From AMORALESPINZON at BWH.HARVARD.EDU Wed Jan 6 12:29:51 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Wed, 6 Jan 2021 17:29:51 +0000 Subject: [Loris-dev] Issues with landing page, data query and BrainBrowser Message-ID: <09C35758-DB2A-41D9-B5B6-94FB0095B4F5@bwh.harvard.edu> Dear LorisDev team, We are experiencing the following issues in Loris. Could you please help me or guide me on how address them. 1. After login into LORIS, the webpage does not allow the user to go to any link until the graph under "Study Progression" is created. This is taking more than one minute to load. I guess this is because we have hundreds of centers. Is it possible to remove the graph from the landing page? (See attachment) 2. When using the Data Query Tool the front-end crashes with error 500. This is what I can see in the loris-error.log === [Wed Jan 06 12:23:31.920274 2021] [php7:error] [pid 12100] [client 216.15.126.108:56023] PHP Fatal error: Uncaught ConfigurationException: NDB_Factory::CouchDB() requires all parameters to be supplied. in /var/www/loris/php/libraries/NDB_Factory.class.inc:297\nStack trace:\n#0 /var/www/loris/modules/dataquery/php/dataquery.class.inc(59): NDB_Factory->couchDB('%COUCH_DATABASE...', '%COUCH_HOSTNAME...', 0, '%COUCH_USERNAME...', '%COUCH_PASSWORD...')\n#1 /var/www/loris/php/libraries/NDB_Form.class.inc(188): LORIS\\dataquery\\Dataquery->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171): NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageDecorationMiddleware.php(49): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), Object(LORIS\\dataquery\\Dataquery))\n#4 /var/www/loris/php/libraries/NDB_Page.class.inc(659): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), Object(LORIS\\dataquery\\Dataquery))\n#5 /var/www/loris/php/libraries/Module.class.inc(341): NDB_Page->process(Object(Zend\\ in /var/www/loris/php/libraries/NDB_Factory.class.inc on line 297, referer: https://ipmsa-loris.bic.mni.mcgill.ca/imaging_browser/viewSession/?sessionID=85935 === 3. In the statistics section (Reports -> Statistics) I can see the following message at the bottom of the page: === Oops It seems like the scan type selected does not have a corresponding column in the mri_parameter_form table in the database. In order to display the statistics for the scan type, make sure the mri_parameter_form table contains a column in the exact format SCANTYPE_Scan_done === In the loris-error.log a see a large list of the following messages: === [Wed Jan 06 12:26:24.730900 2021] [php7:notice] [pid 25824] [client 216.15.126.108:56738] PHP Notice: Undefined index: Female in /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line 137, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ [Wed Jan 06 12:26:24.730935 2021] [php7:notice] [pid 25824] [client 216.15.126.108:56738] PHP Notice: Undefined index: OLYMPUS_CLINICAL_SCREENING in /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ [Wed Jan 06 12:26:24.730944 2021] [php7:notice] [pid 25824] [client 216.15.126.108:56738] PHP Notice: Undefined index: Male in /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ === 4. I am not able to visualiza any image. A message ?LOADING ?? appears but nothing happens. Looking at the loris-error.log I can see that the path to the images is missing a ?/? === PHP Warning: readfile(/data_/ipmsa/loris_data/IPMSA/dataassembly/343633/baseline/mri/native/IPMSA_343633_baseline_flair_001.mnc): failed to open stream: No such file or directory in /var/www/loris/modules/brainbrowser/ajax/image.php on line 56, referer: https://ipmsa-loris.bic.mni.mcgill.ca/brainbrowser/?minc_id=[112603] === Do you know where can this missing ?/? should be set? Thank you in advance for your help. Best regards, Alfredo. [cid:385AE0BA-DCBF-4FFF-985B-4DD28B51BCFD] The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: StudyProgessionGraph.png Type: image/png Size: 65647 bytes Desc: StudyProgessionGraph.png URL: From dave.macfarlane at mcin.ca Wed Jan 6 12:50:39 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Wed, 6 Jan 2021 12:50:39 -0500 Subject: [Loris-dev] Issues with landing page, data query and BrainBrowser In-Reply-To: <09C35758-DB2A-41D9-B5B6-94FB0095B4F5@bwh.harvard.edu> References: <09C35758-DB2A-41D9-B5B6-94FB0095B4F5@bwh.harvard.edu> Message-ID: On Wed, Jan 6, 2021 at 12:30 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team, > > We are experiencing the following issues in Loris. Could you please help > me or guide me on how address them. > > 1. After login into LORIS, the webpage does not allow the user to go to > any link until the graph under "Study Progression" is created. This is > taking more than one minute to load. I guess this is because we have > hundreds of centers. Is it possible to remove the graph from the landing > page? (See attachment) > > I don't believe it should take that long even with a large number of sites. I'll let someone from CCNA handle this part of the question since they also have hundreds of sites and might have more insight.. > > 2. When using the Data Query Tool the front-end crashes with error 500. > > This is what I can see in the loris-error.log > > === > [Wed Jan 06 12:23:31.920274 2021] [php7:error] [pid 12100] [client > 216.15.126.108:56023] PHP Fatal error: Uncaught ConfigurationException: > NDB_Factory::CouchDB() requires all parameters to be supplied. in > /var/www/loris/php/libraries/NDB_Factory.class.inc:297\nStack trace:\n#0 > /var/www/loris/modules/dataquery/php/dataquery.class.inc(59): > NDB_Factory->couchDB('%COUCH_DATABASE...', '%COUCH_HOSTNAME...', 0, > '%COUCH_USERNAME...', '%COUCH_PASSWORD...')\n#1 > /var/www/loris/php/libraries/NDB_Form.class.inc(188): > LORIS\\dataquery\\Dataquery->setup()\n#2 > /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171): > NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#3 > /var/www/loris/src/Middleware/PageDecorationMiddleware.php(49): > LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), > Object(LORIS\\dataquery\\Dataquery))\n#4 > /var/www/loris/php/libraries/NDB_Page.class.inc(659): > LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), > Object(LORIS\\dataquery\\Dataquery))\n#5 > /var/www/loris/php/libraries/Module.class.inc(341): > NDB_Page->process(Object(Zend\\ in > /var/www/loris/php/libraries/NDB_Factory.class.inc on line 297, referer: > https://ipmsa-loris.bic.mni.mcgill.ca/imaging_browser/viewSession/?sessionID=85935 > === > > The DQT currently requires a CouchDB backend with the data imported into it. It looks like the CouchDB hostname/database/username/ password/etc aren't set up. The Configurations section of the file modules/dataquery/README.md should have more information about the setup required. Is the `` tag in project/config.xml setup as described in step 3 of that document? > > 3. In the statistics section (Reports -> Statistics) I can see the > following message at the bottom of the page: > > === > Oops > > It seems like the scan type selected does not have a corresponding column > in the mri_parameter_form table in the database. > In order to display the statistics for the scan type, make sure the > mri_parameter_form table contains a column in the exact format > SCANTYPE_Scan_done > === > > The statistics page using an instrument named "mri_parameter_form" to determine numbers for the scan done. For each scan type in the mri_scan_types table* it expects there to be a column named "SCANTYPE_Scan_Done" to use for reporting statistics. I believe there's somewhere in the MRI documentation that goes into more depth but I'm not entirely sure where, maybe Cecile can chime in.. In the loris-error.log a see a large list of the following messages: > > === > [Wed Jan 06 12:26:24.730900 2021] [php7:notice] [pid 25824] [client > 216.15.126.108:56738] PHP Notice: Undefined index: Female in > /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line > 137, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ > [Wed Jan 06 12:26:24.730935 2021] [php7:notice] [pid 25824] [client > 216.15.126.108:56738] PHP Notice: Undefined index: > OLYMPUS_CLINICAL_SCREENING in > /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line > 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ > [Wed Jan 06 12:26:24.730944 2021] [php7:notice] [pid 25824] [client > 216.15.126.108:56738] PHP Notice: Undefined index: Male in > /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line > 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ > === > > What version of LORIS is this? I think the notices are unrelated and probably harmless but should still be fixed if they haven't been yet. > 4. I am not able to visualiza any image. A message ?LOADING ?? appears but > nothing happens. > Looking at the loris-error.log I can see that the path to the images is > missing a ?/? > > === > PHP Warning: readfile(/data_/ipmsa/loris_data/IPMSA/dataassembly/343633/baseline/mri/native/IPMSA_343633_baseline_flair_001.mnc): > failed to open stream: No such file or directory in > /var/www/loris/modules/brainbrowser/ajax/image.php on line 56, referer: > https://ipmsa-loris.bic.mni.mcgill.ca/brainbrowser/?minc_id=[112603] > === > > Do you know where can this missing ?/? should be set? > > It looks like that code is using the imagePath configuration variable which should have a trailing /. It should be the configuration option labeled "Path to images for display in Imaging Browser (e.g. /data/$project/data/)" in the Configuration module frontend. - Dave -------------- next part -------------- An HTML attachment was scrubbed... URL: From zia.mohades at mcin.ca Thu Jan 7 15:34:50 2021 From: zia.mohades at mcin.ca (Zia Mohades) Date: Thu, 7 Jan 2021 15:34:50 -0500 Subject: [Loris-dev] Issues with landing page, data query and BrainBrowser In-Reply-To: References: <09C35758-DB2A-41D9-B5B6-94FB0095B4F5@bwh.harvard.edu> Message-ID: Hello, Regarding your first question. As Dave mentioned we haven't experienced any issues with loading when we click on the link/site under the graph. We did however noticed some formatting issues which should be fixed in the new version of LORIS but nothing related to the loading functionality. Thank you On Wed, Jan 6, 2021 at 12:51 PM Dave MacFarlane wrote: > On Wed, Jan 6, 2021 at 12:30 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Dear LorisDev team, >> >> We are experiencing the following issues in Loris. Could you please help >> me or guide me on how address them. >> >> 1. After login into LORIS, the webpage does not allow the user to go to >> any link until the graph under "Study Progression" is created. This is >> taking more than one minute to load. I guess this is because we have >> hundreds of centers. Is it possible to remove the graph from the landing >> page? (See attachment) >> >> > I don't believe it should take that long even with a large number of > sites. I'll let someone from CCNA handle this part of the question since > they also have hundreds of sites and might have more insight.. > > >> >> 2. When using the Data Query Tool the front-end crashes with error 500. >> >> This is what I can see in the loris-error.log >> >> === >> [Wed Jan 06 12:23:31.920274 2021] [php7:error] [pid 12100] [client >> 216.15.126.108:56023] PHP Fatal error: Uncaught ConfigurationException: >> NDB_Factory::CouchDB() requires all parameters to be supplied. in >> /var/www/loris/php/libraries/NDB_Factory.class.inc:297\nStack trace:\n#0 >> /var/www/loris/modules/dataquery/php/dataquery.class.inc(59): >> NDB_Factory->couchDB('%COUCH_DATABASE...', '%COUCH_HOSTNAME...', 0, >> '%COUCH_USERNAME...', '%COUCH_PASSWORD...')\n#1 >> /var/www/loris/php/libraries/NDB_Form.class.inc(188): >> LORIS\\dataquery\\Dataquery->setup()\n#2 >> /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171): >> NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#3 >> /var/www/loris/src/Middleware/PageDecorationMiddleware.php(49): >> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), >> Object(LORIS\\dataquery\\Dataquery))\n#4 >> /var/www/loris/php/libraries/NDB_Page.class.inc(659): >> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), >> Object(LORIS\\dataquery\\Dataquery))\n#5 >> /var/www/loris/php/libraries/Module.class.inc(341): >> NDB_Page->process(Object(Zend\\ in >> /var/www/loris/php/libraries/NDB_Factory.class.inc on line 297, referer: >> https://ipmsa-loris.bic.mni.mcgill.ca/imaging_browser/viewSession/?sessionID=85935 >> === >> >> > The DQT currently requires a CouchDB backend with the data imported into > it. It looks like the CouchDB hostname/database/username/ password/etc > aren't set up. The Configurations section of the file > modules/dataquery/README.md should have more information about the setup > required. Is the `` tag in project/config.xml setup as described > in step 3 of that document? > > >> >> 3. In the statistics section (Reports -> Statistics) I can see the >> following message at the bottom of the page: >> >> === >> Oops >> >> It seems like the scan type selected does not have a corresponding column >> in the mri_parameter_form table in the database. >> In order to display the statistics for the scan type, make sure the >> mri_parameter_form table contains a column in the exact format >> SCANTYPE_Scan_done >> === >> >> > The statistics page using an instrument named "mri_parameter_form" to > determine numbers for the scan done. For each scan type in the > mri_scan_types table* it expects there to be a column named > "SCANTYPE_Scan_Done" to use for reporting statistics. I believe there's > somewhere in the MRI documentation that goes into more depth but I'm not > entirely sure where, maybe Cecile can chime in.. > > In the loris-error.log a see a large list of the following messages: >> >> === >> [Wed Jan 06 12:26:24.730900 2021] [php7:notice] [pid 25824] [client >> 216.15.126.108:56738] PHP Notice: Undefined index: Female in >> /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line >> 137, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ >> [Wed Jan 06 12:26:24.730935 2021] [php7:notice] [pid 25824] [client >> 216.15.126.108:56738] PHP Notice: Undefined index: >> OLYMPUS_CLINICAL_SCREENING in >> /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line >> 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ >> [Wed Jan 06 12:26:24.730944 2021] [php7:notice] [pid 25824] [client >> 216.15.126.108:56738] PHP Notice: Undefined index: Male in >> /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line >> 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ >> === >> >> > What version of LORIS is this? I think the notices are unrelated and > probably harmless but should still be fixed if they haven't been yet. > > >> 4. I am not able to visualiza any image. A message ?LOADING ?? appears >> but nothing happens. >> Looking at the loris-error.log I can see that the path to the images is >> missing a ?/? >> >> === >> PHP Warning: readfile(/data_/ipmsa/loris_data/IPMSA/dataassembly/343633/baseline/mri/native/IPMSA_343633_baseline_flair_001.mnc): >> failed to open stream: No such file or directory in >> /var/www/loris/modules/brainbrowser/ajax/image.php on line 56, referer: >> https://ipmsa-loris.bic.mni.mcgill.ca/brainbrowser/?minc_id=[112603] >> === >> >> Do you know where can this missing ?/? should be set? >> >> > It looks like that code is using the imagePath configuration variable > which should have a trailing /. It should be the configuration option > labeled "Path to images for display in Imaging Browser (e.g. > /data/$project/data/)" in the Configuration module frontend. > > - Dave > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ioannis at berkeley.edu Sun Jan 10 12:36:01 2021 From: ioannis at berkeley.edu (Ioannis Pappas) Date: Sun, 10 Jan 2021 09:36:01 -0800 Subject: [Loris-dev] CentOS 8 and Loris Message-ID: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> Dear Loris Support. I hope you are well and happy 2021. We would like to reinstall Loris based on a more recent release of our operating system (CentOS 8). I was wondering if you have specific instructions and/or experience with installing Loris in that environment (I think we could only find instructions for 7). Thank you very much! Best wishes, Ioannis From wangshen.mcin at gmail.com Sun Jan 10 12:46:11 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Sun, 10 Jan 2021 12:46:11 -0500 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> Message-ID: Hi Ioannis, I hope you are well and happy 2021 too. Centos 8 only updates the YUM and Kernel version etc. So the instructions for 7 still work for 8. Best Shen On Sun, 10 Jan 2021 at 12:36, Ioannis Pappas wrote: > Dear Loris Support. > > I hope you are well and happy 2021. > > We would like to reinstall Loris based on a more recent release of our > operating system (CentOS 8). > > I was wondering if you have specific instructions and/or experience with > installing Loris in that environment (I think we could only find > instructions for 7). > > Thank you very much! > > Best wishes, > Ioannis > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From support-cirl at berkeley.edu Sun Jan 10 19:56:22 2021 From: support-cirl at berkeley.edu (Julie Ashworth, HWNI Computing Support) Date: Sun, 10 Jan 2021 16:56:22 -0800 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> Message-ID: <20210111005622.GA44097@oi.attlocal.net> Thanks Shen, I'm installing loris v23.0.2 on CentOS8 using the instructions here: https://loristest.readthedocs.io/en/latest/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/CentOS/README.html I installed php-7.4 including php-fpm (as instructed) # php -v PHP 7.4.6 (cli) (built: May 12 2020 08:09:15) ( NTS ) I installed loris v23.0.2.tar.gz in /var/www/loris I edited the /etc/httpd/conf.d/loris.conf file to include the following line: php_value include_path .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries however, starting httpd produces a syntax error with php_value. Jan 10 16:47:29 loris-c8.priv httpd[7850]: Invalid command 'php_value', perhaps misspelled or defined by a module not included in the server configuration Here is the relevant php module info in /etc/httpd/conf.modules.d: # grep -v "^#" /etc/httpd/conf.modules.d/00-mpm.conf LoadModule mpm_event_module modules/mod_mpm_event.so # grep -v "^#" /etc/httpd/conf.modules.d/15-php.conf LoadModule php7_module modules/libphp7.so # apachectl -M | egrep "fork|php" (produces nothing) What is the recommended way to set the php_value 'invlude_path' with php-fpm? thanks, Julie On 10-01-2021 12.46 -0500, Shen Wang wrote: > Hi Ioannis, > I hope you are well and happy 2021 too. > Centos 8 only updates the YUM and Kernel version etc. > So the instructions for 7 still work??for 8. > Best > Shen > On Sun, 10 Jan 2021 at 12:36, Ioannis Pappas <[1]ioannis at berkeley.edu> > wrote: > > Dear Loris Support. > > I hope you are well and happy 2021. > > We would like to reinstall Loris based on a more recent release of our > operating system (CentOS 8). > > I was wondering if you have specific instructions and/or experience with > installing Loris in that environment (I think we could only find > instructions for 7). > > Thank you very much! > > Best wishes, > Ioannis > _______________________________________________ > Loris-dev mailing list > [2]Loris-dev at bic.mni.mcgill.ca > [3]https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -- > Shen Wang > [4]Loris?? Developer > Montreal Neurological Institute?? > McGill University > > References > > Visible links > 1. mailto:ioannis at berkeley.edu > 2. mailto:Loris-dev at bic.mni.mcgill.ca > 3. https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > 4. https://github.com/aces/Loris > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev ---end quoted text--- From wangshen.mcin at gmail.com Mon Jan 11 10:08:02 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Mon, 11 Jan 2021 10:08:02 -0500 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: <20210111005622.GA44097@oi.attlocal.net> References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> Message-ID: Hi Julie, I recommend reinstalling php 7.4 and apache. https://tecadmin.net/install-apache-php-fpm-centos-8/ this article is helpful. Best Shen -------------- next part -------------- An HTML attachment was scrubbed... URL: From support-cirl at berkeley.edu Mon Jan 11 15:32:46 2021 From: support-cirl at berkeley.edu (Julie Ashworth, HWNI Computing Support) Date: Mon, 11 Jan 2021 12:32:46 -0800 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> Message-ID: <20210111203246.GA49193@oi.attlocal.net> hi Shen, that *is* how I installed apache/php7.4. Please reread my email. I'd like to know how y'all recommend adding the php path for loris libraries using php-fpm. If I use the apache configuration file provided: php_value include_path .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries I get an error: Invalid command 'php_value', perhaps misspelled or defined by a module not included in the server configuration ... because this isn't supported with php-fpm best, Julie On 11-01-2021 10.08 -0500, Shen Wang wrote: > Hi Julie, > I recommend reinstalling php 7.4 and apache. > [1]https://tecadmin.net/install-apache-php-fpm-centos-8/ this article is > helpful. > Best > Shen > > References > > Visible links > 1. https://tecadmin.net/install-apache-php-fpm-centos-8/ ---end quoted text--- From wangshen.mcin at gmail.com Mon Jan 11 16:04:01 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Mon, 11 Jan 2021 16:04:01 -0500 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: <20210111203246.GA49193@oi.attlocal.net> References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> <20210111203246.GA49193@oi.attlocal.net> Message-ID: Hi Julie, We do not support Loris 23.0.2 to run on CentOS 8. You can install 23.0.2 on Centos 7. If you want to try to install it on Centos8. There is no guarantee that it will work on Centos 8. You can try it. step 1 : remove the line of php_value from loris.conf step 2 : add "php_value[include_path] = ....." into */etc/php-fpm.d/loris.conf* step 3: reload php-fpm and httpd. Good Luck! Best Shen On Mon, 11 Jan 2021 at 15:32, Julie Ashworth, HWNI Computing Support < support-cirl at berkeley.edu> wrote: > hi Shen, > that *is* how I installed apache/php7.4. > > Please reread my email. > > I'd like to know how y'all recommend adding the php path for loris > libraries using php-fpm. > > If I use the apache configuration file provided: > php_value include_path > .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries > > I get an error: > Invalid command 'php_value', perhaps misspelled or defined by a module not > included in the server configuration > > > ... because this isn't supported with php-fpm > > best, > Julie > > > > > > > > On 11-01-2021 10.08 -0500, Shen Wang wrote: > > Hi Julie, > > I recommend reinstalling php 7.4 and apache. > > [1]https://tecadmin.net/install-apache-php-fpm-centos-8/ this > article is > > helpful. > > Best > > Shen > > > > References > > > > Visible links > > 1. https://tecadmin.net/install-apache-php-fpm-centos-8/ > ---end quoted text--- > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From support-cirl at berkeley.edu Mon Jan 11 16:27:39 2021 From: support-cirl at berkeley.edu (Julie Ashworth, HWNI Computing Support) Date: Mon, 11 Jan 2021 13:27:39 -0800 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> <20210111203246.GA49193@oi.attlocal.net> Message-ID: <20210111212739.GA49780@oi.attlocal.net> Thanks Shen, Is this documented anywhere? I checked the Ubuntu instructions and the install.sh file, but I don't see it mentioned. You also mentioned to Ioannis that Loris should run find on CentOS8. Which version did you recommend for CentOS8? best, Julie On 11-01-2021 16.04 -0500, Shen Wang wrote: > Hi Julie, > We do not support Loris 23.0.2 to run on CentOS 8. > You can install 23.0.2 on Centos 7. > If you want to try to install it on Centos8. There is no guarantee that it > will work on Centos 8. > You can try it. > step 1 : remove the line of php_value from loris.conf > step 2 : add "php_value[include_path] = > ....."??into??/etc/php-fpm.d/loris.conf > step 3: reload php-fpm and httpd. > Good Luck! > Best?? > Shen > On Mon, 11 Jan 2021 at 15:32, Julie Ashworth, HWNI Computing Support > <[1]support-cirl at berkeley.edu> wrote: > > hi Shen, > that *is* how I installed apache/php7.4. > > Please reread my email. > > I'd like to know how y'all recommend adding the php path for loris > libraries using php-fpm. > > If I use the apache configuration file provided: > ?? ?? ?? ?? php_value include_path > .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries > > I get an error: > Invalid command 'php_value', perhaps misspelled or defined by a module > not included in the server configuration > > ... because this isn't supported with php-fpm > > best, > Julie > > On 11-01-2021 10.08 -0500, Shen Wang wrote: > >?? ?? Hi Julie, > >?? ?? I recommend reinstalling php 7.4 and apache. > >?? ?? [1][2]https://tecadmin.net/install-apache-php-fpm-centos-8/ this > article is > >?? ?? helpful. > >?? ?? Best > >?? ?? Shen > > > > References > > > >?? ?? Visible links > >?? ?? 1. [3]https://tecadmin.net/install-apache-php-fpm-centos-8/ > ---end quoted text--- > > -- > Shen Wang > [4]Loris?? Developer > Montreal Neurological Institute?? > McGill University > > References > > Visible links > 1. mailto:support-cirl at berkeley.edu > 2. https://tecadmin.net/install-apache-php-fpm-centos-8/ > 3. https://tecadmin.net/install-apache-php-fpm-centos-8/ > 4. https://github.com/aces/Loris ---end quoted text--- From AMORALESPINZON at BWH.HARVARD.EDU Mon Jan 11 16:59:19 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 11 Jan 2021 21:59:19 +0000 Subject: [Loris-dev] Error Webpack installing v22.0.0 Message-ID: <72D9F51B-BBAC-497A-9FC7-B64EFF3F7812@bwh.harvard.edu> Dear LorisDev Team, I am upgrading Loris from v21.0.0 to v22.0.0 (https://github.com/aces/Loris/releases/tag/v22.0.0). After installation of node v10.13.0 and npm 6.4.1, and getting the corresponding source code, I am getting the following error when executing ?make all?: === ERROR in ./jsx/DynamicDataTable.js Module build failed (from ./node_modules/babel-loader/lib/index.js): Error: Cannot find module 'babel-plugin-transform-object-rest-spread' from '/var/www/loris' at Function.module.exports [as sync] (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) at resolveStandardizedName (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) at resolvePlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) at loadPlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) at createDescriptor (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) at items.map (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) at Array.map () at createDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) at createPluginDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) at plugins (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) at mergeChainOpts (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) at /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 at buildRootChain (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) at loadPrivatePartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) at Object.loadPartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) at Generator.next () at asyncGeneratorStep (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) at _next (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 at new Promise () at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) at Object._loader (/var/www/loris/node_modules/babel-loader/lib/index.js:224:18) at Object.loader (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) === I am running Ubuntu Xenial 16.04.4 I also tried using node v14.15.4 but got the same error. Do you have suggestions on how to solve this? Regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Tue Jan 12 09:14:46 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Tue, 12 Jan 2021 09:14:46 -0500 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: <20210111212739.GA49780@oi.attlocal.net> References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> <20210111203246.GA49193@oi.attlocal.net> <20210111212739.GA49780@oi.attlocal.net> Message-ID: Hi Julie, The Loris Team only supports Centos7 currently. We don't have Centos8 instructions yet, so you can't find it. If you and Ioannis would like to install loris 23 on centos 8, you can try. I have installed loris 23 on centos 8, although the process is not simple. That is why I mentioned Centos 8, not officially supported yet. Sorry for confusion. best Shen [image: ???? 2021-01-11 ??8.04.56.png] On Mon, 11 Jan 2021 at 16:27, Julie Ashworth, HWNI Computing Support < support-cirl at berkeley.edu> wrote: > Thanks Shen, > Is this documented anywhere? I checked the Ubuntu instructions and the > install.sh file, but I don't see it mentioned. > > You also mentioned to Ioannis that Loris should run find on CentOS8. Which > version did you recommend for CentOS8? > > best, > Julie > > On 11-01-2021 16.04 -0500, Shen Wang wrote: > > Hi Julie, > > We do not support Loris 23.0.2 to run on CentOS 8. > > You can install 23.0.2 on Centos 7. > > If you want to try to install it on Centos8. There is no guarantee > that it > > will work on Centos 8. > > You can try it. > > step 1 : remove the line of php_value from loris.conf > > step 2 : add "php_value[include_path] = > > ....." into /etc/php-fpm.d/loris.conf > > step 3: reload php-fpm and httpd. > > Good Luck! > > Best > > Shen > > On Mon, 11 Jan 2021 at 15:32, Julie Ashworth, HWNI Computing Support > > <[1]support-cirl at berkeley.edu> wrote: > > > > hi Shen, > > that *is* how I installed apache/php7.4. > > > > Please reread my email. > > > > I'd like to know how y'all recommend adding the php path for loris > > libraries using php-fpm. > > > > If I use the apache configuration file provided: > > php_value include_path > > > .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries > > > > I get an error: > > Invalid command 'php_value', perhaps misspelled or defined by a > module > > not included in the server configuration > > > > ... because this isn't supported with php-fpm > > > > best, > > Julie > > > > On 11-01-2021 10.08 -0500, Shen Wang wrote: > > > Hi Julie, > > > I recommend reinstalling php 7.4 and apache. > > > [1][2]https://tecadmin.net/install-apache-php-fpm-centos-8/ > this > > article is > > > helpful. > > > Best > > > Shen > > > > > > References > > > > > > Visible links > > > 1. [3]https://tecadmin.net/install-apache-php-fpm-centos-8/ > > ---end quoted text--- > > > > -- > > Shen Wang > > [4]Loris Developer > > Montreal Neurological Institute > > McGill University > > > > References > > > > Visible links > > 1. mailto:support-cirl at berkeley.edu > > 2. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 3. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 4. https://github.com/aces/Loris > ---end quoted text--- > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: ???? 2021-01-11 ??8.04.56.png Type: image/png Size: 298657 bytes Desc: not available URL: From rogers at bic.mni.mcgill.ca Tue Jan 12 11:35:44 2021 From: rogers at bic.mni.mcgill.ca (Christine Rogers) Date: Tue, 12 Jan 2021 11:35:44 -0500 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: <20210111212739.GA49780@oi.attlocal.net> References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> <20210111203246.GA49193@oi.attlocal.net> <20210111212739.GA49780@oi.attlocal.net> Message-ID: Hi Julie, As my colleague Shen mentioned, we support CentOS 7 currently -- CentOS installation information is linked from the main Readme in LORIS (e.g. for release 23 here ) - including the CentOS Installation Guide found in our main LORIS documentation site . Best, Christine On Mon, Jan 11, 2021 at 4:27 PM Julie Ashworth, HWNI Computing Support < support-cirl at berkeley.edu> wrote: > Thanks Shen, > Is this documented anywhere? I checked the Ubuntu instructions and the > install.sh file, but I don't see it mentioned. > > You also mentioned to Ioannis that Loris should run find on CentOS8. Which > version did you recommend for CentOS8? > > best, > Julie > > On 11-01-2021 16.04 -0500, Shen Wang wrote: > > Hi Julie, > > We do not support Loris 23.0.2 to run on CentOS 8. > > You can install 23.0.2 on Centos 7. > > If you want to try to install it on Centos8. There is no guarantee > that it > > will work on Centos 8. > > You can try it. > > step 1 : remove the line of php_value from loris.conf > > step 2 : add "php_value[include_path] = > > ....."? into? /etc/php-fpm.d/loris.conf > > step 3: reload php-fpm and httpd. > > Good Luck! > > Best? > > Shen > > On Mon, 11 Jan 2021 at 15:32, Julie Ashworth, HWNI Computing Support > > <[1]support-cirl at berkeley.edu> wrote: > > > > hi Shen, > > that *is* how I installed apache/php7.4. > > > > Please reread my email. > > > > I'd like to know how y'all recommend adding the php path for loris > > libraries using php-fpm. > > > > If I use the apache configuration file provided: > > ? ? ? ? php_value include_path > > > .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries > > > > I get an error: > > Invalid command 'php_value', perhaps misspelled or defined by a > module > > not included in the server configuration > > > > ... because this isn't supported with php-fpm > > > > best, > > Julie > > > > On 11-01-2021 10.08 -0500, Shen Wang wrote: > > >? ? Hi Julie, > > >? ? I recommend reinstalling php 7.4 and apache. > > >? ? [1][2]https://tecadmin.net/install-apache-php-fpm-centos-8/ > this > > article is > > >? ? helpful. > > >? ? Best > > >? ? Shen > > > > > > References > > > > > >? ? Visible links > > >? ? 1. [3]https://tecadmin.net/install-apache-php-fpm-centos-8/ > > ---end quoted text--- > > > > -- > > Shen Wang > > [4]Loris? Developer > > Montreal Neurological Institute? > > McGill University > > > > References > > > > Visible links > > 1. mailto:support-cirl at berkeley.edu > > 2. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 3. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 4. https://github.com/aces/Loris > ---end quoted text--- > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -- christine.rogers at mcgill.ca McGill Centre for Integrative Neuroscience | MCIN.ca Montreal Neurological Institute McGill University | Montreal | Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Tue Jan 12 11:40:08 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Tue, 12 Jan 2021 11:40:08 -0500 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: <20210112162730.GA57593@oi.attlocal.net> References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> <20210111203246.GA49193@oi.attlocal.net> <20210111212739.GA49780@oi.attlocal.net> <20210112162730.GA57593@oi.attlocal.net> Message-ID: Hi Julie, We are holding the Loris meeting to discuss whether to support centos in the future. Loris's sub-modules have issues with the Centos system. So Loris team will not support Centos. We will only support Ubuntu in the future. Best Shen On Tue, 12 Jan 2021 at 11:27, Julie Ashworth, HWNI Computing Support < support-cirl at berkeley.edu> wrote: > hi Shen, > I'm looking for documentation of the (useful!) instruction you provided in > your previous email: > > >? ? step 2 : add "php_value[include_path]? = > >? ? ....."? into? /etc/php-fpm.d/loris.conf > > I would appreciate a link to that documentation, because I think it would > be valuable for the future. I can adapt Ubuntu documentation for CentOS. > > thanks, > Julie > > > > On 12-01-2021 09.14 -0500, Shen Wang wrote: > > Hi Julie, > > > > The Loris Team only supports Centos7 currently. > > We don't have Centos8 instructions yet, so you can't find it. > > > > If you and Ioannis would like to install loris 23 on centos 8, you can > > try. > > I have installed loris 23 on centos 8, although the process is not > simple. > > That is why I mentioned Centos 8, not officially supported yet. Sorry > for > > confusion. > > best > > Shen > > [1]?? ????????? 2021-01-11 ???? ?8.04.56.png > > On Mon, 11 Jan 2021 at 16:27, Julie Ashworth, HWNI Computing Support > > <[2]support-cirl at berkeley.edu> wrote: > > > > Thanks Shen, > > Is this documented anywhere? I checked the Ubuntu instructions and > the > > install.sh file, but I don't see it mentioned. > > > > You also mentioned to Ioannis that Loris should run find on CentOS8. > > Which version did you recommend for CentOS8? > > > > best, > > Julie > > > > On 11-01-2021 16.04 -0500, Shen Wang wrote: > > >? ? Hi Julie, > > >? ? We do not support Loris 23.0.2 to run on CentOS 8. > > >? ? You can install 23.0.2 on Centos 7. > > >? ? If you want to try to install it on Centos8. There is no > guarantee > > that it > > >? ? will work on Centos 8. > > >? ? You can try it. > > >? ? step 1 : remove the line of php_value from loris.conf > > >? ? step 2 : add "php_value[include_path]? = > > >? ? ....."? into? /etc/php-fpm.d/loris.conf > > >? ? step 3: reload php-fpm and httpd. > > >? ? Good Luck! > > >? ? Best? > > >? ? Shen > > >? ? On Mon, 11 Jan 2021 at 15:32, Julie Ashworth, HWNI Computing > > Support > > >? ? <[1][3]support-cirl at berkeley.edu> wrote: > > > > > >? ? ? hi Shen, > > >? ? ? that *is* how I installed apache/php7.4. > > > > > >? ? ? Please reread my email. > > > > > >? ? ? I'd like to know how y'all recommend adding the php path > for > > loris > > >? ? ? libraries using php-fpm. > > > > > >? ? ? If I use the apache configuration file provided: > > >? ? ? ? ? ? ? php_value include_path > > >? ? ? > > > .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries > > > > > >? ? ? I get an error: > > >? ? ? Invalid command 'php_value', perhaps misspelled or > defined by a > > module > > >? ? ? not included in the server configuration > > > > > >? ? ? ... because this isn't supported with php-fpm > > > > > >? ? ? best, > > >? ? ? Julie > > > > > >? ? ? On 11-01-2021 10.08 -0500, Shen Wang wrote: > > >? ? ? >? ? Hi Julie, > > >? ? ? >? ? I recommend reinstalling php 7.4 and apache. > > >? ? ? >? ? > > [1][2][4]https://tecadmin.net/install-apache-php-fpm-centos-8/ this > > >? ? ? article is > > >? ? ? >? ? helpful. > > >? ? ? >? ? Best > > >? ? ? >? ? Shen > > >? ? ? > > > >? ? ? > References > > >? ? ? > > > >? ? ? >? ? Visible links > > >? ? ? >? ? 1. > > [3][5]https://tecadmin.net/install-apache-php-fpm-centos-8/ > > >? ? ? ---end quoted text--- > > > > > >? ? -- > > >? ? Shen Wang > > >? ? [4]Loris? Developer > > >? ? Montreal Neurological Institute? > > >? ? McGill University > > > > > > References > > > > > >? ? Visible links > > >? ? 1. mailto:[6]support-cirl at berkeley.edu > > >? ? 2. [7]https://tecadmin.net/install-apache-php-fpm-centos-8/ > > >? ? 3. [8]https://tecadmin.net/install-apache-php-fpm-centos-8/ > > >? ? 4. [9]https://github.com/aces/Loris > > ---end quoted text--- > > > > -- > > Shen Wang > > [10]Loris? Developer > > Montreal Neurological Institute? > > McGill University > > > > References > > > > Visible links > > 2. mailto:support-cirl at berkeley.edu > > 3. mailto:support-cirl at berkeley.edu > > 4. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 5. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 6. mailto:support-cirl at berkeley.edu > > 7. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 8. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 9. https://github.com/aces/Loris > > 10. https://github.com/aces/Loris > > > ---end quoted text--- > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From support-cirl at berkeley.edu Tue Jan 12 11:52:08 2021 From: support-cirl at berkeley.edu (Julie Ashworth, HWNI Computing Support) Date: Tue, 12 Jan 2021 08:52:08 -0800 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> <20210111203246.GA49193@oi.attlocal.net> <20210111212739.GA49780@oi.attlocal.net> <20210112162730.GA57593@oi.attlocal.net> Message-ID: <20210112165208.GB58113@oi.attlocal.net> hi Shen, On 12-01-2021 11.40 -0500, Shen Wang wrote: > So Loris team will not support??Centos. We will only support??Ubuntu in the future.?? That's interesting that CentOS will no longer be supported. Since you previously mentioned that CentOS8 should work, I already started the installation, and I'd like to see if it works. So, please, please... will you please send me a link to the most recent instruction for loris installation that includes the php_value in /etc/php-fpm.d? As I said, I can modify ubuntu instructions. I don't need instructions specific to CentOS. thanks, Julie On 12-01-2021 11.40 -0500, Shen Wang wrote: > Hi Julie, > We are holding the Loris meeting to discuss whether to support centos in > the future.?? > Loris's??sub-modules have issues with the Centos system. So Loris team will > not support??Centos. > We will only support??Ubuntu in the future.?? > Best?? > Shen > On Tue, 12 Jan 2021 at 11:27, Julie Ashworth, HWNI Computing Support > <[1]support-cirl at berkeley.edu> wrote: > > hi Shen, > I'm looking for documentation of the (useful!) instruction you provided > in your previous email: > > >???? ???? step 2 : add "php_value[include_path]???? = > >???? ???? ....."????into????/etc/php-fpm.d/loris.conf > > I would appreciate a link to that documentation, because I think it > would be valuable for the future. I can adapt Ubuntu documentation for > CentOS. > > thanks, > Julie > > On 12-01-2021 09.14 -0500, Shen Wang wrote: > >?? ?? Hi Julie, > > > >?? ?? The Loris Team only supports Centos7 currently. > >?? ?? We don't have Centos8 instructions yet, so you can't find it. > > > >?? ?? If you and Ioannis would like to install loris 23 on centos 8, you > can > >?? ?? try. > >?? ?? I have installed loris 23 on centos 8, although the process is not > simple. > >?? ?? That is why I mentioned Centos 8, not officially supported yet. > Sorry for > >?? ?? confusion. > >?? ?? best > >?? ?? Shen > >?? ?? [1]???? ???????????????????? 2021-01-11 ????????? ??8.04.56.png > >?? ?? On Mon, 11 Jan 2021 at 16:27, Julie Ashworth, HWNI Computing > Support > >?? ?? <[2][2]support-cirl at berkeley.edu> wrote: > > > >?? ?? ?? Thanks Shen, > >?? ?? ?? Is this documented anywhere? I checked the Ubuntu instructions > and the > >?? ?? ?? install.sh file, but I don't see it mentioned. > > > >?? ?? ?? You also mentioned to Ioannis that Loris should run find on > CentOS8. > >?? ?? ?? Which version did you recommend for CentOS8? > > > >?? ?? ?? best, > >?? ?? ?? Julie > > > >?? ?? ?? On 11-01-2021 16.04 -0500, Shen Wang wrote: > >?? ?? ?? >???? ???? Hi Julie, > >?? ?? ?? >???? ???? We do not support Loris 23.0.2 to run on CentOS 8. > >?? ?? ?? >???? ???? You can install 23.0.2 on Centos 7. > >?? ?? ?? >???? ???? If you want to try to install it on Centos8. There is no > guarantee > >?? ?? ?? that it > >?? ?? ?? >???? ???? will work on Centos 8. > >?? ?? ?? >???? ???? You can try it. > >?? ?? ?? >???? ???? step 1 : remove the line of php_value from loris.conf > >?? ?? ?? >???? ???? step 2 : add "php_value[include_path]???? = > >?? ?? ?? >???? ???? ....."????into????/etc/php-fpm.d/loris.conf > >?? ?? ?? >???? ???? step 3: reload php-fpm and httpd. > >?? ?? ?? >???? ???? Good Luck! > >?? ?? ?? >???? ???? Best???? > >?? ?? ?? >???? ???? Shen > >?? ?? ?? >???? ???? On Mon, 11 Jan 2021 at 15:32, Julie Ashworth, HWNI > Computing > >?? ?? ?? Support > >?? ?? ?? >???? ???? <[1][3][3]support-cirl at berkeley.edu> wrote: > >?? ?? ?? > > >?? ?? ?? >???? ???? ???? hi Shen, > >?? ?? ?? >???? ???? ???? that *is* how I installed apache/php7.4. > >?? ?? ?? > > >?? ?? ?? >???? ???? ???? Please reread my email. > >?? ?? ?? > > >?? ?? ?? >???? ???? ???? I'd like to know how y'all recommend adding the php > path for > >?? ?? ?? loris > >?? ?? ?? >???? ???? ???? libraries using php-fpm. > >?? ?? ?? > > >?? ?? ?? >???? ???? ???? If I use the apache configuration file provided: > >?? ?? ?? >???? ???? ???? ???? ???? ???? ???? php_value include_path > >?? ?? ?? >???? ???? ???? > >?? ?? ?? > .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries > >?? ?? ?? > > >?? ?? ?? >???? ???? ???? I get an error: > >?? ?? ?? >???? ???? ???? Invalid command 'php_value', perhaps misspelled or > defined by a > >?? ?? ?? module > >?? ?? ?? >???? ???? ???? not included in the server configuration > >?? ?? ?? > > >?? ?? ?? >???? ???? ???? ... because this isn't supported with php-fpm > >?? ?? ?? > > >?? ?? ?? >???? ???? ???? best, > >?? ?? ?? >???? ???? ???? Julie > >?? ?? ?? > > >?? ?? ?? >???? ???? ???? On 11-01-2021 10.08 -0500, Shen Wang wrote: > >?? ?? ?? >???? ???? ???? >???? ???? Hi Julie, > >?? ?? ?? >???? ???? ???? >???? ???? I recommend reinstalling php 7.4 and apache. > >?? ?? ?? >???? ???? ???? >???? ???? > >?? ?? ?? [1][2][4][4]https://tecadmin.net/install-apache-php-fpm-centos-8/ > this > >?? ?? ?? >???? ???? ???? article is > >?? ?? ?? >???? ???? ???? >???? ???? helpful. > >?? ?? ?? >???? ???? ???? >???? ???? Best > >?? ?? ?? >???? ???? ???? >???? ???? Shen > >?? ?? ?? >???? ???? ???? > > >?? ?? ?? >???? ???? ???? > References > >?? ?? ?? >???? ???? ???? > > >?? ?? ?? >???? ???? ???? >???? ???? Visible links > >?? ?? ?? >???? ???? ???? >???? ???? 1. > >?? ?? ?? [3][5][5]https://tecadmin.net/install-apache-php-fpm-centos-8/ > >?? ?? ?? >???? ???? ???? ---end quoted text--- > >?? ?? ?? > > >?? ?? ?? >???? ???? -- > >?? ?? ?? >???? ???? Shen Wang > >?? ?? ?? >???? ???? [4]Loris???? Developer > >?? ?? ?? >???? ???? Montreal Neurological Institute???? > >?? ?? ?? >???? ???? McGill University > >?? ?? ?? > > >?? ?? ?? > References > >?? ?? ?? > > >?? ?? ?? >???? ???? Visible links > >?? ?? ?? >???? ???? 1. mailto:[6][6]support-cirl at berkeley.edu > >?? ?? ?? >???? ???? 2. > [7][7]https://tecadmin.net/install-apache-php-fpm-centos-8/ > >?? ?? ?? >???? ???? 3. > [8][8]https://tecadmin.net/install-apache-php-fpm-centos-8/ > >?? ?? ?? >???? ???? 4. [9][9]https://github.com/aces/Loris > >?? ?? ?? ---end quoted text--- > > > >?? ?? -- > >?? ?? Shen Wang > >?? ?? [10]Loris???? Developer > >?? ?? Montreal Neurological Institute???? > >?? ?? McGill University > > > > References > > > >?? ?? Visible links > >?? ?? 2. mailto:[10]support-cirl at berkeley.edu > >?? ?? 3. mailto:[11]support-cirl at berkeley.edu > >?? ?? 4. [12]https://tecadmin.net/install-apache-php-fpm-centos-8/ > >?? ?? 5. [13]https://tecadmin.net/install-apache-php-fpm-centos-8/ > >?? ?? 6. mailto:[14]support-cirl at berkeley.edu > >?? ?? 7. [15]https://tecadmin.net/install-apache-php-fpm-centos-8/ > >?? ?? 8. [16]https://tecadmin.net/install-apache-php-fpm-centos-8/ > >?? ?? 9. [17]https://github.com/aces/Loris > >?? ??10. [18]https://github.com/aces/Loris > > ---end quoted text--- > > -- > Shen Wang > [19]Loris?? Developer > Montreal Neurological Institute?? > McGill University > > References > > Visible links > 1. mailto:support-cirl at berkeley.edu > 2. mailto:support-cirl at berkeley.edu > 3. mailto:support-cirl at berkeley.edu > 4. https://tecadmin.net/install-apache-php-fpm-centos-8/ > 5. https://tecadmin.net/install-apache-php-fpm-centos-8/ > 6. mailto:support-cirl at berkeley.edu > 7. https://tecadmin.net/install-apache-php-fpm-centos-8/ > 8. https://tecadmin.net/install-apache-php-fpm-centos-8/ > 9. https://github.com/aces/Loris > 10. mailto:support-cirl at berkeley.edu > 11. mailto:support-cirl at berkeley.edu > 12. https://tecadmin.net/install-apache-php-fpm-centos-8/ > 13. https://tecadmin.net/install-apache-php-fpm-centos-8/ > 14. mailto:support-cirl at berkeley.edu > 15. https://tecadmin.net/install-apache-php-fpm-centos-8/ > 16. https://tecadmin.net/install-apache-php-fpm-centos-8/ > 17. https://github.com/aces/Loris > 18. https://github.com/aces/Loris > 19. https://github.com/aces/Loris ---end quoted text--- From samirdas99 at gmail.com Tue Jan 12 11:58:51 2021 From: samirdas99 at gmail.com (Samir Das) Date: Tue, 12 Jan 2021 17:58:51 +0100 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: <20210112165208.GB58113@oi.attlocal.net> References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> <20210111203246.GA49193@oi.attlocal.net> <20210111212739.GA49780@oi.attlocal.net> <20210112162730.GA57593@oi.attlocal.net> <20210112165208.GB58113@oi.attlocal.net> Message-ID: Hi Julie, We'll do our best to help you with this configuration. :) We'll send you any documentation we have. Regarding CentOS, since RedHat has discontinued its support, we are planning on putting our testing resources elsewhere. We have yet to discuss CentOS-Stream, which we will do next week. But I wouldn't worry too much... we'll help as much as we can given that you have already installed it, etc. If the problems become too tedious, then we can figure out options together. Best, Samir Das On Tue, Jan 12, 2021 at 5:52 PM Julie Ashworth, HWNI Computing Support < support-cirl at berkeley.edu> wrote: > hi Shen, > > On 12-01-2021 11.40 -0500, Shen Wang wrote: > > So Loris team will not support? Centos. We will only support? Ubuntu > in the future.? > > That's interesting that CentOS will no longer be supported. > > Since you previously mentioned that CentOS8 should work, I already started > the installation, and I'd like to see if it works. > > So, please, please... > will you please send me a link to the most recent instruction for loris > installation that includes the php_value in /etc/php-fpm.d? > As I said, I can modify ubuntu instructions. I don't need instructions > specific to CentOS. > > thanks, > Julie > > > > On 12-01-2021 11.40 -0500, Shen Wang wrote: > > Hi Julie, > > We are holding the Loris meeting to discuss whether to support centos > in > > the future.? > > Loris's? sub-modules have issues with the Centos system. So Loris > team will > > not support? Centos. > > We will only support? Ubuntu in the future.? > > Best? > > Shen > > On Tue, 12 Jan 2021 at 11:27, Julie Ashworth, HWNI Computing Support > > <[1]support-cirl at berkeley.edu> wrote: > > > > hi Shen, > > I'm looking for documentation of the (useful!) instruction you > provided > > in your previous email: > > > > >??? ??? step 2 : add "php_value[include_path]??? = > > >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf > > > > I would appreciate a link to that documentation, because I think it > > would be valuable for the future. I can adapt Ubuntu documentation > for > > CentOS. > > > > thanks, > > Julie > > > > On 12-01-2021 09.14 -0500, Shen Wang wrote: > > >? ? Hi Julie, > > > > > >? ? The Loris Team only supports Centos7 currently. > > >? ? We don't have Centos8 instructions yet, so you can't find it. > > > > > >? ? If you and Ioannis would like to install loris 23 on centos > 8, you > > can > > >? ? try. > > >? ? I have installed loris 23 on centos 8, although the process > is not > > simple. > > >? ? That is why I mentioned Centos 8, not officially supported > yet. > > Sorry for > > >? ? confusion. > > >? ? best > > >? ? Shen > > >? ? [1]???? ???????????????????? 2021-01-11 ????????? > ??8.04.56.png > > >? ? On Mon, 11 Jan 2021 at 16:27, Julie Ashworth, HWNI Computing > > Support > > >? ? <[2][2]support-cirl at berkeley.edu> wrote: > > > > > >? ? ? Thanks Shen, > > >? ? ? Is this documented anywhere? I checked the Ubuntu > instructions > > and the > > >? ? ? install.sh file, but I don't see it mentioned. > > > > > >? ? ? You also mentioned to Ioannis that Loris should run find > on > > CentOS8. > > >? ? ? Which version did you recommend for CentOS8? > > > > > >? ? ? best, > > >? ? ? Julie > > > > > >? ? ? On 11-01-2021 16.04 -0500, Shen Wang wrote: > > >? ? ? >??? ??? Hi Julie, > > >? ? ? >??? ??? We do not support Loris 23.0.2 to run on > CentOS 8. > > >? ? ? >??? ??? You can install 23.0.2 on Centos 7. > > >? ? ? >??? ??? If you want to try to install it on Centos8. > There is no > > guarantee > > >? ? ? that it > > >? ? ? >??? ??? will work on Centos 8. > > >? ? ? >??? ??? You can try it. > > >? ? ? >??? ??? step 1 : remove the line of php_value from > loris.conf > > >? ? ? >??? ??? step 2 : add "php_value[include_path]??? = > > >? ? ? >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf > > >? ? ? >??? ??? step 3: reload php-fpm and httpd. > > >? ? ? >??? ??? Good Luck! > > >? ? ? >??? ??? Best??? > > >? ? ? >??? ??? Shen > > >? ? ? >??? ??? On Mon, 11 Jan 2021 at 15:32, Julie Ashworth, > HWNI > > Computing > > >? ? ? Support > > >? ? ? >??? ??? <[1][3][3]support-cirl at berkeley.edu> wrote: > > >? ? ? > > > >? ? ? >??? ??? ??? hi Shen, > > >? ? ? >??? ??? ??? that *is* how I installed apache/php7.4. > > >? ? ? > > > >? ? ? >??? ??? ??? Please reread my email. > > >? ? ? > > > >? ? ? >??? ??? ??? I'd like to know how y'all recommend > adding the php > > path for > > >? ? ? loris > > >? ? ? >??? ??? ??? libraries using php-fpm. > > >? ? ? > > > >? ? ? >??? ??? ??? If I use the apache configuration file > provided: > > >? ? ? >??? ??? ??? ??? ??? ??? ??? php_value include_path > > >? ? ? >??? ??? ??? > > >? ? ? > > > .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries > > >? ? ? > > > >? ? ? >??? ??? ??? I get an error: > > >? ? ? >??? ??? ??? Invalid command 'php_value', perhaps > misspelled or > > defined by a > > >? ? ? module > > >? ? ? >??? ??? ??? not included in the server configuration > > >? ? ? > > > >? ? ? >??? ??? ??? ... because this isn't supported with > php-fpm > > >? ? ? > > > >? ? ? >??? ??? ??? best, > > >? ? ? >??? ??? ??? Julie > > >? ? ? > > > >? ? ? >??? ??? ??? On 11-01-2021 10.08 -0500, Shen Wang > wrote: > > >? ? ? >??? ??? ??? >??? ??? Hi Julie, > > >? ? ? >??? ??? ??? >??? ??? I recommend reinstalling php > 7.4 and apache. > > >? ? ? >??? ??? ??? >??? ??? > > >? ? ? [1][2][4][4] > https://tecadmin.net/install-apache-php-fpm-centos-8/ > > this > > >? ? ? >??? ??? ??? article is > > >? ? ? >??? ??? ??? >??? ??? helpful. > > >? ? ? >??? ??? ??? >??? ??? Best > > >? ? ? >??? ??? ??? >??? ??? Shen > > >? ? ? >??? ??? ??? > > > >? ? ? >??? ??? ??? > References > > >? ? ? >??? ??? ??? > > > >? ? ? >??? ??? ??? >??? ??? Visible links > > >? ? ? >??? ??? ??? >??? ??? 1. > > >? ? ? [3][5][5] > https://tecadmin.net/install-apache-php-fpm-centos-8/ > > >? ? ? >??? ??? ??? ---end quoted text--- > > >? ? ? > > > >? ? ? >??? ??? -- > > >? ? ? >??? ??? Shen Wang > > >? ? ? >??? ??? [4]Loris??? Developer > > >? ? ? >??? ??? Montreal Neurological Institute??? > > >? ? ? >??? ??? McGill University > > >? ? ? > > > >? ? ? > References > > >? ? ? > > > >? ? ? >??? ??? Visible links > > >? ? ? >??? ??? 1. mailto:[6][6]support-cirl at berkeley.edu > > >? ? ? >??? ??? 2. > > [7][7]https://tecadmin.net/install-apache-php-fpm-centos-8/ > > >? ? ? >??? ??? 3. > > [8][8]https://tecadmin.net/install-apache-php-fpm-centos-8/ > > >? ? ? >??? ??? 4. [9][9]https://github.com/aces/Loris > > >? ? ? ---end quoted text--- > > > > > >? ? -- > > >? ? Shen Wang > > >? ? [10]Loris??? Developer > > >? ? Montreal Neurological Institute??? > > >? ? McGill University > > > > > > References > > > > > >? ? Visible links > > >? ? 2. mailto:[10]support-cirl at berkeley.edu > > >? ? 3. mailto:[11]support-cirl at berkeley.edu > > >? ? 4. [12]https://tecadmin.net/install-apache-php-fpm-centos-8/ > > >? ? 5. [13]https://tecadmin.net/install-apache-php-fpm-centos-8/ > > >? ? 6. mailto:[14]support-cirl at berkeley.edu > > >? ? 7. [15]https://tecadmin.net/install-apache-php-fpm-centos-8/ > > >? ? 8. [16]https://tecadmin.net/install-apache-php-fpm-centos-8/ > > >? ? 9. [17]https://github.com/aces/Loris > > >? ? 10. [18]https://github.com/aces/Loris > > > > ---end quoted text--- > > > > -- > > Shen Wang > > [19]Loris? Developer > > Montreal Neurological Institute? > > McGill University > > > > References > > > > Visible links > > 1. mailto:support-cirl at berkeley.edu > > 2. mailto:support-cirl at berkeley.edu > > 3. mailto:support-cirl at berkeley.edu > > 4. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 5. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 6. mailto:support-cirl at berkeley.edu > > 7. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 8. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 9. https://github.com/aces/Loris > > 10. mailto:support-cirl at berkeley.edu > > 11. mailto:support-cirl at berkeley.edu > > 12. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 13. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 14. mailto:support-cirl at berkeley.edu > > 15. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 16. https://tecadmin.net/install-apache-php-fpm-centos-8/ > > 17. https://github.com/aces/Loris > > 18. https://github.com/aces/Loris > > 19. https://github.com/aces/Loris > ---end quoted text--- > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From support-cirl at berkeley.edu Tue Jan 12 12:39:06 2021 From: support-cirl at berkeley.edu (Julie Ashworth, HWNI Computing Support) Date: Tue, 12 Jan 2021 09:39:06 -0800 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> <20210111203246.GA49193@oi.attlocal.net> <20210111212739.GA49780@oi.attlocal.net> <20210112162730.GA57593@oi.attlocal.net> <20210112165208.GB58113@oi.attlocal.net> Message-ID: Thank you, In the last 4 emails I have simply asked for current linux documentation, not centos8 documentation (preferably that mentions php-fpm configuration). Is that available? On Tue, Jan 12, 2021, 8:59 AM Samir Das wrote: > Hi Julie, > > We'll do our best to help you with this configuration. :) We'll send you > any documentation we have. > > Regarding CentOS, since RedHat has discontinued its support, we are > planning on putting our testing resources elsewhere. We have yet to discuss > CentOS-Stream, which we will do next week. But I wouldn't worry too much... > we'll help as much as we can given that you have already installed it, etc. > If the problems become too tedious, then we can figure out options together. > > Best, > > Samir Das > > On Tue, Jan 12, 2021 at 5:52 PM Julie Ashworth, HWNI Computing Support < > support-cirl at berkeley.edu> wrote: > >> hi Shen, >> >> On 12-01-2021 11.40 -0500, Shen Wang wrote: >> > So Loris team will not support? Centos. We will only support? Ubuntu >> in the future.? >> >> That's interesting that CentOS will no longer be supported. >> >> Since you previously mentioned that CentOS8 should work, I already >> started the installation, and I'd like to see if it works. >> >> So, please, please... >> will you please send me a link to the most recent instruction for loris >> installation that includes the php_value in /etc/php-fpm.d? >> As I said, I can modify ubuntu instructions. I don't need instructions >> specific to CentOS. >> >> thanks, >> Julie >> >> >> >> On 12-01-2021 11.40 -0500, Shen Wang wrote: >> > Hi Julie, >> > We are holding the Loris meeting to discuss whether to support >> centos in >> > the future.? >> > Loris's? sub-modules have issues with the Centos system. So Loris >> team will >> > not support? Centos. >> > We will only support? Ubuntu in the future.? >> > Best? >> > Shen >> > On Tue, 12 Jan 2021 at 11:27, Julie Ashworth, HWNI Computing Support >> > <[1]support-cirl at berkeley.edu> wrote: >> > >> > hi Shen, >> > I'm looking for documentation of the (useful!) instruction you >> provided >> > in your previous email: >> > >> > >??? ??? step 2 : add "php_value[include_path]??? = >> > >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf >> > >> > I would appreciate a link to that documentation, because I think it >> > would be valuable for the future. I can adapt Ubuntu documentation >> for >> > CentOS. >> > >> > thanks, >> > Julie >> > >> > On 12-01-2021 09.14 -0500, Shen Wang wrote: >> > >? ? Hi Julie, >> > > >> > >? ? The Loris Team only supports Centos7 currently. >> > >? ? We don't have Centos8 instructions yet, so you can't find >> it. >> > > >> > >? ? If you and Ioannis would like to install loris 23 on centos >> 8, you >> > can >> > >? ? try. >> > >? ? I have installed loris 23 on centos 8, although the process >> is not >> > simple. >> > >? ? That is why I mentioned Centos 8, not officially supported >> yet. >> > Sorry for >> > >? ? confusion. >> > >? ? best >> > >? ? Shen >> > >? ? [1]???? ???????????????????? 2021-01-11 ????????? >> ??8.04.56.png >> > >? ? On Mon, 11 Jan 2021 at 16:27, Julie Ashworth, HWNI Computing >> > Support >> > >? ? <[2][2]support-cirl at berkeley.edu> wrote: >> > > >> > >? ? ? Thanks Shen, >> > >? ? ? Is this documented anywhere? I checked the Ubuntu >> instructions >> > and the >> > >? ? ? install.sh file, but I don't see it mentioned. >> > > >> > >? ? ? You also mentioned to Ioannis that Loris should run find >> on >> > CentOS8. >> > >? ? ? Which version did you recommend for CentOS8? >> > > >> > >? ? ? best, >> > >? ? ? Julie >> > > >> > >? ? ? On 11-01-2021 16.04 -0500, Shen Wang wrote: >> > >? ? ? >??? ??? Hi Julie, >> > >? ? ? >??? ??? We do not support Loris 23.0.2 to run on >> CentOS 8. >> > >? ? ? >??? ??? You can install 23.0.2 on Centos 7. >> > >? ? ? >??? ??? If you want to try to install it on Centos8. >> There is no >> > guarantee >> > >? ? ? that it >> > >? ? ? >??? ??? will work on Centos 8. >> > >? ? ? >??? ??? You can try it. >> > >? ? ? >??? ??? step 1 : remove the line of php_value from >> loris.conf >> > >? ? ? >??? ??? step 2 : add "php_value[include_path]??? = >> > >? ? ? >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf >> > >? ? ? >??? ??? step 3: reload php-fpm and httpd. >> > >? ? ? >??? ??? Good Luck! >> > >? ? ? >??? ??? Best??? >> > >? ? ? >??? ??? Shen >> > >? ? ? >??? ??? On Mon, 11 Jan 2021 at 15:32, Julie Ashworth, >> HWNI >> > Computing >> > >? ? ? Support >> > >? ? ? >??? ??? <[1][3][3]support-cirl at berkeley.edu> wrote: >> > >? ? ? > >> > >? ? ? >??? ??? ??? hi Shen, >> > >? ? ? >??? ??? ??? that *is* how I installed apache/php7.4. >> > >? ? ? > >> > >? ? ? >??? ??? ??? Please reread my email. >> > >? ? ? > >> > >? ? ? >??? ??? ??? I'd like to know how y'all recommend >> adding the php >> > path for >> > >? ? ? loris >> > >? ? ? >??? ??? ??? libraries using php-fpm. >> > >? ? ? > >> > >? ? ? >??? ??? ??? If I use the apache configuration file >> provided: >> > >? ? ? >??? ??? ??? ??? ??? ??? ??? php_value >> include_path >> > >? ? ? >??? ??? ??? >> > >? ? ? >> > >> .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries >> > >? ? ? > >> > >? ? ? >??? ??? ??? I get an error: >> > >? ? ? >??? ??? ??? Invalid command 'php_value', perhaps >> misspelled or >> > defined by a >> > >? ? ? module >> > >? ? ? >??? ??? ??? not included in the server configuration >> > >? ? ? > >> > >? ? ? >??? ??? ??? ... because this isn't supported with >> php-fpm >> > >? ? ? > >> > >? ? ? >??? ??? ??? best, >> > >? ? ? >??? ??? ??? Julie >> > >? ? ? > >> > >? ? ? >??? ??? ??? On 11-01-2021 10.08 -0500, Shen Wang >> wrote: >> > >? ? ? >??? ??? ??? >??? ??? Hi Julie, >> > >? ? ? >??? ??? ??? >??? ??? I recommend reinstalling php >> 7.4 and apache. >> > >? ? ? >??? ??? ??? >??? ??? >> > >? ? ? [1][2][4][4] >> https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > this >> > >? ? ? >??? ??? ??? article is >> > >? ? ? >??? ??? ??? >??? ??? helpful. >> > >? ? ? >??? ??? ??? >??? ??? Best >> > >? ? ? >??? ??? ??? >??? ??? Shen >> > >? ? ? >??? ??? ??? > >> > >? ? ? >??? ??? ??? > References >> > >? ? ? >??? ??? ??? > >> > >? ? ? >??? ??? ??? >??? ??? Visible links >> > >? ? ? >??? ??? ??? >??? ??? 1. >> > >? ? ? [3][5][5] >> https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > >? ? ? >??? ??? ??? ---end quoted text--- >> > >? ? ? > >> > >? ? ? >??? ??? -- >> > >? ? ? >??? ??? Shen Wang >> > >? ? ? >??? ??? [4]Loris??? Developer >> > >? ? ? >??? ??? Montreal Neurological Institute??? >> > >? ? ? >??? ??? McGill University >> > >? ? ? > >> > >? ? ? > References >> > >? ? ? > >> > >? ? ? >??? ??? Visible links >> > >? ? ? >??? ??? 1. mailto:[6][6]support-cirl at berkeley.edu >> > >? ? ? >??? ??? 2. >> > [7][7]https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > >? ? ? >??? ??? 3. >> > [8][8]https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > >? ? ? >??? ??? 4. [9][9]https://github.com/aces/Loris >> > >? ? ? ---end quoted text--- >> > > >> > >? ? -- >> > >? ? Shen Wang >> > >? ? [10]Loris??? Developer >> > >? ? Montreal Neurological Institute??? >> > >? ? McGill University >> > > >> > > References >> > > >> > >? ? Visible links >> > >? ? 2. mailto:[10]support-cirl at berkeley.edu >> > >? ? 3. mailto:[11]support-cirl at berkeley.edu >> > >? ? 4. [12] >> https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > >? ? 5. [13] >> https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > >? ? 6. mailto:[14]support-cirl at berkeley.edu >> > >? ? 7. [15] >> https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > >? ? 8. [16] >> https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > >? ? 9. [17]https://github.com/aces/Loris >> > >? ? 10. [18]https://github.com/aces/Loris >> > >> > ---end quoted text--- >> > >> > -- >> > Shen Wang >> > [19]Loris? Developer >> > Montreal Neurological Institute? >> > McGill University >> > >> > References >> > >> > Visible links >> > 1. mailto:support-cirl at berkeley.edu >> > 2. mailto:support-cirl at berkeley.edu >> > 3. mailto:support-cirl at berkeley.edu >> > 4. https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > 5. https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > 6. mailto:support-cirl at berkeley.edu >> > 7. https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > 8. https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > 9. https://github.com/aces/Loris >> > 10. mailto:support-cirl at berkeley.edu >> > 11. mailto:support-cirl at berkeley.edu >> > 12. https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > 13. https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > 14. mailto:support-cirl at berkeley.edu >> > 15. https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > 16. https://tecadmin.net/install-apache-php-fpm-centos-8/ >> > 17. https://github.com/aces/Loris >> > 18. https://github.com/aces/Loris >> > 19. https://github.com/aces/Loris >> ---end quoted text--- >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From laetitia.fesselier at mcin.ca Tue Jan 12 15:02:59 2021 From: laetitia.fesselier at mcin.ca (Laetitia Fesselier) Date: Tue, 12 Jan 2021 15:02:59 -0500 Subject: [Loris-dev] Error Webpack installing v22.0.0 In-Reply-To: <72D9F51B-BBAC-497A-9FC7-B64EFF3F7812@bwh.harvard.edu> References: <72D9F51B-BBAC-497A-9FC7-B64EFF3F7812@bwh.harvard.edu> Message-ID: Hello Alfredo, I suggest you try the following: - delete the node_modules folder: *rm -R node_modules* - reinstall all the node libraries *npm install* - compile *npm run compile* Let us know if you need further assistance. Regards, Laetitia On Mon, Jan 11, 2021 at 4:59 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev Team, > > I am upgrading Loris from v21.0.0 to v22.0.0 ( > https://github.com/aces/Loris/releases/tag/v22.0.0). After installation > of node v10.13.0 and npm 6.4.1, and getting the corresponding source code, > I am getting the following error when executing ?make all?: > > === > *ERROR in ./jsx/DynamicDataTable.js* > * Module build failed (from ./node_modules/babel-loader/lib/index.js):* > * Error: Cannot find module 'babel-plugin-transform-object-rest-spread' > from '/var/www/loris'* > * at Function.module.exports [as sync] > (/var/www/loris/node_modules/resolve/lib/sync.js:74:15)* > * at resolveStandardizedName > (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31)* > * at resolvePlugin > (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10)* > * at loadPlugin > (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20)* > * at createDescriptor > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9)* > * at items.map > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50)* > * at Array.map ()* > * at createDescriptors > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29)* > * at createPluginDescriptors > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10)* > * at plugins > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19)* > * at mergeChainOpts > (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26)* > * at > /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7* > * at buildRootChain > (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22)* > * at loadPrivatePartialConfig > (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55)* > * at Object.loadPartialConfig > (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18)* > * at Object. > (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26)* > * at Generator.next ()* > * at asyncGeneratorStep > (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103)* > * at _next > (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194)* > * at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364* > * at new Promise ()* > * at Object. > (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97)* > * at Object._loader > (/var/www/loris/node_modules/babel-loader/lib/index.js:224:18)* > * at Object.loader > (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18)* > * at Object. > (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12)* > === > > I am running Ubuntu Xenial 16.04.4 > > I also tried using node v14.15.4 but got the same error. > > Do you have suggestions on how to solve this? > > Regards, > Alfredo. > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Tue Jan 12 15:22:08 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Tue, 12 Jan 2021 15:22:08 -0500 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> <20210111203246.GA49193@oi.attlocal.net> <20210111212739.GA49780@oi.attlocal.net> <20210112162730.GA57593@oi.attlocal.net> <20210112165208.GB58113@oi.attlocal.net> Message-ID: Hi Julie, CentOS is no longer supported (by which I mean the operating system itself has been discontinued, not the LORIS support for it.) The MCIN production servers currently run on CentOS7 which is why the installation procedure is well documented/tested for that system, but given the discontinuation of CentOS the plan is to move our production servers off of CentOS entirely. It's worth noting that CentOS 8 EOL is 2021, while CentOS 7 EOL is 2024. This is the reason why our documentation is tailored to V7. We don't have much experience running LORIS under php-fpm, which is why there's no documentation for that environment. At one point years ago I had written a configuration file in order to use it in Travis CI, but since then testing/development has moved towards using Docker and the built-in PHP web server (I just looked at that configuration file and it's so old it refers to php5..). mod_php is currently the only supported/documented PHP environment as it's all most of the LORIS developers have experience with (though I also regularly develop with the php built in dev server, so I'm confident that that works as well.) The good news is our dependency on apache/mod_php is much weaker than it was when I had worked on it years ago, but the bad news is there's no written documentation that I'm aware of. If you're willing to do the work of debugging the environment we can help where we can, but if you're trying to get a system up and quickly it's likely faster and easier to use something that we have more experience with. For reference, I don't think the php_value setting you're trying to set should be required anywhere by LORIS. LORIS uses an autoloader for class/include resolution and shouldn't depend on the PHP include_path. If you're set on php-fpm you can look at docs/config/apache2-fastcgi as a starting point, but note that that configuration is from 2014 (which as far as I know is the last time anyone tried to use LORIS in that environment.) P.S. (Forgive me if I'm slow to respond to any emails as I'm on vacation until next week..) On Tue, Jan 12, 2021 at 12:39 PM Julie Ashworth, HWNI Computing Support < support-cirl at berkeley.edu> wrote: > Thank you, > In the last 4 emails I have simply asked for current linux documentation, > not centos8 documentation (preferably that mentions php-fpm configuration). > Is that available? > > > > On Tue, Jan 12, 2021, 8:59 AM Samir Das wrote: > >> Hi Julie, >> >> We'll do our best to help you with this configuration. :) We'll send you >> any documentation we have. >> >> Regarding CentOS, since RedHat has discontinued its support, we are >> planning on putting our testing resources elsewhere. We have yet to discuss >> CentOS-Stream, which we will do next week. But I wouldn't worry too much... >> we'll help as much as we can given that you have already installed it, etc. >> If the problems become too tedious, then we can figure out options together. >> >> Best, >> >> Samir Das >> >> On Tue, Jan 12, 2021 at 5:52 PM Julie Ashworth, HWNI Computing Support < >> support-cirl at berkeley.edu> wrote: >> >>> hi Shen, >>> >>> On 12-01-2021 11.40 -0500, Shen Wang wrote: >>> > So Loris team will not support? Centos. We will only >>> support? Ubuntu in the future.? >>> >>> That's interesting that CentOS will no longer be supported. >>> >>> Since you previously mentioned that CentOS8 should work, I already >>> started the installation, and I'd like to see if it works. >>> >>> So, please, please... >>> will you please send me a link to the most recent instruction for loris >>> installation that includes the php_value in /etc/php-fpm.d? >>> As I said, I can modify ubuntu instructions. I don't need instructions >>> specific to CentOS. >>> >>> thanks, >>> Julie >>> >>> >>> >>> On 12-01-2021 11.40 -0500, Shen Wang wrote: >>> > Hi Julie, >>> > We are holding the Loris meeting to discuss whether to support >>> centos in >>> > the future.? >>> > Loris's? sub-modules have issues with the Centos system. So Loris >>> team will >>> > not support? Centos. >>> > We will only support? Ubuntu in the future.? >>> > Best? >>> > Shen >>> > On Tue, 12 Jan 2021 at 11:27, Julie Ashworth, HWNI Computing Support >>> > <[1]support-cirl at berkeley.edu> wrote: >>> > >>> > hi Shen, >>> > I'm looking for documentation of the (useful!) instruction you >>> provided >>> > in your previous email: >>> > >>> > >??? ??? step 2 : add "php_value[include_path]??? = >>> > >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf >>> > >>> > I would appreciate a link to that documentation, because I think >>> it >>> > would be valuable for the future. I can adapt Ubuntu >>> documentation for >>> > CentOS. >>> > >>> > thanks, >>> > Julie >>> > >>> > On 12-01-2021 09.14 -0500, Shen Wang wrote: >>> > >? ? Hi Julie, >>> > > >>> > >? ? The Loris Team only supports Centos7 currently. >>> > >? ? We don't have Centos8 instructions yet, so you can't find >>> it. >>> > > >>> > >? ? If you and Ioannis would like to install loris 23 on >>> centos 8, you >>> > can >>> > >? ? try. >>> > >? ? I have installed loris 23 on centos 8, although the >>> process is not >>> > simple. >>> > >? ? That is why I mentioned Centos 8, not officially supported >>> yet. >>> > Sorry for >>> > >? ? confusion. >>> > >? ? best >>> > >? ? Shen >>> > >? ? [1]???? ???????????????????? 2021-01-11 ????????? >>> ??8.04.56.png >>> > >? ? On Mon, 11 Jan 2021 at 16:27, Julie Ashworth, HWNI >>> Computing >>> > Support >>> > >? ? <[2][2]support-cirl at berkeley.edu> wrote: >>> > > >>> > >? ? ? Thanks Shen, >>> > >? ? ? Is this documented anywhere? I checked the Ubuntu >>> instructions >>> > and the >>> > >? ? ? install.sh file, but I don't see it mentioned. >>> > > >>> > >? ? ? You also mentioned to Ioannis that Loris should run >>> find on >>> > CentOS8. >>> > >? ? ? Which version did you recommend for CentOS8? >>> > > >>> > >? ? ? best, >>> > >? ? ? Julie >>> > > >>> > >? ? ? On 11-01-2021 16.04 -0500, Shen Wang wrote: >>> > >? ? ? >??? ??? Hi Julie, >>> > >? ? ? >??? ??? We do not support Loris 23.0.2 to run on >>> CentOS 8. >>> > >? ? ? >??? ??? You can install 23.0.2 on Centos 7. >>> > >? ? ? >??? ??? If you want to try to install it on Centos8. >>> There is no >>> > guarantee >>> > >? ? ? that it >>> > >? ? ? >??? ??? will work on Centos 8. >>> > >? ? ? >??? ??? You can try it. >>> > >? ? ? >??? ??? step 1 : remove the line of php_value from >>> loris.conf >>> > >? ? ? >??? ??? step 2 : add "php_value[include_path]??? = >>> > >? ? ? >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf >>> > >? ? ? >??? ??? step 3: reload php-fpm and httpd. >>> > >? ? ? >??? ??? Good Luck! >>> > >? ? ? >??? ??? Best??? >>> > >? ? ? >??? ??? Shen >>> > >? ? ? >??? ??? On Mon, 11 Jan 2021 at 15:32, Julie >>> Ashworth, HWNI >>> > Computing >>> > >? ? ? Support >>> > >? ? ? >??? ??? <[1][3][3]support-cirl at berkeley.edu> wrote: >>> > >? ? ? > >>> > >? ? ? >??? ??? ??? hi Shen, >>> > >? ? ? >??? ??? ??? that *is* how I installed apache/php7.4. >>> > >? ? ? > >>> > >? ? ? >??? ??? ??? Please reread my email. >>> > >? ? ? > >>> > >? ? ? >??? ??? ??? I'd like to know how y'all recommend >>> adding the php >>> > path for >>> > >? ? ? loris >>> > >? ? ? >??? ??? ??? libraries using php-fpm. >>> > >? ? ? > >>> > >? ? ? >??? ??? ??? If I use the apache configuration file >>> provided: >>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? php_value >>> include_path >>> > >? ? ? >??? ??? ??? >>> > >? ? ? >>> > >>> .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries >>> > >? ? ? > >>> > >? ? ? >??? ??? ??? I get an error: >>> > >? ? ? >??? ??? ??? Invalid command 'php_value', perhaps >>> misspelled or >>> > defined by a >>> > >? ? ? module >>> > >? ? ? >??? ??? ??? not included in the server configuration >>> > >? ? ? > >>> > >? ? ? >??? ??? ??? ... because this isn't supported with >>> php-fpm >>> > >? ? ? > >>> > >? ? ? >??? ??? ??? best, >>> > >? ? ? >??? ??? ??? Julie >>> > >? ? ? > >>> > >? ? ? >??? ??? ??? On 11-01-2021 10.08 -0500, Shen Wang >>> wrote: >>> > >? ? ? >??? ??? ??? >??? ??? Hi Julie, >>> > >? ? ? >??? ??? ??? >??? ??? I recommend reinstalling php >>> 7.4 and apache. >>> > >? ? ? >??? ??? ??? >??? ??? >>> > >? ? ? [1][2][4][4] >>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > this >>> > >? ? ? >??? ??? ??? article is >>> > >? ? ? >??? ??? ??? >??? ??? helpful. >>> > >? ? ? >??? ??? ??? >??? ??? Best >>> > >? ? ? >??? ??? ??? >??? ??? Shen >>> > >? ? ? >??? ??? ??? > >>> > >? ? ? >??? ??? ??? > References >>> > >? ? ? >??? ??? ??? > >>> > >? ? ? >??? ??? ??? >??? ??? Visible links >>> > >? ? ? >??? ??? ??? >??? ??? 1. >>> > >? ? ? [3][5][5] >>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > >? ? ? >??? ??? ??? ---end quoted text--- >>> > >? ? ? > >>> > >? ? ? >??? ??? -- >>> > >? ? ? >??? ??? Shen Wang >>> > >? ? ? >??? ??? [4]Loris??? Developer >>> > >? ? ? >??? ??? Montreal Neurological Institute??? >>> > >? ? ? >??? ??? McGill University >>> > >? ? ? > >>> > >? ? ? > References >>> > >? ? ? > >>> > >? ? ? >??? ??? Visible links >>> > >? ? ? >??? ??? 1. mailto:[6][6]support-cirl at berkeley.edu >>> > >? ? ? >??? ??? 2. >>> > [7][7]https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > >? ? ? >??? ??? 3. >>> > [8][8]https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > >? ? ? >??? ??? 4. [9][9]https://github.com/aces/Loris >>> > >? ? ? ---end quoted text--- >>> > > >>> > >? ? -- >>> > >? ? Shen Wang >>> > >? ? [10]Loris??? Developer >>> > >? ? Montreal Neurological Institute??? >>> > >? ? McGill University >>> > > >>> > > References >>> > > >>> > >? ? Visible links >>> > >? ? 2. mailto:[10]support-cirl at berkeley.edu >>> > >? ? 3. mailto:[11]support-cirl at berkeley.edu >>> > >? ? 4. [12] >>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > >? ? 5. [13] >>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > >? ? 6. mailto:[14]support-cirl at berkeley.edu >>> > >? ? 7. [15] >>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > >? ? 8. [16] >>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > >? ? 9. [17]https://github.com/aces/Loris >>> > >? ? 10. [18]https://github.com/aces/Loris >>> > >>> > ---end quoted text--- >>> > >>> > -- >>> > Shen Wang >>> > [19]Loris? Developer >>> > Montreal Neurological Institute? >>> > McGill University >>> > >>> > References >>> > >>> > Visible links >>> > 1. mailto:support-cirl at berkeley.edu >>> > 2. mailto:support-cirl at berkeley.edu >>> > 3. mailto:support-cirl at berkeley.edu >>> > 4. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > 5. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > 6. mailto:support-cirl at berkeley.edu >>> > 7. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > 8. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > 9. https://github.com/aces/Loris >>> > 10. mailto:support-cirl at berkeley.edu >>> > 11. mailto:support-cirl at berkeley.edu >>> > 12. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > 13. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > 14. mailto:support-cirl at berkeley.edu >>> > 15. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > 16. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>> > 17. https://github.com/aces/Loris >>> > 18. https://github.com/aces/Loris >>> > 19. https://github.com/aces/Loris >>> ---end quoted text--- >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Tue Jan 12 15:28:09 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Tue, 12 Jan 2021 20:28:09 +0000 Subject: [Loris-dev] Error Webpack installing v22.0.0 In-Reply-To: References: <72D9F51B-BBAC-497A-9FC7-B64EFF3F7812@bwh.harvard.edu> Message-ID: Hi Laetitia, I just executed the steps you suggested and I?m getting the same error (see logs below). Regards, Alfredo. === lorisadmin at ipmsa-loris:/var/www/loris$ npm install > sweetalert2 at 8.18.6 postinstall /var/www/loris/node_modules/sweetalert2 > node bin/postinstall.js Has SweetAlert2 helped you create amazing applications? You can show your <3 and support by making a donation: > https://sweetalert2.github.io/#donations Also, the author of SweetAlert2 (@limonte) is looking for short-term working contracts in front-end, preferably OSS. > https://github.com/limonte npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.9 (node_modules/fsevents): npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents at 1.2.9: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) added 753 packages from 390 contributors and audited 821 packages in 13.253s found 495 vulnerabilities (487 low, 4 moderate, 4 high) run `npm audit fix` to fix them, or `npm audit` for details === === lorisadmin at ipmsa-loris:/var/www/loris$ npm run compile > loris at 1.0.0 compile /var/www/loris > webpack Hash: ef2e2aa8abafb645b741 Version: webpack 4.41.2 Child Hash: ef2e2aa8abafb645b741 Time: 4714ms Built at: 01/12/2021 3:19:49 PM 106 assets Entrypoint ./htdocs/js/components/DynamicDataTable.js = ./htdocs/js/components/DynamicDataTable.js ./htdocs/js/components/DynamicDataTable.js.map Entrypoint ./htdocs/js/components/PaginationLinks.js = ./htdocs/js/components/PaginationLinks.js ./htdocs/js/components/PaginationLinks.js.map Entrypoint ./htdocs/js/components/StaticDataTable.js = ./htdocs/js/components/StaticDataTable.js ./htdocs/js/components/StaticDataTable.js.map . . . . . . ERROR in ./jsx/DynamicDataTable.js Module build failed (from ./node_modules/babel-loader/lib/index.js): Error: Cannot find module 'babel-plugin-transform-object-rest-spread' from '/var/www/loris' at Function.module.exports [as sync] (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) at resolveStandardizedName (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) at resolvePlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) at loadPlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) at createDescriptor (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) at items.map (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) at Array.map () at createDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) at createPluginDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) at plugins (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) at mergeChainOpts (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) at /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 at buildRootChain (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) at loadPrivatePartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) at Object.loadPartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) at Generator.next () at asyncGeneratorStep (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) at _next (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 at new Promise () at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) at Object._loader (/var/www/loris/node_modules/babel-loader/lib/index.js:224:18) at Object.loader (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) ERROR in ./jsx/Form.js Module build failed (from ./node_modules/babel-loader/lib/index.js): Error: Cannot find module 'babel-plugin-transform-object-rest-spread' from '/var/www/loris' at Function.module.exports [as sync] (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) at resolveStandardizedName (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) at resolvePlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) at loadPlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) at createDescriptor (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) at items.map (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) at Array.map () at createDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) at createPluginDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) at plugins (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) at mergeChainOpts (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) at /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 at buildRootChain (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) at loadPrivatePartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) at Object.loadPartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) at Generator.next () at asyncGeneratorStep (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) at _next (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 at new Promise () at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) at Object.loader (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) === On Jan 12, 2021, at 3:02 PM, Laetitia Fesselier > wrote: External Email - Use Caution Hello Alfredo, I suggest you try the following: - delete the node_modules folder: rm -R node_modules - reinstall all the node libraries npm install - compile npm run compile Let us know if you need further assistance. Regards, Laetitia On Mon, Jan 11, 2021 at 4:59 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev Team, I am upgrading Loris from v21.0.0 to v22.0.0 (https://github.com/aces/Loris/releases/tag/v22.0.0). After installation of node v10.13.0 and npm 6.4.1, and getting the corresponding source code, I am getting the following error when executing ?make all?: === ERROR in ./jsx/DynamicDataTable.js Module build failed (from ./node_modules/babel-loader/lib/index.js): Error: Cannot find module 'babel-plugin-transform-object-rest-spread' from '/var/www/loris' at Function.module.exports [as sync] (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) at resolveStandardizedName (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) at resolvePlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) at loadPlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) at createDescriptor (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) at items.map (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) at Array.map () at createDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) at createPluginDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) at plugins (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) at mergeChainOpts (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) at /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 at buildRootChain (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) at loadPrivatePartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) at Object.loadPartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) at Generator.next () at asyncGeneratorStep (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) at _next (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 at new Promise () at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) at Object._loader (/var/www/loris/node_modules/babel-loader/lib/index.js:224:18) at Object.loader (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) === I am running Ubuntu Xenial 16.04.4 I also tried using node v14.15.4 but got the same error. Do you have suggestions on how to solve this? Regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Tue Jan 12 16:03:38 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Tue, 12 Jan 2021 21:03:38 +0000 Subject: [Loris-dev] Error Webpack installing v22.0.0 In-Reply-To: References: <72D9F51B-BBAC-497A-9FC7-B64EFF3F7812@bwh.harvard.edu> Message-ID: Hi Laetitia, I just compiled it in a different folder and it worked. I think I have some some issues with permissions in the /var/www/loris folder. Any ideas? Regards, Alfredo. On Jan 12, 2021, at 3:28 PM, Morales Pinzon, Alfredo > wrote: External Email - Use Caution Hi Laetitia, I just executed the steps you suggested and I?m getting the same error (see logs below). Regards, Alfredo. === lorisadmin at ipmsa-loris:/var/www/loris$ npm install > sweetalert2 at 8.18.6 postinstall /var/www/loris/node_modules/sweetalert2 > node bin/postinstall.js Has SweetAlert2 helped you create amazing applications? You can show your <3 and support by making a donation: > https://sweetalert2.github.io/#donations Also, the author of SweetAlert2 (@limonte) is looking for short-term working contracts in front-end, preferably OSS. > https://github.com/limonte npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.9 (node_modules/fsevents): npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents at 1.2.9: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) added 753 packages from 390 contributors and audited 821 packages in 13.253s found 495 vulnerabilities (487 low, 4 moderate, 4 high) run `npm audit fix` to fix them, or `npm audit` for details === === lorisadmin at ipmsa-loris:/var/www/loris$ npm run compile > loris at 1.0.0 compile /var/www/loris > webpack Hash: ef2e2aa8abafb645b741 Version: webpack 4.41.2 Child Hash: ef2e2aa8abafb645b741 Time: 4714ms Built at: 01/12/2021 3:19:49 PM 106 assets Entrypoint ./htdocs/js/components/DynamicDataTable.js = ./htdocs/js/components/DynamicDataTable.js ./htdocs/js/components/DynamicDataTable.js.map Entrypoint ./htdocs/js/components/PaginationLinks.js = ./htdocs/js/components/PaginationLinks.js ./htdocs/js/components/PaginationLinks.js.map Entrypoint ./htdocs/js/components/StaticDataTable.js = ./htdocs/js/components/StaticDataTable.js ./htdocs/js/components/StaticDataTable.js.map . . . . . . ERROR in ./jsx/DynamicDataTable.js Module build failed (from ./node_modules/babel-loader/lib/index.js): Error: Cannot find module 'babel-plugin-transform-object-rest-spread' from '/var/www/loris' at Function.module.exports [as sync] (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) at resolveStandardizedName (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) at resolvePlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) at loadPlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) at createDescriptor (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) at items.map (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) at Array.map () at createDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) at createPluginDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) at plugins (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) at mergeChainOpts (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) at /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 at buildRootChain (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) at loadPrivatePartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) at Object.loadPartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) at Generator.next () at asyncGeneratorStep (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) at _next (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 at new Promise () at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) at Object._loader (/var/www/loris/node_modules/babel-loader/lib/index.js:224:18) at Object.loader (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) ERROR in ./jsx/Form.js Module build failed (from ./node_modules/babel-loader/lib/index.js): Error: Cannot find module 'babel-plugin-transform-object-rest-spread' from '/var/www/loris' at Function.module.exports [as sync] (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) at resolveStandardizedName (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) at resolvePlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) at loadPlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) at createDescriptor (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) at items.map (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) at Array.map () at createDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) at createPluginDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) at plugins (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) at mergeChainOpts (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) at /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 at buildRootChain (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) at loadPrivatePartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) at Object.loadPartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) at Generator.next () at asyncGeneratorStep (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) at _next (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 at new Promise () at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) at Object.loader (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) === On Jan 12, 2021, at 3:02 PM, Laetitia Fesselier > wrote: External Email - Use Caution Hello Alfredo, I suggest you try the following: - delete the node_modules folder: rm -R node_modules - reinstall all the node libraries npm install - compile npm run compile Let us know if you need further assistance. Regards, Laetitia On Mon, Jan 11, 2021 at 4:59 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev Team, I am upgrading Loris from v21.0.0 to v22.0.0 (https://github.com/aces/Loris/releases/tag/v22.0.0). After installation of node v10.13.0 and npm 6.4.1, and getting the corresponding source code, I am getting the following error when executing ?make all?: === ERROR in ./jsx/DynamicDataTable.js Module build failed (from ./node_modules/babel-loader/lib/index.js): Error: Cannot find module 'babel-plugin-transform-object-rest-spread' from '/var/www/loris' at Function.module.exports [as sync] (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) at resolveStandardizedName (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) at resolvePlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) at loadPlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) at createDescriptor (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) at items.map (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) at Array.map () at createDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) at createPluginDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) at plugins (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) at mergeChainOpts (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) at /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 at buildRootChain (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) at loadPrivatePartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) at Object.loadPartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) at Generator.next () at asyncGeneratorStep (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) at _next (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 at new Promise () at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) at Object._loader (/var/www/loris/node_modules/babel-loader/lib/index.js:224:18) at Object.loader (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) === I am running Ubuntu Xenial 16.04.4 I also tried using node v14.15.4 but got the same error. Do you have suggestions on how to solve this? Regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://secure-web.cisco.com/1bkeKKx5RznkqKIva0HYzoY9MxgvLhGMQxvSLxTHjd66w8yNVGszrvu4KCxIR0Jrk9lR2hJb2vk6VJcKx4tk-YtW6ojgznXup82Lja8z84lzCX7kpH4Ug862eQgGxj9ngmkK7HDSutOq50hga2YFHjg-nj66X-9KfKCb11MZf7cTewb4j8Rc7L-ZWKzLP0WLBMt24FQMlnB9bLmXII8LT5xu9Gjyc2tWSOxGuHLRILZhRJkusC6vj1t1QjeucpKopGGH9A9-GFCDifS9o3pySGQ/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From support-cirl at berkeley.edu Tue Jan 12 16:17:53 2021 From: support-cirl at berkeley.edu (Julie Ashworth, HWNI Computing Support) Date: Tue, 12 Jan 2021 13:17:53 -0800 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> <20210111203246.GA49193@oi.attlocal.net> <20210111212739.GA49780@oi.attlocal.net> <20210112162730.GA57593@oi.attlocal.net> <20210112165208.GB58113@oi.attlocal.net> Message-ID: Thanks Dave, There are many groups taking over development of Centos8, so I thinks it's incorrect to say that it's discontinued. The most active group is Rocky linux, started by Greg Kurtzer, who also founded the original CentOS project 15 years ago. https://rockylinux.org/ I have no personal interest in using php-fpm. I was following the centos7 instructions to install php-fpm, but there was an apache error expecting mod_php. I'm happy to install mod_php but that is not documnted in the centos7 instructions. To be honest, I'm really disappointed in the loris documentation and that my emails aren't being read carefully. On Tue, Jan 12, 2021, 12:22 PM Dave MacFarlane wrote: > Hi Julie, > > CentOS is no longer supported (by which I mean the operating system itself > has been discontinued, not the LORIS support for it.) The MCIN production > servers currently run on CentOS7 which is why the installation procedure is > well documented/tested for that system, but given the discontinuation of > CentOS the plan is to move our production servers off of CentOS entirely. > It's worth noting that CentOS 8 EOL is 2021, while CentOS 7 EOL is 2024. > This is the reason why our documentation is tailored to V7. > > We don't have much experience running LORIS under php-fpm, which is why > there's no documentation for that environment. At one point years ago I had > written a configuration file in order to use it in Travis CI, but since > then testing/development has moved towards using Docker and the built-in > PHP web server (I just looked at that configuration file and it's so old it > refers to php5..). mod_php is currently the only supported/documented PHP > environment as it's all most of the LORIS developers have experience with > (though I also regularly develop with the php built in dev server, so I'm > confident that that works as well.) > > The good news is our dependency on apache/mod_php is much weaker than it > was when I had worked on it years ago, but the bad news is there's no > written documentation that I'm aware of. > > If you're willing to do the work of debugging the environment we can help > where we can, but if you're trying to get a system up and quickly it's > likely faster and easier to use something that we have more experience > with. For reference, I don't think the php_value setting you're trying to > set should be required anywhere by LORIS. LORIS uses an autoloader for > class/include resolution and shouldn't depend on the PHP include_path. If > you're set on php-fpm you can look at docs/config/apache2-fastcgi as a > starting point, but note that that configuration is from 2014 (which as far > as I know is the last time anyone tried to use LORIS in that environment.) > > P.S. (Forgive me if I'm slow to respond to any emails as I'm on vacation > until next week..) > > On Tue, Jan 12, 2021 at 12:39 PM Julie Ashworth, HWNI Computing Support < > support-cirl at berkeley.edu> wrote: > >> Thank you, >> In the last 4 emails I have simply asked for current linux >> documentation, not centos8 documentation (preferably that mentions php-fpm >> configuration). Is that available? >> >> >> >> On Tue, Jan 12, 2021, 8:59 AM Samir Das wrote: >> >>> Hi Julie, >>> >>> We'll do our best to help you with this configuration. :) We'll send you >>> any documentation we have. >>> >>> Regarding CentOS, since RedHat has discontinued its support, we are >>> planning on putting our testing resources elsewhere. We have yet to discuss >>> CentOS-Stream, which we will do next week. But I wouldn't worry too much... >>> we'll help as much as we can given that you have already installed it, etc. >>> If the problems become too tedious, then we can figure out options together. >>> >>> Best, >>> >>> Samir Das >>> >>> On Tue, Jan 12, 2021 at 5:52 PM Julie Ashworth, HWNI Computing Support < >>> support-cirl at berkeley.edu> wrote: >>> >>>> hi Shen, >>>> >>>> On 12-01-2021 11.40 -0500, Shen Wang wrote: >>>> > So Loris team will not support? Centos. We will only >>>> support? Ubuntu in the future.? >>>> >>>> That's interesting that CentOS will no longer be supported. >>>> >>>> Since you previously mentioned that CentOS8 should work, I already >>>> started the installation, and I'd like to see if it works. >>>> >>>> So, please, please... >>>> will you please send me a link to the most recent instruction for loris >>>> installation that includes the php_value in /etc/php-fpm.d? >>>> As I said, I can modify ubuntu instructions. I don't need instructions >>>> specific to CentOS. >>>> >>>> thanks, >>>> Julie >>>> >>>> >>>> >>>> On 12-01-2021 11.40 -0500, Shen Wang wrote: >>>> > Hi Julie, >>>> > We are holding the Loris meeting to discuss whether to support >>>> centos in >>>> > the future.? >>>> > Loris's? sub-modules have issues with the Centos system. So Loris >>>> team will >>>> > not support? Centos. >>>> > We will only support? Ubuntu in the future.? >>>> > Best? >>>> > Shen >>>> > On Tue, 12 Jan 2021 at 11:27, Julie Ashworth, HWNI Computing >>>> Support >>>> > <[1]support-cirl at berkeley.edu> wrote: >>>> > >>>> > hi Shen, >>>> > I'm looking for documentation of the (useful!) instruction you >>>> provided >>>> > in your previous email: >>>> > >>>> > >??? ??? step 2 : add "php_value[include_path]??? = >>>> > >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf >>>> > >>>> > I would appreciate a link to that documentation, because I think >>>> it >>>> > would be valuable for the future. I can adapt Ubuntu >>>> documentation for >>>> > CentOS. >>>> > >>>> > thanks, >>>> > Julie >>>> > >>>> > On 12-01-2021 09.14 -0500, Shen Wang wrote: >>>> > >? ? Hi Julie, >>>> > > >>>> > >? ? The Loris Team only supports Centos7 currently. >>>> > >? ? We don't have Centos8 instructions yet, so you can't find >>>> it. >>>> > > >>>> > >? ? If you and Ioannis would like to install loris 23 on >>>> centos 8, you >>>> > can >>>> > >? ? try. >>>> > >? ? I have installed loris 23 on centos 8, although the >>>> process is not >>>> > simple. >>>> > >? ? That is why I mentioned Centos 8, not officially >>>> supported yet. >>>> > Sorry for >>>> > >? ? confusion. >>>> > >? ? best >>>> > >? ? Shen >>>> > >? ? [1]???? ???????????????????? 2021-01-11 ????????? >>>> ??8.04.56.png >>>> > >? ? On Mon, 11 Jan 2021 at 16:27, Julie Ashworth, HWNI >>>> Computing >>>> > Support >>>> > >? ? <[2][2]support-cirl at berkeley.edu> wrote: >>>> > > >>>> > >? ? ? Thanks Shen, >>>> > >? ? ? Is this documented anywhere? I checked the Ubuntu >>>> instructions >>>> > and the >>>> > >? ? ? install.sh file, but I don't see it mentioned. >>>> > > >>>> > >? ? ? You also mentioned to Ioannis that Loris should run >>>> find on >>>> > CentOS8. >>>> > >? ? ? Which version did you recommend for CentOS8? >>>> > > >>>> > >? ? ? best, >>>> > >? ? ? Julie >>>> > > >>>> > >? ? ? On 11-01-2021 16.04 -0500, Shen Wang wrote: >>>> > >? ? ? >??? ??? Hi Julie, >>>> > >? ? ? >??? ??? We do not support Loris 23.0.2 to run on >>>> CentOS 8. >>>> > >? ? ? >??? ??? You can install 23.0.2 on Centos 7. >>>> > >? ? ? >??? ??? If you want to try to install it on >>>> Centos8. There is no >>>> > guarantee >>>> > >? ? ? that it >>>> > >? ? ? >??? ??? will work on Centos 8. >>>> > >? ? ? >??? ??? You can try it. >>>> > >? ? ? >??? ??? step 1 : remove the line of php_value from >>>> loris.conf >>>> > >? ? ? >??? ??? step 2 : add "php_value[include_path]??? = >>>> > >? ? ? >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf >>>> > >? ? ? >??? ??? step 3: reload php-fpm and httpd. >>>> > >? ? ? >??? ??? Good Luck! >>>> > >? ? ? >??? ??? Best??? >>>> > >? ? ? >??? ??? Shen >>>> > >? ? ? >??? ??? On Mon, 11 Jan 2021 at 15:32, Julie >>>> Ashworth, HWNI >>>> > Computing >>>> > >? ? ? Support >>>> > >? ? ? >??? ??? <[1][3][3]support-cirl at berkeley.edu> wrote: >>>> > >? ? ? > >>>> > >? ? ? >??? ??? ??? hi Shen, >>>> > >? ? ? >??? ??? ??? that *is* how I installed >>>> apache/php7.4. >>>> > >? ? ? > >>>> > >? ? ? >??? ??? ??? Please reread my email. >>>> > >? ? ? > >>>> > >? ? ? >??? ??? ??? I'd like to know how y'all recommend >>>> adding the php >>>> > path for >>>> > >? ? ? loris >>>> > >? ? ? >??? ??? ??? libraries using php-fpm. >>>> > >? ? ? > >>>> > >? ? ? >??? ??? ??? If I use the apache configuration file >>>> provided: >>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? php_value >>>> include_path >>>> > >? ? ? >??? ??? ??? >>>> > >? ? ? >>>> > >>>> .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries >>>> > >? ? ? > >>>> > >? ? ? >??? ??? ??? I get an error: >>>> > >? ? ? >??? ??? ??? Invalid command 'php_value', perhaps >>>> misspelled or >>>> > defined by a >>>> > >? ? ? module >>>> > >? ? ? >??? ??? ??? not included in the server >>>> configuration >>>> > >? ? ? > >>>> > >? ? ? >??? ??? ??? ... because this isn't supported with >>>> php-fpm >>>> > >? ? ? > >>>> > >? ? ? >??? ??? ??? best, >>>> > >? ? ? >??? ??? ??? Julie >>>> > >? ? ? > >>>> > >? ? ? >??? ??? ??? On 11-01-2021 10.08 -0500, Shen Wang >>>> wrote: >>>> > >? ? ? >??? ??? ??? >??? ??? Hi Julie, >>>> > >? ? ? >??? ??? ??? >??? ??? I recommend reinstalling >>>> php 7.4 and apache. >>>> > >? ? ? >??? ??? ??? >??? ??? >>>> > >? ? ? [1][2][4][4] >>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > this >>>> > >? ? ? >??? ??? ??? article is >>>> > >? ? ? >??? ??? ??? >??? ??? helpful. >>>> > >? ? ? >??? ??? ??? >??? ??? Best >>>> > >? ? ? >??? ??? ??? >??? ??? Shen >>>> > >? ? ? >??? ??? ??? > >>>> > >? ? ? >??? ??? ??? > References >>>> > >? ? ? >??? ??? ??? > >>>> > >? ? ? >??? ??? ??? >??? ??? Visible links >>>> > >? ? ? >??? ??? ??? >??? ??? 1. >>>> > >? ? ? [3][5][5] >>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > >? ? ? >??? ??? ??? ---end quoted text--- >>>> > >? ? ? > >>>> > >? ? ? >??? ??? -- >>>> > >? ? ? >??? ??? Shen Wang >>>> > >? ? ? >??? ??? [4]Loris??? Developer >>>> > >? ? ? >??? ??? Montreal Neurological Institute??? >>>> > >? ? ? >??? ??? McGill University >>>> > >? ? ? > >>>> > >? ? ? > References >>>> > >? ? ? > >>>> > >? ? ? >??? ??? Visible links >>>> > >? ? ? >??? ??? 1. mailto:[6][6]support-cirl at berkeley.edu >>>> > >? ? ? >??? ??? 2. >>>> > [7][7]https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > >? ? ? >??? ??? 3. >>>> > [8][8]https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > >? ? ? >??? ??? 4. [9][9]https://github.com/aces/Loris >>>> > >? ? ? ---end quoted text--- >>>> > > >>>> > >? ? -- >>>> > >? ? Shen Wang >>>> > >? ? [10]Loris??? Developer >>>> > >? ? Montreal Neurological Institute??? >>>> > >? ? McGill University >>>> > > >>>> > > References >>>> > > >>>> > >? ? Visible links >>>> > >? ? 2. mailto:[10]support-cirl at berkeley.edu >>>> > >? ? 3. mailto:[11]support-cirl at berkeley.edu >>>> > >? ? 4. [12] >>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > >? ? 5. [13] >>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > >? ? 6. mailto:[14]support-cirl at berkeley.edu >>>> > >? ? 7. [15] >>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > >? ? 8. [16] >>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > >? ? 9. [17]https://github.com/aces/Loris >>>> > >? ? 10. [18]https://github.com/aces/Loris >>>> > >>>> > ---end quoted text--- >>>> > >>>> > -- >>>> > Shen Wang >>>> > [19]Loris? Developer >>>> > Montreal Neurological Institute? >>>> > McGill University >>>> > >>>> > References >>>> > >>>> > Visible links >>>> > 1. mailto:support-cirl at berkeley.edu >>>> > 2. mailto:support-cirl at berkeley.edu >>>> > 3. mailto:support-cirl at berkeley.edu >>>> > 4. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > 5. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > 6. mailto:support-cirl at berkeley.edu >>>> > 7. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > 8. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > 9. https://github.com/aces/Loris >>>> > 10. mailto:support-cirl at berkeley.edu >>>> > 11. mailto:support-cirl at berkeley.edu >>>> > 12. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > 13. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > 14. mailto:support-cirl at berkeley.edu >>>> > 15. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > 16. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>> > 17. https://github.com/aces/Loris >>>> > 18. https://github.com/aces/Loris >>>> > 19. https://github.com/aces/Loris >>>> ---end quoted text--- >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From support-cirl at berkeley.edu Tue Jan 12 16:24:57 2021 From: support-cirl at berkeley.edu (Julie Ashworth, HWNI Computing Support) Date: Tue, 12 Jan 2021 13:24:57 -0800 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: References: <72439D38-0555-4CB1-9098-32CF02979934@berkeley.edu> <20210111005622.GA44097@oi.attlocal.net> <20210111203246.GA49193@oi.attlocal.net> <20210111212739.GA49780@oi.attlocal.net> <20210112162730.GA57593@oi.attlocal.net> <20210112165208.GB58113@oi.attlocal.net> Message-ID: Can you please send me the URL for the most recent linux (ubuntu or centos) installation documentation? Thank you On Tue, Jan 12, 2021, 1:17 PM Julie Ashworth, HWNI Computing Support < support-cirl at berkeley.edu> wrote: > Thanks Dave, > There are many groups taking over development of Centos8, so I thinks it's > incorrect to say that it's discontinued. The most active group is Rocky > linux, started by Greg Kurtzer, who also founded the original CentOS > project 15 years ago. > https://rockylinux.org/ > > I have no personal interest in using php-fpm. I was following the centos7 > instructions to install php-fpm, but there was an apache error expecting mod_php. > I'm happy to install mod_php but that is not documnted in the centos7 > instructions. > To be honest, I'm really disappointed in the loris documentation and that > my emails aren't being read carefully. > > > > On Tue, Jan 12, 2021, 12:22 PM Dave MacFarlane > wrote: > >> Hi Julie, >> >> CentOS is no longer supported (by which I mean the operating system >> itself has been discontinued, not the LORIS support for it.) The MCIN >> production servers currently run on CentOS7 which is why the installation >> procedure is well documented/tested for that system, but given the >> discontinuation of CentOS the plan is to move our production servers off of >> CentOS entirely. It's worth noting that CentOS 8 EOL is 2021, while CentOS >> 7 EOL is 2024. This is the reason why our documentation is tailored to V7. >> >> We don't have much experience running LORIS under php-fpm, which is why >> there's no documentation for that environment. At one point years ago I had >> written a configuration file in order to use it in Travis CI, but since >> then testing/development has moved towards using Docker and the built-in >> PHP web server (I just looked at that configuration file and it's so old it >> refers to php5..). mod_php is currently the only supported/documented PHP >> environment as it's all most of the LORIS developers have experience with >> (though I also regularly develop with the php built in dev server, so I'm >> confident that that works as well.) >> >> The good news is our dependency on apache/mod_php is much weaker than it >> was when I had worked on it years ago, but the bad news is there's no >> written documentation that I'm aware of. >> >> If you're willing to do the work of debugging the environment we can help >> where we can, but if you're trying to get a system up and quickly it's >> likely faster and easier to use something that we have more experience >> with. For reference, I don't think the php_value setting you're trying to >> set should be required anywhere by LORIS. LORIS uses an autoloader for >> class/include resolution and shouldn't depend on the PHP include_path. If >> you're set on php-fpm you can look at docs/config/apache2-fastcgi as a >> starting point, but note that that configuration is from 2014 (which as far >> as I know is the last time anyone tried to use LORIS in that environment.) >> >> P.S. (Forgive me if I'm slow to respond to any emails as I'm on vacation >> until next week..) >> >> On Tue, Jan 12, 2021 at 12:39 PM Julie Ashworth, HWNI Computing Support < >> support-cirl at berkeley.edu> wrote: >> >>> Thank you, >>> In the last 4 emails I have simply asked for current linux >>> documentation, not centos8 documentation (preferably that mentions php-fpm >>> configuration). Is that available? >>> >>> >>> >>> On Tue, Jan 12, 2021, 8:59 AM Samir Das wrote: >>> >>>> Hi Julie, >>>> >>>> We'll do our best to help you with this configuration. :) We'll send >>>> you any documentation we have. >>>> >>>> Regarding CentOS, since RedHat has discontinued its support, we are >>>> planning on putting our testing resources elsewhere. We have yet to discuss >>>> CentOS-Stream, which we will do next week. But I wouldn't worry too much... >>>> we'll help as much as we can given that you have already installed it, etc. >>>> If the problems become too tedious, then we can figure out options together. >>>> >>>> Best, >>>> >>>> Samir Das >>>> >>>> On Tue, Jan 12, 2021 at 5:52 PM Julie Ashworth, HWNI Computing Support < >>>> support-cirl at berkeley.edu> wrote: >>>> >>>>> hi Shen, >>>>> >>>>> On 12-01-2021 11.40 -0500, Shen Wang wrote: >>>>> > So Loris team will not support? Centos. We will only >>>>> support? Ubuntu in the future.? >>>>> >>>>> That's interesting that CentOS will no longer be supported. >>>>> >>>>> Since you previously mentioned that CentOS8 should work, I already >>>>> started the installation, and I'd like to see if it works. >>>>> >>>>> So, please, please... >>>>> will you please send me a link to the most recent instruction for >>>>> loris installation that includes the php_value in /etc/php-fpm.d? >>>>> As I said, I can modify ubuntu instructions. I don't need instructions >>>>> specific to CentOS. >>>>> >>>>> thanks, >>>>> Julie >>>>> >>>>> >>>>> >>>>> On 12-01-2021 11.40 -0500, Shen Wang wrote: >>>>> > Hi Julie, >>>>> > We are holding the Loris meeting to discuss whether to support >>>>> centos in >>>>> > the future.? >>>>> > Loris's? sub-modules have issues with the Centos system. So Loris >>>>> team will >>>>> > not support? Centos. >>>>> > We will only support? Ubuntu in the future.? >>>>> > Best? >>>>> > Shen >>>>> > On Tue, 12 Jan 2021 at 11:27, Julie Ashworth, HWNI Computing >>>>> Support >>>>> > <[1]support-cirl at berkeley.edu> wrote: >>>>> > >>>>> > hi Shen, >>>>> > I'm looking for documentation of the (useful!) instruction you >>>>> provided >>>>> > in your previous email: >>>>> > >>>>> > >??? ??? step 2 : add "php_value[include_path]??? = >>>>> > >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf >>>>> > >>>>> > I would appreciate a link to that documentation, because I >>>>> think it >>>>> > would be valuable for the future. I can adapt Ubuntu >>>>> documentation for >>>>> > CentOS. >>>>> > >>>>> > thanks, >>>>> > Julie >>>>> > >>>>> > On 12-01-2021 09.14 -0500, Shen Wang wrote: >>>>> > >? ? Hi Julie, >>>>> > > >>>>> > >? ? The Loris Team only supports Centos7 currently. >>>>> > >? ? We don't have Centos8 instructions yet, so you can't >>>>> find it. >>>>> > > >>>>> > >? ? If you and Ioannis would like to install loris 23 on >>>>> centos 8, you >>>>> > can >>>>> > >? ? try. >>>>> > >? ? I have installed loris 23 on centos 8, although the >>>>> process is not >>>>> > simple. >>>>> > >? ? That is why I mentioned Centos 8, not officially >>>>> supported yet. >>>>> > Sorry for >>>>> > >? ? confusion. >>>>> > >? ? best >>>>> > >? ? Shen >>>>> > >? ? [1]???? ???????????????????? 2021-01-11 ????????? >>>>> ??8.04.56.png >>>>> > >? ? On Mon, 11 Jan 2021 at 16:27, Julie Ashworth, HWNI >>>>> Computing >>>>> > Support >>>>> > >? ? <[2][2]support-cirl at berkeley.edu> wrote: >>>>> > > >>>>> > >? ? ? Thanks Shen, >>>>> > >? ? ? Is this documented anywhere? I checked the Ubuntu >>>>> instructions >>>>> > and the >>>>> > >? ? ? install.sh file, but I don't see it mentioned. >>>>> > > >>>>> > >? ? ? You also mentioned to Ioannis that Loris should run >>>>> find on >>>>> > CentOS8. >>>>> > >? ? ? Which version did you recommend for CentOS8? >>>>> > > >>>>> > >? ? ? best, >>>>> > >? ? ? Julie >>>>> > > >>>>> > >? ? ? On 11-01-2021 16.04 -0500, Shen Wang wrote: >>>>> > >? ? ? >??? ??? Hi Julie, >>>>> > >? ? ? >??? ??? We do not support Loris 23.0.2 to run on >>>>> CentOS 8. >>>>> > >? ? ? >??? ??? You can install 23.0.2 on Centos 7. >>>>> > >? ? ? >??? ??? If you want to try to install it on >>>>> Centos8. There is no >>>>> > guarantee >>>>> > >? ? ? that it >>>>> > >? ? ? >??? ??? will work on Centos 8. >>>>> > >? ? ? >??? ??? You can try it. >>>>> > >? ? ? >??? ??? step 1 : remove the line of php_value from >>>>> loris.conf >>>>> > >? ? ? >??? ??? step 2 : add "php_value[include_path]??? = >>>>> > >? ? ? >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf >>>>> > >? ? ? >??? ??? step 3: reload php-fpm and httpd. >>>>> > >? ? ? >??? ??? Good Luck! >>>>> > >? ? ? >??? ??? Best??? >>>>> > >? ? ? >??? ??? Shen >>>>> > >? ? ? >??? ??? On Mon, 11 Jan 2021 at 15:32, Julie >>>>> Ashworth, HWNI >>>>> > Computing >>>>> > >? ? ? Support >>>>> > >? ? ? >??? ??? <[1][3][3]support-cirl at berkeley.edu> >>>>> wrote: >>>>> > >? ? ? > >>>>> > >? ? ? >??? ??? ??? hi Shen, >>>>> > >? ? ? >??? ??? ??? that *is* how I installed >>>>> apache/php7.4. >>>>> > >? ? ? > >>>>> > >? ? ? >??? ??? ??? Please reread my email. >>>>> > >? ? ? > >>>>> > >? ? ? >??? ??? ??? I'd like to know how y'all recommend >>>>> adding the php >>>>> > path for >>>>> > >? ? ? loris >>>>> > >? ? ? >??? ??? ??? libraries using php-fpm. >>>>> > >? ? ? > >>>>> > >? ? ? >??? ??? ??? If I use the apache configuration >>>>> file provided: >>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? php_value >>>>> include_path >>>>> > >? ? ? >??? ??? ??? >>>>> > >? ? ? >>>>> > >>>>> .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries >>>>> > >? ? ? > >>>>> > >? ? ? >??? ??? ??? I get an error: >>>>> > >? ? ? >??? ??? ??? Invalid command 'php_value', perhaps >>>>> misspelled or >>>>> > defined by a >>>>> > >? ? ? module >>>>> > >? ? ? >??? ??? ??? not included in the server >>>>> configuration >>>>> > >? ? ? > >>>>> > >? ? ? >??? ??? ??? ... because this isn't supported with >>>>> php-fpm >>>>> > >? ? ? > >>>>> > >? ? ? >??? ??? ??? best, >>>>> > >? ? ? >??? ??? ??? Julie >>>>> > >? ? ? > >>>>> > >? ? ? >??? ??? ??? On 11-01-2021 10.08 -0500, Shen Wang >>>>> wrote: >>>>> > >? ? ? >??? ??? ??? >??? ??? Hi Julie, >>>>> > >? ? ? >??? ??? ??? >??? ??? I recommend reinstalling >>>>> php 7.4 and apache. >>>>> > >? ? ? >??? ??? ??? >??? ??? >>>>> > >? ? ? [1][2][4][4] >>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > this >>>>> > >? ? ? >??? ??? ??? article is >>>>> > >? ? ? >??? ??? ??? >??? ??? helpful. >>>>> > >? ? ? >??? ??? ??? >??? ??? Best >>>>> > >? ? ? >??? ??? ??? >??? ??? Shen >>>>> > >? ? ? >??? ??? ??? > >>>>> > >? ? ? >??? ??? ??? > References >>>>> > >? ? ? >??? ??? ??? > >>>>> > >? ? ? >??? ??? ??? >??? ??? Visible links >>>>> > >? ? ? >??? ??? ??? >??? ??? 1. >>>>> > >? ? ? [3][5][5] >>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > >? ? ? >??? ??? ??? ---end quoted text--- >>>>> > >? ? ? > >>>>> > >? ? ? >??? ??? -- >>>>> > >? ? ? >??? ??? Shen Wang >>>>> > >? ? ? >??? ??? [4]Loris??? Developer >>>>> > >? ? ? >??? ??? Montreal Neurological Institute??? >>>>> > >? ? ? >??? ??? McGill University >>>>> > >? ? ? > >>>>> > >? ? ? > References >>>>> > >? ? ? > >>>>> > >? ? ? >??? ??? Visible links >>>>> > >? ? ? >??? ??? 1. mailto:[6][6]support-cirl at berkeley.edu >>>>> > >? ? ? >??? ??? 2. >>>>> > [7][7]https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > >? ? ? >??? ??? 3. >>>>> > [8][8]https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > >? ? ? >??? ??? 4. [9][9]https://github.com/aces/Loris >>>>> > >? ? ? ---end quoted text--- >>>>> > > >>>>> > >? ? -- >>>>> > >? ? Shen Wang >>>>> > >? ? [10]Loris??? Developer >>>>> > >? ? Montreal Neurological Institute??? >>>>> > >? ? McGill University >>>>> > > >>>>> > > References >>>>> > > >>>>> > >? ? Visible links >>>>> > >? ? 2. mailto:[10]support-cirl at berkeley.edu >>>>> > >? ? 3. mailto:[11]support-cirl at berkeley.edu >>>>> > >? ? 4. [12] >>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > >? ? 5. [13] >>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > >? ? 6. mailto:[14]support-cirl at berkeley.edu >>>>> > >? ? 7. [15] >>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > >? ? 8. [16] >>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > >? ? 9. [17]https://github.com/aces/Loris >>>>> > >? ? 10. [18]https://github.com/aces/Loris >>>>> > >>>>> > ---end quoted text--- >>>>> > >>>>> > -- >>>>> > Shen Wang >>>>> > [19]Loris? Developer >>>>> > Montreal Neurological Institute? >>>>> > McGill University >>>>> > >>>>> > References >>>>> > >>>>> > Visible links >>>>> > 1. mailto:support-cirl at berkeley.edu >>>>> > 2. mailto:support-cirl at berkeley.edu >>>>> > 3. mailto:support-cirl at berkeley.edu >>>>> > 4. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > 5. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > 6. mailto:support-cirl at berkeley.edu >>>>> > 7. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > 8. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > 9. https://github.com/aces/Loris >>>>> > 10. mailto:support-cirl at berkeley.edu >>>>> > 11. mailto:support-cirl at berkeley.edu >>>>> > 12. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > 13. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > 14. mailto:support-cirl at berkeley.edu >>>>> > 15. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > 16. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>> > 17. https://github.com/aces/Loris >>>>> > 18. https://github.com/aces/Loris >>>>> > 19. https://github.com/aces/Loris >>>>> ---end quoted text--- >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From laetitia.fesselier at mcin.ca Tue Jan 12 16:37:07 2021 From: laetitia.fesselier at mcin.ca (Laetitia Fesselier) Date: Tue, 12 Jan 2021 16:37:07 -0500 Subject: [Loris-dev] Error Webpack installing v22.0.0 In-Reply-To: References: <72D9F51B-BBAC-497A-9FC7-B64EFF3F7812@bwh.harvard.edu> Message-ID: Can you check that your .babelrc file is identical to the one on the v22.0 branch: https://github.com/aces/Loris/blob/22.0-release/.babelrc ? Regards, Laetitia On Tue, Jan 12, 2021 at 4:04 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Laetitia, > > I just compiled it in a different folder and it worked. I think I have > some some issues with permissions in the /var/www/loris folder. Any ideas? > > Regards, > Alfredo. > > On Jan 12, 2021, at 3:28 PM, Morales Pinzon, Alfredo < > AMORALESPINZON at BWH.HARVARD.EDU> wrote: > > External Email - Use Caution > > Hi Laetitia, > > I just executed the steps you suggested and I?m getting the same error > (see logs below). > > Regards, > Alfredo. > > === > *lorisadmin at ipmsa-loris*:*/var/www/loris*$ npm install > > > sweetalert2 at 8.18.6 postinstall /var/www/loris/node_modules/sweetalert2 > > node bin/postinstall.js > > > Has SweetAlert2 helped you create amazing applications? > You can show your <3 and support by making a donation: > > > *https://sweetalert2.github.io/#donations > * > > * Also, the author of SweetAlert2 (@limonte) is looking for* > * short-term working contracts in front-end, preferably OSS.* > > * > **https://github.com/limonte > * > > npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.9 > (node_modules/fsevents): > npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for > fsevents at 1.2.9: wanted {"os":"darwin","arch":"any"} (current: > {"os":"linux","arch":"x64"}) > > added 753 packages from 390 contributors and audited 821 packages in > 13.253s > found 495 vulnerabilities (487 *low*, 4 moderate, 4 high) > run `npm audit fix` to fix them, or `npm audit` for details > === > > === > *lorisadmin at ipmsa-loris*:*/var/www/loris*$ npm run compile > > > loris at 1.0.0 compile /var/www/loris > > webpack > > Hash: ef2e2aa8abafb645b741 > Version: webpack 4.41.2 > Child > Hash: ef2e2aa8abafb645b741 > Time: 4714ms > Built at: 01/12/2021 3:19:49 PM > 106 assets > Entrypoint ./htdocs/js/components/DynamicDataTable.js = > ./htdocs/js/components/DynamicDataTable.js > ./htdocs/js/components/DynamicDataTable.js.map > Entrypoint ./htdocs/js/components/PaginationLinks.js = > ./htdocs/js/components/PaginationLinks.js > ./htdocs/js/components/PaginationLinks.js.map > Entrypoint ./htdocs/js/components/StaticDataTable.js = > ./htdocs/js/components/StaticDataTable.js > ./htdocs/js/components/StaticDataTable.js.map > > . . . > . . . > > ERROR in ./jsx/DynamicDataTable.js > Module build failed (from ./node_modules/babel-loader/lib/index.js): > Error: Cannot find module 'babel-plugin-transform-object-rest-spread' > from '/var/www/loris' > at Function.module.exports [as sync] > (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) > at resolveStandardizedName > (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) > at resolvePlugin > (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) > at loadPlugin > (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) > at createDescriptor > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) > at items.map > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) > at Array.map () > at createDescriptors > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) > at createPluginDescriptors > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) > at plugins > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) > at mergeChainOpts > (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) > at > /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 > at buildRootChain > (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) > at loadPrivatePartialConfig > (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) > at Object.loadPartialConfig > (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) > at Object. > (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) > at Generator.next () > at asyncGeneratorStep > (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) > at _next > (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) > at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 > at new Promise () > at Object. > (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) > at Object._loader > (/var/www/loris/node_modules/babel-loader/lib/index.js:224:18) > at Object.loader > (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) > at Object. > (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) > > ERROR in ./jsx/Form.js > Module build failed (from ./node_modules/babel-loader/lib/index.js): > Error: Cannot find module 'babel-plugin-transform-object-rest-spread' > from '/var/www/loris' > at Function.module.exports [as sync] > (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) > at resolveStandardizedName > (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) > at resolvePlugin > (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) > at loadPlugin > (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) > at createDescriptor > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) > at items.map > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) > at Array.map () > at createDescriptors > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) > at createPluginDescriptors > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) > at plugins > (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) > at mergeChainOpts > (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) > at > /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 > at buildRootChain > (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) > at loadPrivatePartialConfig > (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) > at Object.loadPartialConfig > (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) > at Object. > (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) > at Generator.next () > at asyncGeneratorStep > (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) > at _next > (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) > at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 > at new Promise () > at Object. > (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) > at Object.loader > (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) > at Object. > (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) > > === > > On Jan 12, 2021, at 3:02 PM, Laetitia Fesselier < > laetitia.fesselier at mcin.ca> wrote: > > External Email - Use Caution > > Hello Alfredo, > > I suggest you try the following: > - delete the node_modules folder: > *rm -R node_modules* > - reinstall all the node libraries > *npm install* > - compile > *npm run compile* > > Let us know if you need further assistance. > Regards, > > Laetitia > > On Mon, Jan 11, 2021 at 4:59 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Dear LorisDev Team, >> >> I am upgrading Loris from v21.0.0 to v22.0.0 ( >> https://github.com/aces/Loris/releases/tag/v22.0.0 >> ). >> After installation of node v10.13.0 and npm 6.4.1, and getting the >> corresponding source code, I am getting the following error when executing >> ?make all?: >> >> === >> *ERROR in ./jsx/DynamicDataTable.js* >> * Module build failed (from ./node_modules/babel-loader/lib/index.js):* >> * Error: Cannot find module >> 'babel-plugin-transform-object-rest-spread' from '/var/www/loris'* >> * at Function.module.exports [as sync] >> (/var/www/loris/node_modules/resolve/lib/sync.js:74:15)* >> * at resolveStandardizedName >> (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31)* >> * at resolvePlugin >> (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10)* >> * at loadPlugin >> (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20)* >> * at createDescriptor >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9)* >> * at items.map >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50)* >> * at Array.map ()* >> * at createDescriptors >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29)* >> * at createPluginDescriptors >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10)* >> * at plugins >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19)* >> * at mergeChainOpts >> (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26)* >> * at >> /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7* >> * at buildRootChain >> (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22)* >> * at loadPrivatePartialConfig >> (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55)* >> * at Object.loadPartialConfig >> (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18)* >> * at Object. >> (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26)* >> * at Generator.next ()* >> * at asyncGeneratorStep >> (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103)* >> * at _next >> (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194)* >> * at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364* >> * at new Promise ()* >> * at Object. >> (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97)* >> * at Object._loader >> (/var/www/loris/node_modules/babel-loader/lib/index.js:224:18)* >> * at Object.loader >> (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18)* >> * at Object. >> (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12)* >> === >> >> I am running Ubuntu Xenial 16.04.4 >> >> I also tried using node v14.15.4 but got the same error. >> >> Do you have suggestions on how to solve this? >> >> Regards, >> Alfredo. >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.org/complianceline >> >> . If the e-mail was sent to you in error but does not contain patient >> information, please contact the sender and properly dispose of the e-mail. >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > > https://secure-web.cisco.com/1bkeKKx5RznkqKIva0HYzoY9MxgvLhGMQxvSLxTHjd66w8yNVGszrvu4KCxIR0Jrk9lR2hJb2vk6VJcKx4tk-YtW6ojgznXup82Lja8z84lzCX7kpH4Ug862eQgGxj9ngmkK7HDSutOq50hga2YFHjg-nj66X-9KfKCb11MZf7cTewb4j8Rc7L-ZWKzLP0WLBMt24FQMlnB9bLmXII8LT5xu9Gjyc2tWSOxGuHLRILZhRJkusC6vj1t1QjeucpKopGGH9A9-GFCDifS9o3pySGQ/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev > > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Tue Jan 12 17:05:18 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Tue, 12 Jan 2021 22:05:18 +0000 Subject: [Loris-dev] Error Webpack installing v22.0.0 In-Reply-To: References: <72D9F51B-BBAC-497A-9FC7-B64EFF3F7812@bwh.harvard.edu> Message-ID: <16675338-C8BC-444B-B59A-D965FB61F4BE@bwh.harvard.edu> Hi Laetitia, That was it. Some files were not properly copied to the loris folder. Now it?s compiled. Thank you. Alfredo. On Jan 12, 2021, at 4:37 PM, Laetitia Fesselier > wrote: External Email - Use Caution Can you check that your .babelrc file is identical to the one on the v22.0 branch: https://github.com/aces/Loris/blob/22.0-release/.babelrc ? Regards, Laetitia On Tue, Jan 12, 2021 at 4:04 PM Morales Pinzon, Alfredo > wrote: Hi Laetitia, I just compiled it in a different folder and it worked. I think I have some some issues with permissions in the /var/www/loris folder. Any ideas? Regards, Alfredo. On Jan 12, 2021, at 3:28 PM, Morales Pinzon, Alfredo > wrote: External Email - Use Caution Hi Laetitia, I just executed the steps you suggested and I?m getting the same error (see logs below). Regards, Alfredo. === lorisadmin at ipmsa-loris:/var/www/loris$ npm install > sweetalert2 at 8.18.6 postinstall /var/www/loris/node_modules/sweetalert2 > node bin/postinstall.js Has SweetAlert2 helped you create amazing applications? You can show your <3 and support by making a donation: > https://sweetalert2.github.io/#donations Also, the author of SweetAlert2 (@limonte) is looking for short-term working contracts in front-end, preferably OSS. > https://github.com/limonte npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.9 (node_modules/fsevents): npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for fsevents at 1.2.9: wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"}) added 753 packages from 390 contributors and audited 821 packages in 13.253s found 495 vulnerabilities (487 low, 4 moderate, 4 high) run `npm audit fix` to fix them, or `npm audit` for details === === lorisadmin at ipmsa-loris:/var/www/loris$ npm run compile > loris at 1.0.0 compile /var/www/loris > webpack Hash: ef2e2aa8abafb645b741 Version: webpack 4.41.2 Child Hash: ef2e2aa8abafb645b741 Time: 4714ms Built at: 01/12/2021 3:19:49 PM 106 assets Entrypoint ./htdocs/js/components/DynamicDataTable.js = ./htdocs/js/components/DynamicDataTable.js ./htdocs/js/components/DynamicDataTable.js.map Entrypoint ./htdocs/js/components/PaginationLinks.js = ./htdocs/js/components/PaginationLinks.js ./htdocs/js/components/PaginationLinks.js.map Entrypoint ./htdocs/js/components/StaticDataTable.js = ./htdocs/js/components/StaticDataTable.js ./htdocs/js/components/StaticDataTable.js.map . . . . . . ERROR in ./jsx/DynamicDataTable.js Module build failed (from ./node_modules/babel-loader/lib/index.js): Error: Cannot find module 'babel-plugin-transform-object-rest-spread' from '/var/www/loris' at Function.module.exports [as sync] (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) at resolveStandardizedName (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) at resolvePlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) at loadPlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) at createDescriptor (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) at items.map (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) at Array.map () at createDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) at createPluginDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) at plugins (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) at mergeChainOpts (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) at /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 at buildRootChain (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) at loadPrivatePartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) at Object.loadPartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) at Generator.next () at asyncGeneratorStep (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) at _next (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 at new Promise () at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) at Object._loader (/var/www/loris/node_modules/babel-loader/lib/index.js:224:18) at Object.loader (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) ERROR in ./jsx/Form.js Module build failed (from ./node_modules/babel-loader/lib/index.js): Error: Cannot find module 'babel-plugin-transform-object-rest-spread' from '/var/www/loris' at Function.module.exports [as sync] (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) at resolveStandardizedName (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) at resolvePlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) at loadPlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) at createDescriptor (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) at items.map (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) at Array.map () at createDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) at createPluginDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) at plugins (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) at mergeChainOpts (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) at /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 at buildRootChain (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) at loadPrivatePartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) at Object.loadPartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) at Generator.next () at asyncGeneratorStep (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) at _next (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 at new Promise () at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) at Object.loader (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) === On Jan 12, 2021, at 3:02 PM, Laetitia Fesselier > wrote: External Email - Use Caution Hello Alfredo, I suggest you try the following: - delete the node_modules folder: rm -R node_modules - reinstall all the node libraries npm install - compile npm run compile Let us know if you need further assistance. Regards, Laetitia On Mon, Jan 11, 2021 at 4:59 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev Team, I am upgrading Loris from v21.0.0 to v22.0.0 (https://github.com/aces/Loris/releases/tag/v22.0.0). After installation of node v10.13.0 and npm 6.4.1, and getting the corresponding source code, I am getting the following error when executing ?make all?: === ERROR in ./jsx/DynamicDataTable.js Module build failed (from ./node_modules/babel-loader/lib/index.js): Error: Cannot find module 'babel-plugin-transform-object-rest-spread' from '/var/www/loris' at Function.module.exports [as sync] (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) at resolveStandardizedName (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) at resolvePlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) at loadPlugin (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) at createDescriptor (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) at items.map (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) at Array.map () at createDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) at createPluginDescriptors (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) at plugins (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) at mergeChainOpts (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) at /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 at buildRootChain (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) at loadPrivatePartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) at Object.loadPartialConfig (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) at Generator.next () at asyncGeneratorStep (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) at _next (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 at new Promise () at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) at Object._loader (/var/www/loris/node_modules/babel-loader/lib/index.js:224:18) at Object.loader (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) at Object. (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) === I am running Ubuntu Xenial 16.04.4 I also tried using node v14.15.4 but got the same error. Do you have suggestions on how to solve this? Regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://secure-web.cisco.com/1bkeKKx5RznkqKIva0HYzoY9MxgvLhGMQxvSLxTHjd66w8yNVGszrvu4KCxIR0Jrk9lR2hJb2vk6VJcKx4tk-YtW6ojgznXup82Lja8z84lzCX7kpH4Ug862eQgGxj9ngmkK7HDSutOq50hga2YFHjg-nj66X-9KfKCb11MZf7cTewb4j8Rc7L-ZWKzLP0WLBMt24FQMlnB9bLmXII8LT5xu9Gjyc2tWSOxGuHLRILZhRJkusC6vj1t1QjeucpKopGGH9A9-GFCDifS9o3pySGQ/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From laetitia.fesselier at mcin.ca Tue Jan 12 17:11:46 2021 From: laetitia.fesselier at mcin.ca (Laetitia Fesselier) Date: Tue, 12 Jan 2021 17:11:46 -0500 Subject: [Loris-dev] Error Webpack installing v22.0.0 In-Reply-To: <16675338-C8BC-444B-B59A-D965FB61F4BE@bwh.harvard.edu> References: <72D9F51B-BBAC-497A-9FC7-B64EFF3F7812@bwh.harvard.edu> <16675338-C8BC-444B-B59A-D965FB61F4BE@bwh.harvard.edu> Message-ID: Hello Alfredo, I'm glad that your issue is solved. If you copy files manually, hidden files are often a problem. Be extra careful with them. Have a great day, Laetitia On Tue, Jan 12, 2021 at 5:05 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Laetitia, > > That was it. Some files were not properly copied to the loris folder. Now > it?s compiled. > > Thank you. > > Alfredo. > > On Jan 12, 2021, at 4:37 PM, Laetitia Fesselier < > laetitia.fesselier at mcin.ca> wrote: > > External Email - Use Caution > > Can you check that your .babelrc file is identical to the one on the v22.0 > branch: https://github.com/aces/Loris/blob/22.0-release/.babelrc > > ? > Regards, > > Laetitia > > On Tue, Jan 12, 2021 at 4:04 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Hi Laetitia, >> >> I just compiled it in a different folder and it worked. I think I have >> some some issues with permissions in the /var/www/loris folder. Any ideas? >> >> Regards, >> Alfredo. >> >> On Jan 12, 2021, at 3:28 PM, Morales Pinzon, Alfredo < >> AMORALESPINZON at BWH.HARVARD.EDU> wrote: >> >> External Email - Use Caution >> >> Hi Laetitia, >> >> I just executed the steps you suggested and I?m getting the same error >> (see logs below). >> >> Regards, >> Alfredo. >> >> === >> *lorisadmin at ipmsa-loris*:*/var/www/loris*$ npm install >> >> > sweetalert2 at 8.18.6 postinstall /var/www/loris/node_modules/sweetalert2 >> > node bin/postinstall.js >> >> >> Has SweetAlert2 helped you create amazing applications? >> You can show your <3 and support by making a donation: >> >> > *https://sweetalert2.github.io/#donations >> * >> >> * Also, the author of SweetAlert2 (@limonte) is looking for* >> * short-term working contracts in front-end, preferably OSS.* >> >> * > **https://github.com/limonte >> * >> >> npm WARN optional SKIPPING OPTIONAL DEPENDENCY: fsevents at 1.2.9 >> (node_modules/fsevents): >> npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for >> fsevents at 1.2.9: wanted {"os":"darwin","arch":"any"} (current: >> {"os":"linux","arch":"x64"}) >> >> added 753 packages from 390 contributors and audited 821 packages in >> 13.253s >> found 495 vulnerabilities (487 *low*, 4 moderate, 4 high) >> run `npm audit fix` to fix them, or `npm audit` for details >> === >> >> === >> *lorisadmin at ipmsa-loris*:*/var/www/loris*$ npm run compile >> >> > loris at 1.0.0 compile /var/www/loris >> > webpack >> >> Hash: ef2e2aa8abafb645b741 >> Version: webpack 4.41.2 >> Child >> Hash: ef2e2aa8abafb645b741 >> Time: 4714ms >> Built at: 01/12/2021 3:19:49 PM >> 106 assets >> Entrypoint ./htdocs/js/components/DynamicDataTable.js = >> ./htdocs/js/components/DynamicDataTable.js >> ./htdocs/js/components/DynamicDataTable.js.map >> Entrypoint ./htdocs/js/components/PaginationLinks.js = >> ./htdocs/js/components/PaginationLinks.js >> ./htdocs/js/components/PaginationLinks.js.map >> Entrypoint ./htdocs/js/components/StaticDataTable.js = >> ./htdocs/js/components/StaticDataTable.js >> ./htdocs/js/components/StaticDataTable.js.map >> >> . . . >> . . . >> >> ERROR in ./jsx/DynamicDataTable.js >> Module build failed (from ./node_modules/babel-loader/lib/index.js): >> Error: Cannot find module 'babel-plugin-transform-object-rest-spread' >> from '/var/www/loris' >> at Function.module.exports [as sync] >> (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) >> at resolveStandardizedName >> (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) >> at resolvePlugin >> (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) >> at loadPlugin >> (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) >> at createDescriptor >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) >> at items.map >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) >> at Array.map () >> at createDescriptors >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) >> at createPluginDescriptors >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) >> at plugins >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) >> at mergeChainOpts >> (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) >> at >> /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 >> at buildRootChain >> (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) >> at loadPrivatePartialConfig >> (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) >> at Object.loadPartialConfig >> (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) >> at Object. >> (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) >> at Generator.next () >> at asyncGeneratorStep >> (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) >> at _next >> (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) >> at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 >> at new Promise () >> at Object. >> (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) >> at Object._loader >> (/var/www/loris/node_modules/babel-loader/lib/index.js:224:18) >> at Object.loader >> (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) >> at Object. >> (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) >> >> ERROR in ./jsx/Form.js >> Module build failed (from ./node_modules/babel-loader/lib/index.js): >> Error: Cannot find module 'babel-plugin-transform-object-rest-spread' >> from '/var/www/loris' >> at Function.module.exports [as sync] >> (/var/www/loris/node_modules/resolve/lib/sync.js:74:15) >> at resolveStandardizedName >> (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31) >> at resolvePlugin >> (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10) >> at loadPlugin >> (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20) >> at createDescriptor >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9) >> at items.map >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50) >> at Array.map () >> at createDescriptors >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29) >> at createPluginDescriptors >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10) >> at plugins >> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19) >> at mergeChainOpts >> (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26) >> at >> /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7 >> at buildRootChain >> (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22) >> at loadPrivatePartialConfig >> (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55) >> at Object.loadPartialConfig >> (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18) >> at Object. >> (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26) >> at Generator.next () >> at asyncGeneratorStep >> (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103) >> at _next >> (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194) >> at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364 >> at new Promise () >> at Object. >> (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97) >> at Object.loader >> (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18) >> at Object. >> (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12) >> >> === >> >> On Jan 12, 2021, at 3:02 PM, Laetitia Fesselier < >> laetitia.fesselier at mcin.ca> wrote: >> >> External Email - Use Caution >> >> Hello Alfredo, >> >> I suggest you try the following: >> - delete the node_modules folder: >> *rm -R node_modules* >> - reinstall all the node libraries >> *npm install* >> - compile >> *npm run compile* >> >> Let us know if you need further assistance. >> Regards, >> >> Laetitia >> >> On Mon, Jan 11, 2021 at 4:59 PM Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >>> Dear LorisDev Team, >>> >>> I am upgrading Loris from v21.0.0 to v22.0.0 ( >>> https://github.com/aces/Loris/releases/tag/v22.0.0 >>> ). >>> After installation of node v10.13.0 and npm 6.4.1, and getting the >>> corresponding source code, I am getting the following error when executing >>> ?make all?: >>> >>> === >>> *ERROR in ./jsx/DynamicDataTable.js* >>> * Module build failed (from >>> ./node_modules/babel-loader/lib/index.js):* >>> * Error: Cannot find module >>> 'babel-plugin-transform-object-rest-spread' from '/var/www/loris'* >>> * at Function.module.exports [as sync] >>> (/var/www/loris/node_modules/resolve/lib/sync.js:74:15)* >>> * at resolveStandardizedName >>> (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:101:31)* >>> * at resolvePlugin >>> (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:54:10)* >>> * at loadPlugin >>> (/var/www/loris/node_modules/@babel/core/lib/config/files/plugins.js:62:20)* >>> * at createDescriptor >>> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:154:9)* >>> * at items.map >>> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:50)* >>> * at Array.map ()* >>> * at createDescriptors >>> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:109:29)* >>> * at createPluginDescriptors >>> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:105:10)* >>> * at plugins >>> (/var/www/loris/node_modules/@babel/core/lib/config/config-descriptors.js:40:19)* >>> * at mergeChainOpts >>> (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:319:26)* >>> * at >>> /var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:283:7* >>> * at buildRootChain >>> (/var/www/loris/node_modules/@babel/core/lib/config/config-chain.js:120:22)* >>> * at loadPrivatePartialConfig >>> (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:85:55)* >>> * at Object.loadPartialConfig >>> (/var/www/loris/node_modules/@babel/core/lib/config/partial.js:110:18)* >>> * at Object. >>> (/var/www/loris/node_modules/babel-loader/lib/index.js:144:26)* >>> * at Generator.next ()* >>> * at asyncGeneratorStep >>> (/var/www/loris/node_modules/babel-loader/lib/index.js:3:103)* >>> * at _next >>> (/var/www/loris/node_modules/babel-loader/lib/index.js:5:194)* >>> * at /var/www/loris/node_modules/babel-loader/lib/index.js:5:364* >>> * at new Promise ()* >>> * at Object. >>> (/var/www/loris/node_modules/babel-loader/lib/index.js:5:97)* >>> * at Object._loader >>> (/var/www/loris/node_modules/babel-loader/lib/index.js:224:18)* >>> * at Object.loader >>> (/var/www/loris/node_modules/babel-loader/lib/index.js:60:18)* >>> * at Object. >>> (/var/www/loris/node_modules/babel-loader/lib/index.js:55:12)* >>> === >>> >>> I am running Ubuntu Xenial 16.04.4 >>> >>> I also tried using node v14.15.4 but got the same error. >>> >>> Do you have suggestions on how to solve this? >>> >>> Regards, >>> Alfredo. >>> The information in this e-mail is intended only for the person to whom >>> it is addressed. If you believe this e-mail was sent to you in error and >>> the e-mail contains patient information, please contact the Mass General >>> Brigham Compliance HelpLine at >>> http://www.massgeneralbrigham.org/complianceline >>> >>> . If the e-mail was sent to you in error but does not contain patient >>> information, please contact the sender and properly dispose of the e-mail. >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.org/complianceline >> >> . If the e-mail was sent to you in error but does not contain patient >> information, please contact the sender and properly dispose of the e-mail. >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> >> https://secure-web.cisco.com/1bkeKKx5RznkqKIva0HYzoY9MxgvLhGMQxvSLxTHjd66w8yNVGszrvu4KCxIR0Jrk9lR2hJb2vk6VJcKx4tk-YtW6ojgznXup82Lja8z84lzCX7kpH4Ug862eQgGxj9ngmkK7HDSutOq50hga2YFHjg-nj66X-9KfKCb11MZf7cTewb4j8Rc7L-ZWKzLP0WLBMt24FQMlnB9bLmXII8LT5xu9Gjyc2tWSOxGuHLRILZhRJkusC6vj1t1QjeucpKopGGH9A9-GFCDifS9o3pySGQ/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev >> >> >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.org/complianceline >> >> . 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URL: From joh17964 at umn.edu Tue Jan 12 18:05:03 2021 From: joh17964 at umn.edu (Eli Johnson) Date: Tue, 12 Jan 2021 17:05:03 -0600 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: References: Message-ID: Hi Julie, I'm not on the LORIS team, but I referenced this CentOS 7 documentation while installing on RHEL 7 last year -- https://github.com/aces/Loris/tree/main/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/CentOS Most of the documentation can be found in the docs directory within the LORIS project on github. @LORIS team, the links for CENTOS documentation in the github wiki are broken. Best, Eli Johnson Eli Johnson Developer/Data Manager Institute of Child Development University of Minnesota joh17964 at umn.edu On Tue, Jan 12, 2021 at 3:25 PM wrote: > Send Loris-dev mailing list submissions to > loris-dev at bic.mni.mcgill.ca > > To subscribe or unsubscribe via the World Wide Web, visit > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > or, via email, send a message with subject or body 'help' to > loris-dev-request at bic.mni.mcgill.ca > > You can reach the person managing the list at > loris-dev-owner at bic.mni.mcgill.ca > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Loris-dev digest..." > Today's Topics: > > 1. Re: CentOS 8 and Loris (Julie Ashworth, HWNI Computing Support) > > > > ---------- Forwarded message ---------- > From: "Julie Ashworth, HWNI Computing Support" > To: Dave MacFarlane > Cc: loris-dev , Samir Das < > samirdas99 at gmail.com>, Christine Rogers > Bcc: > Date: Tue, 12 Jan 2021 13:24:57 -0800 > Subject: Re: [Loris-dev] CentOS 8 and Loris > Can you please send me the URL for the most recent linux (ubuntu or > centos) installation documentation? > Thank you > > On Tue, Jan 12, 2021, 1:17 PM Julie Ashworth, HWNI Computing Support < > support-cirl at berkeley.edu> wrote: > >> Thanks Dave, >> There are many groups taking over development of Centos8, so I thinks >> it's incorrect to say that it's discontinued. The most active group is >> Rocky linux, started by Greg Kurtzer, who also founded the original CentOS >> project 15 years ago. >> https://rockylinux.org/ >> >> I have no personal interest in using php-fpm. I was following the centos7 >> instructions to install php-fpm, but there was an apache error expecting mod_php. >> I'm happy to install mod_php but that is not documnted in the centos7 >> instructions. >> To be honest, I'm really disappointed in the loris documentation and that >> my emails aren't being read carefully. >> >> >> >> On Tue, Jan 12, 2021, 12:22 PM Dave MacFarlane >> wrote: >> >>> Hi Julie, >>> >>> CentOS is no longer supported (by which I mean the operating system >>> itself has been discontinued, not the LORIS support for it.) The MCIN >>> production servers currently run on CentOS7 which is why the installation >>> procedure is well documented/tested for that system, but given the >>> discontinuation of CentOS the plan is to move our production servers off of >>> CentOS entirely. It's worth noting that CentOS 8 EOL is 2021, while CentOS >>> 7 EOL is 2024. This is the reason why our documentation is tailored to V7. >>> >>> We don't have much experience running LORIS under php-fpm, which is why >>> there's no documentation for that environment. At one point years ago I had >>> written a configuration file in order to use it in Travis CI, but since >>> then testing/development has moved towards using Docker and the built-in >>> PHP web server (I just looked at that configuration file and it's so old it >>> refers to php5..). mod_php is currently the only supported/documented PHP >>> environment as it's all most of the LORIS developers have experience with >>> (though I also regularly develop with the php built in dev server, so I'm >>> confident that that works as well.) >>> >>> The good news is our dependency on apache/mod_php is much weaker than it >>> was when I had worked on it years ago, but the bad news is there's no >>> written documentation that I'm aware of. >>> >>> If you're willing to do the work of debugging the environment we can >>> help where we can, but if you're trying to get a system up and quickly it's >>> likely faster and easier to use something that we have more experience >>> with. For reference, I don't think the php_value setting you're trying to >>> set should be required anywhere by LORIS. LORIS uses an autoloader for >>> class/include resolution and shouldn't depend on the PHP include_path. If >>> you're set on php-fpm you can look at docs/config/apache2-fastcgi as a >>> starting point, but note that that configuration is from 2014 (which as far >>> as I know is the last time anyone tried to use LORIS in that environment.) >>> >>> P.S. (Forgive me if I'm slow to respond to any emails as I'm on vacation >>> until next week..) >>> >>> On Tue, Jan 12, 2021 at 12:39 PM Julie Ashworth, HWNI Computing Support < >>> support-cirl at berkeley.edu> wrote: >>> >>>> Thank you, >>>> In the last 4 emails I have simply asked for current linux >>>> documentation, not centos8 documentation (preferably that mentions php-fpm >>>> configuration). Is that available? >>>> >>>> >>>> >>>> On Tue, Jan 12, 2021, 8:59 AM Samir Das wrote: >>>> >>>>> Hi Julie, >>>>> >>>>> We'll do our best to help you with this configuration. :) We'll send >>>>> you any documentation we have. >>>>> >>>>> Regarding CentOS, since RedHat has discontinued its support, we are >>>>> planning on putting our testing resources elsewhere. We have yet to discuss >>>>> CentOS-Stream, which we will do next week. But I wouldn't worry too much... >>>>> we'll help as much as we can given that you have already installed it, etc. >>>>> If the problems become too tedious, then we can figure out options together. >>>>> >>>>> Best, >>>>> >>>>> Samir Das >>>>> >>>>> On Tue, Jan 12, 2021 at 5:52 PM Julie Ashworth, HWNI Computing Support >>>>> wrote: >>>>> >>>>>> hi Shen, >>>>>> >>>>>> On 12-01-2021 11.40 -0500, Shen Wang wrote: >>>>>> > So Loris team will not support? Centos. We will only >>>>>> support? Ubuntu in the future.? >>>>>> >>>>>> That's interesting that CentOS will no longer be supported. >>>>>> >>>>>> Since you previously mentioned that CentOS8 should work, I already >>>>>> started the installation, and I'd like to see if it works. >>>>>> >>>>>> So, please, please... >>>>>> will you please send me a link to the most recent instruction for >>>>>> loris installation that includes the php_value in /etc/php-fpm.d? >>>>>> As I said, I can modify ubuntu instructions. I don't need >>>>>> instructions specific to CentOS. >>>>>> >>>>>> thanks, >>>>>> Julie >>>>>> >>>>>> >>>>>> >>>>>> On 12-01-2021 11.40 -0500, Shen Wang wrote: >>>>>> > Hi Julie, >>>>>> > We are holding the Loris meeting to discuss whether to support >>>>>> centos in >>>>>> > the future.? >>>>>> > Loris's? sub-modules have issues with the Centos system. So >>>>>> Loris team will >>>>>> > not support? Centos. >>>>>> > We will only support? Ubuntu in the future.? >>>>>> > Best? >>>>>> > Shen >>>>>> > On Tue, 12 Jan 2021 at 11:27, Julie Ashworth, HWNI Computing >>>>>> Support >>>>>> > <[1]support-cirl at berkeley.edu> wrote: >>>>>> > >>>>>> > hi Shen, >>>>>> > I'm looking for documentation of the (useful!) instruction you >>>>>> provided >>>>>> > in your previous email: >>>>>> > >>>>>> > >??? ??? step 2 : add "php_value[include_path]??? = >>>>>> > >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf >>>>>> > >>>>>> > I would appreciate a link to that documentation, because I >>>>>> think it >>>>>> > would be valuable for the future. I can adapt Ubuntu >>>>>> documentation for >>>>>> > CentOS. >>>>>> > >>>>>> > thanks, >>>>>> > Julie >>>>>> > >>>>>> > On 12-01-2021 09.14 -0500, Shen Wang wrote: >>>>>> > >? ? Hi Julie, >>>>>> > > >>>>>> > >? ? The Loris Team only supports Centos7 currently. >>>>>> > >? ? We don't have Centos8 instructions yet, so you can't >>>>>> find it. >>>>>> > > >>>>>> > >? ? If you and Ioannis would like to install loris 23 on >>>>>> centos 8, you >>>>>> > can >>>>>> > >? ? try. >>>>>> > >? ? I have installed loris 23 on centos 8, although the >>>>>> process is not >>>>>> > simple. >>>>>> > >? ? That is why I mentioned Centos 8, not officially >>>>>> supported yet. >>>>>> > Sorry for >>>>>> > >? ? confusion. >>>>>> > >? ? best >>>>>> > >? ? Shen >>>>>> > >? ? [1]???? ???????????????????? 2021-01-11 ????????? >>>>>> ??8.04.56.png >>>>>> > >? ? On Mon, 11 Jan 2021 at 16:27, Julie Ashworth, HWNI >>>>>> Computing >>>>>> > Support >>>>>> > >? ? <[2][2]support-cirl at berkeley.edu> wrote: >>>>>> > > >>>>>> > >? ? ? Thanks Shen, >>>>>> > >? ? ? Is this documented anywhere? I checked the Ubuntu >>>>>> instructions >>>>>> > and the >>>>>> > >? ? ? install.sh file, but I don't see it mentioned. >>>>>> > > >>>>>> > >? ? ? You also mentioned to Ioannis that Loris should run >>>>>> find on >>>>>> > CentOS8. >>>>>> > >? ? ? Which version did you recommend for CentOS8? >>>>>> > > >>>>>> > >? ? ? best, >>>>>> > >? ? ? Julie >>>>>> > > >>>>>> > >? ? ? On 11-01-2021 16.04 -0500, Shen Wang wrote: >>>>>> > >? ? ? >??? ??? Hi Julie, >>>>>> > >? ? ? >??? ??? We do not support Loris 23.0.2 to run on >>>>>> CentOS 8. >>>>>> > >? ? ? >??? ??? You can install 23.0.2 on Centos 7. >>>>>> > >? ? ? >??? ??? If you want to try to install it on >>>>>> Centos8. There is no >>>>>> > guarantee >>>>>> > >? ? ? that it >>>>>> > >? ? ? >??? ??? will work on Centos 8. >>>>>> > >? ? ? >??? ??? You can try it. >>>>>> > >? ? ? >??? ??? step 1 : remove the line of php_value >>>>>> from loris.conf >>>>>> > >? ? ? >??? ??? step 2 : add "php_value[include_path]??? >>>>>> = >>>>>> > >? ? ? >??? ??? >>>>>> ....."??? into??? /etc/php-fpm.d/loris.conf >>>>>> > >? ? ? >??? ??? step 3: reload php-fpm and httpd. >>>>>> > >? ? ? >??? ??? Good Luck! >>>>>> > >? ? ? >??? ??? Best??? >>>>>> > >? ? ? >??? ??? Shen >>>>>> > >? ? ? >??? ??? On Mon, 11 Jan 2021 at 15:32, Julie >>>>>> Ashworth, HWNI >>>>>> > Computing >>>>>> > >? ? ? Support >>>>>> > >? ? ? >??? ??? <[1][3][3]support-cirl at berkeley.edu> >>>>>> wrote: >>>>>> > >? ? ? > >>>>>> > >? ? ? >??? ??? ??? hi Shen, >>>>>> > >? ? ? >??? ??? ??? that *is* how I installed >>>>>> apache/php7.4. >>>>>> > >? ? ? > >>>>>> > >? ? ? >??? ??? ??? Please reread my email. >>>>>> > >? ? ? > >>>>>> > >? ? ? >??? ??? ??? I'd like to know how y'all recommend >>>>>> adding the php >>>>>> > path for >>>>>> > >? ? ? loris >>>>>> > >? ? ? >??? ??? ??? libraries using php-fpm. >>>>>> > >? ? ? > >>>>>> > >? ? ? >??? ??? ??? If I use the apache configuration >>>>>> file provided: >>>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? php_value >>>>>> include_path >>>>>> > >? ? ? >??? ??? ??? >>>>>> > >? ? ? >>>>>> > >>>>>> .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries >>>>>> > >? ? ? > >>>>>> > >? ? ? >??? ??? ??? I get an error: >>>>>> > >? ? ? >??? ??? ??? Invalid command 'php_value', perhaps >>>>>> misspelled or >>>>>> > defined by a >>>>>> > >? ? ? module >>>>>> > >? ? ? >??? ??? ??? not included in the server >>>>>> configuration >>>>>> > >? ? ? > >>>>>> > >? ? ? >??? ??? ??? ... because this isn't supported >>>>>> with php-fpm >>>>>> > >? ? ? > >>>>>> > >? ? ? >??? ??? ??? best, >>>>>> > >? ? ? >??? ??? ??? Julie >>>>>> > >? ? ? > >>>>>> > >? ? ? >??? ??? ??? On 11-01-2021 10.08 -0500, Shen Wang >>>>>> wrote: >>>>>> > >? ? ? >??? ??? ??? >??? ??? Hi Julie, >>>>>> > >? ? ? >??? ??? ??? >??? ??? I recommend reinstalling >>>>>> php 7.4 and apache. >>>>>> > >? ? ? >??? ??? ??? >??? ??? >>>>>> > >? ? ? [1][2][4][4] >>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > this >>>>>> > >? ? ? >??? ??? ??? article is >>>>>> > >? ? ? >??? ??? ??? >??? ??? helpful. >>>>>> > >? ? ? >??? ??? ??? >??? ??? Best >>>>>> > >? ? ? >??? ??? ??? >??? ??? Shen >>>>>> > >? ? ? >??? ??? ??? > >>>>>> > >? ? ? >??? ??? ??? > References >>>>>> > >? ? ? >??? ??? ??? > >>>>>> > >? ? ? >??? ??? ??? >??? ??? Visible links >>>>>> > >? ? ? >??? ??? ??? >??? ??? 1. >>>>>> > >? ? ? [3][5][5] >>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > >? ? ? >??? ??? ??? ---end quoted text--- >>>>>> > >? ? ? > >>>>>> > >? ? ? >??? ??? -- >>>>>> > >? ? ? >??? ??? Shen Wang >>>>>> > >? ? ? >??? ??? [4]Loris??? Developer >>>>>> > >? ? ? >??? ??? Montreal Neurological Institute??? >>>>>> > >? ? ? >??? ??? McGill University >>>>>> > >? ? ? > >>>>>> > >? ? ? > References >>>>>> > >? ? ? > >>>>>> > >? ? ? >??? ??? Visible links >>>>>> > >? ? ? >??? ??? 1. mailto:[6][6]support-cirl at berkeley.edu >>>>>> > >? ? ? >??? ??? 2. >>>>>> > [7][7]https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > >? ? ? >??? ??? 3. >>>>>> > [8][8]https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > >? ? ? >??? ??? 4. [9][9]https://github.com/aces/Loris >>>>>> > >? ? ? ---end quoted text--- >>>>>> > > >>>>>> > >? ? -- >>>>>> > >? ? Shen Wang >>>>>> > >? ? [10]Loris??? Developer >>>>>> > >? ? Montreal Neurological Institute??? >>>>>> > >? ? McGill University >>>>>> > > >>>>>> > > References >>>>>> > > >>>>>> > >? ? Visible links >>>>>> > >? ? 2. mailto:[10]support-cirl at berkeley.edu >>>>>> > >? ? 3. mailto:[11]support-cirl at berkeley.edu >>>>>> > >? ? 4. [12] >>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > >? ? 5. [13] >>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > >? ? 6. mailto:[14]support-cirl at berkeley.edu >>>>>> > >? ? 7. [15] >>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > >? ? 8. [16] >>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > >? ? 9. [17]https://github.com/aces/Loris >>>>>> > >? ? 10. [18]https://github.com/aces/Loris >>>>>> > >>>>>> > ---end quoted text--- >>>>>> > >>>>>> > -- >>>>>> > Shen Wang >>>>>> > [19]Loris? Developer >>>>>> > Montreal Neurological Institute? >>>>>> > McGill University >>>>>> > >>>>>> > References >>>>>> > >>>>>> > Visible links >>>>>> > 1. mailto:support-cirl at berkeley.edu >>>>>> > 2. mailto:support-cirl at berkeley.edu >>>>>> > 3. mailto:support-cirl at berkeley.edu >>>>>> > 4. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > 5. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > 6. mailto:support-cirl at berkeley.edu >>>>>> > 7. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > 8. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > 9. https://github.com/aces/Loris >>>>>> > 10. mailto:support-cirl at berkeley.edu >>>>>> > 11. mailto:support-cirl at berkeley.edu >>>>>> > 12. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > 13. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > 14. mailto:support-cirl at berkeley.edu >>>>>> > 15. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > 16. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>> > 17. https://github.com/aces/Loris >>>>>> > 18. https://github.com/aces/Loris >>>>>> > 19. https://github.com/aces/Loris >>>>>> ---end quoted text--- >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From support-cirl at berkeley.edu Tue Jan 12 18:41:40 2021 From: support-cirl at berkeley.edu (Julie Ashworth, HWNI Computing Support) Date: Tue, 12 Jan 2021 15:41:40 -0800 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: References: Message-ID: Thanks Eli, That is the doc I used which produced the php-fpm error. On Tue, Jan 12, 2021, 3:05 PM Eli Johnson wrote: > Hi Julie, > > I'm not on the LORIS team, but I referenced this CentOS 7 documentation > while installing on RHEL 7 last year -- > > > https://github.com/aces/Loris/tree/main/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/CentOS > > Most of the documentation can be found in the docs directory within the > LORIS project on github. > > @LORIS team, the links for CENTOS documentation in the github wiki are > broken. > > > Best, > Eli Johnson > > Eli Johnson > Developer/Data Manager > Institute of Child Development > University of Minnesota > joh17964 at umn.edu > > > On Tue, Jan 12, 2021 at 3:25 PM > wrote: > >> Send Loris-dev mailing list submissions to >> loris-dev at bic.mni.mcgill.ca >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> or, via email, send a message with subject or body 'help' to >> loris-dev-request at bic.mni.mcgill.ca >> >> You can reach the person managing the list at >> loris-dev-owner at bic.mni.mcgill.ca >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of Loris-dev digest..." >> Today's Topics: >> >> 1. Re: CentOS 8 and Loris (Julie Ashworth, HWNI Computing Support) >> >> >> >> ---------- Forwarded message ---------- >> From: "Julie Ashworth, HWNI Computing Support" > > >> To: Dave MacFarlane >> Cc: loris-dev , Samir Das < >> samirdas99 at gmail.com>, Christine Rogers >> Bcc: >> Date: Tue, 12 Jan 2021 13:24:57 -0800 >> Subject: Re: [Loris-dev] CentOS 8 and Loris >> Can you please send me the URL for the most recent linux (ubuntu or >> centos) installation documentation? >> Thank you >> >> On Tue, Jan 12, 2021, 1:17 PM Julie Ashworth, HWNI Computing Support < >> support-cirl at berkeley.edu> wrote: >> >>> Thanks Dave, >>> There are many groups taking over development of Centos8, so I thinks >>> it's incorrect to say that it's discontinued. The most active group is >>> Rocky linux, started by Greg Kurtzer, who also founded the original CentOS >>> project 15 years ago. >>> https://rockylinux.org/ >>> >>> I have no personal interest in using php-fpm. I was following the >>> centos7 instructions to install php-fpm, but there was an apache error >>> expecting mod_php. I'm happy to install mod_php but that is not >>> documnted in the centos7 instructions. >>> To be honest, I'm really disappointed in the loris documentation and >>> that my emails aren't being read carefully. >>> >>> >>> >>> On Tue, Jan 12, 2021, 12:22 PM Dave MacFarlane >>> wrote: >>> >>>> Hi Julie, >>>> >>>> CentOS is no longer supported (by which I mean the operating system >>>> itself has been discontinued, not the LORIS support for it.) The MCIN >>>> production servers currently run on CentOS7 which is why the installation >>>> procedure is well documented/tested for that system, but given the >>>> discontinuation of CentOS the plan is to move our production servers off of >>>> CentOS entirely. It's worth noting that CentOS 8 EOL is 2021, while CentOS >>>> 7 EOL is 2024. This is the reason why our documentation is tailored to V7. >>>> >>>> We don't have much experience running LORIS under php-fpm, which is why >>>> there's no documentation for that environment. At one point years ago I had >>>> written a configuration file in order to use it in Travis CI, but since >>>> then testing/development has moved towards using Docker and the built-in >>>> PHP web server (I just looked at that configuration file and it's so old it >>>> refers to php5..). mod_php is currently the only supported/documented PHP >>>> environment as it's all most of the LORIS developers have experience with >>>> (though I also regularly develop with the php built in dev server, so I'm >>>> confident that that works as well.) >>>> >>>> The good news is our dependency on apache/mod_php is much weaker than >>>> it was when I had worked on it years ago, but the bad news is there's no >>>> written documentation that I'm aware of. >>>> >>>> If you're willing to do the work of debugging the environment we can >>>> help where we can, but if you're trying to get a system up and quickly it's >>>> likely faster and easier to use something that we have more experience >>>> with. For reference, I don't think the php_value setting you're trying to >>>> set should be required anywhere by LORIS. LORIS uses an autoloader for >>>> class/include resolution and shouldn't depend on the PHP include_path. If >>>> you're set on php-fpm you can look at docs/config/apache2-fastcgi as a >>>> starting point, but note that that configuration is from 2014 (which as far >>>> as I know is the last time anyone tried to use LORIS in that environment.) >>>> >>>> P.S. (Forgive me if I'm slow to respond to any emails as I'm on >>>> vacation until next week..) >>>> >>>> On Tue, Jan 12, 2021 at 12:39 PM Julie Ashworth, HWNI Computing Support >>>> wrote: >>>> >>>>> Thank you, >>>>> In the last 4 emails I have simply asked for current linux >>>>> documentation, not centos8 documentation (preferably that mentions php-fpm >>>>> configuration). Is that available? >>>>> >>>>> >>>>> >>>>> On Tue, Jan 12, 2021, 8:59 AM Samir Das wrote: >>>>> >>>>>> Hi Julie, >>>>>> >>>>>> We'll do our best to help you with this configuration. :) We'll send >>>>>> you any documentation we have. >>>>>> >>>>>> Regarding CentOS, since RedHat has discontinued its support, we are >>>>>> planning on putting our testing resources elsewhere. We have yet to discuss >>>>>> CentOS-Stream, which we will do next week. But I wouldn't worry too much... >>>>>> we'll help as much as we can given that you have already installed it, etc. >>>>>> If the problems become too tedious, then we can figure out options together. >>>>>> >>>>>> Best, >>>>>> >>>>>> Samir Das >>>>>> >>>>>> On Tue, Jan 12, 2021 at 5:52 PM Julie Ashworth, HWNI Computing >>>>>> Support wrote: >>>>>> >>>>>>> hi Shen, >>>>>>> >>>>>>> On 12-01-2021 11.40 -0500, Shen Wang wrote: >>>>>>> > So Loris team will not support? Centos. We will only >>>>>>> support? Ubuntu in the future.? >>>>>>> >>>>>>> That's interesting that CentOS will no longer be supported. >>>>>>> >>>>>>> Since you previously mentioned that CentOS8 should work, I already >>>>>>> started the installation, and I'd like to see if it works. >>>>>>> >>>>>>> So, please, please... >>>>>>> will you please send me a link to the most recent instruction for >>>>>>> loris installation that includes the php_value in /etc/php-fpm.d? >>>>>>> As I said, I can modify ubuntu instructions. I don't need >>>>>>> instructions specific to CentOS. >>>>>>> >>>>>>> thanks, >>>>>>> Julie >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 12-01-2021 11.40 -0500, Shen Wang wrote: >>>>>>> > Hi Julie, >>>>>>> > We are holding the Loris meeting to discuss whether to support >>>>>>> centos in >>>>>>> > the future.? >>>>>>> > Loris's? sub-modules have issues with the Centos system. So >>>>>>> Loris team will >>>>>>> > not support? Centos. >>>>>>> > We will only support? Ubuntu in the future.? >>>>>>> > Best? >>>>>>> > Shen >>>>>>> > On Tue, 12 Jan 2021 at 11:27, Julie Ashworth, HWNI Computing >>>>>>> Support >>>>>>> > <[1]support-cirl at berkeley.edu> wrote: >>>>>>> > >>>>>>> > hi Shen, >>>>>>> > I'm looking for documentation of the (useful!) instruction >>>>>>> you provided >>>>>>> > in your previous email: >>>>>>> > >>>>>>> > >??? ??? step 2 : add "php_value[include_path]??? = >>>>>>> > >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf >>>>>>> > >>>>>>> > I would appreciate a link to that documentation, because I >>>>>>> think it >>>>>>> > would be valuable for the future. I can adapt Ubuntu >>>>>>> documentation for >>>>>>> > CentOS. >>>>>>> > >>>>>>> > thanks, >>>>>>> > Julie >>>>>>> > >>>>>>> > On 12-01-2021 09.14 -0500, Shen Wang wrote: >>>>>>> > >? ? Hi Julie, >>>>>>> > > >>>>>>> > >? ? The Loris Team only supports Centos7 currently. >>>>>>> > >? ? We don't have Centos8 instructions yet, so you can't >>>>>>> find it. >>>>>>> > > >>>>>>> > >? ? If you and Ioannis would like to install loris 23 on >>>>>>> centos 8, you >>>>>>> > can >>>>>>> > >? ? try. >>>>>>> > >? ? I have installed loris 23 on centos 8, although the >>>>>>> process is not >>>>>>> > simple. >>>>>>> > >? ? That is why I mentioned Centos 8, not officially >>>>>>> supported yet. >>>>>>> > Sorry for >>>>>>> > >? ? confusion. >>>>>>> > >? ? best >>>>>>> > >? ? Shen >>>>>>> > >? ? [1]???? ???????????????????? 2021-01-11 ????????? >>>>>>> ??8.04.56.png >>>>>>> > >? ? On Mon, 11 Jan 2021 at 16:27, Julie Ashworth, HWNI >>>>>>> Computing >>>>>>> > Support >>>>>>> > >? ? <[2][2]support-cirl at berkeley.edu> wrote: >>>>>>> > > >>>>>>> > >? ? ? Thanks Shen, >>>>>>> > >? ? ? Is this documented anywhere? I checked the Ubuntu >>>>>>> instructions >>>>>>> > and the >>>>>>> > >? ? ? install.sh file, but I don't see it mentioned. >>>>>>> > > >>>>>>> > >? ? ? You also mentioned to Ioannis that Loris should run >>>>>>> find on >>>>>>> > CentOS8. >>>>>>> > >? ? ? Which version did you recommend for CentOS8? >>>>>>> > > >>>>>>> > >? ? ? best, >>>>>>> > >? ? ? Julie >>>>>>> > > >>>>>>> > >? ? ? On 11-01-2021 16.04 -0500, Shen Wang wrote: >>>>>>> > >? ? ? >??? ??? Hi Julie, >>>>>>> > >? ? ? >??? ??? We do not support Loris 23.0.2 to run on >>>>>>> CentOS 8. >>>>>>> > >? ? ? >??? ??? You can install 23.0.2 on Centos 7. >>>>>>> > >? ? ? >??? ??? If you want to try to install it on >>>>>>> Centos8. There is no >>>>>>> > guarantee >>>>>>> > >? ? ? that it >>>>>>> > >? ? ? >??? ??? will work on Centos 8. >>>>>>> > >? ? ? >??? ??? You can try it. >>>>>>> > >? ? ? >??? ??? step 1 : remove the line of php_value >>>>>>> from loris.conf >>>>>>> > >? ? ? >??? ??? step 2 : add >>>>>>> "php_value[include_path]??? = >>>>>>> > >? ? ? >??? ??? >>>>>>> ....."??? into??? /etc/php-fpm.d/loris.conf >>>>>>> > >? ? ? >??? ??? step 3: reload php-fpm and httpd. >>>>>>> > >? ? ? >??? ??? Good Luck! >>>>>>> > >? ? ? >??? ??? Best??? >>>>>>> > >? ? ? >??? ??? Shen >>>>>>> > >? ? ? >??? ??? On Mon, 11 Jan 2021 at 15:32, Julie >>>>>>> Ashworth, HWNI >>>>>>> > Computing >>>>>>> > >? ? ? Support >>>>>>> > >? ? ? >??? ??? <[1][3][3]support-cirl at berkeley.edu> >>>>>>> wrote: >>>>>>> > >? ? ? > >>>>>>> > >? ? ? >??? ??? ??? hi Shen, >>>>>>> > >? ? ? >??? ??? ??? that *is* how I installed >>>>>>> apache/php7.4. >>>>>>> > >? ? ? > >>>>>>> > >? ? ? >??? ??? ??? Please reread my email. >>>>>>> > >? ? ? > >>>>>>> > >? ? ? >??? ??? ??? I'd like to know how y'all >>>>>>> recommend adding the php >>>>>>> > path for >>>>>>> > >? ? ? loris >>>>>>> > >? ? ? >??? ??? ??? libraries using php-fpm. >>>>>>> > >? ? ? > >>>>>>> > >? ? ? >??? ??? ??? If I use the apache configuration >>>>>>> file provided: >>>>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? php_value >>>>>>> include_path >>>>>>> > >? ? ? >??? ??? ??? >>>>>>> > >? ? ? >>>>>>> > >>>>>>> .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries >>>>>>> > >? ? ? > >>>>>>> > >? ? ? >??? ??? ??? I get an error: >>>>>>> > >? ? ? >??? ??? ??? Invalid command 'php_value', >>>>>>> perhaps misspelled or >>>>>>> > defined by a >>>>>>> > >? ? ? module >>>>>>> > >? ? ? >??? ??? ??? not included in the server >>>>>>> configuration >>>>>>> > >? ? ? > >>>>>>> > >? ? ? >??? ??? ??? ... because this isn't supported >>>>>>> with php-fpm >>>>>>> > >? ? ? > >>>>>>> > >? ? ? >??? ??? ??? best, >>>>>>> > >? ? ? >??? ??? ??? Julie >>>>>>> > >? ? ? > >>>>>>> > >? ? ? >??? ??? ??? On 11-01-2021 10.08 -0500, Shen >>>>>>> Wang wrote: >>>>>>> > >? ? ? >??? ??? ??? >??? ??? Hi Julie, >>>>>>> > >? ? ? >??? ??? ??? >??? ??? I recommend reinstalling >>>>>>> php 7.4 and apache. >>>>>>> > >? ? ? >??? ??? ??? >??? ??? >>>>>>> > >? ? ? [1][2][4][4] >>>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > this >>>>>>> > >? ? ? >??? ??? ??? article is >>>>>>> > >? ? ? >??? ??? ??? >??? ??? helpful. >>>>>>> > >? ? ? >??? ??? ??? >??? ??? Best >>>>>>> > >? ? ? >??? ??? ??? >??? ??? Shen >>>>>>> > >? ? ? >??? ??? ??? > >>>>>>> > >? ? ? >??? ??? ??? > References >>>>>>> > >? ? ? >??? ??? ??? > >>>>>>> > >? ? ? >??? ??? ??? >??? ??? Visible links >>>>>>> > >? ? ? >??? ??? ??? >??? ??? 1. >>>>>>> > >? ? ? [3][5][5] >>>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > >? ? ? >??? ??? ??? ---end quoted text--- >>>>>>> > >? ? ? > >>>>>>> > >? ? ? >??? ??? -- >>>>>>> > >? ? ? >??? ??? Shen Wang >>>>>>> > >? ? ? >??? ??? [4]Loris??? Developer >>>>>>> > >? ? ? >??? ??? Montreal Neurological Institute??? >>>>>>> > >? ? ? >??? ??? McGill University >>>>>>> > >? ? ? > >>>>>>> > >? ? ? > References >>>>>>> > >? ? ? > >>>>>>> > >? ? ? >??? ??? Visible links >>>>>>> > >? ? ? >??? ??? 1. mailto:[6][6] >>>>>>> support-cirl at berkeley.edu >>>>>>> > >? ? ? >??? ??? 2. >>>>>>> > [7][7]https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > >? ? ? >??? ??? 3. >>>>>>> > [8][8]https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > >? ? ? >??? ??? 4. [9][9]https://github.com/aces/Loris >>>>>>> > >? ? ? ---end quoted text--- >>>>>>> > > >>>>>>> > >? ? -- >>>>>>> > >? ? Shen Wang >>>>>>> > >? ? [10]Loris??? Developer >>>>>>> > >? ? Montreal Neurological Institute??? >>>>>>> > >? ? McGill University >>>>>>> > > >>>>>>> > > References >>>>>>> > > >>>>>>> > >? ? Visible links >>>>>>> > >? ? 2. mailto:[10]support-cirl at berkeley.edu >>>>>>> > >? ? 3. mailto:[11]support-cirl at berkeley.edu >>>>>>> > >? ? 4. [12] >>>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > >? ? 5. [13] >>>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > >? ? 6. mailto:[14]support-cirl at berkeley.edu >>>>>>> > >? ? 7. [15] >>>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > >? ? 8. [16] >>>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > >? ? 9. [17]https://github.com/aces/Loris >>>>>>> > >? ? 10. [18]https://github.com/aces/Loris >>>>>>> > >>>>>>> > ---end quoted text--- >>>>>>> > >>>>>>> > -- >>>>>>> > Shen Wang >>>>>>> > [19]Loris? Developer >>>>>>> > Montreal Neurological Institute? >>>>>>> > McGill University >>>>>>> > >>>>>>> > References >>>>>>> > >>>>>>> > Visible links >>>>>>> > 1. mailto:support-cirl at berkeley.edu >>>>>>> > 2. mailto:support-cirl at berkeley.edu >>>>>>> > 3. mailto:support-cirl at berkeley.edu >>>>>>> > 4. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > 5. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > 6. mailto:support-cirl at berkeley.edu >>>>>>> > 7. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > 8. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > 9. https://github.com/aces/Loris >>>>>>> > 10. mailto:support-cirl at berkeley.edu >>>>>>> > 11. mailto:support-cirl at berkeley.edu >>>>>>> > 12. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > 13. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > 14. mailto:support-cirl at berkeley.edu >>>>>>> > 15. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > 16. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>> > 17. https://github.com/aces/Loris >>>>>>> > 18. https://github.com/aces/Loris >>>>>>> > 19. https://github.com/aces/Loris >>>>>>> ---end quoted text--- >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Thu Jan 14 15:27:56 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Thu, 14 Jan 2021 20:27:56 +0000 Subject: [Loris-dev] LORIS - Upload nifti and minc Message-ID: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> Dear LorisDev team, Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format? Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From AMORALESPINZON at BWH.HARVARD.EDU Fri Jan 15 21:38:21 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Sat, 16 Jan 2021 02:38:21 +0000 Subject: [Loris-dev] Errors upgrading LORIS v22.0.4 to v23.0.0 Message-ID: Dear Loris DevTeam, I am upgrading LORIS to the last version 23.0.0. While executing the SQL patch I got the following output with errors (see below). I have followed all the upgrading steps. Any ideas on what can be missing? Regards, Alfredo. === mysql> source /home/bic/moralf/22.0_To_23.0_upgrade.sql +------------------------------------------------------------------------------------+ | Running: SQL/New_patches/2018-05-18-adding_physiological_all_sites_permissions.sql | +------------------------------------------------------------------------------------+ | Running: SQL/New_patches/2018-05-18-adding_physiological_all_sites_permissions.sql | +------------------------------------------------------------------------------------+ 1 row in set (0.01 sec) Query OK, 1 row affected (0.03 sec) Query OK, 1 row affected (0.00 sec) ERROR 1048 (23000): Column 'userID' cannot be null ERROR 1048 (23000): Column 'userID' cannot be null +---------------------------------------------------------------------+ | Running: SQL/New_patches/2018-07-23-battery_manager_permissions.sql | +---------------------------------------------------------------------+ | Running: SQL/New_patches/2018-07-23-battery_manager_permissions.sql | +---------------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.01 sec) Query OK, 0 rows affected (0.00 sec) Records: 0 Duplicates: 0 Warnings: 0 Query OK, 0 rows affected (0.00 sec) Records: 0 Duplicates: 0 Warnings: 0 ERROR 1146 (42S02): Table 'IPMSA_LORIS.modules' doesn't exist +----------------------------------------------------------------+ | Running: SQL/New_patches/2019-02-08-multiple_mri_protocols.sql | +----------------------------------------------------------------+ | Running: SQL/New_patches/2019-02-08-multiple_mri_protocols.sql | +----------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 0 rows affected (0.02 sec) Query OK, 1 row affected (0.00 sec) Query OK, 0 rows affected (0.02 sec) Query OK, 1 row affected (0.01 sec) Query OK, 0 rows affected (0.02 sec) Query OK, 1 row affected (0.00 sec) Query OK, 0 rows affected (0.03 sec) Query OK, 1 row affected (0.00 sec) Query OK, 0 rows affected (0.08 sec) Records: 0 Duplicates: 0 Warnings: 0 Query OK, 9 rows affected (0.01 sec) Rows matched: 9 Changed: 9 Warnings: 0 Query OK, 9 rows affected (0.09 sec) Records: 9 Duplicates: 0 Warnings: 0 Query OK, 0 rows affected (0.05 sec) Records: 0 Duplicates: 0 Warnings: 0 Query OK, 0 rows affected (0.00 sec) Rows matched: 0 Changed: 0 Warnings: 0 Query OK, 0 rows affected (0.05 sec) Records: 0 Duplicates: 0 Warnings: 0 Query OK, 0 rows affected (0.04 sec) Records: 0 Duplicates: 0 Warnings: 0 Query OK, 0 rows affected (0.00 sec) Rows matched: 0 Changed: 0 Warnings: 0 Query OK, 0 rows affected (0.07 sec) Records: 0 Duplicates: 0 Warnings: 0 Query OK, 0 rows affected (0.06 sec) Records: 0 Duplicates: 0 Warnings: 0 Query OK, 0 rows affected (0.00 sec) Rows matched: 0 Changed: 0 Warnings: 0 Query OK, 0 rows affected (0.07 sec) Records: 0 Duplicates: 0 Warnings: 0 +------------------------------------------------------------------+ | Running: SQL/New_patches/2019-07-02-Add_Edit_DoB_Permissions.sql | +------------------------------------------------------------------+ | Running: SQL/New_patches/2019-07-02-Add_Edit_DoB_Permissions.sql | +------------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.01 sec) +---------------------------------------------------------+ | Running: SQL/New_patches/2019-07-04-add_DoD_feature.sql | +---------------------------------------------------------+ | Running: SQL/New_patches/2019-07-04-add_DoD_feature.sql | +---------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 0 rows affected (0.77 sec) Records: 0 Duplicates: 0 Warnings: 0 Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.01 sec) Records: 1 Duplicates: 0 Warnings: 0 Query OK, 1 row affected (0.00 sec) Records: 1 Duplicates: 0 Warnings: 0 +--------------------------------------------------------------+ | Running: SQL/New_patches/2019-07-05-Add_Language_feature.sql | +--------------------------------------------------------------+ | Running: SQL/New_patches/2019-07-05-Add_Language_feature.sql | +--------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 126974 rows affected (4.18 sec) Records: 126974 Duplicates: 0 Warnings: 0 +--------------------------------------------------------------------------------+ | Running: SQL/New_patches/2019-08-06-Add_date_display_format_config_setting.sql | +--------------------------------------------------------------------------------+ | Running: SQL/New_patches/2019-08-06-Add_date_display_format_config_setting.sql | +--------------------------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 1 row affected (0.00 sec) Records: 1 Duplicates: 0 Warnings: 0 Query OK, 1 row affected (0.01 sec) Records: 1 Duplicates: 0 Warnings: 0 +-------------------------------------------------------------------------------------------+ | Running: SQL/New_patches/2019-10-09-move_MINCToolsPath_configuration_to_Config_tables.sql | +-------------------------------------------------------------------------------------------+ | Running: SQL/New_patches/2019-10-09-move_MINCToolsPath_configuration_to_Config_tables.sql | +-------------------------------------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 1 row affected (0.00 sec) Records: 1 Duplicates: 0 Warnings: 0 Query OK, 1 row affected (0.00 sec) Records: 1 Duplicates: 0 Warnings: 0 +-------------------------------------------------------------------------+ | Running: SQL/New_patches/2019-10-29-adding_issues_attachments_table.sql | +-------------------------------------------------------------------------+ | Running: SQL/New_patches/2019-10-29-adding_issues_attachments_table.sql | +-------------------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 0 rows affected (0.03 sec) Query OK, 1 row affected (0.01 sec) Query OK, 1 row affected (0.00 sec) Records: 1 Duplicates: 0 Warnings: 0 +---------------------------------------------------------+ | Running: SQL/New_patches/2019-11-26-AddOtherSexEnum.sql | +---------------------------------------------------------+ | Running: SQL/New_patches/2019-11-26-AddOtherSexEnum.sql | +---------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 0 rows affected (0.00 sec) Records: 0 Duplicates: 0 Warnings: 0 Query OK, 0 rows affected (0.01 sec) Records: 0 Duplicates: 0 Warnings: 0 +----------------------------------------------------------------------------+ | Running: SQL/New_patches/2019-11-29-Add_upload_directory_configuration.sql | +----------------------------------------------------------------------------+ | Running: SQL/New_patches/2019-11-29-Add_upload_directory_configuration.sql | +----------------------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 1 row affected (0.01 sec) Records: 1 Duplicates: 0 Warnings: 0 Query OK, 1 row affected (0.00 sec) Records: 1 Duplicates: 0 Warnings: 0 Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Records: 1 Duplicates: 0 Warnings: 0 Query OK, 1 row affected (0.01 sec) Records: 1 Duplicates: 0 Warnings: 0 +--------------------------------------------------------+ | Running: SQL/New_patches/2019-12-05-AddModuleTable.sql | +--------------------------------------------------------+ | Running: SQL/New_patches/2019-12-05-AddModuleTable.sql | +--------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 0 rows affected (0.02 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.01 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.01 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.01 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.01 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.01 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.01 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.01 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.01 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.01 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) +-------------------------------------------------------+ | Running: SQL/New_patches/2020-01-16-ModuleManager.sql | +-------------------------------------------------------+ | Running: SQL/New_patches/2020-01-16-ModuleManager.sql | +-------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) Query OK, 1 row affected (0.00 sec) ERROR 1048 (23000): Column 'userID' cannot be null ERROR 1048 (23000): Column 'userID' cannot be null +-------------------------------------------------------------------------------------------+ | Running: SQL/New_patches/2020-01-20-adding_electrophysiology_browser_to_modules_table.sql | +-------------------------------------------------------------------------------------------+ | Running: SQL/New_patches/2020-01-20-adding_electrophysiology_browser_to_modules_table.sql | +-------------------------------------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 1 row affected (0.00 sec) +------------------------------------------------------+ | Running: SQL/New_patches/2020-02-18-MyPrefModule.sql | +------------------------------------------------------+ | Running: SQL/New_patches/2020-02-18-MyPrefModule.sql | +------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 1 row affected (0.00 sec) +----------------------------------------------------------------+ | Running: SQL/New_patches/2020-02-24-CandidateProfileModule.sql | +----------------------------------------------------------------+ | Running: SQL/New_patches/2020-02-24-CandidateProfileModule.sql | +----------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 1 row affected (0.00 sec) +----------------------------------------------------------------------+ | Running: SQL/New_patches/2020-04-20-Rename_highlander_permission.sql | +----------------------------------------------------------------------+ | Running: SQL/New_patches/2020-04-20-Rename_highlander_permission.sql | +----------------------------------------------------------------------+ 1 row in set (0.01 sec) Query OK, 1 row affected (0.00 sec) Rows matched: 1 Changed: 1 Warnings: 0 +---------------------------------------------------------------------------+ | Running: SQL/New_patches/2020-04-27-AddViolatedScansOwnSitePermission.sql | +---------------------------------------------------------------------------+ | Running: SQL/New_patches/2020-04-27-AddViolatedScansOwnSitePermission.sql | +---------------------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 1 row affected (0.00 sec) ERROR 1048 (23000): Column 'userID' cannot be null +------------------------------------------------------------------------------+ | Running: SQL/New_patches/2020-05-08-ChangeDefaultMPCGForMriViolationsLog.sql | +------------------------------------------------------------------------------+ | Running: SQL/New_patches/2020-05-08-ChangeDefaultMPCGForMriViolationsLog.sql | +------------------------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 0 rows affected (0.06 sec) Records: 0 Duplicates: 0 Warnings: 0 +---------------------------------------------------------------+ | Running: SQL/New_patches/2020-05-11-AddViolationsResolved.sql | +---------------------------------------------------------------+ | Running: SQL/New_patches/2020-05-11-AddViolationsResolved.sql | +---------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 0 rows affected (0.00 sec) Records: 0 Duplicates: 0 Warnings: 0 +------------------------------------------------------------------------+ | Running: SQL/New_patches/2020-05-15-RemoveObsoleteMriViolationsLog.sql | +------------------------------------------------------------------------+ | Running: SQL/New_patches/2020-05-15-RemoveObsoleteMriViolationsLog.sql | +------------------------------------------------------------------------+ 1 row in set (0.00 sec) Query OK, 0 rows affected (0.00 sec) Query OK, 0 rows affected (2.04 sec) Rows matched: 0 Changed: 0 Warnings: 0 mysql> notee === The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Mon Jan 18 10:52:13 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Mon, 18 Jan 2021 10:52:13 -0500 Subject: [Loris-dev] CentOS 8 and Loris In-Reply-To: References: Message-ID: Hi Julie, At what point are you getting the php-fpm error? I just tried going through the documentation that Eli linked on a cleanly installed CentOS 7 VM and while it is odd that it's installing php-fpm and then telling you to use a config file made mod_php, when I followed the documentation it seemed to work. (I got as far as accessing http://localhost/installdb.php then couldn't go further because I don't have a web browser on the VM I was using to test, but if there's a problem with the php configuration I don't think that page should load either and I accessed it with curl to verify. Note that when install.sh asked me if I wanted to set up the config files automatically I said 'n' in my test since it was set up manually in the section above of the documentation..) - Dave On Tue, Jan 12, 2021 at 6:42 PM Julie Ashworth, HWNI Computing Support < support-cirl at berkeley.edu> wrote: > Thanks Eli, > That is the doc I used which produced the php-fpm error. > > On Tue, Jan 12, 2021, 3:05 PM Eli Johnson wrote: > >> Hi Julie, >> >> I'm not on the LORIS team, but I referenced this CentOS 7 documentation >> while installing on RHEL 7 last year -- >> >> >> https://github.com/aces/Loris/tree/main/docs/wiki/00_SERVER_INSTALL_AND_CONFIGURATION/01_LORIS_Install/CentOS >> >> Most of the documentation can be found in the docs directory within the >> LORIS project on github. >> >> @LORIS team, the links for CENTOS documentation in the github wiki are >> broken. >> >> >> Best, >> Eli Johnson >> >> Eli Johnson >> Developer/Data Manager >> Institute of Child Development >> University of Minnesota >> joh17964 at umn.edu >> >> >> On Tue, Jan 12, 2021 at 3:25 PM >> wrote: >> >>> Send Loris-dev mailing list submissions to >>> loris-dev at bic.mni.mcgill.ca >>> >>> To subscribe or unsubscribe via the World Wide Web, visit >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> or, via email, send a message with subject or body 'help' to >>> loris-dev-request at bic.mni.mcgill.ca >>> >>> You can reach the person managing the list at >>> loris-dev-owner at bic.mni.mcgill.ca >>> >>> When replying, please edit your Subject line so it is more specific >>> than "Re: Contents of Loris-dev digest..." >>> Today's Topics: >>> >>> 1. Re: CentOS 8 and Loris (Julie Ashworth, HWNI Computing Support) >>> >>> >>> >>> ---------- Forwarded message ---------- >>> From: "Julie Ashworth, HWNI Computing Support" < >>> support-cirl at berkeley.edu> >>> To: Dave MacFarlane >>> Cc: loris-dev , Samir Das < >>> samirdas99 at gmail.com>, Christine Rogers >>> Bcc: >>> Date: Tue, 12 Jan 2021 13:24:57 -0800 >>> Subject: Re: [Loris-dev] CentOS 8 and Loris >>> Can you please send me the URL for the most recent linux (ubuntu or >>> centos) installation documentation? >>> Thank you >>> >>> On Tue, Jan 12, 2021, 1:17 PM Julie Ashworth, HWNI Computing Support < >>> support-cirl at berkeley.edu> wrote: >>> >>>> Thanks Dave, >>>> There are many groups taking over development of Centos8, so I thinks >>>> it's incorrect to say that it's discontinued. The most active group is >>>> Rocky linux, started by Greg Kurtzer, who also founded the original CentOS >>>> project 15 years ago. >>>> https://rockylinux.org/ >>>> >>>> I have no personal interest in using php-fpm. I was following the >>>> centos7 instructions to install php-fpm, but there was an apache error >>>> expecting mod_php. I'm happy to install mod_php but that is not >>>> documnted in the centos7 instructions. >>>> To be honest, I'm really disappointed in the loris documentation and >>>> that my emails aren't being read carefully. >>>> >>>> >>>> >>>> On Tue, Jan 12, 2021, 12:22 PM Dave MacFarlane >>>> wrote: >>>> >>>>> Hi Julie, >>>>> >>>>> CentOS is no longer supported (by which I mean the operating system >>>>> itself has been discontinued, not the LORIS support for it.) The MCIN >>>>> production servers currently run on CentOS7 which is why the installation >>>>> procedure is well documented/tested for that system, but given the >>>>> discontinuation of CentOS the plan is to move our production servers off of >>>>> CentOS entirely. It's worth noting that CentOS 8 EOL is 2021, while CentOS >>>>> 7 EOL is 2024. This is the reason why our documentation is tailored to V7. >>>>> >>>>> We don't have much experience running LORIS under php-fpm, which is >>>>> why there's no documentation for that environment. At one point years ago I >>>>> had written a configuration file in order to use it in Travis CI, but since >>>>> then testing/development has moved towards using Docker and the built-in >>>>> PHP web server (I just looked at that configuration file and it's so old it >>>>> refers to php5..). mod_php is currently the only supported/documented PHP >>>>> environment as it's all most of the LORIS developers have experience with >>>>> (though I also regularly develop with the php built in dev server, so I'm >>>>> confident that that works as well.) >>>>> >>>>> The good news is our dependency on apache/mod_php is much weaker than >>>>> it was when I had worked on it years ago, but the bad news is there's no >>>>> written documentation that I'm aware of. >>>>> >>>>> If you're willing to do the work of debugging the environment we can >>>>> help where we can, but if you're trying to get a system up and quickly it's >>>>> likely faster and easier to use something that we have more experience >>>>> with. For reference, I don't think the php_value setting you're trying to >>>>> set should be required anywhere by LORIS. LORIS uses an autoloader for >>>>> class/include resolution and shouldn't depend on the PHP include_path. If >>>>> you're set on php-fpm you can look at docs/config/apache2-fastcgi as a >>>>> starting point, but note that that configuration is from 2014 (which as far >>>>> as I know is the last time anyone tried to use LORIS in that environment.) >>>>> >>>>> P.S. (Forgive me if I'm slow to respond to any emails as I'm on >>>>> vacation until next week..) >>>>> >>>>> On Tue, Jan 12, 2021 at 12:39 PM Julie Ashworth, HWNI Computing >>>>> Support wrote: >>>>> >>>>>> Thank you, >>>>>> In the last 4 emails I have simply asked for current linux >>>>>> documentation, not centos8 documentation (preferably that mentions php-fpm >>>>>> configuration). Is that available? >>>>>> >>>>>> >>>>>> >>>>>> On Tue, Jan 12, 2021, 8:59 AM Samir Das wrote: >>>>>> >>>>>>> Hi Julie, >>>>>>> >>>>>>> We'll do our best to help you with this configuration. :) We'll send >>>>>>> you any documentation we have. >>>>>>> >>>>>>> Regarding CentOS, since RedHat has discontinued its support, we are >>>>>>> planning on putting our testing resources elsewhere. We have yet to discuss >>>>>>> CentOS-Stream, which we will do next week. But I wouldn't worry too much... >>>>>>> we'll help as much as we can given that you have already installed it, etc. >>>>>>> If the problems become too tedious, then we can figure out options together. >>>>>>> >>>>>>> Best, >>>>>>> >>>>>>> Samir Das >>>>>>> >>>>>>> On Tue, Jan 12, 2021 at 5:52 PM Julie Ashworth, HWNI Computing >>>>>>> Support wrote: >>>>>>> >>>>>>>> hi Shen, >>>>>>>> >>>>>>>> On 12-01-2021 11.40 -0500, Shen Wang wrote: >>>>>>>> > So Loris team will not support? Centos. We will only >>>>>>>> support? Ubuntu in the future.? >>>>>>>> >>>>>>>> That's interesting that CentOS will no longer be supported. >>>>>>>> >>>>>>>> Since you previously mentioned that CentOS8 should work, I already >>>>>>>> started the installation, and I'd like to see if it works. >>>>>>>> >>>>>>>> So, please, please... >>>>>>>> will you please send me a link to the most recent instruction for >>>>>>>> loris installation that includes the php_value in /etc/php-fpm.d? >>>>>>>> As I said, I can modify ubuntu instructions. I don't need >>>>>>>> instructions specific to CentOS. >>>>>>>> >>>>>>>> thanks, >>>>>>>> Julie >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 12-01-2021 11.40 -0500, Shen Wang wrote: >>>>>>>> > Hi Julie, >>>>>>>> > We are holding the Loris meeting to discuss whether to support >>>>>>>> centos in >>>>>>>> > the future.? >>>>>>>> > Loris's? sub-modules have issues with the Centos system. So >>>>>>>> Loris team will >>>>>>>> > not support? Centos. >>>>>>>> > We will only support? Ubuntu in the future.? >>>>>>>> > Best? >>>>>>>> > Shen >>>>>>>> > On Tue, 12 Jan 2021 at 11:27, Julie Ashworth, HWNI Computing >>>>>>>> Support >>>>>>>> > <[1]support-cirl at berkeley.edu> wrote: >>>>>>>> > >>>>>>>> > hi Shen, >>>>>>>> > I'm looking for documentation of the (useful!) instruction >>>>>>>> you provided >>>>>>>> > in your previous email: >>>>>>>> > >>>>>>>> > >??? ??? step 2 : add "php_value[include_path]??? = >>>>>>>> > >??? ??? ....."??? into??? /etc/php-fpm.d/loris.conf >>>>>>>> > >>>>>>>> > I would appreciate a link to that documentation, because I >>>>>>>> think it >>>>>>>> > would be valuable for the future. I can adapt Ubuntu >>>>>>>> documentation for >>>>>>>> > CentOS. >>>>>>>> > >>>>>>>> > thanks, >>>>>>>> > Julie >>>>>>>> > >>>>>>>> > On 12-01-2021 09.14 -0500, Shen Wang wrote: >>>>>>>> > >? ? Hi Julie, >>>>>>>> > > >>>>>>>> > >? ? The Loris Team only supports Centos7 currently. >>>>>>>> > >? ? We don't have Centos8 instructions yet, so you can't >>>>>>>> find it. >>>>>>>> > > >>>>>>>> > >? ? If you and Ioannis would like to install loris 23 on >>>>>>>> centos 8, you >>>>>>>> > can >>>>>>>> > >? ? try. >>>>>>>> > >? ? I have installed loris 23 on centos 8, although the >>>>>>>> process is not >>>>>>>> > simple. >>>>>>>> > >? ? That is why I mentioned Centos 8, not officially >>>>>>>> supported yet. >>>>>>>> > Sorry for >>>>>>>> > >? ? confusion. >>>>>>>> > >? ? best >>>>>>>> > >? ? Shen >>>>>>>> > >? ? [1]???? ???????????????????? 2021-01-11 ????????? >>>>>>>> ??8.04.56.png >>>>>>>> > >? ? On Mon, 11 Jan 2021 at 16:27, Julie Ashworth, HWNI >>>>>>>> Computing >>>>>>>> > Support >>>>>>>> > >? ? <[2][2]support-cirl at berkeley.edu> wrote: >>>>>>>> > > >>>>>>>> > >? ? ? Thanks Shen, >>>>>>>> > >? ? ? Is this documented anywhere? I checked the Ubuntu >>>>>>>> instructions >>>>>>>> > and the >>>>>>>> > >? ? ? install.sh file, but I don't see it mentioned. >>>>>>>> > > >>>>>>>> > >? ? ? You also mentioned to Ioannis that Loris should >>>>>>>> run find on >>>>>>>> > CentOS8. >>>>>>>> > >? ? ? Which version did you recommend for CentOS8? >>>>>>>> > > >>>>>>>> > >? ? ? best, >>>>>>>> > >? ? ? Julie >>>>>>>> > > >>>>>>>> > >? ? ? On 11-01-2021 16.04 -0500, Shen Wang wrote: >>>>>>>> > >? ? ? >??? ??? Hi Julie, >>>>>>>> > >? ? ? >??? ??? We do not support Loris 23.0.2 to run >>>>>>>> on CentOS 8. >>>>>>>> > >? ? ? >??? ??? You can install 23.0.2 on Centos 7. >>>>>>>> > >? ? ? >??? ??? If you want to try to install it on >>>>>>>> Centos8. There is no >>>>>>>> > guarantee >>>>>>>> > >? ? ? that it >>>>>>>> > >? ? ? >??? ??? will work on Centos 8. >>>>>>>> > >? ? ? >??? ??? You can try it. >>>>>>>> > >? ? ? >??? ??? step 1 : remove the line of php_value >>>>>>>> from loris.conf >>>>>>>> > >? ? ? >??? ??? step 2 : add >>>>>>>> "php_value[include_path]??? = >>>>>>>> > >? ? ? >??? ??? >>>>>>>> ....."??? into??? /etc/php-fpm.d/loris.conf >>>>>>>> > >? ? ? >??? ??? step 3: reload php-fpm and httpd. >>>>>>>> > >? ? ? >??? ??? Good Luck! >>>>>>>> > >? ? ? >??? ??? Best??? >>>>>>>> > >? ? ? >??? ??? Shen >>>>>>>> > >? ? ? >??? ??? On Mon, 11 Jan 2021 at 15:32, Julie >>>>>>>> Ashworth, HWNI >>>>>>>> > Computing >>>>>>>> > >? ? ? Support >>>>>>>> > >? ? ? >??? ??? <[1][3][3]support-cirl at berkeley.edu> >>>>>>>> wrote: >>>>>>>> > >? ? ? > >>>>>>>> > >? ? ? >??? ??? ??? hi Shen, >>>>>>>> > >? ? ? >??? ??? ??? that *is* how I installed >>>>>>>> apache/php7.4. >>>>>>>> > >? ? ? > >>>>>>>> > >? ? ? >??? ??? ??? Please reread my email. >>>>>>>> > >? ? ? > >>>>>>>> > >? ? ? >??? ??? ??? I'd like to know how y'all >>>>>>>> recommend adding the php >>>>>>>> > path for >>>>>>>> > >? ? ? loris >>>>>>>> > >? ? ? >??? ??? ??? libraries using php-fpm. >>>>>>>> > >? ? ? > >>>>>>>> > >? ? ? >??? ??? ??? If I use the apache configuration >>>>>>>> file provided: >>>>>>>> > >? ? ? >??? ??? ??? ??? ??? ??? ??? php_value >>>>>>>> include_path >>>>>>>> > >? ? ? >??? ??? ??? >>>>>>>> > >? ? ? >>>>>>>> > >>>>>>>> .:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries >>>>>>>> > >? ? ? > >>>>>>>> > >? ? ? >??? ??? ??? I get an error: >>>>>>>> > >? ? ? >??? ??? ??? Invalid command 'php_value', >>>>>>>> perhaps misspelled or >>>>>>>> > defined by a >>>>>>>> > >? ? ? module >>>>>>>> > >? ? ? >??? ??? ??? not included in the server >>>>>>>> configuration >>>>>>>> > >? ? ? > >>>>>>>> > >? ? ? >??? ??? ??? ... because this isn't supported >>>>>>>> with php-fpm >>>>>>>> > >? ? ? > >>>>>>>> > >? ? ? >??? ??? ??? best, >>>>>>>> > >? ? ? >??? ??? ??? Julie >>>>>>>> > >? ? ? > >>>>>>>> > >? ? ? >??? ??? ??? On 11-01-2021 10.08 -0500, Shen >>>>>>>> Wang wrote: >>>>>>>> > >? ? ? >??? ??? ??? >??? ??? Hi Julie, >>>>>>>> > >? ? ? >??? ??? ??? >??? ??? I recommend >>>>>>>> reinstalling php 7.4 and apache. >>>>>>>> > >? ? ? >??? ??? ??? >??? ??? >>>>>>>> > >? ? ? [1][2][4][4] >>>>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > this >>>>>>>> > >? ? ? >??? ??? ??? article is >>>>>>>> > >? ? ? >??? ??? ??? >??? ??? helpful. >>>>>>>> > >? ? ? >??? ??? ??? >??? ??? Best >>>>>>>> > >? ? ? >??? ??? ??? >??? ??? Shen >>>>>>>> > >? ? ? >??? ??? ??? > >>>>>>>> > >? ? ? >??? ??? ??? > References >>>>>>>> > >? ? ? >??? ??? ??? > >>>>>>>> > >? ? ? >??? ??? ??? >??? ??? Visible links >>>>>>>> > >? ? ? >??? ??? ??? >??? ??? 1. >>>>>>>> > >? ? ? [3][5][5] >>>>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > >? ? ? >??? ??? ??? ---end quoted text--- >>>>>>>> > >? ? ? > >>>>>>>> > >? ? ? >??? ??? -- >>>>>>>> > >? ? ? >??? ??? Shen Wang >>>>>>>> > >? ? ? >??? ??? [4]Loris??? Developer >>>>>>>> > >? ? ? >??? ??? Montreal Neurological Institute??? >>>>>>>> > >? ? ? >??? ??? McGill University >>>>>>>> > >? ? ? > >>>>>>>> > >? ? ? > References >>>>>>>> > >? ? ? > >>>>>>>> > >? ? ? >??? ??? Visible links >>>>>>>> > >? ? ? >??? ??? 1. mailto:[6][6] >>>>>>>> support-cirl at berkeley.edu >>>>>>>> > >? ? ? >??? ??? 2. >>>>>>>> > [7][7]https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > >? ? ? >??? ??? 3. >>>>>>>> > [8][8]https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > >? ? ? >??? ??? 4. [9][9]https://github.com/aces/Loris >>>>>>>> > >? ? ? ---end quoted text--- >>>>>>>> > > >>>>>>>> > >? ? -- >>>>>>>> > >? ? Shen Wang >>>>>>>> > >? ? [10]Loris??? Developer >>>>>>>> > >? ? Montreal Neurological Institute??? >>>>>>>> > >? ? McGill University >>>>>>>> > > >>>>>>>> > > References >>>>>>>> > > >>>>>>>> > >? ? Visible links >>>>>>>> > >? ? 2. mailto:[10]support-cirl at berkeley.edu >>>>>>>> > >? ? 3. mailto:[11]support-cirl at berkeley.edu >>>>>>>> > >? ? 4. [12] >>>>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > >? ? 5. [13] >>>>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > >? ? 6. mailto:[14]support-cirl at berkeley.edu >>>>>>>> > >? ? 7. [15] >>>>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > >? ? 8. [16] >>>>>>>> https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > >? ? 9. [17]https://github.com/aces/Loris >>>>>>>> > >? ? 10. [18]https://github.com/aces/Loris >>>>>>>> > >>>>>>>> > ---end quoted text--- >>>>>>>> > >>>>>>>> > -- >>>>>>>> > Shen Wang >>>>>>>> > [19]Loris? Developer >>>>>>>> > Montreal Neurological Institute? >>>>>>>> > McGill University >>>>>>>> > >>>>>>>> > References >>>>>>>> > >>>>>>>> > Visible links >>>>>>>> > 1. mailto:support-cirl at berkeley.edu >>>>>>>> > 2. mailto:support-cirl at berkeley.edu >>>>>>>> > 3. mailto:support-cirl at berkeley.edu >>>>>>>> > 4. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > 5. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > 6. mailto:support-cirl at berkeley.edu >>>>>>>> > 7. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > 8. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > 9. https://github.com/aces/Loris >>>>>>>> > 10. mailto:support-cirl at berkeley.edu >>>>>>>> > 11. mailto:support-cirl at berkeley.edu >>>>>>>> > 12. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > 13. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > 14. mailto:support-cirl at berkeley.edu >>>>>>>> > 15. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > 16. https://tecadmin.net/install-apache-php-fpm-centos-8/ >>>>>>>> > 17. https://github.com/aces/Loris >>>>>>>> > 18. https://github.com/aces/Loris >>>>>>>> > 19. https://github.com/aces/Loris >>>>>>>> ---end quoted text--- >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Mon Jan 18 10:58:47 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Mon, 18 Jan 2021 10:58:47 -0500 Subject: [Loris-dev] Errors upgrading LORIS v22.0.4 to v23.0.0 In-Reply-To: References: Message-ID: Hi Alfredo, It seems like you have an issue with the user_perm_rel table. I need more information to debug this issue. Could you send me the data in the table (22.0.4)? Thanks. Best regards Shen On Fri, 15 Jan 2021 at 21:38, Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear Loris DevTeam, > > I am upgrading LORIS to the last version 23.0.0. While executing the SQL > patch I got the following output with errors (see below). I have followed > all the upgrading steps. Any ideas on what can be missing? > > Regards, > Alfredo. > > === > mysql> source /home/bic/moralf/22.0_To_23.0_upgrade.sql > > +------------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2018-05-18-adding_physiological_all_sites_permissions.sql | > > +------------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2018-05-18-adding_physiological_all_sites_permissions.sql | > > +------------------------------------------------------------------------------------+ > 1 row in set (0.01 sec) > > Query OK, 1 row affected (0.03 sec) > > Query OK, 1 row affected (0.00 sec) > > ERROR 1048 (23000): Column 'userID' cannot be null > ERROR 1048 (23000): Column 'userID' cannot be null > +---------------------------------------------------------------------+ > | Running: SQL/New_patches/2018-07-23-battery_manager_permissions.sql | > +---------------------------------------------------------------------+ > | Running: SQL/New_patches/2018-07-23-battery_manager_permissions.sql | > +---------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 0 rows affected (0.00 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.00 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > ERROR 1146 (42S02): Table 'IPMSA_LORIS.modules' doesn't exist > +----------------------------------------------------------------+ > | Running: SQL/New_patches/2019-02-08-multiple_mri_protocols.sql | > +----------------------------------------------------------------+ > | Running: SQL/New_patches/2019-02-08-multiple_mri_protocols.sql | > +----------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.02 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 0 rows affected (0.02 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 0 rows affected (0.02 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 0 rows affected (0.03 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 0 rows affected (0.08 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 9 rows affected (0.01 sec) > Rows matched: 9 Changed: 9 Warnings: 0 > > Query OK, 9 rows affected (0.09 sec) > Records: 9 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.05 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.00 sec) > Rows matched: 0 Changed: 0 Warnings: 0 > > Query OK, 0 rows affected (0.05 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.04 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.00 sec) > Rows matched: 0 Changed: 0 Warnings: 0 > > Query OK, 0 rows affected (0.07 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.06 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.00 sec) > Rows matched: 0 Changed: 0 Warnings: 0 > > Query OK, 0 rows affected (0.07 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > +------------------------------------------------------------------+ > | Running: SQL/New_patches/2019-07-02-Add_Edit_DoB_Permissions.sql | > +------------------------------------------------------------------+ > | Running: SQL/New_patches/2019-07-02-Add_Edit_DoB_Permissions.sql | > +------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > +---------------------------------------------------------+ > | Running: SQL/New_patches/2019-07-04-add_DoD_feature.sql | > +---------------------------------------------------------+ > | Running: SQL/New_patches/2019-07-04-add_DoD_feature.sql | > +---------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.77 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > +--------------------------------------------------------------+ > | Running: SQL/New_patches/2019-07-05-Add_Language_feature.sql | > +--------------------------------------------------------------+ > | Running: SQL/New_patches/2019-07-05-Add_Language_feature.sql | > +--------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 126974 rows affected (4.18 sec) > Records: 126974 Duplicates: 0 Warnings: 0 > > > +--------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2019-08-06-Add_date_display_format_config_setting.sql | > > +--------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2019-08-06-Add_date_display_format_config_setting.sql | > > +--------------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.01 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > > +-------------------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2019-10-09-move_MINCToolsPath_configuration_to_Config_tables.sql > | > > +-------------------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2019-10-09-move_MINCToolsPath_configuration_to_Config_tables.sql > | > > +-------------------------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > +-------------------------------------------------------------------------+ > | Running: SQL/New_patches/2019-10-29-adding_issues_attachments_table.sql | > +-------------------------------------------------------------------------+ > | Running: SQL/New_patches/2019-10-29-adding_issues_attachments_table.sql | > +-------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.03 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > +---------------------------------------------------------+ > | Running: SQL/New_patches/2019-11-26-AddOtherSexEnum.sql | > +---------------------------------------------------------+ > | Running: SQL/New_patches/2019-11-26-AddOtherSexEnum.sql | > +---------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.00 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.01 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > > +----------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2019-11-29-Add_upload_directory_configuration.sql | > > +----------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2019-11-29-Add_upload_directory_configuration.sql | > > +----------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.01 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > +--------------------------------------------------------+ > | Running: SQL/New_patches/2019-12-05-AddModuleTable.sql | > +--------------------------------------------------------+ > | Running: SQL/New_patches/2019-12-05-AddModuleTable.sql | > +--------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.02 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > +-------------------------------------------------------+ > | Running: SQL/New_patches/2020-01-16-ModuleManager.sql | > +-------------------------------------------------------+ > | Running: SQL/New_patches/2020-01-16-ModuleManager.sql | > +-------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > ERROR 1048 (23000): Column 'userID' cannot be null > ERROR 1048 (23000): Column 'userID' cannot be null > > +-------------------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2020-01-20-adding_electrophysiology_browser_to_modules_table.sql > | > > +-------------------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2020-01-20-adding_electrophysiology_browser_to_modules_table.sql > | > > +-------------------------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > +------------------------------------------------------+ > | Running: SQL/New_patches/2020-02-18-MyPrefModule.sql | > +------------------------------------------------------+ > | Running: SQL/New_patches/2020-02-18-MyPrefModule.sql | > +------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > +----------------------------------------------------------------+ > | Running: SQL/New_patches/2020-02-24-CandidateProfileModule.sql | > +----------------------------------------------------------------+ > | Running: SQL/New_patches/2020-02-24-CandidateProfileModule.sql | > +----------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > +----------------------------------------------------------------------+ > | Running: SQL/New_patches/2020-04-20-Rename_highlander_permission.sql | > +----------------------------------------------------------------------+ > | Running: SQL/New_patches/2020-04-20-Rename_highlander_permission.sql | > +----------------------------------------------------------------------+ > 1 row in set (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > Rows matched: 1 Changed: 1 Warnings: 0 > > > +---------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2020-04-27-AddViolatedScansOwnSitePermission.sql | > > +---------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2020-04-27-AddViolatedScansOwnSitePermission.sql | > > +---------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > ERROR 1048 (23000): Column 'userID' cannot be null > > +------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2020-05-08-ChangeDefaultMPCGForMriViolationsLog.sql | > > +------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2020-05-08-ChangeDefaultMPCGForMriViolationsLog.sql | > > +------------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.06 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > +---------------------------------------------------------------+ > | Running: SQL/New_patches/2020-05-11-AddViolationsResolved.sql | > +---------------------------------------------------------------+ > | Running: SQL/New_patches/2020-05-11-AddViolationsResolved.sql | > +---------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.00 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > +------------------------------------------------------------------------+ > | Running: SQL/New_patches/2020-05-15-RemoveObsoleteMriViolationsLog.sql | > +------------------------------------------------------------------------+ > | Running: SQL/New_patches/2020-05-15-RemoveObsoleteMriViolationsLog.sql | > +------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.00 sec) > > Query OK, 0 rows affected (2.04 sec) > Rows matched: 0 Changed: 0 Warnings: 0 > > mysql> notee > > === > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Mon Jan 18 11:58:26 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Mon, 18 Jan 2021 11:58:26 -0500 Subject: [Loris-dev] Errors upgrading LORIS v22.0.4 to v23.0.0 In-Reply-To: References: Message-ID: Hi Alfredo, Looking at the patch it looks like both of the sections that have the error message are doing a subselect for the user named "admin" in a part where it's trying to give newly created permissions to the admin user so that they can be selected in the frontend. Do you have a user named "admin" or did you rename it? In either case, I don't think it will affect your upgrade. You can manually give the electrophysiology_browser_view_site, electrophysiology_browser_view_allsites, module_manager_view, and module_manager_edit to whichever user you use to manage user accounts based on the insert statements in the script by changing "admin" to whatever username you're using. If you don't plan on using the electrophysiology browser or module manager modules, I don't think anything else should be affected other than the ability to grant the permissions in the frontend. The permissions themselves were created so the code shouldn't break. On Fri, Jan 15, 2021 at 9:38 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear Loris DevTeam, > > I am upgrading LORIS to the last version 23.0.0. While executing the SQL > patch I got the following output with errors (see below). I have followed > all the upgrading steps. Any ideas on what can be missing? > > Regards, > Alfredo. > > === > mysql> source /home/bic/moralf/22.0_To_23.0_upgrade.sql > > +------------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2018-05-18-adding_physiological_all_sites_permissions.sql | > > +------------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2018-05-18-adding_physiological_all_sites_permissions.sql | > > +------------------------------------------------------------------------------------+ > 1 row in set (0.01 sec) > > Query OK, 1 row affected (0.03 sec) > > Query OK, 1 row affected (0.00 sec) > > ERROR 1048 (23000): Column 'userID' cannot be null > ERROR 1048 (23000): Column 'userID' cannot be null > +---------------------------------------------------------------------+ > | Running: SQL/New_patches/2018-07-23-battery_manager_permissions.sql | > +---------------------------------------------------------------------+ > | Running: SQL/New_patches/2018-07-23-battery_manager_permissions.sql | > +---------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 0 rows affected (0.00 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.00 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > ERROR 1146 (42S02): Table 'IPMSA_LORIS.modules' doesn't exist > +----------------------------------------------------------------+ > | Running: SQL/New_patches/2019-02-08-multiple_mri_protocols.sql | > +----------------------------------------------------------------+ > | Running: SQL/New_patches/2019-02-08-multiple_mri_protocols.sql | > +----------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.02 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 0 rows affected (0.02 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 0 rows affected (0.02 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 0 rows affected (0.03 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 0 rows affected (0.08 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 9 rows affected (0.01 sec) > Rows matched: 9 Changed: 9 Warnings: 0 > > Query OK, 9 rows affected (0.09 sec) > Records: 9 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.05 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.00 sec) > Rows matched: 0 Changed: 0 Warnings: 0 > > Query OK, 0 rows affected (0.05 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.04 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.00 sec) > Rows matched: 0 Changed: 0 Warnings: 0 > > Query OK, 0 rows affected (0.07 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.06 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.00 sec) > Rows matched: 0 Changed: 0 Warnings: 0 > > Query OK, 0 rows affected (0.07 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > +------------------------------------------------------------------+ > | Running: SQL/New_patches/2019-07-02-Add_Edit_DoB_Permissions.sql | > +------------------------------------------------------------------+ > | Running: SQL/New_patches/2019-07-02-Add_Edit_DoB_Permissions.sql | > +------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > +---------------------------------------------------------+ > | Running: SQL/New_patches/2019-07-04-add_DoD_feature.sql | > +---------------------------------------------------------+ > | Running: SQL/New_patches/2019-07-04-add_DoD_feature.sql | > +---------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.77 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > +--------------------------------------------------------------+ > | Running: SQL/New_patches/2019-07-05-Add_Language_feature.sql | > +--------------------------------------------------------------+ > | Running: SQL/New_patches/2019-07-05-Add_Language_feature.sql | > +--------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 126974 rows affected (4.18 sec) > Records: 126974 Duplicates: 0 Warnings: 0 > > > +--------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2019-08-06-Add_date_display_format_config_setting.sql | > > +--------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2019-08-06-Add_date_display_format_config_setting.sql | > > +--------------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.01 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > > +-------------------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2019-10-09-move_MINCToolsPath_configuration_to_Config_tables.sql > | > > +-------------------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2019-10-09-move_MINCToolsPath_configuration_to_Config_tables.sql > | > > +-------------------------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > +-------------------------------------------------------------------------+ > | Running: SQL/New_patches/2019-10-29-adding_issues_attachments_table.sql | > +-------------------------------------------------------------------------+ > | Running: SQL/New_patches/2019-10-29-adding_issues_attachments_table.sql | > +-------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.03 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > +---------------------------------------------------------+ > | Running: SQL/New_patches/2019-11-26-AddOtherSexEnum.sql | > +---------------------------------------------------------+ > | Running: SQL/New_patches/2019-11-26-AddOtherSexEnum.sql | > +---------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.00 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > Query OK, 0 rows affected (0.01 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > > +----------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2019-11-29-Add_upload_directory_configuration.sql | > > +----------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2019-11-29-Add_upload_directory_configuration.sql | > > +----------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > Query OK, 1 row affected (0.01 sec) > Records: 1 Duplicates: 0 Warnings: 0 > > +--------------------------------------------------------+ > | Running: SQL/New_patches/2019-12-05-AddModuleTable.sql | > +--------------------------------------------------------+ > | Running: SQL/New_patches/2019-12-05-AddModuleTable.sql | > +--------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.02 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > +-------------------------------------------------------+ > | Running: SQL/New_patches/2020-01-16-ModuleManager.sql | > +-------------------------------------------------------+ > | Running: SQL/New_patches/2020-01-16-ModuleManager.sql | > +-------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > ERROR 1048 (23000): Column 'userID' cannot be null > ERROR 1048 (23000): Column 'userID' cannot be null > > +-------------------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2020-01-20-adding_electrophysiology_browser_to_modules_table.sql > | > > +-------------------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2020-01-20-adding_electrophysiology_browser_to_modules_table.sql > | > > +-------------------------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > +------------------------------------------------------+ > | Running: SQL/New_patches/2020-02-18-MyPrefModule.sql | > +------------------------------------------------------+ > | Running: SQL/New_patches/2020-02-18-MyPrefModule.sql | > +------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > +----------------------------------------------------------------+ > | Running: SQL/New_patches/2020-02-24-CandidateProfileModule.sql | > +----------------------------------------------------------------+ > | Running: SQL/New_patches/2020-02-24-CandidateProfileModule.sql | > +----------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > +----------------------------------------------------------------------+ > | Running: SQL/New_patches/2020-04-20-Rename_highlander_permission.sql | > +----------------------------------------------------------------------+ > | Running: SQL/New_patches/2020-04-20-Rename_highlander_permission.sql | > +----------------------------------------------------------------------+ > 1 row in set (0.01 sec) > > Query OK, 1 row affected (0.00 sec) > Rows matched: 1 Changed: 1 Warnings: 0 > > > +---------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2020-04-27-AddViolatedScansOwnSitePermission.sql | > > +---------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2020-04-27-AddViolatedScansOwnSitePermission.sql | > > +---------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 1 row affected (0.00 sec) > > ERROR 1048 (23000): Column 'userID' cannot be null > > +------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2020-05-08-ChangeDefaultMPCGForMriViolationsLog.sql | > > +------------------------------------------------------------------------------+ > | Running: > SQL/New_patches/2020-05-08-ChangeDefaultMPCGForMriViolationsLog.sql | > > +------------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.06 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > +---------------------------------------------------------------+ > | Running: SQL/New_patches/2020-05-11-AddViolationsResolved.sql | > +---------------------------------------------------------------+ > | Running: SQL/New_patches/2020-05-11-AddViolationsResolved.sql | > +---------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.00 sec) > Records: 0 Duplicates: 0 Warnings: 0 > > +------------------------------------------------------------------------+ > | Running: SQL/New_patches/2020-05-15-RemoveObsoleteMriViolationsLog.sql | > +------------------------------------------------------------------------+ > | Running: SQL/New_patches/2020-05-15-RemoveObsoleteMriViolationsLog.sql | > +------------------------------------------------------------------------+ > 1 row in set (0.00 sec) > > Query OK, 0 rows affected (0.00 sec) > > Query OK, 0 rows affected (2.04 sec) > Rows matched: 0 Changed: 0 Warnings: 0 > > mysql> notee > > === > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Tue Jan 19 13:59:54 2021 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 19 Jan 2021 13:59:54 -0500 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> Message-ID: Hi Alfredo, Very sorry for the late reply. In short, yes, it is possible to do both. It is possible to insert MINC files in LORIS by using the LORIS-MRI script called minc_insertion.pl in the uploadNeuroDB folder. If you run perl minc_insertion.pl -h; you will see the explanation on how to run the script. Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called imaging_non_minc_insertion.pl in the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl should give you all the information you need in order to run the script. Hope this helps, C?cile On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team, > > Is is possible to upload nifti and minc files into LORIS, for instance to > a given visit, without having the files in BIDS format? > > Best regards, > Alfredo. > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Mon Jan 25 08:35:46 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 25 Jan 2021 13:35:46 +0000 Subject: [Loris-dev] Issues with landing page, data query and BrainBrowser In-Reply-To: References: <09C35758-DB2A-41D9-B5B6-94FB0095B4F5@bwh.harvard.edu> Message-ID: Dear Zia, The issue is when loading the landing page once a user had logged in into LORIS. The systems remains unresponsive until the graph is loaded. I am moving to the last version of LORIS right now, I will inform if the issues persists in the latests version. Thank you. Alfredo. On Jan 7, 2021, at 3:34 PM, Zia Mohades > wrote: External Email - Use Caution Hello, Regarding your first question. As Dave mentioned we haven't experienced any issues with loading when we click on the link/site under the graph. We did however noticed some formatting issues which should be fixed in the new version of LORIS but nothing related to the loading functionality. Thank you On Wed, Jan 6, 2021 at 12:51 PM Dave MacFarlane > wrote: On Wed, Jan 6, 2021 at 12:30 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, We are experiencing the following issues in Loris. Could you please help me or guide me on how address them. 1. After login into LORIS, the webpage does not allow the user to go to any link until the graph under "Study Progression" is created. This is taking more than one minute to load. I guess this is because we have hundreds of centers. Is it possible to remove the graph from the landing page? (See attachment) I don't believe it should take that long even with a large number of sites. I'll let someone from CCNA handle this part of the question since they also have hundreds of sites and might have more insight.. 2. When using the Data Query Tool the front-end crashes with error 500. This is what I can see in the loris-error.log === [Wed Jan 06 12:23:31.920274 2021] [php7:error] [pid 12100] [client 216.15.126.108:56023] PHP Fatal error: Uncaught ConfigurationException: NDB_Factory::CouchDB() requires all parameters to be supplied. in /var/www/loris/php/libraries/NDB_Factory.class.inc:297\nStack trace:\n#0 /var/www/loris/modules/dataquery/php/dataquery.class.inc(59): NDB_Factory->couchDB('%COUCH_DATABASE...', '%COUCH_HOSTNAME...', 0, '%COUCH_USERNAME...', '%COUCH_PASSWORD...')\n#1 /var/www/loris/php/libraries/NDB_Form.class.inc(188): LORIS\\dataquery\\Dataquery->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171): NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageDecorationMiddleware.php(49): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), Object(LORIS\\dataquery\\Dataquery))\n#4 /var/www/loris/php/libraries/NDB_Page.class.inc(659): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), Object(LORIS\\dataquery\\Dataquery))\n#5 /var/www/loris/php/libraries/Module.class.inc(341): NDB_Page->process(Object(Zend\\ in /var/www/loris/php/libraries/NDB_Factory.class.inc on line 297, referer: https://ipmsa-loris.bic.mni.mcgill.ca/imaging_browser/viewSession/?sessionID=85935 === The DQT currently requires a CouchDB backend with the data imported into it. It looks like the CouchDB hostname/database/username/ password/etc aren't set up. The Configurations section of the file modules/dataquery/README.md should have more information about the setup required. Is the `` tag in project/config.xml setup as described in step 3 of that document? 3. In the statistics section (Reports -> Statistics) I can see the following message at the bottom of the page: === Oops It seems like the scan type selected does not have a corresponding column in the mri_parameter_form table in the database. In order to display the statistics for the scan type, make sure the mri_parameter_form table contains a column in the exact format SCANTYPE_Scan_done === The statistics page using an instrument named "mri_parameter_form" to determine numbers for the scan done. For each scan type in the mri_scan_types table* it expects there to be a column named "SCANTYPE_Scan_Done" to use for reporting statistics. I believe there's somewhere in the MRI documentation that goes into more depth but I'm not entirely sure where, maybe Cecile can chime in.. In the loris-error.log a see a large list of the following messages: === [Wed Jan 06 12:26:24.730900 2021] [php7:notice] [pid 25824] [client 216.15.126.108:56738] PHP Notice: Undefined index: Female in /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line 137, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ [Wed Jan 06 12:26:24.730935 2021] [php7:notice] [pid 25824] [client 216.15.126.108:56738] PHP Notice: Undefined index: OLYMPUS_CLINICAL_SCREENING in /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ [Wed Jan 06 12:26:24.730944 2021] [php7:notice] [pid 25824] [client 216.15.126.108:56738] PHP Notice: Undefined index: Male in /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ === What version of LORIS is this? I think the notices are unrelated and probably harmless but should still be fixed if they haven't been yet. 4. I am not able to visualiza any image. A message ?LOADING ?? appears but nothing happens. Looking at the loris-error.log I can see that the path to the images is missing a ?/? === PHP Warning: readfile(/data_/ipmsa/loris_data/IPMSA/dataassembly/343633/baseline/mri/native/IPMSA_343633_baseline_flair_001.mnc): failed to open stream: No such file or directory in /var/www/loris/modules/brainbrowser/ajax/image.php on line 56, referer: https://ipmsa-loris.bic.mni.mcgill.ca/brainbrowser/?minc_id=[112603] === Do you know where can this missing ?/? should be set? It looks like that code is using the imagePath configuration variable which should have a trailing /. It should be the configuration option labeled "Path to images for display in Imaging Browser (e.g. /data/$project/data/)" in the Configuration module frontend. - Dave _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Mon Jan 25 14:48:43 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 25 Jan 2021 19:48:43 +0000 Subject: [Loris-dev] Cannot connect to the database Message-ID: <33D50627-0F5C-4518-A224-DC4740EA6118@bwh.harvard.edu> Dear LorisDev team, I upgraded the PHP version for apache from 7.2.28 to 7.3.26 in order to avoid errors with trailing-comma in functions. Now that it's upgraded I am getting the following error: === [Sun Jan 24 09:43:47.375992 2021] [php7:notice] [pid 26182] [client 216.15.126.108:50170] Could not execute . Stack trace#0 /var/www/loris/php/libraries/Database.class.inc(106): Database->connect('AAA', 'BBB', 'CCC', '111.111.111.11', true)\n#1 /var/www/loris/php/libraries/NDB_Client.class.inc(66): Database::singleton('AAA', 'BBB', 'CCC', '111.111.111.11', true)\n#2 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#3 {main} [Sun Jan 24 09:43:47.376142 2021] [php7:error] [pid 26182] [client 216.15.126.108:50170] PHP Fatal error: Uncaught DatabaseException: Could not establish a PDO object using the following values: username: `AAA`, dbname: `BBB`, host: `111.111.111.11` and the supplied password. in /var/www/loris/php/libraries/Database.class.inc:173\nStack trace:\n#0 /var/www/loris/php/libraries/Database.class.inc(106): Database->connect('AAA', 'BBB', 'CCC', '111.111.111.11', true)\n#1 /var/www/loris/php/libraries/NDB_Client.class.inc(66): Database::singleton('AAA', 'BBB', 'CCC', '111.111.111.11', true)\n#2 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#3 {main}\n thrown in /var/www/loris/php/libraries/Database.class.inc on line 173 Merge state === I manually tested the connection from the LORIS server to the server hosting the database and it works. Do you have ideas on how to solve this issue? Maybe I?m missing some updates? I am running Ubuntu Xenial 16.04.4 and LORIS is in version 22.0.0. Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. From wangshen.mcin at gmail.com Mon Jan 25 15:05:33 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Mon, 25 Jan 2021 15:05:33 -0500 Subject: [Loris-dev] Cannot connect to the database In-Reply-To: <33D50627-0F5C-4518-A224-DC4740EA6118@bwh.harvard.edu> References: <33D50627-0F5C-4518-A224-DC4740EA6118@bwh.harvard.edu> Message-ID: Hi Alfredo, After you upgrade the PHP version, you need to upgrade some libraries to support the new PHP version as well. 1. sudo apt-get install -y php7.3 php7.3-mysql php7.3-xml php7.3-json php7.3-mbstring php7.3-gd php-ast 2. sudo apt-get install -y libapache2-mod-php7.3 3. sudo a2enmod php7.3 4. sudo service apache2 restart I hope these steps will help you. best Shen On Mon, 25 Jan 2021 at 14:52, Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team, > > I upgraded the PHP version for apache from 7.2.28 to 7.3.26 in order to > avoid errors with trailing-comma in functions. Now that it's upgraded I am > getting the following error: > > === > [Sun Jan 24 09:43:47.375992 2021] [php7:notice] [pid 26182] [client > 216.15.126.108:50170] Could not execute . Stack trace#0 > /var/www/loris/php/libraries/Database.class.inc(106): > Database->connect('AAA', 'BBB', 'CCC', '111.111.111.11', true)\n#1 > /var/www/loris/php/libraries/NDB_Client.class.inc(66): > Database::singleton('AAA', 'BBB', 'CCC', '111.111.111.11', true)\n#2 > /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#3 {main} > > [Sun Jan 24 09:43:47.376142 2021] [php7:error] [pid 26182] [client > 216.15.126.108:50170] PHP Fatal error: Uncaught DatabaseException: Could > not establish a PDO object using the following values: username: `AAA`, > dbname: `BBB`, host: `111.111.111.11` and the supplied password. in > /var/www/loris/php/libraries/Database.class.inc:173\nStack trace:\n#0 > /var/www/loris/php/libraries/Database.class.inc(106): > Database->connect('AAA', 'BBB', 'CCC', '111.111.111.11', true)\n#1 > /var/www/loris/php/libraries/NDB_Client.class.inc(66): > Database::singleton('AAA', 'BBB', 'CCC', '111.111.111.11', true)\n#2 > /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#3 {main}\n > thrown in /var/www/loris/php/libraries/Database.class.inc on line 173 > Merge state > === > > I manually tested the connection from the LORIS server to the server > hosting the database and it works. Do you have ideas on how to solve this > issue? Maybe I?m missing some updates? > > I am running Ubuntu Xenial 16.04.4 and LORIS is in version 22.0.0. > > Best, > Alfredo. > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Mon Jan 25 15:14:49 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 25 Jan 2021 20:14:49 +0000 Subject: [Loris-dev] LORIS ~ 2.500 errors uploading In-Reply-To: <82AA8E32-614D-4866-98EE-EA3D40F7383D@bwh.harvard.edu> References: <82AA8E32-614D-4866-98EE-EA3D40F7383D@bwh.harvard.edu> Message-ID: <83FAFD49-B7A8-44AB-AF5C-D6A046CD13C4@bwh.harvard.edu> Hi Nicolas, I am following up on this issue. I can share some dicom files through the loris sftp if needed. Best, Alfredo. On Jan 14, 2021, at 2:33 PM, Morales Pinzon, Alfredo > wrote: Hi Nicolas, We uploaded another study in LORIS with 7.554 visits. Out of those visits, 825 don't have any images uploaded and 1.700 have missing images. I am checking the log files but most of the time they don?t have an ERROR or WARNING message which makes finding issues very time consuming . So far these are my findings: For the 825 visit where no images were uploaded this is what I can see in the logs: Error Cases 'inserting into the database: 0' 350 'Visit label does not exist? (Issues on Alfredo?s side) 265 'inserting into the database: 0' & 'Visit label does not exist' 12 patient-name doesn\'t match 99 The \'PatientName\' DICOM field cannot be extracted 19 You can\'t use it with data from multiple studies 23 Dicom to Minc conversion failed 10 Log not created 1 Unknown 46 For the 350 cases where the logs say 'inserting into the database: 0? I have found so far the following messages: - No data could be converted into valid MINC files. - The candidate info validation has failed. I check 5 cases with the instructions you provided in a previous email and all the conversion to dcm2minc worked. I reran 2 of those cases, and the log files suggested to run the following command (with different parameters for each case): === \/data_\/ipmsa\/loris_data\/IPMSA\/bin\/mri/uploadNeuroDB/tarchiveLoader.pl -globLocation -profile prod \/data_\/ipmsa\/loris_data\/IPMSA\/data\/tarchive\/DCM_2014\-02\-04_ImagingUpload\-22\-30\-pKguhD\.tar -uploadID 44052 -verbose === After the execution the images were properly uploaded for one case and the other one is missing a flair image. For the 1.700 that have missing images I have been looking at some log files but I haven?t found warnings or errors, as happened previously with the missing t1c in a previous study. What do you suggest to help me go through all these cases? We can start working with some examples and figure out what is happening and how can we fixed. Based on this current situation, I strongly suggest to improve the error and warning logging in the uploading process for LORIS. Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Mon Jan 25 15:45:23 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 25 Jan 2021 20:45:23 +0000 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> Message-ID: Hi Cecile, Thank you for your answer. I am sorry I was not enough specific regarding what we are looking for. We are actually looking for a solution to avoid importing the ?raw? images in minc and nifti images instead of DICOM. We are having a lot of issues importing DICOM (~1.700 visits with issues) and we want to explore options for uploading the original images (e.g., t1) using minc and nifti without them being in BIDS formar. Do you have scripts for this? Best, Alfredo. On Jan 19, 2021, at 1:59 PM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Very sorry for the late reply. In short, yes, it is possible to do both. It is possible to insert MINC files in LORIS by using the LORIS-MRI script called minc_insertion.pl in the uploadNeuroDB folder. If you run perl minc_insertion.pl -h; you will see the explanation on how to run the script. Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called imaging_non_minc_insertion.pl in the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl should give you all the information you need in order to run the script. Hope this helps, C?cile On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format? Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Mon Jan 25 15:53:05 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 25 Jan 2021 20:53:05 +0000 Subject: [Loris-dev] Cannot connect to the database In-Reply-To: References: <33D50627-0F5C-4518-A224-DC4740EA6118@bwh.harvard.edu> Message-ID: Hi Shen, Thank you! The server is now running but now there is another error. I will send a separate email for that. Best, Alfredo. On Jan 25, 2021, at 3:05 PM, Shen Wang > wrote: External Email - Use Caution Hi Alfredo, After you upgrade the PHP version, you need to upgrade some libraries to support the new PHP version as well. 1. sudo apt-get install -y php7.3 php7.3-mysql php7.3-xml php7.3-json php7.3-mbstring php7.3-gd php-ast 2. sudo apt-get install -y libapache2-mod-php7.3 3. sudo a2enmod php7.3 4. sudo service apache2 restart I hope these steps will help you. best Shen On Mon, 25 Jan 2021 at 14:52, Morales Pinzon, Alfredo > wrote: Dear LorisDev team, I upgraded the PHP version for apache from 7.2.28 to 7.3.26 in order to avoid errors with trailing-comma in functions. Now that it's upgraded I am getting the following error: === [Sun Jan 24 09:43:47.375992 2021] [php7:notice] [pid 26182] [client 216.15.126.108:50170] Could not execute . Stack trace#0 /var/www/loris/php/libraries/Database.class.inc(106): Database->connect('AAA', 'BBB', 'CCC', '111.111.111.11', true)\n#1 /var/www/loris/php/libraries/NDB_Client.class.inc(66): Database::singleton('AAA', 'BBB', 'CCC', '111.111.111.11', true)\n#2 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#3 {main} [Sun Jan 24 09:43:47.376142 2021] [php7:error] [pid 26182] [client 216.15.126.108:50170] PHP Fatal error: Uncaught DatabaseException: Could not establish a PDO object using the following values: username: `AAA`, dbname: `BBB`, host: `111.111.111.11` and the supplied password. in /var/www/loris/php/libraries/Database.class.inc:173\nStack trace:\n#0 /var/www/loris/php/libraries/Database.class.inc(106): Database->connect('AAA', 'BBB', 'CCC', '111.111.111.11', true)\n#1 /var/www/loris/php/libraries/NDB_Client.class.inc(66): Database::singleton('AAA', 'BBB', 'CCC', '111.111.111.11', true)\n#2 /var/www/loris/htdocs/index.php(27): NDB_Client->initialize()\n#3 {main}\n thrown in /var/www/loris/php/libraries/Database.class.inc on line 173 Merge state === I manually tested the connection from the LORIS server to the server hosting the database and it works. Do you have ideas on how to solve this issue? Maybe I?m missing some updates? I am running Ubuntu Xenial 16.04.4 and LORIS is in version 22.0.0. Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -- Shen Wang Loris Developer Montreal Neurological Institute McGill University The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Mon Jan 25 17:01:57 2021 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Mon, 25 Jan 2021 17:01:57 -0500 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> Message-ID: Hi Alfredo, I am a bit confused by your email. The two perl scripts I mentioned last week do not require the data to be organized in BIDS to insert them. Did you look into them? Sorry, maybe I am missing something. C?cile On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Cecile, > > Thank you for your answer. I am sorry I was not enough specific regarding > what we are looking for. We are actually looking for a solution to avoid > importing the ?raw? images in minc and nifti images instead of DICOM. We > are having a lot of issues importing DICOM (~1.700 visits with issues) and > we want to explore options for uploading the original images (e.g., t1) > using minc and nifti without them being in BIDS formar. > > Do you have scripts for this? > > Best, > Alfredo. > > On Jan 19, 2021, at 1:59 PM, Cecile Madjar wrote: > > External Email - Use Caution > > Hi Alfredo, > > Very sorry for the late reply. In short, yes, it is possible to do both. > > It is possible to insert MINC files in LORIS by using the LORIS-MRI script > called minc_insertion.pl > in > the uploadNeuroDB folder. If you run perl minc_insertion.pl > > -h; you will see the explanation on how to run the script. > > Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI > script called imaging_non_minc_insertion.pl > in > the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl > > should give you all the information you need in order to run the script. > > Hope this helps, > > C?cile > > On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Dear LorisDev team, >> >> Is is possible to upload nifti and minc files into LORIS, for instance to >> a given visit, without having the files in BIDS format? >> >> Best regards, >> Alfredo. >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.org/complianceline >> >> . If the e-mail was sent to you in error but does not contain patient >> information, please contact the sender and properly dispose of the e-mail. >> >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sridar.narayanan at mcgill.ca Mon Jan 25 17:16:05 2021 From: sridar.narayanan at mcgill.ca (Sridar Narayanan, Dr.) Date: Mon, 25 Jan 2021 22:16:05 +0000 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> Message-ID: <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> Hi Cecile, Just to clarify, many import issues seem to stem from problems with the implementation of dcm2mnc used by Loris. These DICOM files can be successfully converted to MINC and NifTI with other tools, and so we were wondering if it would be possible to import MRI data into Loris as MINC & NifTI files instead of importing the DICOMs. Alternatively, we could convert these files to BIDS and import that instead of DICOM. The important point is whether we can avoid importing DICOM for new scan/participant instances, but import only BIDS or MINC + NiFTI data and generate a new Loris ID from this. We are not asking about attaching a MINC or NifTI file to an existing record, which we know can be done (e.g. for label files associated with the images). Thanks, Sridar On Jan 25, 2021, at 5:01 PM, Cecile Madjar > wrote: Hi Alfredo, I am a bit confused by your email. The two perl scripts I mentioned last week do not require the data to be organized in BIDS to insert them. Did you look into them? Sorry, maybe I am missing something. C?cile On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, Thank you for your answer. I am sorry I was not enough specific regarding what we are looking for. We are actually looking for a solution to avoid importing the ?raw? images in minc and nifti images instead of DICOM. We are having a lot of issues importing DICOM (~1.700 visits with issues) and we want to explore options for uploading the original images (e.g., t1) using minc and nifti without them being in BIDS formar. Do you have scripts for this? Best, Alfredo. On Jan 19, 2021, at 1:59 PM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Very sorry for the late reply. In short, yes, it is possible to do both. It is possible to insert MINC files in LORIS by using the LORIS-MRI script called minc_insertion.pl in the uploadNeuroDB folder. If you run perl minc_insertion.pl -h; you will see the explanation on how to run the script. Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called imaging_non_minc_insertion.pl in the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl should give you all the information you need in order to run the script. Hope this helps, C?cile On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format? Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From nicolasbrossard.mni at gmail.com Tue Jan 26 07:53:54 2021 From: nicolasbrossard.mni at gmail.com (Nicolas Brossard) Date: Tue, 26 Jan 2021 07:53:54 -0500 Subject: [Loris-dev] LORIS ~ 2.500 errors uploading In-Reply-To: <83FAFD49-B7A8-44AB-AF5C-D6A046CD13C4@bwh.harvard.edu> References: <82AA8E32-614D-4866-98EE-EA3D40F7383D@bwh.harvard.edu> <83FAFD49-B7A8-44AB-AF5C-D6A046CD13C4@bwh.harvard.edu> Message-ID: Hi Alfredo, Sorry for the late reply. I'll be able to address this tomorrow. I'll keep in touch. Best, Nicolas On Mon, Jan 25, 2021 at 3:14 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Nicolas, > > I am following up on this issue. I can share some dicom files through the > loris sftp if needed. > > Best, > Alfredo. > > On Jan 14, 2021, at 2:33 PM, Morales Pinzon, Alfredo < > AMORALESPINZON at BWH.HARVARD.EDU> wrote: > > Hi Nicolas, > > We uploaded another study in LORIS with 7.554 visits. Out of those visits, > 825 don't have any images uploaded and 1.700 have missing images. I am > checking the log files but most of the time they don?t have an ERROR or > WARNING message which makes finding issues very time consuming . > > So far these are my findings: > > For the 825 visit where no images were uploaded this is what I can see in > the logs: > > Error Cases > 'inserting into the database: 0' 350 > 'Visit label does not exist? (Issues on Alfredo?s side) 265 > 'inserting into the database: 0' & 'Visit label does not exist' 12 > patient-name doesn\'t match 99 > The \'PatientName\' DICOM field cannot be extracted 19 > You can\'t use it with data from multiple studies 23 > Dicom to Minc conversion failed 10 > Log not created 1 > Unknown 46 > > For the 350 cases where the logs say 'inserting into the database: 0? I > have found so far the following messages: > > - No data could be converted into valid MINC files. > - The candidate info validation has failed. > > I check 5 cases with the instructions you provided in a previous email and > all the conversion to dcm2minc worked. I reran 2 of those cases, and > the log files suggested to run the following command (with different > parameters for each case): > > === > \/data_\/ipmsa\/loris_data\/IPMSA\/bin\/mri/uploadNeuroDB/tarchiveLoader.pl > -globLocation -profile prod > \/data_\/ipmsa\/loris_data\/IPMSA\/data\/tarchive\/DCM_2014\-02\-04_ImagingUpload\-22\-30\-pKguhD\.tar > -uploadID 44052 -verbose > === > > After the execution the images were properly uploaded for one case and > the other one is missing a flair image. > > > For the 1.700 that have missing images I have been looking at some log > files but I haven?t found warnings or errors, as happened previously with > the missing t1c in a previous study. > > What do you suggest to help me go through all these cases? We can start > working with some examples and figure out what is happening and how can we > fixed. > > Based on this current situation, I strongly suggest to improve the error > and warning logging in the uploading process for LORIS. > > Best, > Alfredo. > > > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Tue Jan 26 16:33:51 2021 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 26 Jan 2021 16:33:51 -0500 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> Message-ID: Hi, Thank you for the clarification. I think I understand better the confusion. You can insert MINC files without having to insert DICOM files by running the minc_insertion.pl script with the -force option. Basically, the force option will bypass checks to see if there are DICOMs to attach the file to. minc_insertion.pl -profile -mincPath -force -create_minc_pics For the NIfTI files alone, because of the nature of that file format (no header information like MINC...), you will have to specify a lot of the information when calling the script imaging_non_minc_insertion.pl (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... Basically all the columns of the files table). It needs to be associated with an upload_id for the logging in the database but the upload_id does not necessarily need to be DICOM files. It could be a zipped archive of all the NIfTI files of the session uploaded for example. Then you would just need to create a little wrapper script to run imaging_non_minc_insertion.pl on the loaded NIfTI files. Does that clarify the steps? Thanks! C?cile On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. < sridar.narayanan at mcgill.ca> wrote: > Hi Cecile, > > Just to clarify, many import issues seem to stem from problems with the > implementation of dcm2mnc used by Loris. These DICOM files can be > successfully converted to MINC and NifTI with other tools, and so we were > wondering if it would be possible to import MRI data into Loris as MINC & > NifTI files *instead of* importing the DICOMs. Alternatively, we could > convert these files to BIDS and import that instead of DICOM. The important > point is whether we can *avoid importing DICOM* for new scan/participant > instances, but import only BIDS or MINC + NiFTI data and generate a new > Loris ID from this. We are not asking about attaching a MINC or NifTI file > to an existing record, which we know can be done (e.g. for label files > associated with the images). > > Thanks, > > Sridar > > > On Jan 25, 2021, at 5:01 PM, Cecile Madjar wrote: > > Hi Alfredo, > > I am a bit confused by your email. The two perl scripts I mentioned last > week do not require the data to be organized in BIDS to insert them. Did > you look into them? > > Sorry, maybe I am missing something. > > C?cile > > On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Hi Cecile, >> >> Thank you for your answer. I am sorry I was not enough specific regarding >> what we are looking for. We are actually looking for a solution to avoid >> importing the ?raw? images in minc and nifti images instead of DICOM. We >> are having a lot of issues importing DICOM (~1.700 visits with issues) and >> we want to explore options for uploading the original images (e.g., t1) >> using minc and nifti without them being in BIDS formar. >> >> Do you have scripts for this? >> >> Best, >> Alfredo. >> >> On Jan 19, 2021, at 1:59 PM, Cecile Madjar wrote: >> >> External Email - Use Caution >> >> Hi Alfredo, >> >> Very sorry for the late reply. In short, yes, it is possible to do both. >> >> It is possible to insert MINC files in LORIS by using the LORIS-MRI >> script called minc_insertion.pl >> in >> the uploadNeuroDB folder. If you run perl minc_insertion.pl >> >> -h; you will see the explanation on how to run the script. >> >> Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI >> script called imaging_non_minc_insertion.pl >> in >> the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl >> >> should give you all the information you need in order to run the script. >> >> Hope this helps, >> >> C?cile >> >> On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >>> Dear LorisDev team, >>> >>> Is is possible to upload nifti and minc files into LORIS, for instance >>> to a given visit, without having the files in BIDS format? >>> >>> Best regards, >>> Alfredo. >>> The information in this e-mail is intended only for the person to whom >>> it is addressed. If you believe this e-mail was sent to you in error and >>> the e-mail contains patient information, please contact the Mass General >>> Brigham Compliance HelpLine at >>> http://www.massgeneralbrigham.org/complianceline >>> >>> . If the e-mail was sent to you in error but does not contain patient >>> information, please contact the sender and properly dispose of the e-mail. >>> >>> >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >>> >> >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.org/complianceline . If the e-mail was >> sent to you in error but does not contain patient information, please >> contact the sender and properly dispose of the e-mail. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sridar.narayanan at mcgill.ca Tue Jan 26 16:49:23 2021 From: sridar.narayanan at mcgill.ca (Sridar Narayanan, Dr.) Date: Tue, 26 Jan 2021 21:49:23 +0000 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> Message-ID: <47F601DB-460C-48D9-9D66-A00F6CA4D75A@mcgill.ca> Hi Cecile, Yes, that is very helpful. We would not import a NIfTI file alone, however. The options would be: MINC + NIfTI; BIDS alone; BIDS + MINC (if the BIDS import does not create a MINC file automatically). My understanding is that when DICOM files are imported for a new visit, both a MINC file and a NIfTI file are created automatically. If, instead of importing DICOM, a MINC file is imported, will a corresponding NIfTI file also be created internally? If not, can we just attached the NIfTI file to the record created when the MINC file is uploaded? What happens when a BIDS file is imported - will a MINC file also be created, or would BIDS be the only image representation? Are BIDS to MINC converters available? Thanks! Sridar On Jan 26, 2021, at 4:33 PM, Cecile Madjar > wrote: Hi, Thank you for the clarification. I think I understand better the confusion. You can insert MINC files without having to insert DICOM files by running the minc_insertion.pl script with the -force option. Basically, the force option will bypass checks to see if there are DICOMs to attach the file to. minc_insertion.pl -profile -mincPath -force -create_minc_pics For the NIfTI files alone, because of the nature of that file format (no header information like MINC...), you will have to specify a lot of the information when calling the script imaging_non_minc_insertion.pl (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... Basically all the columns of the files table). It needs to be associated with an upload_id for the logging in the database but the upload_id does not necessarily need to be DICOM files. It could be a zipped archive of all the NIfTI files of the session uploaded for example. Then you would just need to create a little wrapper script to run imaging_non_minc_insertion.pl on the loaded NIfTI files. Does that clarify the steps? Thanks! C?cile On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. > wrote: Hi Cecile, Just to clarify, many import issues seem to stem from problems with the implementation of dcm2mnc used by Loris. These DICOM files can be successfully converted to MINC and NifTI with other tools, and so we were wondering if it would be possible to import MRI data into Loris as MINC & NifTI files instead of importing the DICOMs. Alternatively, we could convert these files to BIDS and import that instead of DICOM. The important point is whether we can avoid importing DICOM for new scan/participant instances, but import only BIDS or MINC + NiFTI data and generate a new Loris ID from this. We are not asking about attaching a MINC or NifTI file to an existing record, which we know can be done (e.g. for label files associated with the images). Thanks, Sridar On Jan 25, 2021, at 5:01 PM, Cecile Madjar > wrote: Hi Alfredo, I am a bit confused by your email. The two perl scripts I mentioned last week do not require the data to be organized in BIDS to insert them. Did you look into them? Sorry, maybe I am missing something. C?cile On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, Thank you for your answer. I am sorry I was not enough specific regarding what we are looking for. We are actually looking for a solution to avoid importing the ?raw? images in minc and nifti images instead of DICOM. We are having a lot of issues importing DICOM (~1.700 visits with issues) and we want to explore options for uploading the original images (e.g., t1) using minc and nifti without them being in BIDS formar. Do you have scripts for this? Best, Alfredo. On Jan 19, 2021, at 1:59 PM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Very sorry for the late reply. In short, yes, it is possible to do both. It is possible to insert MINC files in LORIS by using the LORIS-MRI script called minc_insertion.pl in the uploadNeuroDB folder. If you run perl minc_insertion.pl -h; you will see the explanation on how to run the script. Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called imaging_non_minc_insertion.pl in the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl should give you all the information you need in order to run the script. Hope this helps, C?cile On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format? Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Tue Jan 26 17:21:36 2021 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 26 Jan 2021 17:21:36 -0500 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: <47F601DB-460C-48D9-9D66-A00F6CA4D75A@mcgill.ca> References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> <47F601DB-460C-48D9-9D66-A00F6CA4D75A@mcgill.ca> Message-ID: Hi, Indeed, after importing the MINC file, a NIfTI file can be created and associated with it by running the mass_nii.pl script on a range of FileIDs. Be sure to have the configuration option "Create NIfTI files" set to yes in the imaging pipeline part of the config module. Although, this is probably the case if you were having MINC + NIfTI with DICOM uploads. In LORIS-MRI, there is also a python pipeline (bids_import.py in the python directory) that allows the import of BIDS datasets (EEG and MRI currently supported). Unfortunately, we do not have a BIDS to MINC converter though. However, we have an example tool to convert MINC files into a BIDS dataset but it has to be customized for each project depending on the acquisition particulars. Hope this helps, C?cile On Tue, Jan 26, 2021 at 4:49 PM Sridar Narayanan, Dr. < sridar.narayanan at mcgill.ca> wrote: > Hi Cecile, > > Yes, that is very helpful. > > We would not import a NIfTI file alone, however. The options would be: > MINC + NIfTI; BIDS alone; BIDS + MINC (if the BIDS import does not create a > MINC file automatically). > > My understanding is that when DICOM files are imported for a new visit, > both a MINC file and a NIfTI file are created automatically. If, instead of > importing DICOM, a MINC file is imported, will a corresponding NIfTI file > also be created internally? If not, can we just attached the NIfTI file to > the record created when the MINC file is uploaded? > > What happens when a BIDS file is imported - will a MINC file also be > created, or would BIDS be the only image representation? Are BIDS to MINC > converters available? > > Thanks! > > Sridar > > > On Jan 26, 2021, at 4:33 PM, Cecile Madjar wrote: > > Hi, > > Thank you for the clarification. I think I understand better the confusion. > > You can insert MINC files without having to insert DICOM files by running > the minc_insertion.pl script with the -force option. Basically, the force > option will bypass checks to see if there are DICOMs to attach the file to. > > minc_insertion.pl -profile > -mincPath -force -create_minc_pics > > For the NIfTI files alone, because of the nature of that file format (no > header information like MINC...), you will have to specify a lot of the > information when calling the script imaging_non_minc_insertion.pl > (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... > Basically all the columns of the files table). It needs to be associated > with an upload_id for the logging in the database but the upload_id does > not necessarily need to be DICOM files. It could be a zipped archive of all > the NIfTI files of the session uploaded for example. Then you would just > need to create a little wrapper script to run > imaging_non_minc_insertion.pl on the loaded NIfTI files. > > Does that clarify the steps? > > Thanks! > > C?cile > > On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. < > sridar.narayanan at mcgill.ca> wrote: > >> Hi Cecile, >> >> Just to clarify, many import issues seem to stem from problems with the >> implementation of dcm2mnc used by Loris. These DICOM files can be >> successfully converted to MINC and NifTI with other tools, and so we were >> wondering if it would be possible to import MRI data into Loris as MINC & >> NifTI files *instead of* importing the DICOMs. Alternatively, we could >> convert these files to BIDS and import that instead of DICOM. The important >> point is whether we can *avoid importing DICOM* for new scan/participant >> instances, but import only BIDS or MINC + NiFTI data and generate a new >> Loris ID from this. We are not asking about attaching a MINC or NifTI file >> to an existing record, which we know can be done (e.g. for label files >> associated with the images). >> >> Thanks, >> >> Sridar >> >> >> On Jan 25, 2021, at 5:01 PM, Cecile Madjar wrote: >> >> Hi Alfredo, >> >> I am a bit confused by your email. The two perl scripts I mentioned last >> week do not require the data to be organized in BIDS to insert them. Did >> you look into them? >> >> Sorry, maybe I am missing something. >> >> C?cile >> >> On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >>> Hi Cecile, >>> >>> Thank you for your answer. I am sorry I was not enough specific >>> regarding what we are looking for. We are actually looking for a solution >>> to avoid importing the ?raw? images in minc and nifti images instead of >>> DICOM. We are having a lot of issues importing DICOM (~1.700 visits with >>> issues) and we want to explore options for uploading the original images >>> (e.g., t1) using minc and nifti without them being in BIDS formar. >>> >>> Do you have scripts for this? >>> >>> Best, >>> Alfredo. >>> >>> On Jan 19, 2021, at 1:59 PM, Cecile Madjar >>> wrote: >>> >>> External Email - Use Caution >>> >>> Hi Alfredo, >>> >>> Very sorry for the late reply. In short, yes, it is possible to do both. >>> >>> It is possible to insert MINC files in LORIS by using the LORIS-MRI >>> script called minc_insertion.pl >>> in >>> the uploadNeuroDB folder. If you run perl minc_insertion.pl >>> >>> -h; you will see the explanation on how to run the script. >>> >>> Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI >>> script called imaging_non_minc_insertion.pl >>> in >>> the same uploadNeuroDB folder. Running perl >>> imaging_non_minc_insertion.pl >>> >>> should give you all the information you need in order to run the script. >>> >>> Hope this helps, >>> >>> C?cile >>> >>> On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo < >>> AMORALESPINZON at bwh.harvard.edu> wrote: >>> >>>> Dear LorisDev team, >>>> >>>> Is is possible to upload nifti and minc files into LORIS, for instance >>>> to a given visit, without having the files in BIDS format? >>>> >>>> Best regards, >>>> Alfredo. >>>> The information in this e-mail is intended only for the person to whom >>>> it is addressed. If you believe this e-mail was sent to you in error and >>>> the e-mail contains patient information, please contact the Mass General >>>> Brigham Compliance HelpLine at >>>> http://www.massgeneralbrigham.org/complianceline >>>> >>>> . If the e-mail was sent to you in error but does not contain patient >>>> information, please contact the sender and properly dispose of the e-mail. >>>> >>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is addressed. If you believe this e-mail was sent to you in error and >>> the e-mail contains patient information, please contact the Mass General >>> Brigham Compliance HelpLine at >>> http://www.massgeneralbrigham.org/complianceline . If the e-mail was >>> sent to you in error but does not contain patient information, please >>> contact the sender and properly dispose of the e-mail. >>> >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Fri Jan 29 01:18:41 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Fri, 29 Jan 2021 06:18:41 +0000 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> Message-ID: <0863DD40-4B8E-498C-816E-E28E25A8FCCA@bwh.harvard.edu> Hi Cecile, I tried the script minc_insertion.pl but it seems that the Candidate should not exist before the execution of the script. Is this the case? This would be problematic in order to upload multiple sequences for a given Candidate. This is the error I am getting: === $ perl minc_insertion.pl -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w -mincPath /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists. SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 Spool message is: ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists === Best, Alfredo. P.S. The file /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log is not being written. On Jan 26, 2021, at 4:33 PM, Cecile Madjar > wrote: External Email - Use Caution Hi, Thank you for the clarification. I think I understand better the confusion. You can insert MINC files without having to insert DICOM files by running the minc_insertion.pl script with the -force option. Basically, the force option will bypass checks to see if there are DICOMs to attach the file to. minc_insertion.pl -profile -mincPath -force -create_minc_pics For the NIfTI files alone, because of the nature of that file format (no header information like MINC...), you will have to specify a lot of the information when calling the script imaging_non_minc_insertion.pl (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... Basically all the columns of the files table). It needs to be associated with an upload_id for the logging in the database but the upload_id does not necessarily need to be DICOM files. It could be a zipped archive of all the NIfTI files of the session uploaded for example. Then you would just need to create a little wrapper script to run imaging_non_minc_insertion.pl on the loaded NIfTI files. Does that clarify the steps? Thanks! C?cile On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. > wrote: Hi Cecile, Just to clarify, many import issues seem to stem from problems with the implementation of dcm2mnc used by Loris. These DICOM files can be successfully converted to MINC and NifTI with other tools, and so we were wondering if it would be possible to import MRI data into Loris as MINC & NifTI files instead of importing the DICOMs. Alternatively, we could convert these files to BIDS and import that instead of DICOM. The important point is whether we can avoid importing DICOM for new scan/participant instances, but import only BIDS or MINC + NiFTI data and generate a new Loris ID from this. We are not asking about attaching a MINC or NifTI file to an existing record, which we know can be done (e.g. for label files associated with the images). Thanks, Sridar On Jan 25, 2021, at 5:01 PM, Cecile Madjar > wrote: Hi Alfredo, I am a bit confused by your email. The two perl scripts I mentioned last week do not require the data to be organized in BIDS to insert them. Did you look into them? Sorry, maybe I am missing something. C?cile On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, Thank you for your answer. I am sorry I was not enough specific regarding what we are looking for. We are actually looking for a solution to avoid importing the ?raw? images in minc and nifti images instead of DICOM. We are having a lot of issues importing DICOM (~1.700 visits with issues) and we want to explore options for uploading the original images (e.g., t1) using minc and nifti without them being in BIDS formar. Do you have scripts for this? Best, Alfredo. On Jan 19, 2021, at 1:59 PM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Very sorry for the late reply. In short, yes, it is possible to do both. It is possible to insert MINC files in LORIS by using the LORIS-MRI script called minc_insertion.pl in the uploadNeuroDB folder. If you run perl minc_insertion.pl -h; you will see the explanation on how to run the script. Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called imaging_non_minc_insertion.pl in the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl should give you all the information you need in order to run the script. Hope this helps, C?cile On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format? Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Fri Jan 29 11:09:22 2021 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Fri, 29 Jan 2021 11:09:22 -0500 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: <0863DD40-4B8E-498C-816E-E28E25A8FCCA@bwh.harvard.edu> References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> <0863DD40-4B8E-498C-816E-E28E25A8FCCA@bwh.harvard.edu> Message-ID: Hi Alfredo, I was able to reproduce your bug on version 22.0 of LORIS-MRI and it was maybe present in older versions as well. This was fixed in release 23.0 with better logging information. I just sent a PR with a fix for 22.0 that you can find here: https://github.com/aces/Loris-MRI/pull/573/files That should resolve the issue you were having. Let me know how it goes. Best, C?cile On Fri, Jan 29, 2021 at 1:18 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Cecile, > > I tried the script minc_insertion.pl but it seems that the Candidate > should not exist before the execution of the script. Is this the case? This > would be problematic in order to upload multiple sequences for a given > Candidate. This is the error I am getting: > > === > $ perl minc_insertion.pl -profile prod -force -verbose -create_minc_pics > -acquisition_protocol t2w -mincPath > /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc > > log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is > /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log > ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with > PSCID=AZH101303 already exists. > SELECT ArchiveLocation FROM tarchive WHERE > TarchiveID = ( SELECT TarchiveID > FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? > ) PSCID is: AZH101303 > CandID id: 814099 > visit_label is: 105ms302w48 > PSCID is: AZH101303 > CandID id: 814099 > visit_label is: 105ms302w48 > Spool message is: ERROR: Cannot create candidate (AZH101303, 814099) as a > candidate with PSCID=AZH101303 already exists > === > > Best, > Alfredo. > > P.S. The file /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log > is not being written. > > On Jan 26, 2021, at 4:33 PM, Cecile Madjar wrote: > > External Email - Use Caution > > Hi, > > Thank you for the clarification. I think I understand better the confusion. > > You can insert MINC files without having to insert DICOM files by running > the minc_insertion.pl > > script with the -force option. Basically, the force option will bypass > checks to see if there are DICOMs to attach the file to. > > minc_insertion.pl > > -profile -mincPath your MINC file> -force -create_minc_pics > > For the NIfTI files alone, because of the nature of that file format (no > header information like MINC...), you will have to specify a lot of the > information when calling the script imaging_non_minc_insertion.pl > > (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... > Basically all the columns of the files table). It needs to be associated > with an upload_id for the logging in the database but the upload_id does > not necessarily need to be DICOM files. It could be a zipped archive of all > the NIfTI files of the session uploaded for example. Then you would just > need to create a little wrapper script to run > imaging_non_minc_insertion.pl > > on the loaded NIfTI files. > > Does that clarify the steps? > > Thanks! > > C?cile > > On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. < > sridar.narayanan at mcgill.ca> wrote: > >> Hi Cecile, >> >> Just to clarify, many import issues seem to stem from problems with the >> implementation of dcm2mnc used by Loris. These DICOM files can be >> successfully converted to MINC and NifTI with other tools, and so we were >> wondering if it would be possible to import MRI data into Loris as MINC & >> NifTI files *instead of* importing the DICOMs. Alternatively, we could >> convert these files to BIDS and import that instead of DICOM. The important >> point is whether we can *avoid importing DICOM* for new scan/participant >> instances, but import only BIDS or MINC + NiFTI data and generate a new >> Loris ID from this. We are not asking about attaching a MINC or NifTI file >> to an existing record, which we know can be done (e.g. for label files >> associated with the images). >> >> Thanks, >> >> Sridar >> >> >> On Jan 25, 2021, at 5:01 PM, Cecile Madjar wrote: >> >> Hi Alfredo, >> >> I am a bit confused by your email. The two perl scripts I mentioned last >> week do not require the data to be organized in BIDS to insert them. Did >> you look into them? >> >> Sorry, maybe I am missing something. >> >> C?cile >> >> On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >>> Hi Cecile, >>> >>> Thank you for your answer. I am sorry I was not enough specific >>> regarding what we are looking for. We are actually looking for a solution >>> to avoid importing the ?raw? images in minc and nifti images instead of >>> DICOM. We are having a lot of issues importing DICOM (~1.700 visits with >>> issues) and we want to explore options for uploading the original images >>> (e.g., t1) using minc and nifti without them being in BIDS formar. >>> >>> Do you have scripts for this? >>> >>> Best, >>> Alfredo. >>> >>> On Jan 19, 2021, at 1:59 PM, Cecile Madjar >>> wrote: >>> >>> External Email - Use Caution >>> >>> Hi Alfredo, >>> >>> Very sorry for the late reply. In short, yes, it is possible to do both. >>> >>> It is possible to insert MINC files in LORIS by using the LORIS-MRI >>> script called minc_insertion.pl >>> in >>> the uploadNeuroDB folder. If you run perl minc_insertion.pl >>> >>> -h; you will see the explanation on how to run the script. >>> >>> Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI >>> script called imaging_non_minc_insertion.pl >>> in >>> the same uploadNeuroDB folder. Running perl >>> imaging_non_minc_insertion.pl >>> >>> should give you all the information you need in order to run the script. >>> >>> Hope this helps, >>> >>> C?cile >>> >>> On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo < >>> AMORALESPINZON at bwh.harvard.edu> wrote: >>> >>>> Dear LorisDev team, >>>> >>>> Is is possible to upload nifti and minc files into LORIS, for instance >>>> to a given visit, without having the files in BIDS format? >>>> >>>> Best regards, >>>> Alfredo. >>>> The information in this e-mail is intended only for the person to whom >>>> it is addressed. If you believe this e-mail was sent to you in error and >>>> the e-mail contains patient information, please contact the Mass General >>>> Brigham Compliance HelpLine at >>>> http://www.massgeneralbrigham.org/complianceline >>>> >>>> . If the e-mail was sent to you in error but does not contain patient >>>> information, please contact the sender and properly dispose of the e-mail. >>>> >>>> >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is addressed. If you believe this e-mail was sent to you in error and >>> the e-mail contains patient information, please contact the Mass General >>> Brigham Compliance HelpLine at >>> http://www.massgeneralbrigham.org/complianceline >>> >>> . If the e-mail was sent to you in error but does not contain patient >>> information, please contact the sender and properly dispose of the e-mail. >>> >> >> > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Fri Jan 29 11:44:11 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Fri, 29 Jan 2021 16:44:11 +0000 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> <0863DD40-4B8E-498C-816E-E28E25A8FCCA@bwh.harvard.edu> Message-ID: <7D1CB8B1-10C2-458F-8D9E-A683471D3F2A@bwh.harvard.edu> Hi Cecile, Thank you. This is great. I will move to v23 regardless of some small issues I had in the migration SQL that don?t impact our project as we are not using the electrophysiology browser or module manager modules. I?ll test it one I?m in v23 and let you know. Best, Alfredo. On Jan 29, 2021, at 11:09 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, I was able to reproduce your bug on version 22.0 of LORIS-MRI and it was maybe present in older versions as well. This was fixed in release 23.0 with better logging information. I just sent a PR with a fix for 22.0 that you can find here: https://github.com/aces/Loris-MRI/pull/573/files That should resolve the issue you were having. Let me know how it goes. Best, C?cile On Fri, Jan 29, 2021 at 1:18 AM Morales Pinzon, Alfredo > wrote: Hi Cecile, I tried the script minc_insertion.pl but it seems that the Candidate should not exist before the execution of the script. Is this the case? This would be problematic in order to upload multiple sequences for a given Candidate. This is the error I am getting: === $ perl minc_insertion.pl -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w -mincPath /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists. SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 Spool message is: ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists === Best, Alfredo. P.S. The file /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log is not being written. On Jan 26, 2021, at 4:33 PM, Cecile Madjar > wrote: External Email - Use Caution Hi, Thank you for the clarification. I think I understand better the confusion. You can insert MINC files without having to insert DICOM files by running the minc_insertion.pl script with the -force option. Basically, the force option will bypass checks to see if there are DICOMs to attach the file to. minc_insertion.pl -profile -mincPath -force -create_minc_pics For the NIfTI files alone, because of the nature of that file format (no header information like MINC...), you will have to specify a lot of the information when calling the script imaging_non_minc_insertion.pl (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... Basically all the columns of the files table). It needs to be associated with an upload_id for the logging in the database but the upload_id does not necessarily need to be DICOM files. It could be a zipped archive of all the NIfTI files of the session uploaded for example. Then you would just need to create a little wrapper script to run imaging_non_minc_insertion.pl on the loaded NIfTI files. Does that clarify the steps? Thanks! C?cile On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. > wrote: Hi Cecile, Just to clarify, many import issues seem to stem from problems with the implementation of dcm2mnc used by Loris. These DICOM files can be successfully converted to MINC and NifTI with other tools, and so we were wondering if it would be possible to import MRI data into Loris as MINC & NifTI files instead of importing the DICOMs. Alternatively, we could convert these files to BIDS and import that instead of DICOM. The important point is whether we can avoid importing DICOM for new scan/participant instances, but import only BIDS or MINC + NiFTI data and generate a new Loris ID from this. We are not asking about attaching a MINC or NifTI file to an existing record, which we know can be done (e.g. for label files associated with the images). Thanks, Sridar On Jan 25, 2021, at 5:01 PM, Cecile Madjar > wrote: Hi Alfredo, I am a bit confused by your email. The two perl scripts I mentioned last week do not require the data to be organized in BIDS to insert them. Did you look into them? Sorry, maybe I am missing something. C?cile On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, Thank you for your answer. I am sorry I was not enough specific regarding what we are looking for. We are actually looking for a solution to avoid importing the ?raw? images in minc and nifti images instead of DICOM. We are having a lot of issues importing DICOM (~1.700 visits with issues) and we want to explore options for uploading the original images (e.g., t1) using minc and nifti without them being in BIDS formar. Do you have scripts for this? Best, Alfredo. On Jan 19, 2021, at 1:59 PM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Very sorry for the late reply. In short, yes, it is possible to do both. It is possible to insert MINC files in LORIS by using the LORIS-MRI script called minc_insertion.pl in the uploadNeuroDB folder. If you run perl minc_insertion.pl -h; you will see the explanation on how to run the script. Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called imaging_non_minc_insertion.pl in the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl should give you all the information you need in order to run the script. Hope this helps, C?cile On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format? Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sridar.narayanan at mcgill.ca Fri Jan 29 12:15:31 2021 From: sridar.narayanan at mcgill.ca (Sridar Narayanan, Dr.) Date: Fri, 29 Jan 2021 17:15:31 +0000 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> <0863DD40-4B8E-498C-816E-E28E25A8FCCA@bwh.harvard.edu> Message-ID: Hi Cecile, I think Alfredo?s plan was to upgrade to 23.0 as soon as the upgrade to 22.0 was completed successfully (since a direct upgrade was not possible). Since 23.0 appears to fix some bugs in 22.0, when would it be most efficient to perform the 22.0 -> 23.0 upgrade? Should Alfredo ensure that 22.0 is functional with all patches applied first, to be safe, or will the upgrade to 23.0 take care of many of these issues? Thanks, Sridar On Jan 29, 2021, at 11:09 AM, Cecile Madjar > wrote: Hi Alfredo, I was able to reproduce your bug on version 22.0 of LORIS-MRI and it was maybe present in older versions as well. This was fixed in release 23.0 with better logging information. I just sent a PR with a fix for 22.0 that you can find here: https://github.com/aces/Loris-MRI/pull/573/files That should resolve the issue you were having. Let me know how it goes. Best, C?cile On Fri, Jan 29, 2021 at 1:18 AM Morales Pinzon, Alfredo > wrote: Hi Cecile, I tried the script minc_insertion.pl but it seems that the Candidate should not exist before the execution of the script. Is this the case? This would be problematic in order to upload multiple sequences for a given Candidate. This is the error I am getting: === $ perl minc_insertion.pl -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w -mincPath /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists. SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 Spool message is: ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists === Best, Alfredo. P.S. The file /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log is not being written. On Jan 26, 2021, at 4:33 PM, Cecile Madjar > wrote: External Email - Use Caution Hi, Thank you for the clarification. I think I understand better the confusion. You can insert MINC files without having to insert DICOM files by running the minc_insertion.pl script with the -force option. Basically, the force option will bypass checks to see if there are DICOMs to attach the file to. minc_insertion.pl -profile -mincPath -force -create_minc_pics For the NIfTI files alone, because of the nature of that file format (no header information like MINC...), you will have to specify a lot of the information when calling the script imaging_non_minc_insertion.pl (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... Basically all the columns of the files table). It needs to be associated with an upload_id for the logging in the database but the upload_id does not necessarily need to be DICOM files. It could be a zipped archive of all the NIfTI files of the session uploaded for example. Then you would just need to create a little wrapper script to run imaging_non_minc_insertion.pl on the loaded NIfTI files. Does that clarify the steps? Thanks! C?cile On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. > wrote: Hi Cecile, Just to clarify, many import issues seem to stem from problems with the implementation of dcm2mnc used by Loris. These DICOM files can be successfully converted to MINC and NifTI with other tools, and so we were wondering if it would be possible to import MRI data into Loris as MINC & NifTI files instead of importing the DICOMs. Alternatively, we could convert these files to BIDS and import that instead of DICOM. The important point is whether we can avoid importing DICOM for new scan/participant instances, but import only BIDS or MINC + NiFTI data and generate a new Loris ID from this. We are not asking about attaching a MINC or NifTI file to an existing record, which we know can be done (e.g. for label files associated with the images). Thanks, Sridar On Jan 25, 2021, at 5:01 PM, Cecile Madjar > wrote: Hi Alfredo, I am a bit confused by your email. The two perl scripts I mentioned last week do not require the data to be organized in BIDS to insert them. Did you look into them? Sorry, maybe I am missing something. C?cile On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, Thank you for your answer. I am sorry I was not enough specific regarding what we are looking for. We are actually looking for a solution to avoid importing the ?raw? images in minc and nifti images instead of DICOM. We are having a lot of issues importing DICOM (~1.700 visits with issues) and we want to explore options for uploading the original images (e.g., t1) using minc and nifti without them being in BIDS formar. Do you have scripts for this? Best, Alfredo. On Jan 19, 2021, at 1:59 PM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Very sorry for the late reply. In short, yes, it is possible to do both. It is possible to insert MINC files in LORIS by using the LORIS-MRI script called minc_insertion.pl in the uploadNeuroDB folder. If you run perl minc_insertion.pl -h; you will see the explanation on how to run the script. Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called imaging_non_minc_insertion.pl in the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl should give you all the information you need in order to run the script. Hope this helps, C?cile On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format? Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Fri Jan 29 12:57:01 2021 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Fri, 29 Jan 2021 12:57:01 -0500 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> <0863DD40-4B8E-498C-816E-E28E25A8FCCA@bwh.harvard.edu> Message-ID: I see. There are significant changes between 22 and 23 on LORIS-MRI (mainly the ability to set specific MRI protocols based on Visit label, Projects or subprojects requiring changes to the MRI protocol tables). However, I do not foresee any major blocker as to proceed to upgrading to 23.0 for LORIS-MRI. Hope this helps, C?cile On Fri, Jan 29, 2021 at 12:15 PM Sridar Narayanan, Dr. < sridar.narayanan at mcgill.ca> wrote: > Hi Cecile, > > I think Alfredo?s plan was to upgrade to 23.0 as soon as the upgrade to > 22.0 was completed successfully (since a direct upgrade was not possible). > Since 23.0 appears to fix some bugs in 22.0, when would it be most > efficient to perform the 22.0 -> 23.0 upgrade? Should Alfredo ensure that > 22.0 is functional with all patches applied first, to be safe, or will the > upgrade to 23.0 take care of many of these issues? > > Thanks, > > Sridar > > > On Jan 29, 2021, at 11:09 AM, Cecile Madjar wrote: > > Hi Alfredo, > > I was able to reproduce your bug on version 22.0 of LORIS-MRI and it was > maybe present in older versions as well. This was fixed in release 23.0 > with better logging information. > > I just sent a PR with a fix for 22.0 that you can find here: > https://github.com/aces/Loris-MRI/pull/573/files > > That should resolve the issue you were having. Let me know how it goes. > > Best, > > C?cile > > On Fri, Jan 29, 2021 at 1:18 AM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Hi Cecile, >> >> I tried the script minc_insertion.pl but it seems that the Candidate >> should not exist before the execution of the script. Is this the case? This >> would be problematic in order to upload multiple sequences for a given >> Candidate. This is the error I am getting: >> >> === >> $ perl minc_insertion.pl -profile prod -force -verbose -create_minc_pics >> -acquisition_protocol t2w -mincPath >> /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc >> >> log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is >> /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log >> ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with >> PSCID=AZH101303 already exists. >> SELECT ArchiveLocation FROM tarchive WHERE >> TarchiveID = ( SELECT TarchiveID >> FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? >> ) PSCID is: AZH101303 >> CandID id: 814099 >> visit_label is: 105ms302w48 >> PSCID is: AZH101303 >> CandID id: 814099 >> visit_label is: 105ms302w48 >> Spool message is: ERROR: Cannot create candidate (AZH101303, 814099) as a >> candidate with PSCID=AZH101303 already exists >> === >> >> Best, >> Alfredo. >> >> P.S. The file /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log >> is not being written. >> >> On Jan 26, 2021, at 4:33 PM, Cecile Madjar wrote: >> >> External Email - Use Caution >> >> Hi, >> >> Thank you for the clarification. I think I understand better >> the confusion. >> >> You can insert MINC files without having to insert DICOM files by running >> the minc_insertion.pl >> >> script with the -force option. Basically, the force option will bypass >> checks to see if there are DICOMs to attach the file to. >> >> minc_insertion.pl >> >> -profile -mincPath > your MINC file> -force -create_minc_pics >> >> For the NIfTI files alone, because of the nature of that file format (no >> header information like MINC...), you will have to specify a lot of the >> information when calling the script imaging_non_minc_insertion.pl >> >> (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... >> Basically all the columns of the files table). It needs to be associated >> with an upload_id for the logging in the database but the upload_id does >> not necessarily need to be DICOM files. It could be a zipped archive of all >> the NIfTI files of the session uploaded for example. Then you would just >> need to create a little wrapper script to run >> imaging_non_minc_insertion.pl >> >> on the loaded NIfTI files. >> >> Does that clarify the steps? >> >> Thanks! >> >> C?cile >> >> On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. < >> sridar.narayanan at mcgill.ca> wrote: >> >>> Hi Cecile, >>> >>> Just to clarify, many import issues seem to stem from problems with the >>> implementation of dcm2mnc used by Loris. These DICOM files can be >>> successfully converted to MINC and NifTI with other tools, and so we were >>> wondering if it would be possible to import MRI data into Loris as MINC & >>> NifTI files *instead of* importing the DICOMs. Alternatively, we could >>> convert these files to BIDS and import that instead of DICOM. The important >>> point is whether we can *avoid importing DICOM* for new >>> scan/participant instances, but import only BIDS or MINC + NiFTI data and >>> generate a new Loris ID from this. We are not asking about attaching a MINC >>> or NifTI file to an existing record, which we know can be done (e.g. for >>> label files associated with the images). >>> >>> Thanks, >>> >>> Sridar >>> >>> >>> On Jan 25, 2021, at 5:01 PM, Cecile Madjar >>> wrote: >>> >>> Hi Alfredo, >>> >>> I am a bit confused by your email. The two perl scripts I mentioned last >>> week do not require the data to be organized in BIDS to insert them. Did >>> you look into them? >>> >>> Sorry, maybe I am missing something. >>> >>> C?cile >>> >>> On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo < >>> AMORALESPINZON at bwh.harvard.edu> wrote: >>> >>>> Hi Cecile, >>>> >>>> Thank you for your answer. I am sorry I was not enough specific >>>> regarding what we are looking for. We are actually looking for a solution >>>> to avoid importing the ?raw? images in minc and nifti images instead of >>>> DICOM. We are having a lot of issues importing DICOM (~1.700 visits with >>>> issues) and we want to explore options for uploading the original images >>>> (e.g., t1) using minc and nifti without them being in BIDS formar. >>>> >>>> Do you have scripts for this? >>>> >>>> Best, >>>> Alfredo. >>>> >>>> On Jan 19, 2021, at 1:59 PM, Cecile Madjar >>>> wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Hi Alfredo, >>>> >>>> Very sorry for the late reply. In short, yes, it is possible to do both. >>>> >>>> It is possible to insert MINC files in LORIS by using the LORIS-MRI >>>> script called minc_insertion.pl >>>> in >>>> the uploadNeuroDB folder. If you run perl minc_insertion.pl >>>> >>>> -h; you will see the explanation on how to run the script. >>>> >>>> Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI >>>> script called imaging_non_minc_insertion.pl >>>> in >>>> the same uploadNeuroDB folder. Running perl >>>> imaging_non_minc_insertion.pl >>>> >>>> should give you all the information you need in order to run the script. >>>> >>>> Hope this helps, >>>> >>>> C?cile >>>> >>>> On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo < >>>> AMORALESPINZON at bwh.harvard.edu> wrote: >>>> >>>>> Dear LorisDev team, >>>>> >>>>> Is is possible to upload nifti and minc files into LORIS, for instance >>>>> to a given visit, without having the files in BIDS format? >>>>> >>>>> Best regards, >>>>> Alfredo. >>>>> The information in this e-mail is intended only for the person to whom >>>>> it is addressed. If you believe this e-mail was sent to you in error and >>>>> the e-mail contains patient information, please contact the Mass General >>>>> Brigham Compliance HelpLine at >>>>> http://www.massgeneralbrigham.org/complianceline >>>>> >>>>> . If the e-mail was sent to you in error but does not contain patient >>>>> information, please contact the sender and properly dispose of the e-mail. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>>> >>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it is addressed. If you believe this e-mail was sent to you in error and >>>> the e-mail contains patient information, please contact the Mass General >>>> Brigham Compliance HelpLine at >>>> http://www.massgeneralbrigham.org/complianceline >>>> >>>> . If the e-mail was sent to you in error but does not contain patient >>>> information, please contact the sender and properly dispose of the e-mail. >>>> >>> >>> >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.org/complianceline . If the e-mail was >> sent to you in error but does not contain patient information, please >> contact the sender and properly dispose of the e-mail. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Fri Jan 29 18:19:14 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Fri, 29 Jan 2021 23:19:14 +0000 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> <0863DD40-4B8E-498C-816E-E28E25A8FCCA@bwh.harvard.edu> Message-ID: Hi Cecile, I am now running LORIS-MRI v23.0.3 and LORIS v23.0.2. I am getting the following output for the same command line: Command line === perl /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/minc_insertion.pl -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w -mincPath /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc === Output === log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-17-32-M9vqyU.log Can't locate object method "selectall_array" via package "DBI::db" at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1819. SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 === Log file (/data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-17-32-M9vqyU.log) === ==> Loading file from disk /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc --> mapping DICOM parameter for /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc --> filters out parameters of length > 1000 for /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc === I think issue is coming from this line: https://github.com/aces/Loris-MRI/blob/8c7e41549fb10a845caa96f31c8e505ef3adca52/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm#L1819 Maybe ?selectall_array? has to be replaced by ?selectall_arrayref?? Thank you for all your help. Best, Alfredo. On Jan 29, 2021, at 12:57 PM, Cecile Madjar > wrote: External Email - Use Caution I see. There are significant changes between 22 and 23 on LORIS-MRI (mainly the ability to set specific MRI protocols based on Visit label, Projects or subprojects requiring changes to the MRI protocol tables). However, I do not foresee any major blocker as to proceed to upgrading to 23.0 for LORIS-MRI. Hope this helps, C?cile On Fri, Jan 29, 2021 at 12:15 PM Sridar Narayanan, Dr. > wrote: Hi Cecile, I think Alfredo?s plan was to upgrade to 23.0 as soon as the upgrade to 22.0 was completed successfully (since a direct upgrade was not possible). Since 23.0 appears to fix some bugs in 22.0, when would it be most efficient to perform the 22.0 -> 23.0 upgrade? Should Alfredo ensure that 22.0 is functional with all patches applied first, to be safe, or will the upgrade to 23.0 take care of many of these issues? Thanks, Sridar On Jan 29, 2021, at 11:09 AM, Cecile Madjar > wrote: Hi Alfredo, I was able to reproduce your bug on version 22.0 of LORIS-MRI and it was maybe present in older versions as well. This was fixed in release 23.0 with better logging information. I just sent a PR with a fix for 22.0 that you can find here: https://github.com/aces/Loris-MRI/pull/573/files That should resolve the issue you were having. Let me know how it goes. Best, C?cile On Fri, Jan 29, 2021 at 1:18 AM Morales Pinzon, Alfredo > wrote: Hi Cecile, I tried the script minc_insertion.pl but it seems that the Candidate should not exist before the execution of the script. Is this the case? This would be problematic in order to upload multiple sequences for a given Candidate. This is the error I am getting: === $ perl minc_insertion.pl -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w -mincPath /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists. SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 Spool message is: ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists === Best, Alfredo. P.S. The file /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log is not being written. On Jan 26, 2021, at 4:33 PM, Cecile Madjar > wrote: External Email - Use Caution Hi, Thank you for the clarification. I think I understand better the confusion. You can insert MINC files without having to insert DICOM files by running the minc_insertion.pl script with the -force option. Basically, the force option will bypass checks to see if there are DICOMs to attach the file to. minc_insertion.pl -profile -mincPath -force -create_minc_pics For the NIfTI files alone, because of the nature of that file format (no header information like MINC...), you will have to specify a lot of the information when calling the script imaging_non_minc_insertion.pl (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... Basically all the columns of the files table). It needs to be associated with an upload_id for the logging in the database but the upload_id does not necessarily need to be DICOM files. It could be a zipped archive of all the NIfTI files of the session uploaded for example. Then you would just need to create a little wrapper script to run imaging_non_minc_insertion.pl on the loaded NIfTI files. Does that clarify the steps? Thanks! C?cile On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. > wrote: Hi Cecile, Just to clarify, many import issues seem to stem from problems with the implementation of dcm2mnc used by Loris. These DICOM files can be successfully converted to MINC and NifTI with other tools, and so we were wondering if it would be possible to import MRI data into Loris as MINC & NifTI files instead of importing the DICOMs. Alternatively, we could convert these files to BIDS and import that instead of DICOM. The important point is whether we can avoid importing DICOM for new scan/participant instances, but import only BIDS or MINC + NiFTI data and generate a new Loris ID from this. We are not asking about attaching a MINC or NifTI file to an existing record, which we know can be done (e.g. for label files associated with the images). Thanks, Sridar On Jan 25, 2021, at 5:01 PM, Cecile Madjar > wrote: Hi Alfredo, I am a bit confused by your email. The two perl scripts I mentioned last week do not require the data to be organized in BIDS to insert them. Did you look into them? Sorry, maybe I am missing something. C?cile On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, Thank you for your answer. I am sorry I was not enough specific regarding what we are looking for. We are actually looking for a solution to avoid importing the ?raw? images in minc and nifti images instead of DICOM. We are having a lot of issues importing DICOM (~1.700 visits with issues) and we want to explore options for uploading the original images (e.g., t1) using minc and nifti without them being in BIDS formar. Do you have scripts for this? Best, Alfredo. On Jan 19, 2021, at 1:59 PM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Very sorry for the late reply. In short, yes, it is possible to do both. It is possible to insert MINC files in LORIS by using the LORIS-MRI script called minc_insertion.pl in the uploadNeuroDB folder. If you run perl minc_insertion.pl -h; you will see the explanation on how to run the script. Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called imaging_non_minc_insertion.pl in the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl should give you all the information you need in order to run the script. Hope this helps, C?cile On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format? Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: