From wangshen.mcin at gmail.com Mon Jul 3 14:07:01 2017 From: wangshen.mcin at gmail.com (Shen Wang) Date: Mon, 3 Jul 2017 14:07:01 -0400 Subject: [Loris-dev] Fwd: LORIS Document Repository In-Reply-To: References: <30266241-3ADA-44AC-9C51-1897BD7E64EB@childmind.org> <1076585160.28116.1498710071701.JavaMail.zimbra@cbr.iisc.ac.in> <1E5C55CC-A0F2-4CD7-98C9-81A1B7D744DE@childmind.org> Message-ID: Hi Bonhwang, I tested Loris 17.0 on my VM, it works fine. It is difficult to debug without error log. Could you show me more error log or error message? 1, Run "sudo tail -f /var/log/apache2/loris-error.log" when you add a category. Please show me the message. 2, Or Run "insert into document_repository_categories (id,category_name,parent_id,comments) values('777','test','0',null)" in your loris database. You should see the new test category. Then try upload a file under test category. Tell me the result. Best wishes On 3 July 2017 at 11:08, Shen Wang wrote: > Hi Ganesh > You can get the "Document Repository" module functional without email > server. > Could you show me the error log or error message when you want to add a > category? > > Shen > > On 3 July 2017 at 10:14, Bonhwang Koo wrote: > >> 17.0.3 >> >> >> >> -- >> >> Bonhwang Koo >> >> Research Assistant, CDB >> >> Child Mind Institute >> >> childmind.org >> >> 445 Park Avenue (entrance on 56th Street) >> >> New York, NY 10022 >> >> E: Bonhwang.Koo at childmind.org >> >> p: 646.625.4398 <(646)%20625-4398> >> >> f: 646.625.4348 <(646)%20625-4348> >> >> >> >> Facebook: facebook.com/ChildMindInstitute | Follow us on Twitter: >> twitter.com/ChildMindDotOrg >> >> >> >> --- >> >> >> >> This email message, including any attachments, is for the sole use of the >> intended recipient(s) and may contain information that is proprietary, >> confidential, and exempt from disclosure under applicable law. Any >> unauthorized review, use, disclosure, or distribution is prohibited. If you >> have received this email in error please notify the sender by return email >> and delete the original message. Please note, the recipient should check >> this email and any attachments for the presence of viruses. The >> organization accepts no liability for any damage caused by any virus >> transmitted by this email. >> >> >> >> *From: *Shen Wang >> *Date: *Monday, July 3, 2017 at 10:04 AM >> *To: *Bonhwang Koo >> *Cc: *"Ganesh Chauhan (CBR)" , Samir Das < >> samir.das at mcgill.ca>, loris-dev >> >> *Subject: *Re: [Loris-dev] Fwd: LORIS Document Repository >> >> >> >> Hi >> >> Could you tell me which version of Loris do you have? I will check it. >> >> >> >> Best wishes >> >> Shen >> >> >> >> On 29 June 2017 at 17:03, Bonhwang Koo >> wrote: >> >> I followed your suggestion, although I ran the command for a slightly >> different directory: ?sudo chmod 777 /var/www/loris/modules/document_repository/user_uploads?, >> and I still have the same issue. This isn?t working even though I have a >> mail server installed via PostFix. I took a look at the console on my >> browser, and this is the error I?m getting: >> >> >> >> >> >> >> >> This is the corresponding code in document_repository_helper.js:89 : >> >> $.ajax({ >> >> url: loris.BaseURL + "/document_repository/ajax/addCategory.php", >> >> type: "POST", >> >> data: $("#addCategoryForm").serialize(), >> >> success: function() { >> >> $("#addCategoryModal").modal('hide'); >> >> $("#addCategoryCategory").removeClass("has-error"); >> >> $("#categoryAddError").hide(); >> >> $('.add-success').show(); >> >> setTimeout(function() { >> >> $('.add-success').hide(); >> >> }, 3000); >> >> setTimeout(function() { >> >> location.reload(); >> >> }, 3000); >> >> }, >> >> error: function(jqXHR, textStatus, errorThrown) { >> >> if (jqXHR.status === 400) { >> >> $("#addCategoryCategory").addClass("has-error"); >> >> $("#categoryAddError").show() >> >> } >> >> } >> >> }); >> >> >> >> >> >> >> >> -- >> >> Bonhwang Koo >> >> Research Assistant, CDB >> >> Child Mind Institute >> >> childmind.org >> >> 445 Park Avenue (entrance on 56th Street) >> >> New York, NY 10022 >> >> E: Bonhwang.Koo at childmind.org >> >> p: 646.625.4398 <(646)%20625-4398> >> >> f: 646.625.4348 <(646)%20625-4348> >> >> >> >> Facebook: facebook.com/ChildMindInstitute | Follow us on Twitter: >> twitter.com/ChildMindDotOrg >> >> >> >> --- >> >> >> >> This email message, including any attachments, is for the sole use of the >> intended recipient(s) and may contain information that is proprietary, >> confidential, and exempt from disclosure under applicable law. Any >> unauthorized review, use, disclosure, or distribution is prohibited. If you >> have received this email in error please notify the sender by return email >> and delete the original message. Please note, the recipient should check >> this email and any attachments for the presence of viruses. The >> organization accepts no liability for any damage caused by any virus >> transmitted by this email. >> >> >> >> *From: *"Ganesh Chauhan (CBR)" >> *Date: *Thursday, June 29, 2017 at 12:21 AM >> *To: *Shen Wang >> *Cc: *Samir Das , loris-dev < >> Loris-dev at bic.mni.mcgill.ca>, Bonhwang Koo >> >> >> *Subject: *Re: [Loris-dev] Fwd: LORIS Document Repository >> >> >> >> Hi, >> >> >> >> I have had the same problem of not being able to add a category despite >> having file permissions. >> >> Though I still do not have the email server setup for LORIS. Hence do you >> think that without the email server we cannot get the "Document Repository" >> module functional. >> >> >> >> Thanks for your suggestion. >> >> >> >> With best regards, >> >> Ganesh >> >> >> ------------------------------ >> >> *From: *"Shen Wang" >> *To: *"Samir Das" >> *Cc: *"loris-dev" , "Bonhwang Koo" < >> Bonhwang.Koo at childmind.org> >> *Sent: *Thursday, June 29, 2017 12:52:48 AM >> *Subject: *Re: [Loris-dev] Fwd: LORIS Document Repository >> >> >> >> Hello: >> >> Maybe you need to have file system permission to create the upload >> directory. >> >> I think It is not a Loris issue. >> >> As a quick fix, you can do: "sudo chmod 777 /var/www/loris/ >> document_repository/user_uploads". >> >> /var/www/loris/ will be replaced by your loris directory. >> >> I hope this can help you. >> >> >> >> Shen >> >> >> >> On 27 June 2017 at 16:09, Samir Das wrote: >> >> >> >> ---------- Forwarded message ---------- >> From: *Bonhwang Koo* >> Date: Mon, Jun 26, 2017 at 8:28 AM >> Subject: LORIS Document Repository >> To: "loris.info at mcin.ca" >> >> Hello, >> >> >> >> I am working with the Child Mind Institute?s Healthy Brain Network >> initiative, and we created a LORIS instance to allow users query data from >> our recent data release. I want to use the document repository feature, but >> it won?t allow me to upload a file without a category, so when I try to add >> a new category, nothing happens. Can you help me resolve this issue? >> >> >> >> Best, >> >> -- >> >> Bonhwang Koo >> >> Research Assistant, CDB >> >> Child Mind Institute >> >> childmind.org >> >> 445 Park Avenue (entrance on 56th Street) >> >> New York, NY 10022 >> >> E: Bonhwang.Koo at childmind.org >> >> p: 646.625.4398 <(646)%20625-4398> >> >> f: 646.625.4348 <(646)%20625-4348> >> >> >> >> Facebook: facebook.com/ChildMindInstitute | Follow us on Twitter: >> twitter.com/ChildMindDotOrg >> >> >> >> --- >> >> >> >> This email message, including any attachments, is for the sole use of the >> intended recipient(s) and may contain information that is proprietary, >> confidential, and exempt from disclosure under applicable law. Any >> unauthorized review, use, disclosure, or distribution is prohibited. If you >> have received this email in error please notify the sender by return email >> and delete the original message. Please note, the recipient should check >> this email and any attachments for the presence of viruses. The >> organization accepts no liability for any damage caused by any virus >> transmitted by this email. >> >> >> >> >> >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> >> >> -- >> >> Ganesh Chauhan (PhD) >> Scientist >> Centre for Brain Research (CBR) >> Indian Institute of Science (IISc) >> Bengaluru, INDIA >> +91 80 2293 3009 <+91%2080%202293%203009> >> https://www.cbr.iisc.ac.in >> >> >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.png Type: image/png Size: 27544 bytes Desc: not available URL: From michael.joseph at sickkids.ca Tue Jul 4 13:01:13 2017 From: michael.joseph at sickkids.ca (Michael Joseph) Date: Tue, 4 Jul 2017 17:01:13 +0000 Subject: [Loris-dev] CouchDB MRI Importer errors on Loris v17.0.5 Message-ID: Hi Loris dev team, I received some errors when running the CouchDB_Import_MRI.php script. I've attached a log of the errors. It seems like a MySQL 5.7 issue and disabling "ONLY_FULL_GROUP_BY" mode fixed it. Without disabling the mode, the script wasn't able to populate the CouchDB database. Michael ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: couchdb_import_mri_errors.txt URL: From ganesh.chauhan at cbr.iisc.ac.in Wed Jul 5 07:18:41 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Wed, 5 Jul 2017 16:48:41 +0530 (IST) Subject: [Loris-dev] Pre-processing MRI DICOM files and Insertion into Loris Message-ID: <285280006.33249.1499253521426.JavaMail.zimbra@cbr.iisc.ac.in> Dear team Loris, I uploaded a zipped file containing DICOM image files via the front end using "Imaging Uploader". The file got uploaded but the "Progress" section in the table displayed "Failure". Then I wanted to process the image files through the back end. For which I typed the following command: /data/Loris/bin/mri/uploadNeuroDB/imaging_upload_file.pl /data/incoming/CBR035_734440_V1.zip -upload_id 3 -profile prod I got the error message: ERROR: You don't have a configuration file named 'prod' in: /data/Loris/bin/mri/dicom-archive/.loris_mri/ Since I am sure I have this file in the desired location and I can view the configuration file called "prod", I do not understand why I get this error. Your help is highly appreciated. With best regards, Ganesh -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA +91 80 2293 3009 https://www.cbr.iisc.ac.in -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -------------- next part -------------- An HTML attachment was scrubbed... URL: From gluneau.mcin at gmail.com Wed Jul 5 08:01:15 2017 From: gluneau.mcin at gmail.com (Gregory Luneau) Date: Wed, 5 Jul 2017 08:01:15 -0400 Subject: [Loris-dev] Pre-processing MRI DICOM files and Insertion into Loris In-Reply-To: <285280006.33249.1499253521426.JavaMail.zimbra@cbr.iisc.ac.in> References: <285280006.33249.1499253521426.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: Hello Ganesh, as for processing the image on the command line, you'll need to source the environment file first, like this: source /data/Loris/bin/mri/environment Take a look at that environment file first and make sure everything seems ok. Then as a second step, run the imaging upload script. Good day, On Wed, Jul 5, 2017 at 7:18 AM, Ganesh Chauhan (CBR) < ganesh.chauhan at cbr.iisc.ac.in> wrote: > Dear team Loris, > > I uploaded a zipped file containing DICOM image files via the front end > using "Imaging Uploader". The file got uploaded but the "Progress" section > in the table displayed "Failure". > Then I wanted to process the image files through the back end. For which I > typed the following command: > > /data/Loris/bin/mri/uploadNeuroDB/imaging_upload_file.pl > /data/incoming/CBR035_734440_V1.zip -upload_id 3 -profile prod > > I got the error message: > > ERROR: You don't have a > configuration file named 'prod' in: > /data/Loris/bin/mri/dicom-archive/.loris_mri/ > > Since I am sure I have this file in the desired location and I can view > the configuration file called "prod", I do not understand why I get this > error. > > Your help is highly appreciated. > > With best regards, > Ganesh > > > -- > Ganesh Chauhan (PhD) > Scientist > Centre for Brain Research (CBR) > Indian Institute of Science (IISc) > Bengaluru, INDIA > +91 80 2293 3009 <+91%2080%202293%203009> > https://www.cbr.iisc.ac.in > > -- > This message has been scanned for viruses and > dangerous content by *MailScanner* , and is > believed to be clean. > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -- Gregory Luneau McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montreal, Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From ganesh.chauhan at cbr.iisc.ac.in Wed Jul 5 08:58:24 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Wed, 5 Jul 2017 18:28:24 +0530 (IST) Subject: [Loris-dev] Pre-processing MRI DICOM files and Insertion into Loris In-Reply-To: References: <285280006.33249.1499253521426.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: <2080257853.33314.1499259504726.JavaMail.zimbra@cbr.iisc.ac.in> Dear Gregory, I am not sure what should go into the following line in the file environment export PERL5LIB=/data/Loris/bin/mri/uploadNeuroDB:$PERL5LIB Any suggestions like should it be: export PERL5LIB=/usr/share/perl/5.22:$PERL5LIB Many thanks. With best regards, Ganesh From: "Gregory Luneau" To: "Ganesh Chauhan, CBR" Cc: "loris-dev" Sent: Wednesday, July 5, 2017 5:31:15 PM Subject: Re: [Loris-dev] Pre-processing MRI DICOM files and Insertion into Loris Hello Ganesh, as for processing the image on the command line, you'll need to source the environment file first, like this: source /data/Loris/bin/mri/environment Take a look at that environment file first and make sure everything seems ok. Then as a second step, run the imaging upload script. Good day, On Wed, Jul 5, 2017 at 7:18 AM, Ganesh Chauhan (CBR) < [ mailto:ganesh.chauhan at cbr.iisc.ac.in | ganesh.chauhan at cbr.iisc.ac.in ] > wrote: Dear team Loris, I uploaded a zipped file containing DICOM image files via the front end using "Imaging Uploader". The file got uploaded but the "Progress" section in the table displayed "Failure". Then I wanted to process the image files through the back end. For which I typed the following command: /data/Loris/bin/mri/uploadNeuroDB/ [ http://imaging_upload_file.pl/ | imaging_upload_file.pl ] /data/incoming/CBR035_734440_V1.zip -upload_id 3 -profile prod I got the error message: ERROR: You don't have a configuration file named 'prod' in: /data/Loris/bin/mri/dicom-archive/.loris_mri/ Since I am sure I have this file in the desired location and I can view the configuration file called "prod", I do not understand why I get this error. Your help is highly appreciated. With best regards, Ganesh -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA [ tel:+91%2080%202293%203009 | +91 80 2293 3009 ] [ https://www.cbr.iisc.ac.in/ | https://www.cbr.iisc.ac.in ] -- This message has been scanned for viruses and dangerous content by [ http://www.mailscanner.info/ | MailScanner ] , and is believed to be clean. _______________________________________________ Loris-dev mailing list [ mailto:Loris-dev at bic.mni.mcgill.ca | Loris-dev at bic.mni.mcgill.ca ] [ http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev | http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev ] -- Gregory Luneau McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montreal, Canada -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA +91 80 2293 3009 https://www.cbr.iisc.ac.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From gluneau.mcin at gmail.com Wed Jul 5 09:27:02 2017 From: gluneau.mcin at gmail.com (Gregory Luneau) Date: Wed, 5 Jul 2017 09:27:02 -0400 Subject: [Loris-dev] Pre-processing MRI DICOM files and Insertion into Loris In-Reply-To: <2080257853.33314.1499259504726.JavaMail.zimbra@cbr.iisc.ac.in> References: <285280006.33249.1499253521426.JavaMail.zimbra@cbr.iisc.ac.in> <2080257853.33314.1499259504726.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: Hi Ganesh, it is good like this: export PERL5LIB=/data/Loris/bin/mri/uploadNeuroDB:$PERL5LIB it will add the uploadNeuroDB perl libraries to those already in the variable $PERL5LIB. On Wed, Jul 5, 2017 at 8:58 AM, Ganesh Chauhan (CBR) < ganesh.chauhan at cbr.iisc.ac.in> wrote: > Dear Gregory, > > I am not sure what should go into the following line in the file > environment > > export PERL5LIB=/data/Loris/bin/mri/uploadNeuroDB:$PERL5LIB > > Any suggestions like should it be: > > export PERL5LIB=/usr/share/perl/5.22:$PERL5LIB > > > Many thanks. > > With best regards, > Ganesh > ------------------------------ > *From: *"Gregory Luneau" > *To: *"Ganesh Chauhan, CBR" > *Cc: *"loris-dev" > *Sent: *Wednesday, July 5, 2017 5:31:15 PM > *Subject: *Re: [Loris-dev] Pre-processing MRI DICOM files and Insertion > into Loris > > Hello Ganesh, as for processing the image on the command line, you'll need > to source the environment file first, like this: > source /data/Loris/bin/mri/environment > Take a look at that environment file first and make sure everything seems > ok. > > Then as a second step, run the imaging upload script. > > Good day, > > > On Wed, Jul 5, 2017 at 7:18 AM, Ganesh Chauhan (CBR) < > ganesh.chauhan at cbr.iisc.ac.in> wrote: > >> Dear team Loris, >> >> I uploaded a zipped file containing DICOM image files via the front end >> using "Imaging Uploader". The file got uploaded but the "Progress" section >> in the table displayed "Failure". >> Then I wanted to process the image files through the back end. For which >> I typed the following command: >> >> /data/Loris/bin/mri/uploadNeuroDB/imaging_upload_file.pl >> /data/incoming/CBR035_734440_V1.zip -upload_id 3 -profile prod >> >> I got the error message: >> >> ERROR: You don't have a >> configuration file named 'prod' in: >> /data/Loris/bin/mri/dicom-archive/.loris_mri/ >> >> Since I am sure I have this file in the desired location and I can view >> the configuration file called "prod", I do not understand why I get this >> error. >> >> Your help is highly appreciated. >> >> With best regards, >> Ganesh >> >> >> -- >> Ganesh Chauhan (PhD) >> Scientist >> Centre for Brain Research (CBR) >> Indian Institute of Science (IISc) >> Bengaluru, INDIA >> +91 80 2293 3009 <+91%2080%202293%203009> >> https://www.cbr.iisc.ac.in >> >> -- >> This message has been scanned for viruses and >> dangerous content by *MailScanner* , and >> is >> believed to be clean. >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> > > > -- > > Gregory Luneau > > McGill Centre for Integrative Neuroscience (MCIN), > Ludmer Centre for Neuroinformatics and Mental Health, > Montreal Neurological Institute (MNI), > McGill University, Montreal, Canada > > > -- > Ganesh Chauhan (PhD) > Scientist > Centre for Brain Research (CBR) > Indian Institute of Science (IISc) > Bengaluru, INDIA > +91 80 2293 3009 <+91%2080%202293%203009> > https://www.cbr.iisc.ac.in > -- Gregory Luneau McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montreal, Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From mouna.safi-harb at mail.mcgill.ca Wed Jul 5 09:54:14 2017 From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab) Date: Wed, 5 Jul 2017 13:54:14 +0000 Subject: [Loris-dev] CouchDB MRI Importer errors on Loris v17.0.5 In-Reply-To: References: Message-ID: Hi Michael, In general, to fix the problem, we would add the columns causing the issues to the SELECT statement (as opposed to disabling the full_group_by mode). I tagged you on a Loris pull request that has made changes to the MRI importer script, so you can track progress there for an eventual solution! Thanks, - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Michael Joseph Sent: Tuesday, July 4, 2017 1:01:13 PM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] CouchDB MRI Importer errors on Loris v17.0.5 Hi Loris dev team, I received some errors when running the CouchDB_Import_MRI.php script. I've attached a log of the errors. It seems like a MySQL 5.7 issue and disabling "ONLY_FULL_GROUP_BY" mode fixed it. Without disabling the mode, the script wasn't able to populate the CouchDB database. Michael ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Tue Jul 4 15:28:43 2017 From: wangshen.mcin at gmail.com (Shen Wang) Date: Tue, 4 Jul 2017 15:28:43 -0400 Subject: [Loris-dev] Fwd: LORIS Document Repository In-Reply-To: <1811119841.31833.1499158096005.JavaMail.zimbra@cbr.iisc.ac.in> References: <30266241-3ADA-44AC-9C51-1897BD7E64EB@childmind.org> <1076585160.28116.1498710071701.JavaMail.zimbra@cbr.iisc.ac.in> <1E5C55CC-A0F2-4CD7-98C9-81A1B7D744DE@childmind.org> <5C1E2D0C-EA84-416E-8257-49466C65C45E@childmind.org> <1811119841.31833.1499158096005.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: Hi Bonhwang, Ganesh Thank you for helping me debug this issue. This is a bug. After Loris updates from MySQL 5.6 to MySQL 5.7, The null data can not insert into the database. It causes the 500 error. And I have fixed it, "https://github.com/aces/Loris/pull/2924" this is my pull request to fix the issue. It is waiting to test and merge. You could update your Loris manually or wait for new Loris release. Thank guys! Best regards Shen On 4 July 2017 at 04:48, Ganesh Chauhan (CBR) wrote: > Hi, > > The errors that I got are as follows: > > [Tue Jul 04 14:12:59.397979 2017] [:error] [pid 4223] [client > 10.150.10.76:45030] PHP Notice: Undefined index: openAccordion in > /var/www/lorisinstall/Loris/modules/document_repository/ > php/NDB_Menu_Filter_document_repository.class.inc on line 61, referer: > http://alzheimersproject.cns.iisc.ac.in/main.php? > [Tue Jul 04 14:12:59.398064 2017] [:error] [pid 4223] [client > 10.150.10.76:45030] PHP Notice: Undefined index: filtered in > /var/www/lorisinstall/Loris/modules/document_repository/ > php/NDB_Menu_Filter_document_repository.class.inc on line 63, referer: > http://alzheimersproject.cns.iisc.ac.in/main.php? > [Tue Jul 04 14:12:59.446023 2017] [:error] [pid 4223] [client > 10.150.10.76:45030] PHP Notice: Undefined variable: fileCategories in > /var/www/lorisinstall/Loris/modules/document_repository/ > php/NDB_Menu_Filter_document_repository.class.inc on line 125, referer: > http://alzheimersproject.cns.iisc.ac.in/main.php? > [Tue Jul 04 14:12:59.447476 2017] [:error] [pid 4223] [client > 10.150.10.76:45030] PHP Warning: Invalid argument supplied for foreach() > in /var/www/lorisinstall/Loris/modules/document_repository/ > php/NDB_Menu_Filter_document_repository.class.inc on line 152, referer: > http://alzheimersproject.cns.iisc.ac.in/main.php? > [Tue Jul 04 14:12:59.447527 2017] [:error] [pid 4223] [client > 10.150.10.76:45030] PHP Notice: Undefined variable: fileCategories in > /var/www/lorisinstall/Loris/modules/document_repository/ > php/NDB_Menu_Filter_document_repository.class.inc on line 261, referer: > http://alzheimersproject.cns.iisc.ac.in/main.php? > [Tue Jul 04 14:12:59.462133 2017] [:error] [pid 4223] [client > 10.150.10.76:45030] PHP Warning: Invalid argument supplied for foreach() > in /var/www/lorisinstall/Loris/php/libraries/LorisForm.class.inc on line > 685, referer: http://alzheimersproject.cns.iisc.ac.in/main.php? > [Tue Jul 04 14:13:14.657022 2017] [:error] [pid 4715] [client > 10.150.10.76:45036] PHP Notice: A session had already been started - > ignoring session_start() in /var/www/lorisinstall/Loris/ > php/libraries/NDB_Client.class.inc on line 122, referer: > http://alzheimersproject.cns.iisc.ac.in/document_repository/ > [Tue Jul 04 14:13:14.657118 2017] [:error] [pid 4715] [client > 10.150.10.76:45036] PHP Notice: Undefined variable: comments in > /var/www/lorisinstall/Loris/modules/document_repository/ajax/addCategory.php > on line 60, referer: http://alzheimersproject.cns.iisc.ac.in/document_ > repository/ > [Tue Jul 04 14:13:14.657489 2017] [:error] [pid 4715] [client > 10.150.10.76:45036] PHP Warning: PDOStatement::execute(): > SQLSTATE[HY000]: General error: 1366 Incorrect integer value: ' ' for > column 'parent_id' at row 1 in /var/www/lorisinstall/Loris/ > php/libraries/Database.class.inc on line 312, referer: > http://alzheimersproject.cns.iisc.ac.in/document_repository/ > [Tue Jul 04 14:13:14.666803 2017] [:error] [pid 4715] [client > 10.150.10.76:45036] Could not execute INSERT INTO > document_repository_categories SET `category_name`=:category_ > name,`parent_id`=:parent_id,`comments`=:comments. Stack trace#0 > /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(243): > Database->_realinsert('document_reposi...', Array, true)\n#1 > /var/www/lorisinstall/Loris/modules/document_repository/ajax/addCategory.php(60): > Database->insert('document_reposi...', Array)\n#2 > /var/www/lorisinstall/Loris/htdocs/AjaxHelper.php(93): > require('/var/www/lorisi...')\n#3 {main}, referer: > http://alzheimersproject.cns.iisc.ac.in/document_repository/ > [Tue Jul 04 14:13:14.666897 2017] [:error] [pid 4715] [client > 10.150.10.76:45036] PHP Fatal error: Uncaught DatabaseException: Insert > statement did not execute successfully: Array\n(\n [0] => HY000\n [1] > => 1366\n [2] => Incorrect integer value: ' ' for column 'parent_id' at > row 1\n)\n in /var/www/lorisinstall/Loris/php/libraries/Database.class.inc:314\nStack > trace:\n#0 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(243): > Database->_realinsert('document_reposi...', Array, true)\n#1 > /var/www/lorisinstall/Loris/modules/document_repository/ajax/addCategory.php(60): > Database->insert('document_reposi...', Array)\n#2 > /var/www/lorisinstall/Loris/htdocs/AjaxHelper.php(93): > require('/var/www/lorisi...')\n#3 {main}\n thrown in > /var/www/lorisinstall/Loris/php/libraries/Database.class.inc on line 314, > referer: http://alzheimersproject.cns.iisc.ac.in/document_repository/ > [Tue Jul 04 14:13:16.091641 2017] [:error] [pid 4716] [client > 10.150.10.76:45038] PHP Notice: A session had already been started - > ignoring session_start() in /var/www/lorisinstall/Loris/ > php/libraries/NDB_Client.class.inc on line 122, referer: > http://alzheimersproject.cns.iisc.ac.in/document_repository/ > [Tue Jul 04 14:13:16.091692 2017] [:error] [pid 4716] [client > 10.150.10.76:45038] PHP Notice: Undefined variable: comments in > /var/www/lorisinstall/Loris/modules/document_repository/ajax/addCategory.php > on line 60, referer: http://alzheimersproject.cns.iisc.ac.in/document_ > repository/ > [Tue Jul 04 14:13:16.091878 2017] [:error] [pid 4716] [client > 10.150.10.76:45038] PHP Warning: PDOStatement::execute(): > SQLSTATE[HY000]: General error: 1366 Incorrect integer value: ' ' for > column 'parent_id' at row 1 in /var/www/lorisinstall/Loris/ > php/libraries/Database.class.inc on line 312, referer: > http://alzheimersproject.cns.iisc.ac.in/document_repository/ > [Tue Jul 04 14:13:16.091930 2017] [:error] [pid 4716] [client > 10.150.10.76:45038] Could not execute INSERT INTO > document_repository_categories SET `category_name`=:category_ > name,`parent_id`=:parent_id,`comments`=:comments. Stack trace#0 > /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(243): > Database->_realinsert('document_reposi...', Array, true)\n#1 > /var/www/lorisinstall/Loris/modules/document_repository/ajax/addCategory.php(60): > Database->insert('document_reposi...', Array)\n#2 > /var/www/lorisinstall/Loris/htdocs/AjaxHelper.php(93): > require('/var/www/lorisi...')\n#3 {main}, referer: > http://alzheimersproject.cns.iisc.ac.in/document_repository/ > [Tue Jul 04 14:13:16.091969 2017] [:error] [pid 4716] [client > 10.150.10.76:45038] PHP Fatal error: Uncaught DatabaseException: Insert > statement did not execute successfully: Array\n(\n [0] => HY000\n [1] > => 1366\n [2] => Incorrect integer value: ' ' for column 'parent_id' at > row 1\n)\n in /var/www/lorisinstall/Loris/php/libraries/Database.class.inc:314\nStack > trace:\n#0 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(243): > Database->_realinsert('document_reposi...', Array, true)\n#1 > /var/www/lorisinstall/Loris/modules/document_repository/ajax/addCategory.php(60): > Database->insert('document_reposi...', Array)\n#2 > /var/www/lorisinstall/Loris/htdocs/AjaxHelper.php(93): > require('/var/www/lorisi...')\n#3 {main}\n thrown in > /var/www/lorisinstall/Loris/php/libraries/Database.class.inc on line 314, > referer: http://alzheimersproject.cns.iisc.ac.in/document_repository/ > > > Thanks for your help. > > With best reagrds, > Ganesh > > ------------------------------ > *From: *"Bonhwang Koo" > *To: *"Shen Wang" > *Cc: *"Ganesh Chauhan, CBR" , "Samir Das" < > samir.das at mcgill.ca>, "loris-dev" > *Sent: *Monday, July 3, 2017 11:51:33 PM > > *Subject: *Re: [Loris-dev] Fwd: LORIS Document Repository > > Here?s the error message: > > > > [Mon Jul 03 18:06:11.093590 2017] [:error] [pid 19414] [client > 67.220.146.162:22132] PHP Notice: Undefined variable: fileCategories in > /var/www/loris/modules/document_repository/php/NDB_Menu_Filter_document_repository.class.inc > on line 125, referer: http://data.healthybrainnetwork.org/ > document_repository/ > > [Mon Jul 03 18:06:11.093883 2017] [:error] [pid 19414] [client > 67.220.146.162:22132] PHP Notice: Undefined variable: tree in > /var/www/loris/modules/document_repository/php/NDB_Menu_Filter_document_repository.class.inc > on line 244, referer: http://data.healthybrainnetwork.org/ > document_repository/ > > [Mon Jul 03 18:06:11.093897 2017] [:error] [pid 19414] [client > 67.220.146.162:22132] PHP Warning: Invalid argument supplied for > foreach() in /var/www/loris/modules/document_repository/php/NDB_ > Menu_Filter_document_repository.class.inc on line 152, referer: > http://data.healthybrainnetwork.org/document_repository/ > > [Mon Jul 03 18:06:11.093903 2017] [:error] [pid 19414] [client > 67.220.146.162:22132] PHP Notice: Undefined variable: fileCategories in > /var/www/loris/modules/document_repository/php/NDB_Menu_Filter_document_repository.class.inc > on line 261, referer: http://data.healthybrainnetwork.org/ > document_repository/ > > [Mon Jul 03 18:06:11.099870 2017] [:error] [pid 19414] [client > 67.220.146.162:22132] PHP Warning: Invalid argument supplied for > foreach() in /var/www/loris/php/libraries/LorisForm.class.inc on line > 685, referer: http://data.healthybrainnetwork.org/document_repository/ > > [Mon Jul 03 18:06:23.562950 2017] [:error] [pid 3629] [client > 67.220.146.162:48512] PHP Notice: A session had already been started - > ignoring session_start() in /var/www/loris/php/libraries/NDB_Client.class.inc > on line 122, referer: http://data.healthybrainnetwork.org/ > document_repository/?filtered=true > > [Mon Jul 03 18:06:23.562988 2017] [:error] [pid 3629] [client > 67.220.146.162:48512] PHP Notice: Undefined variable: comments in > /var/www/loris/modules/document_repository/ajax/addCategory.php on line > 60, referer: http://data.healthybrainnetwork.org/ > document_repository/?filtered=true > > [Mon Jul 03 18:06:23.563178 2017] [:error] [pid 3629] [client > 67.220.146.162:48512] PHP Warning: PDOStatement::execute(): > SQLSTATE[HY000]: General error: 1366 Incorrect integer value: ' ' for > column 'parent_id' at row 1 in /var/www/loris/php/libraries/Database.class.inc > on line 312, referer: http://data.healthybrainnetwork.org/ > document_repository/?filtered=true > > [Mon Jul 03 18:06:23.563229 2017] [:error] [pid 3629] [client > 67.220.146.162:48512] Could not execute INSERT INTO > document_repository_categories SET `category_name`=:category_ > name,`parent_id`=:parent_id,`comments`=:comments. Stack trace#0 > /var/www/loris/php/libraries/Database.class.inc(243): > Database->_realinsert('document_reposi...', Array, true)\n#1 > /var/www/loris/modules/document_repository/ajax/addCategory.php(60): > Database->insert('document_reposi...', Array)\n#2 /var/www/loris/htdocs/AjaxHelper.php(93): > require('/var/www/loris/...')\n#3 {main}, referer: http://data. > healthybrainnetwork.org/document_repository/?filtered=true > > [Mon Jul 03 18:06:23.563249 2017] [:error] [pid 3629] [client > 67.220.146.162:48512] PHP Fatal error: Uncaught DatabaseException: > Insert statement did not execute successfully: Array\n(\n [0] => > HY000\n [1] => 1366\n [2] => Incorrect integer value: ' ' for column > 'parent_id' at row 1\n)\n in /var/www/loris/php/libraries/Database.class.inc:314\nStack > trace:\n#0 /var/www/loris/php/libraries/Database.class.inc(243): > Database->_realinsert('document_reposi...', Array, true)\n#1 > /var/www/loris/modules/document_repository/ajax/addCategory.php(60): > Database->insert('document_reposi...', Array)\n#2 /var/www/loris/htdocs/AjaxHelper.php(93): > require('/var/www/loris/...')\n#3 {main}\n thrown in > /var/www/loris/php/libraries/Database.class.inc on line 314, referer: > http://data.healthybrainnetwork.org/document_repository/?filtered=true > > > > I tried the second suggestion as well?the ?test? category shows up in the > document repository, but when I try to add a file, it takes me to a broken > link (document_repository/ajax/documentEditUpload.php), and the error log > gives me the following message: > > > > [Mon Jul 03 18:17:27.494508 2017] [:error] [pid 14300] [client > 67.220.146.162:39842] PHP Notice: Only variables should be passed by > reference in /var/www/loris/modules/document_repository/ajax/documentEditUpload.php > on line 39, referer: http://data.healthybrainnetwork.org/ > document_repository/ > > [Mon Jul 03 18:17:27.494866 2017] [:error] [pid 14300] [client > 67.220.146.162:39842] PHP Warning: PDOStatement::execute(): > SQLSTATE[HY000]: General error: 1366 Incorrect integer value: '' for column > 'For_site' at row 1 in /var/www/loris/php/libraries/Database.class.inc on > line 312, referer: http://data.healthybrainnetwork.org/ > document_repository/ > > [Mon Jul 03 18:17:27.494920 2017] [:error] [pid 14300] [client > 67.220.146.162:39842] Could not execute INSERT INTO document_repository > SET `File_category`=:File_category,`For_site`=:For_site, > `comments`=:comments,`version`=:version,`File_name`=:File_ > name,`File_size`=:File_size,`Data_dir`=:Data_dir,`uploaded_ > by`=:uploaded_by,`Instrument`=:Instrument,`PSCID`=:PSCID,` > visitLabel`=:visitLabel,`File_type`=:File_type. Stack trace#0 > /var/www/loris/php/libraries/Database.class.inc(243): > Database->_realinsert('document_reposi...', Array, true)\n#1 > /var/www/loris/modules/document_repository/ajax/documentEditUpload.php(61): > Database->insert('document_reposi...', Array)\n#2 /var/www/loris/htdocs/AjaxHelper.php(93): > require('/var/www/loris/...')\n#3 {main}, referer: http://data. > healthybrainnetwork.org/document_repository/ > > [Mon Jul 03 18:17:27.494941 2017] [:error] [pid 14300] [client > 67.220.146.162:39842] PHP Fatal error: Uncaught DatabaseException: > Insert statement did not execute successfully: Array\n(\n [0] => > HY000\n [1] => 1366\n [2] => Incorrect integer value: '' for column > 'For_site' at row 1\n)\n in /var/www/loris/php/libraries/Database.class.inc:314\nStack > trace:\n#0 /var/www/loris/php/libraries/Database.class.inc(243): > Database->_realinsert('document_reposi...', Array, true)\n#1 > /var/www/loris/modules/document_repository/ajax/documentEditUpload.php(61): > Database->insert('document_reposi...', Array)\n#2 /var/www/loris/htdocs/AjaxHelper.php(93): > require('/var/www/loris/...')\n#3 {main}\n thrown in > /var/www/loris/php/libraries/Database.class.inc on line 314, referer: > http://data.healthybrainnetwork.org/document_repository/ > > > > > > -- > > Bonhwang Koo > > Research Assistant, CDB > > Child Mind Institute > > childmind.org > > 445 Park Avenue (entrance on 56th Street) > > New York, NY 10022 > > E: Bonhwang.Koo at childmind.org > > p: 646.625.4398 <(646)%20625-4398> > > f: 646.625.4348 <(646)%20625-4348> > > > > Facebook: facebook.com/ChildMindInstitute | Follow us on Twitter: > twitter.com/ChildMindDotOrg > > > > --- > > > > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. Please note, the recipient should check > this email and any attachments for the presence of viruses. The > organization accepts no liability for any damage caused by any virus > transmitted by this email. > > > > *From: *Shen Wang > *Date: *Monday, July 3, 2017 at 2:07 PM > *To: *Bonhwang Koo > *Cc: *"Ganesh Chauhan (CBR)" , Samir Das < > samir.das at mcgill.ca>, loris-dev > *Subject: *Re: [Loris-dev] Fwd: LORIS Document Repository > > > > Hi Bonhwang, > > > > I tested Loris 17.0 on my VM, it works fine. It is difficult to debug > without error log. > > Could you show me more error log or error message? > > 1, Run "sudo tail -f /var/log/apache2/loris-error.log" when you add a > category. Please show me the message. > > 2, Or Run "insert into document_repository_categories > (id,category_name,parent_id,comments) values('777','test','0',null)" in > your loris database. You should see the new test category. Then try upload > a file under test category. Tell me the result. > > > > Best wishes > > > > On 3 July 2017 at 11:08, Shen Wang wrote: > > Hi Ganesh > > You can get the "Document Repository" module functional without email > server. > > Could you show me the error log or error message when you want to add a > category? > > > > Shen > > > > On 3 July 2017 at 10:14, Bonhwang Koo wrote: > > 17.0.3 > > > > -- > > Bonhwang Koo > > Research Assistant, CDB > > Child Mind Institute > > childmind.org > > 445 Park Avenue (entrance on 56th Street) > > New York, NY 10022 > > E: Bonhwang.Koo at childmind.org > > p: 646.625.4398 <(646)%20625-4398> > > f: 646.625.4348 <(646)%20625-4348> > > > > Facebook: facebook.com/ChildMindInstitute | Follow us on Twitter: > twitter.com/ChildMindDotOrg > > > > --- > > > > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. Please note, the recipient should check > this email and any attachments for the presence of viruses. The > organization accepts no liability for any damage caused by any virus > transmitted by this email. > > > > *From: *Shen Wang > *Date: *Monday, July 3, 2017 at 10:04 AM > *To: *Bonhwang Koo > *Cc: *"Ganesh Chauhan (CBR)" , Samir Das < > samir.das at mcgill.ca>, loris-dev > > > *Subject: *Re: [Loris-dev] Fwd: LORIS Document Repository > > > > Hi > > Could you tell me which version of Loris do you have? I will check it. > > > > Best wishes > > Shen > > > > On 29 June 2017 at 17:03, Bonhwang Koo wrote: > > I followed your suggestion, although I ran the command for a slightly > different directory: ?sudo chmod 777 /var/www/loris/modules/ > document_repository/user_uploads?, and I still have the same issue. This > isn?t working even though I have a mail server installed via PostFix. I > took a look at the console on my browser, and this is the error I?m getting: > > > > > > > > This is the corresponding code in document_repository_helper.js:89 : > > $.ajax({ > > url: loris.BaseURL + "/document_repository/ajax/addCategory.php", > > type: "POST", > > data: $("#addCategoryForm").serialize(), > > success: function() { > > $("#addCategoryModal").modal('hide'); > > $("#addCategoryCategory").removeClass("has-error"); > > $("#categoryAddError").hide(); > > $('.add-success').show(); > > setTimeout(function() { > > $('.add-success').hide(); > > }, 3000); > > setTimeout(function() { > > location.reload(); > > }, 3000); > > }, > > error: function(jqXHR, textStatus, errorThrown) { > > if (jqXHR.status === 400) { > > $("#addCategoryCategory").addClass("has-error"); > > $("#categoryAddError").show() > > } > > } > > }); > > > > > > > > -- > > Bonhwang Koo > > Research Assistant, CDB > > Child Mind Institute > > childmind.org > > 445 Park Avenue (entrance on 56th Street) > > New York, NY 10022 > > E: Bonhwang.Koo at childmind.org > > p: 646.625.4398 <(646)%20625-4398> > > f: 646.625.4348 <(646)%20625-4348> > > > > Facebook: facebook.com/ChildMindInstitute | Follow us on Twitter: > twitter.com/ChildMindDotOrg > > > > --- > > > > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. Please note, the recipient should check > this email and any attachments for the presence of viruses. The > organization accepts no liability for any damage caused by any virus > transmitted by this email. > > > > *From: *"Ganesh Chauhan (CBR)" > *Date: *Thursday, June 29, 2017 at 12:21 AM > *To: *Shen Wang > *Cc: *Samir Das , loris-dev < > Loris-dev at bic.mni.mcgill.ca>, Bonhwang Koo > > > *Subject: *Re: [Loris-dev] Fwd: LORIS Document Repository > > > > Hi, > > > > I have had the same problem of not being able to add a category despite > having file permissions. > > Though I still do not have the email server setup for LORIS. Hence do you > think that without the email server we cannot get the "Document Repository" > module functional. > > > > Thanks for your suggestion. > > > > With best regards, > > Ganesh > > > ------------------------------ > > *From: *"Shen Wang" > *To: *"Samir Das" > *Cc: *"loris-dev" , "Bonhwang Koo" < > Bonhwang.Koo at childmind.org> > *Sent: *Thursday, June 29, 2017 12:52:48 AM > *Subject: *Re: [Loris-dev] Fwd: LORIS Document Repository > > > > Hello: > > Maybe you need to have file system permission to create the upload > directory. > > I think It is not a Loris issue. > > As a quick fix, you can do: "sudo chmod 777 /var/www/loris/document_ > repository/user_uploads". > > /var/www/loris/ will be replaced by your loris directory. > > I hope this can help you. > > > > Shen > > > > On 27 June 2017 at 16:09, Samir Das wrote: > > > > ---------- Forwarded message ---------- > From: *Bonhwang Koo* > Date: Mon, Jun 26, 2017 at 8:28 AM > Subject: LORIS Document Repository > To: "loris.info at mcin.ca" > > Hello, > > > > I am working with the Child Mind Institute?s Healthy Brain Network > initiative, and we created a LORIS instance to allow users query data from > our recent data release. I want to use the document repository feature, but > it won?t allow me to upload a file without a category, so when I try to add > a new category, nothing happens. Can you help me resolve this issue? > > > > Best, > > -- > > Bonhwang Koo > > Research Assistant, CDB > > Child Mind Institute > > childmind.org > > 445 Park Avenue (entrance on 56th Street) > > New York, NY 10022 > > E: Bonhwang.Koo at childmind.org > > p: 646.625.4398 <(646)%20625-4398> > > f: 646.625.4348 <(646)%20625-4348> > > > > Facebook: facebook.com/ChildMindInstitute | Follow us on Twitter: > twitter.com/ChildMindDotOrg > > > > --- > > > > This email message, including any attachments, is for the sole use of the > intended recipient(s) and may contain information that is proprietary, > confidential, and exempt from disclosure under applicable law. Any > unauthorized review, use, disclosure, or distribution is prohibited. If you > have received this email in error please notify the sender by return email > and delete the original message. Please note, the recipient should check > this email and any attachments for the presence of viruses. The > organization accepts no liability for any damage caused by any virus > transmitted by this email. > > > > > > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > > > -- > > Ganesh Chauhan (PhD) > Scientist > Centre for Brain Research (CBR) > Indian Institute of Science (IISc) > Bengaluru, INDIA > +91 80 2293 3009 <+91%2080%202293%203009> > https://www.cbr.iisc.ac.in > > > > > > > > > -- > Ganesh Chauhan (PhD) > Scientist > Centre for Brain Research (CBR) > Indian Institute of Science (IISc) > Bengaluru, INDIA > +91 80 2293 3009 <+91%2080%202293%203009> > https://www.cbr.iisc.ac.in > -------------- next part -------------- An HTML attachment was scrubbed... URL: From istvan.morocz at mcgill.ca Wed Jul 5 17:15:36 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Wed, 5 Jul 2017 17:15:36 -0400 (EDT) Subject: [Loris-dev] where to find Vagrantfile for newest LORIS 17.1 ? Message-ID: dear LORIS team, where can i download the Vagrantfile that corresponds with the newest LORIS version 17.1 ? the current Vagrantfile looks 5 months old - which is perhaps fine. just is then the git MASTER clone up to date to pull version 17.1 ? thanks much, bye, pisti ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : http://noisis.com ` istvan.morocz at noisis.com : +1-514-927-1169 : istvan.morocz at mcgill.ca : http://cafe.spl.harvard.edu , http://www.pistikem.org : pistikem at gmail.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" From ganesh.chauhan at cbr.iisc.ac.in Wed Jul 5 00:17:39 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Wed, 5 Jul 2017 09:47:39 +0530 (IST) Subject: [Loris-dev] Fwd: LORIS Document Repository In-Reply-To: References: <30266241-3ADA-44AC-9C51-1897BD7E64EB@childmind.org> <5C1E2D0C-EA84-416E-8257-49466C65C45E@childmind.org> <1811119841.31833.1499158096005.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: <1605586845.32667.1499228259245.JavaMail.zimbra@cbr.iisc.ac.in> Dear Shen, Excellent. I made the changes you suggested and it works for me. Now I can add a category and upload files. Many thanks. With best regards, Ganesh From: "Shen Wang" To: "Ganesh Chauhan, CBR" Cc: "Bonhwang Koo" , "Samir Das" , "loris-dev" Sent: Wednesday, July 5, 2017 12:58:43 AM Subject: Re: [Loris-dev] Fwd: LORIS Document Repository Hi Bonhwang, Ganesh Thank you for helping me debug this issue. This is a bug. After Loris updates from MySQL 5.6 to MySQL 5.7, The null data can not insert into the database. It causes the 500 error. And I have fixed it, " [ https://github.com/aces/Loris/pull/2924 | https://github.com/aces/Loris/pull/2924 ] " this is my pull request to fix the issue. It is waiting to test and merge. You could update your Loris manually or wait for new Loris release. Thank guys! Best regards Shen On 4 July 2017 at 04:48, Ganesh Chauhan (CBR) < [ mailto:ganesh.chauhan at cbr.iisc.ac.in | ganesh.chauhan at cbr.iisc.ac.in ] > wrote: Hi, The errors that I got are as follows: [Tue Jul 04 14:12:59.397979 2017] [:error] [pid 4223] [client [ http://10.150.10.76:45030/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45030 ] ] PHP Notice: Undefined index: openAccordion in /var/www/lorisinstall/Loris/modules/document_repository/php/NDB_Menu_Filter_document_repository.class.inc on line 61, referer: [ http://alzheimersproject.cns.iisc.ac.in/main.php | http://alzheimersproject.cns.iisc.ac.in/main.php ] ? [Tue Jul 04 14:12:59.398064 2017] [:error] [pid 4223] [client [ http://10.150.10.76:45030/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45030 ] ] PHP Notice: Undefined index: filtered in /var/www/lorisinstall/Loris/modules/document_repository/php/NDB_Menu_Filter_document_repository.class.inc on line 63, referer: [ http://alzheimersproject.cns.iisc.ac.in/main.php | http://alzheimersproject.cns.iisc.ac.in/main.php ] ? [Tue Jul 04 14:12:59.446023 2017] [:error] [pid 4223] [client [ http://10.150.10.76:45030/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45030 ] ] PHP Notice: Undefined variable: fileCategories in /var/www/lorisinstall/Loris/modules/document_repository/php/NDB_Menu_Filter_document_repository.class.inc on line 125, referer: [ http://alzheimersproject.cns.iisc.ac.in/main.php | http://alzheimersproject.cns.iisc.ac.in/main.php ] ? [Tue Jul 04 14:12:59.447476 2017] [:error] [pid 4223] [client [ http://10.150.10.76:45030/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45030 ] ] PHP Warning: Invalid argument supplied for foreach() in /var/www/lorisinstall/Loris/modules/document_repository/php/NDB_Menu_Filter_document_repository.class.inc on line 152, referer: [ http://alzheimersproject.cns.iisc.ac.in/main.php | http://alzheimersproject.cns.iisc.ac.in/main.php ] ? [Tue Jul 04 14:12:59.447527 2017] [:error] [pid 4223] [client [ http://10.150.10.76:45030/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45030 ] ] PHP Notice: Undefined variable: fileCategories in /var/www/lorisinstall/Loris/modules/document_repository/php/NDB_Menu_Filter_document_repository.class.inc on line 261, referer: [ http://alzheimersproject.cns.iisc.ac.in/main.php | http://alzheimersproject.cns.iisc.ac.in/main.php ] ? [Tue Jul 04 14:12:59.462133 2017] [:error] [pid 4223] [client [ http://10.150.10.76:45030/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45030 ] ] PHP Warning: Invalid argument supplied for foreach() in /var/www/lorisinstall/Loris/php/libraries/LorisForm.class.inc on line 685, referer: [ http://alzheimersproject.cns.iisc.ac.in/main.php | http://alzheimersproject.cns.iisc.ac.in/main.php ] ? [Tue Jul 04 14:13:14.657022 2017] [:error] [pid 4715] [client [ http://10.150.10.76:45036/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45036 ] ] PHP Notice: A session had already been started - ignoring session_start() in /var/www/lorisinstall/Loris/php/libraries/NDB_Client.class.inc on line 122, referer: [ http://alzheimersproject.cns.iisc.ac.in/document_repository/ | http://alzheimersproject.cns.iisc.ac.in/document_repository/ ] [Tue Jul 04 14:13:14.657118 2017] [:error] [pid 4715] [client [ http://10.150.10.76:45036/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45036 ] ] PHP Notice: Undefined variable: comments in /var/www/lorisinstall/Loris/modules/document_repository/ajax/addCategory.php on line 60, referer: [ http://alzheimersproject.cns.iisc.ac.in/document_repository/ | http://alzheimersproject.cns.iisc.ac.in/document_repository/ ] [Tue Jul 04 14:13:14.657489 2017] [:error] [pid 4715] [client [ http://10.150.10.76:45036/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45036 ] ] PHP Warning: PDOStatement::execute(): SQLSTATE[HY000]: General error: 1366 Incorrect integer value: ' ' for column 'parent_id' at row 1 in /var/www/lorisinstall/Loris/php/libraries/Database.class.inc on line 312, referer: [ http://alzheimersproject.cns.iisc.ac.in/document_repository/ | http://alzheimersproject.cns.iisc.ac.in/document_repository/ ] [Tue Jul 04 14:13:14.666803 2017] [:error] [pid 4715] [client [ http://10.150.10.76:45036/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45036 ] ] Could not execute INSERT INTO document_repository_categories SET `category_name`=:category_name,`parent_id`=:parent_id,`comments`=:comments. Stack trace#0 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(243): Database->_realinsert('document_reposi...', Array, true)\n#1 /var/www/lorisinstall/Loris/modules/document_repository/ajax/addCategory.php(60): Database->insert('document_reposi...', Array)\n#2 /var/www/lorisinstall/Loris/htdocs/AjaxHelper.php(93): require('/var/www/lorisi...')\n#3 {main}, referer: [ http://alzheimersproject.cns.iisc.ac.in/document_repository/ | http://alzheimersproject.cns.iisc.ac.in/document_repository/ ] [Tue Jul 04 14:13:14.666897 2017] [:error] [pid 4715] [client [ http://10.150.10.76:45036/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45036 ] ] PHP Fatal error: Uncaught DatabaseException: Insert statement did not execute successfully: Array\n(\n [0] => HY000\n [1] => 1366\n [2] => Incorrect integer value: ' ' for column 'parent_id' at row 1\n)\n in /var/www/lorisinstall/Loris/php/libraries/Database.class.inc:314\nStack trace:\n#0 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(243): Database->_realinsert('document_reposi...', Array, true)\n#1 /var/www/lorisinstall/Loris/modules/document_repository/ajax/addCategory.php(60): Database->insert('document_reposi...', Array)\n#2 /var/www/lorisinstall/Loris/htdocs/AjaxHelper.php(93): require('/var/www/lorisi...')\n#3 {main}\n thrown in /var/www/lorisinstall/Loris/php/libraries/Database.class.inc on line 314, referer: [ http://alzheimersproject.cns.iisc.ac.in/document_repository/ | http://alzheimersproject.cns.iisc.ac.in/document_repository/ ] [Tue Jul 04 14:13:16.091641 2017] [:error] [pid 4716] [client [ http://10.150.10.76:45038/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45038 ] ] PHP Notice: A session had already been started - ignoring session_start() in /var/www/lorisinstall/Loris/php/libraries/NDB_Client.class.inc on line 122, referer: [ http://alzheimersproject.cns.iisc.ac.in/document_repository/ | http://alzheimersproject.cns.iisc.ac.in/document_repository/ ] [Tue Jul 04 14:13:16.091692 2017] [:error] [pid 4716] [client [ http://10.150.10.76:45038/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45038 ] ] PHP Notice: Undefined variable: comments in /var/www/lorisinstall/Loris/modules/document_repository/ajax/addCategory.php on line 60, referer: [ http://alzheimersproject.cns.iisc.ac.in/document_repository/ | http://alzheimersproject.cns.iisc.ac.in/document_repository/ ] [Tue Jul 04 14:13:16.091878 2017] [:error] [pid 4716] [client [ http://10.150.10.76:45038/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45038 ] ] PHP Warning: PDOStatement::execute(): SQLSTATE[HY000]: General error: 1366 Incorrect integer value: ' ' for column 'parent_id' at row 1 in /var/www/lorisinstall/Loris/php/libraries/Database.class.inc on line 312, referer: [ http://alzheimersproject.cns.iisc.ac.in/document_repository/ | http://alzheimersproject.cns.iisc.ac.in/document_repository/ ] [Tue Jul 04 14:13:16.091930 2017] [:error] [pid 4716] [client [ http://10.150.10.76:45038/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45038 ] ] Could not execute INSERT INTO document_repository_categories SET `category_name`=:category_name,`parent_id`=:parent_id,`comments`=:comments. Stack trace#0 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(243): Database->_realinsert('document_reposi...', Array, true)\n#1 /var/www/lorisinstall/Loris/modules/document_repository/ajax/addCategory.php(60): Database->insert('document_reposi...', Array)\n#2 /var/www/lorisinstall/Loris/htdocs/AjaxHelper.php(93): require('/var/www/lorisi...')\n#3 {main}, referer: [ http://alzheimersproject.cns.iisc.ac.in/document_repository/ | http://alzheimersproject.cns.iisc.ac.in/document_repository/ ] [Tue Jul 04 14:13:16.091969 2017] [:error] [pid 4716] [client [ http://10.150.10.76:45038/ | MailScanner warning: numerical links are often malicious: 10.150.10.76:45038 ] ] PHP Fatal error: Uncaught DatabaseException: Insert statement did not execute successfully: Array\n(\n [0] => HY000\n [1] => 1366\n [2] => Incorrect integer value: ' ' for column 'parent_id' at row 1\n)\n in /var/www/lorisinstall/Loris/php/libraries/Database.class.inc:314\nStack trace:\n#0 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(243): Database->_realinsert('document_reposi...', Array, true)\n#1 /var/www/lorisinstall/Loris/modules/document_repository/ajax/addCategory.php(60): Database->insert('document_reposi...', Array)\n#2 /var/www/lorisinstall/Loris/htdocs/AjaxHelper.php(93): require('/var/www/lorisi...')\n#3 {main}\n thrown in /var/www/lorisinstall/Loris/php/libraries/Database.class.inc on line 314, referer: [ http://alzheimersproject.cns.iisc.ac.in/document_repository/ | http://alzheimersproject.cns.iisc.ac.in/document_repository/ ] Thanks for your help. With best reagrds, Ganesh From: "Bonhwang Koo" < [ mailto:Bonhwang.Koo at childmind.org | Bonhwang.Koo at childmind.org ] > To: "Shen Wang" < [ mailto:wangshen.mcin at gmail.com | wangshen.mcin at gmail.com ] > Cc: "Ganesh Chauhan, CBR" < [ mailto:ganesh.chauhan at cbr.iisc.ac.in | ganesh.chauhan at cbr.iisc.ac.in ] >, "Samir Das" < [ mailto:samir.das at mcgill.ca | samir.das at mcgill.ca ] >, "loris-dev" < [ mailto:Loris-dev at bic.mni.mcgill.ca | Loris-dev at bic.mni.mcgill.ca ] > Sent: Monday, July 3, 2017 11:51:33 PM Subject: Re: [Loris-dev] Fwd: LORIS Document Repository Here?s the error message: [Mon Jul 03 18:06:11.093590 2017] [:error] [pid 19414] [client [ http://67.220.146.162:22132/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:22132 ] ] PHP Notice: Undefined variable: fileCategories in /var/www/loris/modules/document_repository/php/NDB_Menu_Filter_document_repository.class.inc on line 125, referer: [ http://data.healthybrainnetwork.org/document_repository/ | http://data.healthybrainnetwork.org/document_repository/ ] [Mon Jul 03 18:06:11.093883 2017] [:error] [pid 19414] [client [ http://67.220.146.162:22132/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:22132 ] ] PHP Notice: Undefined variable: tree in /var/www/loris/modules/document_repository/php/NDB_Menu_Filter_document_repository.class.inc on line 244, referer: [ http://data.healthybrainnetwork.org/document_repository/ | http://data.healthybrainnetwork.org/document_repository/ ] [Mon Jul 03 18:06:11.093897 2017] [:error] [pid 19414] [client [ http://67.220.146.162:22132/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:22132 ] ] PHP Warning: Invalid argument supplied for foreach() in /var/www/loris/modules/document_repository/php/NDB_Menu_Filter_document_repository.class.inc on line 152, referer: [ http://data.healthybrainnetwork.org/document_repository/ | http://data.healthybrainnetwork.org/document_repository/ ] [Mon Jul 03 18:06:11.093903 2017] [:error] [pid 19414] [client [ http://67.220.146.162:22132/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:22132 ] ] PHP Notice: Undefined variable: fileCategories in /var/www/loris/modules/document_repository/php/NDB_Menu_Filter_document_repository.class.inc on line 261, referer: [ http://data.healthybrainnetwork.org/document_repository/ | http://data.healthybrainnetwork.org/document_repository/ ] [Mon Jul 03 18:06:11.099870 2017] [:error] [pid 19414] [client [ http://67.220.146.162:22132/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:22132 ] ] PHP Warning: Invalid argument supplied for foreach() in /var/www/loris/php/libraries/LorisForm.class.inc on line 685, referer: [ http://data.healthybrainnetwork.org/document_repository/ | http://data.healthybrainnetwork.org/document_repository/ ] [Mon Jul 03 18:06:23.562950 2017] [:error] [pid 3629] [client [ http://67.220.146.162:48512/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:48512 ] ] PHP Notice: A session had already been started - ignoring session_start() in /var/www/loris/php/libraries/NDB_Client.class.inc on line 122, referer: [ http://data.healthybrainnetwork.org/document_repository/?filtered=true | http://data.healthybrainnetwork.org/document_repository/?filtered=true ] [Mon Jul 03 18:06:23.562988 2017] [:error] [pid 3629] [client [ http://67.220.146.162:48512/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:48512 ] ] PHP Notice: Undefined variable: comments in /var/www/loris/modules/document_repository/ajax/addCategory.php on line 60, referer: [ http://data.healthybrainnetwork.org/document_repository/?filtered=true | http://data.healthybrainnetwork.org/document_repository/?filtered=true ] [Mon Jul 03 18:06:23.563178 2017] [:error] [pid 3629] [client [ http://67.220.146.162:48512/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:48512 ] ] PHP Warning: PDOStatement::execute(): SQLSTATE[HY000]: General error: 1366 Incorrect integer value: ' ' for column 'parent_id' at row 1 in /var/www/loris/php/libraries/Database.class.inc on line 312, referer: [ http://data.healthybrainnetwork.org/document_repository/?filtered=true | http://data.healthybrainnetwork.org/document_repository/?filtered=true ] [Mon Jul 03 18:06:23.563229 2017] [:error] [pid 3629] [client [ http://67.220.146.162:48512/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:48512 ] ] Could not execute INSERT INTO document_repository_categories SET `category_name`=:category_name,`parent_id`=:parent_id,`comments`=:comments. Stack trace#0 /var/www/loris/php/libraries/Database.class.inc(243): Database->_realinsert('document_reposi...', Array, true)\n#1 /var/www/loris/modules/document_repository/ajax/addCategory.php(60): Database->insert('document_reposi...', Array)\n#2 /var/www/loris/htdocs/AjaxHelper.php(93): require('/var/www/loris/...')\n#3 {main}, referer: [ http://data.healthybrainnetwork.org/document_repository/?filtered=true | http://data.healthybrainnetwork.org/document_repository/?filtered=true ] [Mon Jul 03 18:06:23.563249 2017] [:error] [pid 3629] [client [ http://67.220.146.162:48512/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:48512 ] ] PHP Fatal error: Uncaught DatabaseException: Insert statement did not execute successfully: Array\n(\n [0] => HY000\n [1] => 1366\n [2] => Incorrect integer value: ' ' for column 'parent_id' at row 1\n)\n in /var/www/loris/php/libraries/Database.class.inc:314\nStack trace:\n#0 /var/www/loris/php/libraries/Database.class.inc(243): Database->_realinsert('document_reposi...', Array, true)\n#1 /var/www/loris/modules/document_repository/ajax/addCategory.php(60): Database->insert('document_reposi...', Array)\n#2 /var/www/loris/htdocs/AjaxHelper.php(93): require('/var/www/loris/...')\n#3 {main}\n thrown in /var/www/loris/php/libraries/Database.class.inc on line 314, referer: [ http://data.healthybrainnetwork.org/document_repository/?filtered=true | http://data.healthybrainnetwork.org/document_repository/?filtered=true ] I tried the second suggestion as well?the ?test? category shows up in the document repository, but when I try to add a file, it takes me to a broken link (document_repository/ajax/documentEditUpload.php), and the error log gives me the following message: [Mon Jul 03 18:17:27.494508 2017] [:error] [pid 14300] [client [ http://67.220.146.162:39842/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:39842 ] ] PHP Notice: Only variables should be passed by reference in /var/www/loris/modules/document_repository/ajax/documentEditUpload.php on line 39, referer: [ http://data.healthybrainnetwork.org/document_repository/ | http://data.healthybrainnetwork.org/document_repository/ ] [Mon Jul 03 18:17:27.494866 2017] [:error] [pid 14300] [client [ http://67.220.146.162:39842/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:39842 ] ] PHP Warning: PDOStatement::execute(): SQLSTATE[HY000]: General error: 1366 Incorrect integer value: '' for column 'For_site' at row 1 in /var/www/loris/php/libraries/Database.class.inc on line 312, referer: [ http://data.healthybrainnetwork.org/document_repository/ | http://data.healthybrainnetwork.org/document_repository/ ] [Mon Jul 03 18:17:27.494920 2017] [:error] [pid 14300] [client [ http://67.220.146.162:39842/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:39842 ] ] Could not execute INSERT INTO document_repository SET `File_category`=:File_category,`For_site`=:For_site,`comments`=:comments,`version`=:version,`File_name`=:File_name,`File_size`=:File_size,`Data_dir`=:Data_dir,`uploaded_by`=:uploaded_by,`Instrument`=:Instrument,`PSCID`=:PSCID,`visitLabel`=:visitLabel,`File_type`=:File_type. Stack trace#0 /var/www/loris/php/libraries/Database.class.inc(243): Database->_realinsert('document_reposi...', Array, true)\n#1 /var/www/loris/modules/document_repository/ajax/documentEditUpload.php(61): Database->insert('document_reposi...', Array)\n#2 /var/www/loris/htdocs/AjaxHelper.php(93): require('/var/www/loris/...')\n#3 {main}, referer: [ http://data.healthybrainnetwork.org/document_repository/ | http://data.healthybrainnetwork.org/document_repository/ ] [Mon Jul 03 18:17:27.494941 2017] [:error] [pid 14300] [client [ http://67.220.146.162:39842/ | MailScanner warning: numerical links are often malicious: 67.220.146.162:39842 ] ] PHP Fatal error: Uncaught DatabaseException: Insert statement did not execute successfully: Array\n(\n [0] => HY000\n [1] => 1366\n [2] => Incorrect integer value: '' for column 'For_site' at row 1\n)\n in /var/www/loris/php/libraries/Database.class.inc:314\nStack trace:\n#0 /var/www/loris/php/libraries/Database.class.inc(243): Database->_realinsert('document_reposi...', Array, true)\n#1 /var/www/loris/modules/document_repository/ajax/documentEditUpload.php(61): Database->insert('document_reposi...', Array)\n#2 /var/www/loris/htdocs/AjaxHelper.php(93): require('/var/www/loris/...')\n#3 {main}\n thrown in /var/www/loris/php/libraries/Database.class.inc on line 314, referer: [ http://data.healthybrainnetwork.org/document_repository/ | http://data.healthybrainnetwork.org/document_repository/ ] -- Bonhwang Koo Research Assistant, CDB Child Mind Institute [ http://childmind.org/ | childmind.org ] 445 Park Avenue (entrance on 56th Street) New York, NY 10022 E: [ mailto:Bonhwang.Koo at childmind.org | Bonhwang.Koo at childmind.org ] p: [ tel:(646)%20625-4398 | 646.625.4398 ] f: [ tel:(646)%20625-4348 | 646.625.4348 ] Facebook: [ http://facebook.com/ChildMindInstitute | facebook.com/ChildMindInstitute ] | Follow us on Twitter: [ http://twitter.com/ChildMindDotOrg | twitter.com/ChildMindDotOrg ] --- This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. From: Shen Wang < [ mailto:wangshen.mcin at gmail.com | wangshen.mcin at gmail.com ] > Date: Monday, July 3, 2017 at 2:07 PM To: Bonhwang Koo < [ mailto:Bonhwang.Koo at childmind.org | Bonhwang.Koo at childmind.org ] > Cc: "Ganesh Chauhan (CBR)" < [ mailto:ganesh.chauhan at cbr.iisc.ac.in | ganesh.chauhan at cbr.iisc.ac.in ] >, Samir Das < [ mailto:samir.das at mcgill.ca | samir.das at mcgill.ca ] >, loris-dev < [ mailto:Loris-dev at bic.mni.mcgill.ca | Loris-dev at bic.mni.mcgill.ca ] > Subject: Re: [Loris-dev] Fwd: LORIS Document Repository Hi Bonhwang, I tested Loris 17.0 on my VM, it works fine. It is difficult to debug without error log. Could you show me more error log or error message ? 1, Run "sudo tail -f /var/log/apache2/loris-error.log" when you add a category. Please show me the message. 2, Or Run "insert into document_repository_categories (id,category_name,parent_id,comments) values('777','test','0',null)" in your loris database. You should see the new test category. Then try upload a file under test category. Tell me the result. Best wishes On 3 July 2017 at 11:08, Shen Wang < [ mailto:wangshen.mcin at gmail.com | wangshen.mcin at gmail.com ] > wrote: BQ_BEGIN Hi Ganesh You can get the "Document Repository" module functional without email server. Could you show me the error log or error message when you want to add a category? Shen On 3 July 2017 at 10:14, Bonhwang Koo < [ mailto:Bonhwang.Koo at childmind.org | Bonhwang.Koo at childmind.org ] > wrote: BQ_BEGIN 17.0.3 -- Bonhwang Koo Research Assistant, CDB Child Mind Institute [ http://childmind.org/ | childmind.org ] 445 Park Avenue (entrance on 56th Street) New York, NY 10022 E: [ mailto:Bonhwang.Koo at childmind.org | Bonhwang.Koo at childmind.org ] p: [ tel:(646)%20625-4398 | 646.625.4398 ] f: [ tel:(646)%20625-4348 | 646.625.4348 ] Facebook: [ http://facebook.com/ChildMindInstitute | facebook.com/ChildMindInstitute ] | Follow us on Twitter: [ http://twitter.com/ChildMindDotOrg | twitter.com/ChildMindDotOrg ] --- This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. From: Shen Wang < [ mailto:wangshen.mcin at gmail.com | wangshen.mcin at gmail.com ] > Date: Monday, July 3, 2017 at 10:04 AM To: Bonhwang Koo < [ mailto:Bonhwang.Koo at childmind.org | Bonhwang.Koo at childmind.org ] > Cc: "Ganesh Chauhan (CBR)" < [ mailto:ganesh.chauhan at cbr.iisc.ac.in | ganesh.chauhan at cbr.iisc.ac.in ] >, Samir Das < [ mailto:samir.das at mcgill.ca | samir.das at mcgill.ca ] >, loris-dev < [ mailto:Loris-dev at bic.mni.mcgill.ca | Loris-dev at bic.mni.mcgill.ca ] > Subject: Re: [Loris-dev] Fwd: LORIS Document Repository Hi Could you tell me which version of Loris do you have? I will check it. Best wishes Shen On 29 June 2017 at 17:03, Bonhwang Koo < [ mailto:Bonhwang.Koo at childmind.org | Bonhwang.Koo at childmind.org ] > wrote: BQ_BEGIN I followed your suggestion, although I ran the command for a slightly different directory: ?sudo chmod 777 /var/www/loris/modules/document_repository/user_uploads?, and I still have the same issue. This isn?t working even though I have a mail server installed via PostFix. I took a look at the console on my browser, and this is the error I?m getting: This is the corresponding code in document_repository_helper.js:89 : $.ajax( { url: loris.BaseURL + "/document_repository/ajax/addCategory.php" , type: "POST" , data: $( "#addCategoryForm" ).serialize(), success: function () { $( "#addCategoryModal" ).modal( 'hide' ); $( "#addCategoryCategory" ).removeClass( "has-error" ); $( "#categoryAddError" ).hide(); $( '.add-success' ).show(); setTimeout( function () { $( '.add-success' ).hide(); } , 3000); setTimeout( function () { location .reload(); } , 3000); } , error: function (jqXHR, textStatus, errorThrown) { if (jqXHR. status === 400) { $( "#addCategoryCategory" ).addClass( "has-error" ); $( "#categoryAddError" ).show() } } } ); -- Bonhwang Koo Research Assistant, CDB Child Mind Institute [ http://childmind.org/ | childmind.org ] 445 Park Avenue (entrance on 56th Street) New York, NY 10022 E: [ mailto:Bonhwang.Koo at childmind.org | Bonhwang.Koo at childmind.org ] p: [ tel:(646)%20625-4398 | 646.625.4398 ] f: [ tel:(646)%20625-4348 | 646.625.4348 ] Facebook: [ http://facebook.com/ChildMindInstitute | facebook.com/ChildMindInstitute ] | Follow us on Twitter: [ http://twitter.com/ChildMindDotOrg | twitter.com/ChildMindDotOrg ] --- This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. From: "Ganesh Chauhan (CBR)" < [ mailto:ganesh.chauhan at cbr.iisc.ac.in | ganesh.chauhan at cbr.iisc.ac.in ] > Date: Thursday, June 29, 2017 at 12:21 AM To: Shen Wang < [ mailto:wangshen.mcin at gmail.com | wangshen.mcin at gmail.com ] > Cc: Samir Das < [ mailto:samir.das at mcgill.ca | samir.das at mcgill.ca ] >, loris-dev < [ mailto:Loris-dev at bic.mni.mcgill.ca | Loris-dev at bic.mni.mcgill.ca ] >, Bonhwang Koo < [ mailto:Bonhwang.Koo at childmind.org | Bonhwang.Koo at childmind.org ] > Subject: Re: [Loris-dev] Fwd: LORIS Document Repository Hi, I have had the same problem of not being able to add a category despite having file permissions. Though I still do not have the email server setup for LORIS. Hence do you think that without the email server we cannot get the "Document Repository" module functional. Thanks for your suggestion. With best regards, Ganesh From: "Shen Wang" < [ mailto:wangshen.mcin at gmail.com | wangshen.mcin at gmail.com ] > To: "Samir Das" < [ mailto:samir.das at mcgill.ca | samir.das at mcgill.ca ] > Cc: "loris-dev" < [ mailto:Loris-dev at bic.mni.mcgill.ca | Loris-dev at bic.mni.mcgill.ca ] >, "Bonhwang Koo" < [ mailto:Bonhwang.Koo at childmind.org | Bonhwang.Koo at childmind.org ] > Sent: Thursday, June 29, 2017 12:52:48 AM Subject: Re: [Loris-dev] Fwd: LORIS Document Repository Hello: Maybe you need to have file system permission to create the upload directory. I think It is not a Loris issue. As a quick fix, you can do: "sudo chmod 777 /var/www/loris/ document_repository/user_uploads". /var/www/loris/ will be replaced by your loris directory. I hope this can help you. Shen On 27 June 2017 at 16:09, Samir Das < [ mailto:samir.das at mcgill.ca | samir.das at mcgill.ca ] > wrote: BQ_BEGIN ---------- Forwarded message ---------- From: Bonhwang Koo < [ mailto:Bonhwang.Koo at childmind.org | Bonhwang.Koo at childmind.org ] > Date: Mon, Jun 26, 2017 at 8:28 AM Subject: LORIS Document Repository To: " [ mailto:loris.info at mcin.ca | loris.info at mcin.ca ] " < [ mailto:loris.info at mcin.ca | loris.info at mcin.ca ] > Hello, I am working with the Child Mind Institute?s Healthy Brain Network initiative, and we created a LORIS instance to allow users query data from our recent data release. I want to use the document repository feature, but it won?t allow me to upload a file without a category, so when I try to add a new category, nothing happens. Can you help me resolve this issue? Best, -- Bonhwang Koo Research Assistant, CDB Child Mind Institute [ http://childmind.org/ | childmind.org ] 445 Park Avenue (entrance on 56th Street) New York, NY 10022 E: [ mailto:Bonhwang.Koo at childmind.org | Bonhwang.Koo at childmind.org ] p: [ tel:(646)%20625-4398 | 646.625.4398 ] f: [ tel:(646)%20625-4348 | 646.625.4348 ] Facebook: [ http://facebook.com/ChildMindInstitute | facebook.com/ChildMindInstitute ] | Follow us on Twitter: [ http://twitter.com/ChildMindDotOrg | twitter.com/ChildMindDotOrg ] --- This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. _______________________________________________ Loris-dev mailing list [ mailto:Loris-dev at bic.mni.mcgill.ca | Loris-dev at bic.mni.mcgill.ca ] [ http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev | http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev ] _______________________________________________ Loris-dev mailing list [ mailto:Loris-dev at bic.mni.mcgill.ca | Loris-dev at bic.mni.mcgill.ca ] [ http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev | http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev ] -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA [ tel:+91%2080%202293%203009 | +91 80 2293 3009 ] [ https://www.cbr.iisc.ac.in/ | https://www.cbr.iisc.ac.in ] BQ_END BQ_END BQ_END -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA [ tel:+91%2080%202293%203009 | +91 80 2293 3009 ] [ https://www.cbr.iisc.ac.in/ | https://www.cbr.iisc.ac.in ] BQ_END -- Ganesh Chauhan (PhD) Scientist Centre for Brain Research (CBR) Indian Institute of Science (IISc) Bengaluru, INDIA +91 80 2293 3009 https://www.cbr.iisc.ac.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From istvan.morocz at mcgill.ca Wed Jul 12 13:16:37 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Wed, 12 Jul 2017 13:16:37 -0400 (EDT) Subject: [Loris-dev] adding a new project to LORIS ? Message-ID: dear LORIS folks, how do i add new PROJECTS to a brandnew LORIS db ? the LORIS GUI seems to hold onto 'New Project' so that i can't specificy any new project names : "failed to save, same name already exists!" pushing the 'NewProjectID' button does not help either. 'Use projects' is enabled on the Study configuration page. i also 'refreshed' that page, as per instructions. any help ? bye, pisti specs : mini-Ubuntu 16.04 VM on VirtualBox, Loris 17.0.5 ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : http://noisis.com ` istvan.morocz at noisis.com : +1-514-927-1169 : istvan.morocz at mcgill.ca : http://cafe.spl.harvard.edu , http://www.pistikem.org : pistikem at gmail.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" From istvan.morocz at mcgill.ca Wed Jul 12 13:24:17 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Wed, 12 Jul 2017 13:24:17 -0400 (EDT) Subject: [Loris-dev] adding a new project to LORIS ? In-Reply-To: References: Message-ID: could this explain my probelm ? root ownership ? drwxrwx--- 8 root www-data 4096 Jul 11 20:02 project On Wed, 12 Jul 2017, Istv?n ?kos M?rocz wrote: > dear LORIS folks, > > how do i add new PROJECTS to a brandnew LORIS db ? the LORIS GUI > seems to hold onto 'New Project' so that i can't specificy any new > project names : > > "failed to save, same name already exists!" > > pushing the 'NewProjectID' button does not help either. > > 'Use projects' is enabled on the Study configuration page. i also > 'refreshed' that page, as per instructions. > > any help ? bye, pisti > > > > specs : mini-Ubuntu 16.04 VM on VirtualBox, Loris 17.0.5 > > > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ > ' > : http://noisis.com > ` istvan.morocz at noisis.com > : +1-514-927-1169 > : istvan.morocz at mcgill.ca > : http://cafe.spl.harvard.edu > , http://www.pistikem.org > : pistikem at gmail.com > . > `~*-,._.,-*~'`^`'~*-,._.,-*~'`" > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : http://noisis.com ` istvan.morocz at noisis.com : +1-514-927-1169 : istvan.morocz at mcgill.ca : http://cafe.spl.harvard.edu , http://www.pistikem.org : pistikem at gmail.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" From istvan.morocz at mcgill.ca Wed Jul 12 21:30:05 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Wed, 12 Jul 2017 21:30:05 -0400 (EDT) Subject: [Loris-dev] LORIS Jason API for Candidate & Visit creation Message-ID: dear LORIS developers, here a kind of a d?j? vue problem : it's the issue of using LORIS' Jason API for Candiate and Visits creation. we installed the new 17.0.5 LORIS version on an mini-Ubuntu v16.04 VM on VirtualBox. things went fine till we tried to make use of this API - but, again the same problem as a month ago with v17.0.1 : error 400 after the command : curl -i -H "Authorization: Bearer xyzXYZ" -H "Content-type:application/json" -X POST -d @newCand.json http://192.168.49.10/api/v0.0.2/candidates/ Warning: Couldn't read data from file "newCand.json", this makes an empty Warning: POST. HTTP/1.1 400 Bad Request Date: Thu, 13 Jul 2017 01:04:57 GMT Server: Apache/2.4.18 (Ubuntu) Access-Control-Allow-Origin: * Access-Control-Allow-Headers: * Content-Security-Policy: default-src 'self' 'unsafe-inline'; script-src 'self' 'unsafe-inline' 'unsafe-eval'; font-src 'self' data:; img-src 'self' data:; Set-Cookie: PHPSESSID=f0o3kdoevt1g9hhtjlh0ns8b07; path=/ Expires: Thu, 19 Nov 1981 08:52:00 GMT Cache-Control: no-store, no-cache, must-revalidate Pragma: no-cache Content-Length: 0 Connection: close Content-Type: text/html; charset=UTF-8 cat newCand.json { "Candidate" : { "Project" : "BRAVO", "PSCID" : "ABC123", "DoB" : "1980-01-01", "Gender" : "Male" } } grep Version /var/www/IPMSA/Loris/htdocs/api/v0.0.2/candidates/Candidate.php * PHP Version 5 ...while the Candidate.php script in LORIS v17.0.3 (a developer version to our understanding) makes use of PHP Version 5.5 - and the file itself is obviously completely different too. last time Jordan was very helpful in pointing this out to us ! QUESTIONS : 1) what do you suggest ? retro-up-grading v17.0.5 --> 17.0.3 ? 2) how will LORIS-MRI work after such a version change which we still need to install and configure ? thanks for helping ! bye, pisti ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : http://noisis.com ` istvan.morocz at noisis.com : +1-514-927-1169 : istvan.morocz at mcgill.ca : http://cafe.spl.harvard.edu , http://www.pistikem.org : pistikem at gmail.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" From michael.joseph at sickkids.ca Fri Jul 14 13:01:47 2017 From: michael.joseph at sickkids.ca (Michael Joseph) Date: Fri, 14 Jul 2017 17:01:47 +0000 Subject: [Loris-dev] Adding candidates involved in multiple projects Message-ID: Hi Loris dev team, We have some candidates who are involved in multiple projects on LORIS. I was wondering how to go about inserting them into the 'candidate' table. I originally thought I could give the candidates the same CandID but change the PSCID. However, the CandID is the primary key and must be unique. Could I create a composite key with both CandID and PSCID or would that break something else? Thanks, Michael ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Fri Jul 14 14:05:24 2017 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Fri, 14 Jul 2017 14:05:24 -0400 Subject: [Loris-dev] Adding candidates involved in multiple projects In-Reply-To: References: Message-ID: Hi Michael, Enabling candidates to be recruited into multiple projects is on our 2017 roadmap - we're quite far along with developing the multi-project candidate model for specific initiatives, but have not integrated this into a release version yet. For the moment the best solution could be to create separate candidate records, perhaps with similar PSCIDs e.g. MTL0001a, MTL0001b. Another alternative is if your studies are related under one initiative, you could use the subproject/cohort level to associate the candidate to different project cohorts at the visit level (session level), but this may not be ideal in the long term. Best, Christine On Fri, Jul 14, 2017 at 1:01 PM, Michael Joseph wrote: > Hi Loris dev team, > > > We have some candidates who are involved in multiple projects on LORIS. I > was wondering how to go about inserting them into the 'candidate' table. I > originally thought I could give the candidates the same CandID but change > the PSCID. However, the CandID is the primary key and must be unique. Could > I create a composite key with both CandID and PSCID or would that break > something else? > > > Thanks, > > Michael > > ------------------------------ > > This e-mail may contain confidential, personal and/or health > information(information which may be subject to legal restrictions on use, > retention and/or disclosure) for the sole use of the intended recipient. > Any review or distribution by anyone other than the person for whom it was > originally intended is strictly prohibited. If you have received this > e-mail in error, please contact the sender and delete all copies. > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.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 michael.joseph at sickkids.ca Fri Jul 14 14:42:22 2017 From: michael.joseph at sickkids.ca (Michael Joseph) Date: Fri, 14 Jul 2017 18:42:22 +0000 Subject: [Loris-dev] Adding candidates involved in multiple projects In-Reply-To: References: , Message-ID: Thanks Christine, Maybe I'll try similar PSCID's so they can at least be easily searchable. That's great to hear that multi-project candidate support will be coming soon. For our instance, the raw images for the candidates will be the same. However, the processed data (eg. scan to study registration) would be different for each project the candidate is a part of. Is this something that could be accounted for? Michael ________________________________ From: Christine Rogers Sent: July 14, 2017 2:05:24 PM To: Michael Joseph Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] Adding candidates involved in multiple projects Hi Michael, Enabling candidates to be recruited into multiple projects is on our 2017 roadmap - we're quite far along with developing the multi-project candidate model for specific initiatives, but have not integrated this into a release version yet. For the moment the best solution could be to create separate candidate records, perhaps with similar PSCIDs e.g. MTL0001a, MTL0001b. Another alternative is if your studies are related under one initiative, you could use the subproject/cohort level to associate the candidate to different project cohorts at the visit level (session level), but this may not be ideal in the long term. Best, Christine On Fri, Jul 14, 2017 at 1:01 PM, Michael Joseph > wrote: Hi Loris dev team, We have some candidates who are involved in multiple projects on LORIS. I was wondering how to go about inserting them into the 'candidate' table. I originally thought I could give the candidates the same CandID but change the PSCID. However, the CandID is the primary key and must be unique. Could I create a composite key with both CandID and PSCID or would that break something else? Thanks, Michael ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca http://www.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 ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. -------------- next part -------------- An HTML attachment was scrubbed... URL: From istvan.morocz at mcgill.ca Fri Jul 14 15:42:45 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Fri, 14 Jul 2017 15:42:45 -0400 (EDT) Subject: [Loris-dev] LORIS jason API for CANDIDATE creation - leading to incorrect PROJECT entry Message-ID: dear LORIS developers, we try to insert new CANDIDATES into LORIS via its API, either with jason scripts or jason strings included in the curl call. example: cat /var/www/IPMSA/Loris/newCand.json { "Candidate" : { "Project" : "BRAVO", "PSCID" : "xSVwx1At", "EDC" : "1971-01-01", "DoB" : "1981-01-01", "Gender" : "Female" } } the problem is that nor in the LORIS GUI nor in the mySQL database is our Project entry 'BRAVO' found. it simply defaults to ProjectID 1. is there a way to adjust this PROJECT at a later stage via the LORIS API and jason PUT calls ? we also intend to adjust the same way many other fields such as SUBPROJECT (or COHORT) and more. specs : LORIS 17.0.5 on mini-Ubuntu/Xenial 16.04 VM and VirtualBox thanks for looking into this, bye, pisti ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : http://noisis.com ` istvan.morocz at noisis.com : +1-514-927-1169 : istvan.morocz at mcgill.ca : http://cafe.spl.harvard.edu , http://www.pistikem.org : pistikem at gmail.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" From istvan.morocz at mcgill.ca Mon Jul 17 11:35:30 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Mon, 17 Jul 2017 11:35:30 -0400 (EDT) Subject: [Loris-dev] MINC toolkit version 64bit ubuntu 16.04 ? Message-ID: bonjour Vladimir, i am again playing - as usual - with LORIS installations and configurations. i am installing the LORIS-MRI suite but have some trouble to locate the MINC toolkit file needed for my distro as per LORIS instructions : http://bic-mni.github.io/ where i am referred to : http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.15-20170529-Ubuntu_15.04-x86_64.deb ==> file not found on this server... ? where should i go from here ? can you help ? thanks much, bye, pisti ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : http://noisis.com ` istvan.morocz at noisis.com : +1-514-927-1169 : istvan.morocz at mcgill.ca : http://cafe.spl.harvard.edu , http://www.pistikem.org : pistikem at gmail.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" From xavier.lecoursboucher at mcgill.ca Mon Jul 17 11:59:32 2017 From: xavier.lecoursboucher at mcgill.ca (Xavier Lecours Boucher, Mr) Date: Mon, 17 Jul 2017 15:59:32 +0000 Subject: [Loris-dev] LORIS jason API for CANDIDATE creation - leading to incorrect PROJECT entry In-Reply-To: References: Message-ID: Hi, The API version in 17.0.5 does not implement PUT nor PATCH request at the candidate level. The good thing about that is that you are free to implement it the way you want. Here is an basic example : https://github.com/aces/Loris/compare/17.1-dev...xlecours:candidate_patch?expand=1 that allow to update any field of the candidate table provided in a object of the form {Candidate: { field1: value1, field2...}} `curl -H "Authorization: Bearer $token" http://localhost/api/v0.0.2/candidates/273164 -X PATCH -d '{"Candidate": {"DoB": "1992-07-02", "EDC": "1992-07-01"}}'` ** Please not that this is not really secure since it allow to replace ANY fields in the candidate table. On a side note, in 17.1 the project name will be attach right after the candidate creation; see https://github.com/aces/Loris/pull/2863/files#diff-27f79abaa4a78d1688dcfce2eca6eadaR161 I am hopping this helps. Thank you for your interest in LORIS. Feel free to ask any other question. Regards, - Xavier L. ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Istv?n ?kos M?rocz Sent: July 14, 2017 2:42 PM To: loris-dev Cc: Jordan Stirling; Haz-Edine Assemlal Subject: [Loris-dev] LORIS jason API for CANDIDATE creation - leading to incorrect PROJECT entry dear LORIS developers, we try to insert new CANDIDATES into LORIS via its API, either with jason scripts or jason strings included in the curl call. example: cat /var/www/IPMSA/Loris/newCand.json { "Candidate" : { "Project" : "BRAVO", "PSCID" : "xSVwx1At", "EDC" : "1971-01-01", "DoB" : "1981-01-01", "Gender" : "Female" } } the problem is that nor in the LORIS GUI nor in the mySQL database is our Project entry 'BRAVO' found. it simply defaults to ProjectID 1. is there a way to adjust this PROJECT at a later stage via the LORIS API and jason PUT calls ? we also intend to adjust the same way many other fields such as SUBPROJECT (or COHORT) and more. specs : LORIS 17.0.5 on mini-Ubuntu/Xenial 16.04 VM and VirtualBox thanks for looking into this, bye, pisti ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : http://noisis.com ` istvan.morocz at noisis.com : +1-514-927-1169 : istvan.morocz at mcgill.ca : http://cafe.spl.harvard.edu [http://cafe.spl.harvard.edu/img/fig.dyscalculia_paper_040913.model3D_animated.gif] Laboratory for Cognition And Functional Evidence cafe.spl.harvard.edu Laboratory for Cognition And Functional Evidence Home | Contact Us | Credits. About CAFE Mission; Projects; Collaborations; fMRI Facilities , http://www.pistikem.org pistik?m.org pistikem.org www.pistikem.org photography photographie fenykep f?nyk?p fotografie fotografia pisti pistikem pistik?m istvan akos morocz Istv?n ?kos M?rocz boston harvard montreal montr?al : pistikem at gmail.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From mouna.safi-harb at mail.mcgill.ca Mon Jul 17 12:14:10 2017 From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab) Date: Mon, 17 Jul 2017 16:14:10 +0000 Subject: [Loris-dev] MINC toolkit version 64bit ubuntu 16.04 ? In-Reply-To: References: Message-ID: Hi, It looks like the link has a typo in it whereby it refers you to Ubuntu 15.04 whereas the partial path (http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/) seems to expect either 14.04 or 16.04. You can probably go the partial link above, and select the proper version yourself which would then trigger the download. But yes, the link needs to be corrected (which I assume Vlad will do?). - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Istv?n ?kos M?rocz Sent: Monday, July 17, 2017 11:35:30 AM To: Vladimir Fonov; loris-dev Cc: Haz-Edine Assemlal Subject: [Loris-dev] MINC toolkit version 64bit ubuntu 16.04 ? bonjour Vladimir, i am again playing - as usual - with LORIS installations and configurations. i am installing the LORIS-MRI suite but have some trouble to locate the MINC toolkit file needed for my distro as per LORIS instructions : http://bic-mni.github.io/ where i am referred to : http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.15-20170529-Ubuntu_15.04-x86_64.deb ==> file not found on this server... ? where should i go from here ? can you help ? thanks much, bye, pisti ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : http://noisis.com ` istvan.morocz at noisis.com : +1-514-927-1169 : istvan.morocz at mcgill.ca : http://cafe.spl.harvard.edu , http://www.pistikem.org : pistikem at gmail.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev -------------- next part -------------- An HTML attachment was scrubbed... URL: From istvan.morocz at mcgill.ca Mon Jul 17 12:24:05 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Mon, 17 Jul 2017 12:24:05 -0400 (EDT) Subject: [Loris-dev] MINC toolkit version 64bit ubuntu 16.04 ? In-Reply-To: References: Message-ID: thanks, Mouna - Alfredo in fact knew already about this typo and sent me few minutes ago 'his' correct link : http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.15-20170529-Ubuntu_16.04-x86_64.deb bye, pisti On Mon, 17 Jul 2017, Mouna Safi-Harab wrote: > > Hi, > > > It looks like the link has a typo in it whereby it refers you to Ubuntu 15.04 whereas the partial path > (http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/)?seems to expect either 14.04 or 16.04. > > You can probably go the partial link above, and select the proper version yourself which would then trigger the > download. > > > But yes, the link needs to be corrected (which I assume Vlad will do?). > > > - Mouna > > ______________________________________________________________________________________________________________________ > From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Istv?n ?kos M?rocz > > Sent: Monday, July 17, 2017 11:35:30 AM > To: Vladimir Fonov; loris-dev > Cc: Haz-Edine Assemlal > Subject: [Loris-dev] MINC toolkit version 64bit ubuntu 16.04 ? ? > bonjour Vladimir, > > i am again playing - as usual - with LORIS installations and > configurations.? i am installing the LORIS-MRI suite but have some > trouble to locate the MINC toolkit file needed for my distro as per > LORIS instructions : > > ???? http://bic-mni.github.io/ > > where i am referred to : > > ???? http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.15-20170529-Ubuntu_15.04-x86_64.deb > > ==> file not found on this server... ? > > > where should i go from here ?? can you help ? > > thanks much, bye, pisti > > > ?? ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ > ? ' > :??????? http://noisis.com > ? `??? istvan.morocz at noisis.com > ? :??????? +1-514-927-1169 > ? :??? istvan.morocz at mcgill.ca > ? :? http://cafe.spl.harvard.edu > ? ,??? http://www.pistikem.org > :?????? pistikem at gmail.com > ? . > ?? `~*-,._.,-*~'`^`'~*-,._.,-*~'`" > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : http://noisis.com ` istvan.morocz at noisis.com : +1-514-927-1169 : istvan.morocz at mcgill.ca : http://cafe.spl.harvard.edu , http://www.pistikem.org : pistikem at gmail.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" From istvan.morocz at mcgill.ca Mon Jul 17 12:48:43 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Mon, 17 Jul 2017 12:48:43 -0400 (EDT) Subject: [Loris-dev] LORIS jason API for CANDIDATE creation - leading to incorrect PROJECT entry In-Reply-To: References: Message-ID: thanks for your note, Xavier - we will have a look at your links ! on the other hand i should have said PUSH (and not PUT) as this is the command included - like here in our example curl call : curl -i -H "Authorization: Bearer ABCDEFGHUJKLMNOP" -H "Content-type:application/json" -X POST -d @newCand.json http://192.168.49.10/api/v0.0.2/candidates/ so, with PUSH it seems to work partially but as said below it's the PROJECT field that doesn't get updated as expected. thanks much, bye, pisti On Mon, 17 Jul 2017, Xavier Lecours Boucher, Mr wrote: > > Hi, > > > The API version in 17.0.5 does not implement PUT nor PATCH request at the candidate level. The good thing about that > is that you are free to implement it the way you want. > > Here is an basic example : https://github.com/aces/Loris/compare/17.1-dev...xlecours:candidate_patch?expand=1 > > that allow to update any field of the candidate table provided in a object of the form {Candidate: { field1: value1, > field2...}} > > > `curl -H "Authorization: Bearer $token" http://localhost/api/v0.0.2/candidates/273164 -X PATCH -d '{"Candidate": > {"DoB": "1992-07-02", "EDC": "1992-07-01"}}'` > > > ** Please not that this is not really secure since it allow to replace ANY fields in the candidate table. > > > On a side note, in 17.1 the project name will be attach right after the candidate creation; > see?https://github.com/aces/Loris/pull/2863/files#diff-27f79abaa4a78d1688dcfce2eca6eadaR161 > > > I am hopping this helps. > > > Thank you for your interest in LORIS. Feel free to ask any other question. > > > Regards, > > - Xavier L. > > > ______________________________________________________________________________________________________________________ > From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Istv?n ?kos M?rocz > > Sent: July 14, 2017 2:42 PM > To: loris-dev > Cc: Jordan Stirling; Haz-Edine Assemlal > Subject: [Loris-dev] LORIS jason API for CANDIDATE creation - leading to incorrect PROJECT entry ? > dear LORIS developers, > > we try to insert new CANDIDATES into LORIS via its API, either with > jason scripts or jason strings included in the curl call.? example: > > cat /var/www/IPMSA/Loris/newCand.json > > { > ???? "Candidate" : { > ???????? "Project" : "BRAVO", > ???????? "PSCID"?? : "xSVwx1At", > ???????? "EDC"???? : "1971-01-01", > ???????? "DoB"???? : "1981-01-01", > ???????? "Gender"? : "Female" > ???? } > } > > the problem is that nor in the LORIS GUI nor in the mySQL database is > our Project entry 'BRAVO' found.? it simply defaults to ProjectID 1. > > is there a way to adjust this PROJECT at a later stage via the LORIS > API and jason PUT calls ?? we also intend to adjust the same way many > other fields such as SUBPROJECT (or COHORT) and more. > > specs : LORIS 17.0.5 on mini-Ubuntu/Xenial 16.04 VM and VirtualBox > > thanks for looking into this, bye, pisti > > > ?? ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ > ? ' > :??????? http://noisis.com > ? `??? istvan.morocz at noisis.com > ? :??????? +1-514-927-1169 > ? :??? istvan.morocz at mcgill.ca > ? :? http://cafe.spl.harvard.edu > [fig.dyscalculia_paper_040913.model3D_animated.gif] > Laboratory for Cognition And Functional Evidence > cafe.spl.harvard.edu > Laboratory for Cognition And Functional Evidence Home | Contact Us | Credits. About CAFE Mission; Projects; > Collaborations; fMRI Facilities > > ? ,??? http://www.pistikem.org > pistik?m.org pistikem.org > www.pistikem.org > photography photographie fenykep f?nyk?p fotografie fotografia pisti pistikem pistik?m istvan akos morocz Istv?n ?kos > M?rocz boston harvard montreal montr?al > > :?????? pistikem at gmail.com > ? . > ?? `~*-,._.,-*~'`^`'~*-,._.,-*~'`" > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : http://noisis.com ` istvan.morocz at noisis.com : +1-514-927-1169 : istvan.morocz at mcgill.ca : http://cafe.spl.harvard.edu , http://www.pistikem.org : pistikem at gmail.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" From sylvain at bic.mni.mcgill.ca Mon Jul 17 12:06:35 2017 From: sylvain at bic.mni.mcgill.ca (Sylvain MILOT) Date: Mon, 17 Jul 2017 12:06:35 -0400 (EDT) Subject: [Loris-dev] MINC toolkit version 64bit ubuntu 16.04 ? In-Reply-To: References: Message-ID: Salut pisti, there are packages there for Ubuntu trusty (14.04) and xenial (16.04) - I suggest you change/upgrade your distro to trusty as last I checked loris required trusty but if they changed/upgraded to 15.04, then I'm somewhat baffled as to why and why they wouldn't choose xenial instead. Anyway, you can always compile from source - use the tar file in http://packages.bic.mni.mcgill.ca/minc-toolkit/minc-toolkit-v2-1.9.15.tar.bz2 Sylvain On Mon, 17 Jul 2017, Istv?n ?kos M?rocz wrote: > bonjour Vladimir, > > i am again playing - as usual - with LORIS installations and > configurations. i am installing the LORIS-MRI suite but have some > trouble to locate the MINC toolkit file needed for my distro as per > LORIS instructions : > > http://bic-mni.github.io/ > > where i am referred to : > > http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.15-20170529-Ubuntu_15.04-x86_64.deb > > ==> file not found on this server... ? > > > where should i go from here ? can you help ? > > thanks much, bye, pisti > > > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ > ' > : http://noisis.com > ` istvan.morocz at noisis.com > : +1-514-927-1169 > : istvan.morocz at mcgill.ca > : http://cafe.spl.harvard.edu > , http://www.pistikem.org > : pistikem at gmail.com > . > `~*-,._.,-*~'`^`'~*-,._.,-*~'`" > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > --- If you need services: workstation maintenance or a storage lease, please fill out https://www.mcgill.ca/bic/core-facilities/access/bic-neuroinformatics-application-form If you have other questions or requests, please contact You may also find some useful online documention here: http://wiki.bic.mni.mcgill.ca Our ssh login server is login.bic.mni.mcgill.ca ssh RSA key fingerprint is 3a:e3:32:f3:2e:7f:cf:94:1c:47:50:4f:c2:b5:93:9b ssh DSA key fingerprint is 44:8b:92:b8:ef:cb:88:76:96:11:aa:1c:d1:a2:1f:9a ssh ECDSA key fingerprint is 9c:84:34:1f:1a:84:bb:f7:45:a2:df:88:3e:49:c4:3e --- Sylvain Milot (sylvain at bic.mni.mcgill.ca) (sylvain.milot at mcgill.ca) Brain Imaging Centre Montreal Neurological Institute 3801 University Street Webster 2B, Room 206 Montreal, Qc., Canada, H3A 2B4 Phone : (514) 398-4965, Fax: 398-8948 Mobile : (514) 712-1768 Office : 527 Av Des Pins O., Room 104 Montreal, Qc., H2W 1S4 From vladimir.fonov at mcgill.ca Mon Jul 17 16:10:54 2017 From: vladimir.fonov at mcgill.ca (Vladimir Fonov, Dr) Date: Mon, 17 Jul 2017 20:10:54 +0000 Subject: [Loris-dev] MINC toolkit version 64bit ubuntu 16.04 ? Message-ID: minc-toolkit-1.9.15-20170529-Ubuntu_16.04-x86_64.deb best regards, Vladimir S. Fonov ~ Vladimir.fonov (at) McGill.ca On Jul 17, 2017 11:36 AM, Istv?n ?kos M?rocz wrote: bonjour Vladimir, i am again playing - as usual - with LORIS installations and configurations. i am installing the LORIS-MRI suite but have some trouble to locate the MINC toolkit file needed for my distro as per LORIS instructions : http://bic-mni.github.io/ where i am referred to : http://packages.bic.mni.mcgill.ca/minc-toolkit/Debian/minc-toolkit-1.9.15-20170529-Ubuntu_15.04-x86_64.deb ==> file not found on this server... ? where should i go from here ? can you help ? thanks much, bye, pisti ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : http://noisis.com ` istvan.morocz at noisis.com : +1-514-927-1169 : istvan.morocz at mcgill.ca : http://cafe.spl.harvard.edu , http://www.pistikem.org : pistikem at gmail.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Mon Jul 17 16:46:23 2017 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Mon, 17 Jul 2017 16:46:23 -0400 Subject: [Loris-dev] Adding candidates involved in multiple projects In-Reply-To: References: Message-ID: Hi Michael, Thanks for your followup comments. We definitely appreciate that when subjects participate in multiple projects, ideally the raw anatomicals and some basic data fields would be stored/shared in a "baseline" timepoint or dataset accessible to different projects. There are many questions about how this model would appropriately apply controls for consent and data dissemination, so we are developing the architectural plans over the next few major releases, piloted on a few key projects. For the short term we could recommend duplication of imaging data for different PSCID/Projects. Alternatively, subproject/cohort (as mentioned before) can be used at the visit level to define datasets generated by different protocols/analyses run on the same subjects. Best, Christine On Fri, Jul 14, 2017 at 2:42 PM, Michael Joseph wrote: > Thanks Christine, > > > Maybe I'll try similar PSCID's so they can at least be easily searchable. > That's great to hear that multi-project candidate support will be coming > soon. For our instance, the raw images for the candidates will be the same. > However, the processed data (eg. scan to study registration) would be > different for each project the candidate is a part of. Is this something > that could be accounted for? > > > Michael > ------------------------------ > *From:* Christine Rogers > *Sent:* July 14, 2017 2:05:24 PM > *To:* Michael Joseph > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] Adding candidates involved in multiple projects > > Hi Michael, > Enabling candidates to be recruited into multiple projects is on our 2017 > roadmap - we're quite far along with developing the multi-project candidate > model for specific initiatives, but have not integrated this into a release > version yet. > For the moment the best solution could be to create separate candidate > records, perhaps with similar PSCIDs e.g. MTL0001a, MTL0001b. Another > alternative is if your studies are related under one initiative, you could > use the subproject/cohort level to associate the candidate to different > project cohorts at the visit level (session level), but this may not be > ideal in the long term. > Best, > Christine > > On Fri, Jul 14, 2017 at 1:01 PM, Michael Joseph < > michael.joseph at sickkids.ca> wrote: > >> Hi Loris dev team, >> >> >> We have some candidates who are involved in multiple projects on LORIS. I >> was wondering how to go about inserting them into the 'candidate' table. I >> originally thought I could give the candidates the same CandID but change >> the PSCID. However, the CandID is the primary key and must be unique. Could >> I create a composite key with both CandID and PSCID or would that break >> something else? >> >> >> Thanks, >> >> Michael >> >> ------------------------------ >> >> This e-mail may contain confidential, personal and/or health >> information(information which may be subject to legal restrictions on use, >> retention and/or disclosure) for the sole use of the intended recipient. >> Any review or distribution by anyone other than the person for whom it was >> originally intended is strictly prohibited. If you have received this >> e-mail in error, please contact the sender and delete all copies. >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> http://www.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 > > ------------------------------ > > This e-mail may contain confidential, personal and/or health > information(information which may be subject to legal restrictions on use, > retention and/or disclosure) for the sole use of the intended recipient. > Any review or distribution by anyone other than the person for whom it was > originally intended is strictly prohibited. If you have received this > e-mail in error, please contact the sender and delete all copies. > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.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 istvan.morocz at mcgill.ca Tue Jul 18 10:23:29 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Tue, 18 Jul 2017 10:23:29 -0400 (EDT) Subject: [Loris-dev] LORIS jason API for CANDIDATE creation - leading to incorrect PROJECT entry In-Reply-To: References: Message-ID: i meant of course 'POST' - and not 'PUSH', sorry about that... here again our example : curl -i -H "Authorization: Bearer ABCDEFGHUJKLMNOP" -H "Content-type:application/json" -X POST -d @newCand.json http://192.168.49.10/api/v0.0.2/candidates/ - or did you want to say that in LORIS 16.0.5 all three POST/PUSH/PUT jason curl API requests will not work ? bye, pisti On Mon, 17 Jul 2017, Istv?n ?kos M?rocz wrote: > thanks for your note, Xavier - we > will have a look at your links ! > > on the other hand i should have said > PUSH (and not PUT) as this is the > command included - like here in our > example curl call : > > curl -i -H "Authorization: Bearer ABCDEFGHUJKLMNOP" -H > "Content-type:application/json" -X POST -d @newCand.json > http://192.168.49.10/api/v0.0.2/candidates/ > > so, with PUSH it seems to work > partially but as said below it's the > PROJECT field that doesn't get > updated as expected. > > thanks much, bye, pisti > > > On Mon, 17 Jul 2017, Xavier Lecours Boucher, Mr wrote: > >> >> Hi, >> >> >> The API version in 17.0.5 does not implement PUT nor PATCH request at the >> candidate level. The good thing about that >> is that you are free to implement it the way you want. >> >> Here is an basic example : >> https://github.com/aces/Loris/compare/17.1-dev...xlecours:candidate_patch?expand=1 >> >> that allow to update any field of the candidate table provided in a object >> of the form {Candidate: { field1: value1, >> field2...}} >> >> >> `curl -H "Authorization: Bearer $token" >> http://localhost/api/v0.0.2/candidates/273164 -X PATCH -d '{"Candidate": >> {"DoB": "1992-07-02", "EDC": "1992-07-01"}}'` >> >> >> ** Please not that this is not really secure since it allow to replace ANY >> fields in the candidate table. >> >> >> On a side note, in 17.1 the project name will be attach right after the >> candidate creation; >> see?https://github.com/aces/Loris/pull/2863/files#diff-27f79abaa4a78d1688dcfce2eca6eadaR161 >> >> >> I am hopping this helps. >> >> >> Thank you for your interest in LORIS. Feel free to ask any other question. >> >> >> Regards, >> >> - Xavier L. >> >> >> ______________________________________________________________________________________________________________________ >> From: loris-dev-bounces at bic.mni.mcgill.ca >> on behalf of Istv?n ?kos M?rocz >> >> Sent: July 14, 2017 2:42 PM >> To: loris-dev >> Cc: Jordan Stirling; Haz-Edine Assemlal >> Subject: [Loris-dev] LORIS jason API for CANDIDATE creation - leading to >> incorrect PROJECT entry ? >> dear LORIS developers, >> >> we try to insert new CANDIDATES into LORIS via its API, either with >> jason scripts or jason strings included in the curl call.? example: >> >> cat /var/www/IPMSA/Loris/newCand.json >> >> { >> ???? "Candidate" : { >> ???????? "Project" : "BRAVO", >> ???????? "PSCID"?? : "xSVwx1At", >> ???????? "EDC"???? : "1971-01-01", >> ???????? "DoB"???? : "1981-01-01", >> ???????? "Gender"? : "Female" >> ???? } >> } >> >> the problem is that nor in the LORIS GUI nor in the mySQL database is >> our Project entry 'BRAVO' found.? it simply defaults to ProjectID 1. >> >> is there a way to adjust this PROJECT at a later stage via the LORIS >> API and jason PUT calls ?? we also intend to adjust the same way many >> other fields such as SUBPROJECT (or COHORT) and more. >> >> specs : LORIS 17.0.5 on mini-Ubuntu/Xenial 16.04 VM and VirtualBox >> >> thanks for looking into this, bye, pisti >> >> >> ?? ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ >> ? ' >> :??????? http://noisis.com >> ? `??? istvan.morocz at noisis.com >> ? :??????? +1-514-927-1169 >> ? :??? istvan.morocz at mcgill.ca >> ? :? http://cafe.spl.harvard.edu >> [fig.dyscalculia_paper_040913.model3D_animated.gif] >> Laboratory for Cognition And Functional Evidence >> cafe.spl.harvard.edu >> Laboratory for Cognition And Functional Evidence Home | Contact Us | >> Credits. About CAFE Mission; Projects; >> Collaborations; fMRI Facilities >> >> ? ,??? http://www.pistikem.org >> pistik?m.org pistikem.org >> www.pistikem.org >> photography photographie fenykep f?nyk?p fotografie fotografia pisti >> pistikem pistik?m istvan akos morocz Istv?n ?kos >> M?rocz boston harvard montreal montr?al >> >> :?????? pistikem at gmail.com >> ? . >> ?? `~*-,._.,-*~'`^`'~*-,._.,-*~'`" >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> >> > > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ > ' > : http://noisis.com > ` istvan.morocz at noisis.com > : +1-514-927-1169 > : istvan.morocz at mcgill.ca > : http://cafe.spl.harvard.edu > , http://www.pistikem.org > : pistikem at gmail.com > . > `~*-,._.,-*~'`^`'~*-,._.,-*~'`" ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : http://noisis.com ` istvan.morocz at noisis.com : +1-514-927-1169 : istvan.morocz at mcgill.ca : http://cafe.spl.harvard.edu , http://www.pistikem.org : pistikem at gmail.com . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" From gluneau.mcin at gmail.com Tue Jul 18 10:29:39 2017 From: gluneau.mcin at gmail.com (Gregory Luneau) Date: Tue, 18 Jul 2017 10:29:39 -0400 Subject: [Loris-dev] adding a new project to LORIS ? In-Reply-To: References: Message-ID: Hello Pisti, the project directory should be owned by the same user that you used to run the install. Did you create a lorisadmin user? If so, you can run this command to fix the ownership: sudo chown lorisadmin.lorisadmin /var/www/loris/project As for the previous question, It does look like you were able to create a project. Then you tried to create a new project with the same name, and loris is preventing you from doing that. You may just need to reload the page and look for the new project name on the left, above the "New ProjectID" link. I would suggest you look at what was created in your mysql database: select * from Project You can modify what you find there as well. Good day, Greg On Wed, Jul 12, 2017 at 1:24 PM, Istv?n ?kos M?rocz wrote: > could this explain my probelm ? root ownership ? > > drwxrwx--- 8 root www-data 4096 Jul 11 20:02 project > > > > > On Wed, 12 Jul 2017, Istv?n ?kos M?rocz wrote: > > dear LORIS folks, >> >> how do i add new PROJECTS to a brandnew LORIS db ? the LORIS GUI >> seems to hold onto 'New Project' so that i can't specificy any new >> project names : >> >> "failed to save, same name already exists!" >> >> pushing the 'NewProjectID' button does not help either. >> >> 'Use projects' is enabled on the Study configuration page. i also >> 'refreshed' that page, as per instructions. >> >> any help ? bye, pisti >> >> >> >> specs : mini-Ubuntu 16.04 VM on VirtualBox, Loris 17.0.5 >> >> >> ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ >> ' >> : http://noisis.com >> ` istvan.morocz at noisis.com >> : +1-514-927-1169 >> : istvan.morocz at mcgill.ca >> : http://cafe.spl.harvard.edu >> , http://www.pistikem.org >> : pistikem at gmail.com >> . >> `~*-,._.,-*~'`^`'~*-,._.,-*~'`" >> >> > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ > ' > : http://noisis.com > ` istvan.morocz at noisis.com > : +1-514-927-1169 > : istvan.morocz at mcgill.ca > : http://cafe.spl.harvard.edu > , http://www.pistikem.org > : pistikem at gmail.com > . > `~*-,._.,-*~'`^`'~*-,._.,-*~'`" > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > > -- Gregory Luneau McGill Centre for Integrative Neuroscience (MCIN), Ludmer Centre for Neuroinformatics and Mental Health, Montreal Neurological Institute (MNI), McGill University, Montreal, Canada -------------- next part -------------- An HTML attachment was scrubbed... URL: From Bonhwang.Koo at childmind.org Wed Jul 19 19:19:33 2017 From: Bonhwang.Koo at childmind.org (Bonhwang Koo) Date: Wed, 19 Jul 2017 23:19:33 +0000 Subject: [Loris-dev] Adding second dataset to LORIS with different access permissions Message-ID: Hi all, My group is currently using LORIS to house phenotypic data for one project, the Healthy Brain Network. The data for this project is protected so when users request an account, they are required to submit an agreement before the admin allows them access to our LORIS instance and download data via the data query tool. However, we are looking to add another separate dataset to our LORIS instance. This dataset would not require users to submit an agreement and thus they shouldn?t have to waste time waiting for their request to be approved in order to access the data. Would it be possible to host both of these datasets on the same instance and modify the account request page such that if a user requests access to the second dataset, the request is immediately approved? Thanks! -- Bonhwang Koo -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.joseph at sickkids.ca Thu Jul 27 11:19:57 2017 From: michael.joseph at sickkids.ca (Michael Joseph) Date: Thu, 27 Jul 2017 15:19:57 +0000 Subject: [Loris-dev] Registering minc files to LORIS Message-ID: Hi Loris dev team, For our Loris instance, we have a bunch of mouse imaging data in minc files. I created a wrapper around the registerFile.pl script to add the files to the database. The files are added successfully and all the metadata is in the parameter_file table. However, I can't see the images through the Imaging Browser module. They are only visible by viewing imaging data through the candidate Access Profile page. Would you have any thoughts as to why that is? Should the make_pics and make_jiv subroutines from MRI.pm also be added to view the files in Brainbrowser? Also, I occasionally get some errors from HDF5. I've attached them here. Michael ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: loris_hdf5errors.txt URL: From mouna.safi-harb at mail.mcgill.ca Thu Jul 27 16:06:29 2017 From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab) Date: Thu, 27 Jul 2017 20:06:29 +0000 Subject: [Loris-dev] Registering minc files to LORIS In-Reply-To: References: Message-ID: Hi Michael, Yes, what you see in Imaging browser is the jpg version (in /data/$PROJ/data/pics/ folder) of the minc file (from the /data/$PROJ/data/assembly/...etc folder). If you do not generate those using make_pics, they won't show in Imaging Browser because they don't exist in the first place. Clicking on the image, once it shows up, will launch brainbrowser with the corresponding minc file for browsing/viewing. make_jiv() is needed if you are using the jiv version to view images, otherwise, it is not necessary. - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Michael Joseph Sent: Thursday, July 27, 2017 11:19:57 AM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] Registering minc files to LORIS Hi Loris dev team, For our Loris instance, we have a bunch of mouse imaging data in minc files. I created a wrapper around the registerFile.pl script to add the files to the database. The files are added successfully and all the metadata is in the parameter_file table. However, I can't see the images through the Imaging Browser module. They are only visible by viewing imaging data through the candidate Access Profile page. Would you have any thoughts as to why that is? Should the make_pics and make_jiv subroutines from MRI.pm also be added to view the files in Brainbrowser? Also, I occasionally get some errors from HDF5. I've attached them here. Michael ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mouna.safi-harb at mail.mcgill.ca Thu Jul 27 16:09:58 2017 From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab) Date: Thu, 27 Jul 2017 20:09:58 +0000 Subject: [Loris-dev] Registering minc files to LORIS In-Reply-To: References: , Message-ID: One thing I should add to the email below is to click on the "all_types" under "Links" in Imaging Browser (as opposed to "native"; in case this is where your issue is coming from). - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Mouna Safi-Harab Sent: Thursday, July 27, 2017 4:06:29 PM To: Michael Joseph; loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] Registering minc files to LORIS Hi Michael, Yes, what you see in Imaging browser is the jpg version (in /data/$PROJ/data/pics/ folder) of the minc file (from the /data/$PROJ/data/assembly/...etc folder). If you do not generate those using make_pics, they won't show in Imaging Browser because they don't exist in the first place. Clicking on the image, once it shows up, will launch brainbrowser with the corresponding minc file for browsing/viewing. make_jiv() is needed if you are using the jiv version to view images, otherwise, it is not necessary. - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Michael Joseph Sent: Thursday, July 27, 2017 11:19:57 AM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] Registering minc files to LORIS Hi Loris dev team, For our Loris instance, we have a bunch of mouse imaging data in minc files. I created a wrapper around the registerFile.pl script to add the files to the database. The files are added successfully and all the metadata is in the parameter_file table. However, I can't see the images through the Imaging Browser module. They are only visible by viewing imaging data through the candidate Access Profile page. Would you have any thoughts as to why that is? Should the make_pics and make_jiv subroutines from MRI.pm also be added to view the files in Brainbrowser? Also, I occasionally get some errors from HDF5. I've attached them here. Michael ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.joseph at sickkids.ca Thu Jul 27 16:39:43 2017 From: michael.joseph at sickkids.ca (Michael Joseph) Date: Thu, 27 Jul 2017 20:39:43 +0000 Subject: [Loris-dev] Registering minc files to LORIS In-Reply-To: References: , , Message-ID: Thank you Mouna. I'll add the make_pics subroutine. I thought the jiv files were necessary for Brainbrowser but the minc files seem to be working. I had the data paths configured wrong. Michael ________________________________ From: Mouna Safi-Harab Sent: July 27, 2017 4:09:58 PM To: Michael Joseph; loris-dev at bic.mni.mcgill.ca Subject: Re: Registering minc files to LORIS One thing I should add to the email below is to click on the "all_types" under "Links" in Imaging Browser (as opposed to "native"; in case this is where your issue is coming from). - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Mouna Safi-Harab Sent: Thursday, July 27, 2017 4:06:29 PM To: Michael Joseph; loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] Registering minc files to LORIS Hi Michael, Yes, what you see in Imaging browser is the jpg version (in /data/$PROJ/data/pics/ folder) of the minc file (from the /data/$PROJ/data/assembly/...etc folder). If you do not generate those using make_pics, they won't show in Imaging Browser because they don't exist in the first place. Clicking on the image, once it shows up, will launch brainbrowser with the corresponding minc file for browsing/viewing. make_jiv() is needed if you are using the jiv version to view images, otherwise, it is not necessary. - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Michael Joseph Sent: Thursday, July 27, 2017 11:19:57 AM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] Registering minc files to LORIS Hi Loris dev team, For our Loris instance, we have a bunch of mouse imaging data in minc files. I created a wrapper around the registerFile.pl script to add the files to the database. The files are added successfully and all the metadata is in the parameter_file table. However, I can't see the images through the Imaging Browser module. They are only visible by viewing imaging data through the candidate Access Profile page. Would you have any thoughts as to why that is? Should the make_pics and make_jiv subroutines from MRI.pm also be added to view the files in Brainbrowser? Also, I occasionally get some errors from HDF5. I've attached them here. Michael ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies. -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Mon Jul 31 13:34:38 2017 From: waveflux at gmail.com (Tom Beaudry) Date: Mon, 31 Jul 2017 13:34:38 -0400 Subject: [Loris-dev] renaming PSCIDs Message-ID: Hi Everyone, I want to rename all of my existing candidates PSCDIDs. Currently they are of the form MTLXXXX and they will become PERFXXXX Can i just edit everyone's info in the candidate table, or would i need to make a modification somewhere else? I have already modified the psc table to change the alias. Thanks, Tom -------------- next part -------------- An HTML attachment was scrubbed... URL: From christine.rogers at mcgill.ca Mon Jul 31 13:44:09 2017 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Mon, 31 Jul 2017 13:44:09 -0400 Subject: [Loris-dev] renaming PSCIDs In-Reply-To: References: Message-ID: Hi Tom, First, assuming you don't have imaging data loaded -- The candidate table is indeed the primary place to change the PSCID values. You'll also want to tweak *config.xml* to allow a longer PSCID (*regex* and *length*), and re-populate the DQT. If you use the Document Repository, you may have specific PSCIDs attached to files there. If you do have imaging data loaded, note that typically the PSCID already stored in DICOM and MINC headers within each file. One option is to back up all your QC information, re-label and then re-load your scans. If you take another approach, note that the mri_protocol_violated_scans table contains a PSCID field. Best, Christine On Mon, Jul 31, 2017 at 1:34 PM, Tom Beaudry wrote: > Hi Everyone, > > I want to rename all of my existing candidates PSCDIDs. > > Currently they are of the form MTLXXXX and they will become PERFXXXX > > Can i just edit everyone's info in the candidate table, or would i need to > make a modification somewhere else? I have already modified the psc table > to change the alias. > > Thanks, > Tom > > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.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 AMORALESPINZON at bwh.harvard.edu Mon Jul 31 15:30:17 2017 From: AMORALESPINZON at bwh.harvard.edu (Morales Pinzon, Alfredo) Date: Mon, 31 Jul 2017 19:30:17 +0000 Subject: [Loris-dev] renaming PSCIDs In-Reply-To: References: , Message-ID: <6943CC45EE5DEC4089174E22E547836934887A47@PHSX10MB8.partners.org> Hi Tom, I can be wrong, but I think you have to use only three letters for your center Alias inside the PSCID. Best, Alfredo. ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca [loris-dev-bounces at bic.mni.mcgill.ca] on behalf of Christine Rogers [christine.rogers at mcgill.ca] Sent: Monday, July 31, 2017 1:44 PM To: Tom Beaudry Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] renaming PSCIDs Hi Tom, First, assuming you don't have imaging data loaded -- The candidate table is indeed the primary place to change the PSCID values. You'll also want to tweak config.xml to allow a longer PSCID (regex and length), and re-populate the DQT. If you use the Document Repository, you may have specific PSCIDs attached to files there. If you do have imaging data loaded, note that typically the PSCID already stored in DICOM and MINC headers within each file. One option is to back up all your QC information, re-label and then re-load your scans. If you take another approach, note that the mri_protocol_violated_scans table contains a PSCID field. Best, Christine On Mon, Jul 31, 2017 at 1:34 PM, Tom Beaudry > wrote: Hi Everyone, I want to rename all of my existing candidates PSCDIDs. Currently they are of the form MTLXXXX and they will become PERFXXXX Can i just edit everyone's info in the candidate table, or would i need to make a modification somewhere else? I have already modified the psc table to change the alias. Thanks, Tom _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca http://www.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 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 Partners Compliance HelpLine at http://www.partners.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 waveflux at gmail.com Mon Jul 31 15:43:53 2017 From: waveflux at gmail.com (Tom Beaudry) Date: Mon, 31 Jul 2017 15:43:53 -0400 Subject: [Loris-dev] renaming PSCIDs In-Reply-To: <6943CC45EE5DEC4089174E22E547836934887A47@PHSX10MB8.partners.org> References: <6943CC45EE5DEC4089174E22E547836934887A47@PHSX10MB8.partners.org> Message-ID: oh yes only 3, it was a typo, I just used PERXXXX On Mon, Jul 31, 2017 at 3:30 PM, Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Tom, > > I can be wrong, but I think you *have* to use only three letters for your > center Alias inside the PSCID. > > Best, > Alfredo. > ------------------------------ > *From:* loris-dev-bounces at bic.mni.mcgill.ca [loris-dev-bounces at bic.mni. > mcgill.ca] on behalf of Christine Rogers [christine.rogers at mcgill.ca] > *Sent:* Monday, July 31, 2017 1:44 PM > *To:* Tom Beaudry > *Cc:* loris-dev at bic.mni.mcgill.ca > *Subject:* Re: [Loris-dev] renaming PSCIDs > > Hi Tom, > > First, assuming you don't have imaging data loaded -- > The candidate table is indeed the primary place to change the PSCID > values. You'll also want to tweak *config.xml* to allow a longer PSCID ( > *regex* and *length*), and re-populate the DQT. > If you use the Document Repository, you may have specific PSCIDs attached > to files there. > > If you do have imaging data loaded, note that typically the PSCID already > stored in DICOM and MINC headers within each file. One option is to back > up all your QC information, re-label and then re-load your scans. If you > take another approach, note that the mri_protocol_violated_scans table > contains a PSCID field. > > Best, > Christine > > On Mon, Jul 31, 2017 at 1:34 PM, Tom Beaudry wrote: > >> Hi Everyone, >> >> I want to rename all of my existing candidates PSCDIDs. >> >> Currently they are of the form MTLXXXX and they will become PERFXXXX >> >> Can i just edit everyone's info in the candidate table, or would i need >> to make a modification somewhere else? I have already modified the psc >> table to change the alias. >> >> Thanks, >> Tom >> >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> http://www.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 > > 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 Partners Compliance > HelpLine at > http://www.partners.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: