From michael.joseph at sickkids.ca Thu Jun 1 10:13:09 2017 From: michael.joseph at sickkids.ca (Michael Joseph) Date: Thu, 1 Jun 2017 14:13:09 +0000 Subject: [Loris-dev] Create DCCID and Organizing CIVET outputs In-Reply-To: References: , , , Message-ID: Hi Mouna, Thank you for your help and sorry for the delay in getting back to you. I disabled "ONLY_FULL_GROUP_BY mode" in MySQL but I'm still getting a few errors. DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`loris`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`CenterID`) REFERENCES `psc` (`CenterID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1041. print() on unopened filehandle LOG at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1181. DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`loris`.`session`, CONSTRAINT `FK_session_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 266. The logs also show that the "CandID does not exist" and "No centerID" In my prod file, I have the following code. The PSCID and visitLabel are retrieved from the dicom header. I've assigned a CandID for testing. } elsif ($patientID =~ /(.*)-([^-]+$)/) { $subjectID{'PSCID'} = NeuroDB::MRI::my_trim($1); $subjectID{'CandID'} = 123456; $subjectID{'visitLabel'} = NeuroDB::MRI::my_trim($2); $subjectID{'createVisitLabel'} = 1; print "PSCID is: " . $subjectID{'PSCID'} . "\nCandID id: " . $subjectID{'CandID'} . "\nvisit_label is: " . $subjectID{'visitLabel'} . "\n"; } Thanks, Michael ________________________________ From: Mouna Safi-Harab Sent: May 9, 2017 2:02:35 PM To: Michael Joseph; loris-dev at bic.mni.mcgill.ca Subject: Re: Create DCCID and Organizing CIVET outputs Hi Michael, Sorry for the delays in getting back to you on this. The LORIS-MRI codebase does the generation of the CandID for you (check the function CreateMRICandidates in tarchive_validation which calls createNewCandID in MRI.pm). The PSCID, however, is not created (LORIS supports multiple ways in which you can create the PSCID, this is usually read from the config.xml file in the LORIS project directory, so it is a bit trickier than creating the CandID). But since your project would have the PSCID_VisitLabel already known and in the DICOM header, and the prod file is made to parse this, I have a workaround for your project needs. In the determineSubjectID() routine in MRIProcessingUtility.pm, after line 241 (on version 17.0.0), you can add a few lines that selects the CandID the pipeline created a step earlier to be used for the execution of the rest of the steps, while relying on your parsed PSCID from the prod file; as follows: # if the candidate was created from the backend, it won't be in the tarchiveInfo, so add it here my $dbh = &NeuroDB::DBI::connect_to_db(@Settings::db); if (!defined($subjectIDsref->{'CandID'}) && $Settings::createCandidates) { my $query = "SELECT CandID FROM candidate WHERE PSCID=?"; my $sth = ${$this->{'dbhr'}}->prepare($query); $sth->execute($subjectIDsref->{'PSCID'}); if ( $sth->rows > 0 ) { $subjectIDsref->{'CandID'} = $sth->fetchrow_array; } } This should allow you to proceed with candidate creation from the backend based on your project assumptions. Please note this is very specific to your project (in particular, due to the fact that you know the PSCID, but not the CandID, while there is a one-to-one correspondence between these two in LORIS). But I believe it addresses your request. Let me know if you have any further questions. - Mouna ________________________________ From: Michael Joseph Sent: Friday, April 28, 2017 12:49:50 PM To: Mouna Safi-Harab; loris-dev at bic.mni.mcgill.ca Subject: Re: Create DCCID and Organizing CIVET outputs Hi Mouna, Thank you for your reply. Your answers certainly help. For our images, the PatientName header is labeled as PSCID-VisitLabel. I've modified the regex in the prod file to parse this out. I didn't want to modify the header to also include a DCCID because there are other groups sharing the images. I was wondering if there's another way to create a DCCID when images are uploaded (similar to how the scanner is registered). The Imaging Uploader GUI isn't as important to us as we'll be relying on the Perl scripts to upload all our images. Thank you for directing me to the DTIPrep directory. It definitely helps as an example for registering processed data. Michael ________________________________ From: Mouna Safi-Harab Sent: April 27, 2017 2:06:58 PM To: Michael Joseph; loris-dev at bic.mni.mcgill.ca Subject: Re: Create DCCID and Organizing CIVET outputs Hi Michael, Here are my answers to your questions: 1) Setting createCandidates to 1 in the prod file does indeed allow for creation of the candidate from the MRI pipeline. You will need to make sure that 1) the PatientName header is anonymized properly in the DICOM files, and 2) getSubjectIDs() function in this prod file is a) splitting the PatientName header information in a way that is consistent with the anonymization and your project DCCID/PSCID/VisitLabel convention, and b) has the $subjectID{'createVisitLabel'} option set to 1 as you will also likely need the MRI pipeline to create the visit for that candidate as well. However, projects using the Imaging Uploader GUI unfortunately does not allow for this option. If you want a way to make it work for now, you can disable the check on Lines 378-395 in NDB_Menu_Filter_imaging_uploader.class.inc (which sole purpose is to check if the CandID is registered in the database). We can look at this from our end, and make sure the option createCandidate is propagated to the Imaging Uploader GUI as well in a seamless manner to the user (will discuss this at our internal meeting). 2) Loris-MRI codebase provides an example of how to insert files from another processing pipeline into the database. Check the DTIPrep/ directory for an example you can follow. Essentially, inserting processed files into LORIS is a two-step process: you will need a 1) wrapper script that "understands" or "knows" how/where the processed files are stored (this step is processing pipeline dependent), and then 2) have that wrapper script call a generic file called uploadNeuroDB/register_processed_data.pl. The register_processed_data.pl file would take in many required arguments, some of which are the full path of the file you are going to register. Other parameters are the acquisition protocol ID. So yes, the"white_matter", "pve", "tal_mask" were initially created to allow for CIVET outputs to be registered with the correct acquisition protocol. Other required parameters are the sourceFileID which would be the ID of the initial file you sent to CIVET for processing. The second step should be processing pipeline independent. I hope the above answers your questions, or at least, gives you a starting point. - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Michael Joseph Sent: Wednesday, April 19, 2017 4:03 PM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] Create DCCID and Organizing CIVET outputs Hi Loris dev community, I have 2 questions: 1) Is there a way to register new candidates into Loris from the back-end without a DCCID? Essentially, I'd like to add candidates and sessions while running the tarchiveLoader script. I noticed that the prod file has a createCandidates variable. Is there anything else that needs to be modified? 2) How are CIVET outputs typically organized in Loris? I noticed that in the mri_scan_type table, there are labels like "white_matter", "pve", "tal_msk". I'm assuming the most of the files from CIVET would get registered using these labels. Also, is there a good way of linking to the htmls from the CIVET QC pipeline? 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. ________________________________ 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 michael.joseph at sickkids.ca Thu Jun 1 10:21:34 2017 From: michael.joseph at sickkids.ca (Michael Joseph) Date: Thu, 1 Jun 2017 14:21:34 +0000 Subject: [Loris-dev] Data Dissemination with LORIS Message-ID: Hi Loris dev team, In our Loris instance, some of the imaging data comes from different collaborators. Once the data is uploaded to Loris, we'd like to share it with the collaborators. Specifically, they should only be able to access the relevant project. I was wondering how this is currently handled in Loris. Assigning new user permissions (though I didn't see the ability to grant access only to certain projects)? The data query tool? Deploying another Loris instance with just the relevant data? 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 Thu Jun 1 12:40:45 2017 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Thu, 1 Jun 2017 12:40:45 -0400 Subject: [Loris-dev] Data Dissemination with LORIS In-Reply-To: References: Message-ID: Hi Michael, User-Project permissions is a feature we're piloting on a few Loris instances this year. We're looking into planning its rollout in a future Loris release. Certainly their application in the Data Query Tool will be an important part of the requirements. In the shorter term, deploying another Loris instance with distinct user account for datasets is one solution. Another: if you can distinctly classify your data by "Site" (aka psc aka CenterID), then basic permissions generally will prevent site-users from accessing other sites' data. (We're also conducting a review this summer for these features.) Best, Christine On Thu, Jun 1, 2017 at 10:21 AM, Michael Joseph wrote: > Hi Loris dev team, > > > In our Loris instance, some of the imaging data comes from different > collaborators. Once the data is uploaded to Loris, we'd like to share it > with the collaborators. Specifically, they should only be able to access > the relevant project. I was wondering how this is currently handled in > Loris. Assigning new user permissions (though I didn't see the ability to > grant access only to certain projects)? The data query tool? Deploying > another Loris instance with just the relevant data? > > > 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 carolina.mak3 at gmail.com Thu Jun 1 12:59:25 2017 From: carolina.mak3 at gmail.com (Carolina Makowski) Date: Thu, 1 Jun 2017 09:59:25 -0700 Subject: [Loris-dev] Fwd: using media module through front end In-Reply-To: References: <49687b198ff64b4dad2ddaee934d01f5@BY2PR0301MB0662.namprd03.prod.outlook.com> Message-ID: Hi Christine, Just to provide some more info on the steps I have taken: 1) Here are the most recent errors I am getting in my loris-error.log file: [Thu Jun 01 09:44:46.935475 2017] [:error] [pid 1786] [client 169.228.191.13:62450] PHP Warning: move_uploaded_file(/data/uploads/DCC0000_baselineyear1arm1_CBCL_test.txt): failed to open stream: Permission denied in /var/www/abcd/modules/media/ajax/FileUpload.php on line 146, referer: http://169.228.56.161/media/ [Thu Jun 01 09:44:46.935557 2017] [:error] [pid 1786] [client 169.228.191.13:62450] PHP Warning: move_uploaded_file(): Unable to move '/tmp/phpCY7laj' to '/data/uploads/DCC0000_baselineyear1arm1_CBCL_test.txt' in /var/www/abcd/modules/media/ajax/FileUpload.php on line 146, referer: http://169.228.56.161/media/ It does seem like a permissions issue. Below you will see the permissions on my /data/uploads/ directory and my FileUpload.php file in /var/www/abcd/modules/media/ajax/ drwxr-xr-x 2 lorisadmin www-data 4096 Mar 27 10:34 *uploads* -rwxr-xr-x 1 lorisadmin lorisadmin 8319 Feb 3 10:13 *FileUpload.php* 2) I also tried to do a "chown lorisadmin:www-data FileUpload.php" to match with the ownership of /data/uploads. This also did not work and the file is "uploaded 100%" as indicated by the front end but the screen freezes at this point, and no file can be found in /data/uploads. As you can see, I switched to testing out an instrument that had no underscores in the name, just to double check this wasn't an issue. Let me know if you or anyone else on the team have any other suggestions to fix the permissions error. Thanks, Carolina ---------- Forwarded message ---------- From: Carolina Makowski Date: Wed, May 31, 2017 at 3:42 PM Subject: Re: [Loris-dev] using media module through front end To: Christine Rogers Cc: "loris-dev at bic.mni.mcgill.ca" Hi Christine, Here are the last two warnings pertaining to the upload (there are no "true" errors): [Wed May 31 15:40:23.721871 2017] [:error] [pid 30667] [client 137.110.9.195:57908] PHP Warning: move_uploaded_file(/data/ uploads/NDARINV1K3LDK3L_baselineyear1arm1_eprime_data_ upload_ABCD-nBack-fMRI_run-20161010142333-EventRelatedInformation.csv): failed to open stream: Permission denied in /var/www/abcd/modules/media/ajax/FileUpload.php on line 146, referer: http://169.228.56.161/media/ [Wed May 31 15:40:23.721935 2017] [:error] [pid 30667] [client 137.110.9.195:57908] PHP Warning: move_uploaded_file(): Unable to move '/tmp/phpNAaV2G' to '/data/uploads/NDARINV1K3LDK3L_ baselineyear1arm1_eprime_data_upload_ABCD-nBack-fMRI_run-20161010142333-EventRelatedInformation.csv' in /var/www/abcd/modules/media/ajax/FileUpload.php on line 146, referer: http://169.228.56.161/media/ And here is a screenshot of the front end, where you see the progress bar but the "Upload file" button is highlighted blue and the progress bar just seems to stall. Carolina On Wed, May 31, 2017 at 3:33 PM, Christine Rogers < christine.rogers at mcgill.ca> wrote: > Hi Carolina, > Thanks, great to know. > What does the Apache error log say? That would be the next thing for the > team to know. > Cheers, > Christine > > > > On May 31, 2017, at 6:13 PM, Carolina Makowski > wrote: > > Hi Christine, > No, there was no file uploaded onto the server and nothing on the database > regarding status of the upload - after about 10 minutes I just navigated > away from the page, so there doesn't seem to be a trace of the attempt. > > Carolina > > On Wed, May 31, 2017 at 3:06 PM, Christine Rogers < > christine.rogers at mcgill.ca> wrote: > >> Hi Carolina, >> >> Do you see the file on the server? >> Also does the database have an entry written to it recording the upload >> of this file? >> These two things could help with troubleshooting... >> C >> >> >> >> > On May 31, 2017, at 5:15 PM, Carolina Makowski >> wrote: >> > >> > Hi there, >> > I have a question about properly setting up the Media Module in LORIS. >> I am having trouble uploading a file through the front end of the database. >> > I have gone through the readme in the /modules directory, and have >> ensured my path in the front end Configuration module matches where the >> data is expected to come in (i.e. /data/uploads/) and I have ensured >> /data/uploads has 775 permission and www-data permissions. >> > >> > On the front end, the file is uploading and the progress bar reaches >> 100%, but at this point nothing happens and progress simply stalls there >> (not sure if a "successfully uploaded" message or something of the like is >> supposed to appear here). Moving to the Browse tab shows that nothing was >> uploaded. It is only a 200K file and is well within the upload limits we >> set for our database. >> > >> > I know this is a relatively new module - let me know if something jumps >> out at you here. Thanks! >> > >> > Carolina >> > _______________________________________________ >> > 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 carolina.mak3 at gmail.com Thu Jun 1 13:16:45 2017 From: carolina.mak3 at gmail.com (Carolina Makowski) Date: Thu, 1 Jun 2017 10:16:45 -0700 Subject: [Loris-dev] radiology reviews - error in saving data Message-ID: Hi LORIS team! I've started a thread with Christine regarding this but thought I would bring this to the larger group as well since Christine is heading off on vacation. I am having trouble saving data for a candidate's radiology review, although I can enter data with no problems through the front end. The last error in my loris-error.log is: [Thu Jun 01 10:07:32.133258 2017] [:error] [pid 844] [client 169.228.191.13:62590] Could not execute UPDATE radiology_review SET `Date_taken`=:set_Date_taken,`Examiner`=:set_Examiner,`Scan_done`=:set_Scan_done,`MRI_date`=:set_MRI_date,`MRI_date_status`=:set_MRI_date_status,`Review_date`=:set_Review_date,`Review_date_status`=:set_Review_date_status,`Review_results`=:set_Review_results,`abnormal_atypical_exclusionary`=:set_abnormal_atypical_exclusionary,`Incidental_findings`=:set_Incidental_findings,`Incidental_findings_status`=:set_Incidental_findings_status,`Candidate_Age`=:set_Candidate_Age,`Window_Difference`=:set_Window_Difference WHERE `CommentID`=:where_CommentID. Stack trace#0 /var/www/abcd/php/libraries/Database.class.inc(391): Database->_realupdate('radiology_revie...', Array, Array, true)\n#1 /var/www/abcd/php/libraries/NDB_BVL_Instrument.class.inc(706): Database->update('radiology_revie...', Array, Array)\n#2 /var/www/abcd/php/libraries/NDB_BVL_Instrument.class.inc(681): NDB_BVL_Instrument->_save(Array)\n#3 /var/www/abcd/php/libraries/LorisForm.class.inc(1326): NDB_BVL_Instrument->_saveValues(Array)\n#4 /var/www/abcd/php/libraries/NDB_BVL_Instrument.class.inc(486): LorisForm->process(Array, true)\n#5 /var/www/abcd/php/libraries/NDB_Caller.class.inc(484): NDB_BVL_Instrument->save()\n#6 /var/www/abcd/php/libraries/NDB_Caller.class.inc(288): NDB_Caller->loadInstrument('radiology_revie...', '', '152475NDARINV1K...', NULL)\n#7 /var/www/abcd/htdocs/main.php(180): NDB_Caller->load('radiology_revie...', '')\n#8 {main}, referer: http://169.228.56.161/radiology_review/?commentID=152475NDARINV1K3LDK3L112261496267818&sessionID=11&candID=152475 I can confirm that this commentID exists in the flag table and I have an instrument table for radiology_review. Let me know if one of you might have some insight into this. Thanks a lot! Carolina -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.joseph at sickkids.ca Thu Jun 1 13:29:00 2017 From: michael.joseph at sickkids.ca (Michael Joseph) Date: Thu, 1 Jun 2017 17:29:00 +0000 Subject: [Loris-dev] Data Dissemination with LORIS In-Reply-To: References: , Message-ID: Thank you Christine. Classifying data by "Site" should work for us. I saw site access in the user permissions but was curious about project access as well. Michael ________________________________ From: Christine Rogers Sent: June 1, 2017 12:40:45 PM To: Michael Joseph Cc: loris-dev at bic.mni.mcgill.ca Subject: Re: [Loris-dev] Data Dissemination with LORIS Hi Michael, User-Project permissions is a feature we're piloting on a few Loris instances this year. We're looking into planning its rollout in a future Loris release. Certainly their application in the Data Query Tool will be an important part of the requirements. In the shorter term, deploying another Loris instance with distinct user account for datasets is one solution. Another: if you can distinctly classify your data by "Site" (aka psc aka CenterID), then basic permissions generally will prevent site-users from accessing other sites' data. (We're also conducting a review this summer for these features.) Best, Christine On Thu, Jun 1, 2017 at 10:21 AM, Michael Joseph > wrote: Hi Loris dev team, In our Loris instance, some of the imaging data comes from different collaborators. Once the data is uploaded to Loris, we'd like to share it with the collaborators. Specifically, they should only be able to access the relevant project. I was wondering how this is currently handled in Loris. Assigning new user permissions (though I didn't see the ability to grant access only to certain projects)? The data query tool? Deploying another Loris instance with just the relevant data? 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 justinkat at gmail.com Thu Jun 1 21:54:02 2017 From: justinkat at gmail.com (Justin Kat) Date: Thu, 1 Jun 2017 21:54:02 -0400 Subject: [Loris-dev] Fwd: using media module through front end In-Reply-To: References: <49687b198ff64b4dad2ddaee934d01f5@BY2PR0301MB0662.namprd03.prod.outlook.com> Message-ID: I've never looked at the Media module code but looks like you either need www-data to be part of lorisadmin or add group write permissions on /data/uploads On Thu, Jun 1, 2017 at 12:59 PM, Carolina Makowski wrote: > Hi Christine, > > Just to provide some more info on the steps I have taken: > > 1) Here are the most recent errors I am getting in my loris-error.log file: > > [Thu Jun 01 09:44:46.935475 2017] [:error] [pid 1786] [client > 169.228.191.13:62450] PHP Warning: move_uploaded_file(/data/ > uploads/DCC0000_baselineyear1arm1_CBCL_test.txt): failed to open stream: > Permission denied in /var/www/abcd/modules/media/ajax/FileUpload.php on > line 146, referer: http://169.228.56.161/media/ > > [Thu Jun 01 09:44:46.935557 2017] [:error] [pid 1786] [client > 169.228.191.13:62450] PHP Warning: move_uploaded_file(): Unable to move > '/tmp/phpCY7laj' to '/data/uploads/DCC0000_baselineyear1arm1_CBCL_test.txt' > in /var/www/abcd/modules/media/ajax/FileUpload.php on line 146, referer: > http://169.228.56.161/media/ > > It does seem like a permissions issue. Below you will see the permissions > on my /data/uploads/ directory and my FileUpload.php file in > /var/www/abcd/modules/media/ajax/ > > drwxr-xr-x 2 lorisadmin www-data 4096 Mar 27 10:34 *uploads* > > -rwxr-xr-x 1 lorisadmin lorisadmin 8319 Feb 3 10:13 *FileUpload.php* > > 2) I also tried to do a "chown lorisadmin:www-data FileUpload.php" to > match with the ownership of /data/uploads. This also did not work and the > file is "uploaded 100%" as indicated by the front end but the screen > freezes at this point, and no file can be found in /data/uploads. > > As you can see, I switched to testing out an instrument that had no > underscores in the name, just to double check this wasn't an issue. Let me > know if you or anyone else on the team have any other suggestions to fix > the permissions error. > > Thanks, > Carolina > > ---------- Forwarded message ---------- > From: Carolina Makowski > Date: Wed, May 31, 2017 at 3:42 PM > Subject: Re: [Loris-dev] using media module through front end > To: Christine Rogers > Cc: "loris-dev at bic.mni.mcgill.ca" > > > Hi Christine, > Here are the last two warnings pertaining to the upload (there are no > "true" errors): > > [Wed May 31 15:40:23.721871 2017] [:error] [pid 30667] [client > 137.110.9.195:57908] PHP Warning: move_uploaded_file(/data/uploa > ds/NDARINV1K3LDK3L_baselineyear1arm1_eprime_data_upload_ > ABCD-nBack-fMRI_run-20161010142333-EventRelatedInformation.csv): failed > to open stream: Permission denied in /var/www/abcd/modules/media/ajax/FileUpload.php > on line 146, referer: http://169.228.56.161/media/ > > [Wed May 31 15:40:23.721935 2017] [:error] [pid 30667] [client > 137.110.9.195:57908] PHP Warning: move_uploaded_file(): Unable to move > '/tmp/phpNAaV2G' to '/data/uploads/NDARINV1K3LDK3L > _baselineyear1arm1_eprime_data_upload_ABCD-nBack-fMRI_ > run-20161010142333-EventRelatedInformation.csv' in > /var/www/abcd/modules/media/ajax/FileUpload.php on line 146, referer: > http://169.228.56.161/media/ > > > And here is a screenshot of the front end, where you see the progress bar > but the "Upload file" button is highlighted blue and the progress bar just > seems to stall. > > Carolina > > On Wed, May 31, 2017 at 3:33 PM, Christine Rogers < > christine.rogers at mcgill.ca> wrote: > >> Hi Carolina, >> Thanks, great to know. >> What does the Apache error log say? That would be the next thing for the >> team to know. >> Cheers, >> Christine >> >> >> >> On May 31, 2017, at 6:13 PM, Carolina Makowski >> wrote: >> >> Hi Christine, >> No, there was no file uploaded onto the server and nothing on the >> database regarding status of the upload - after about 10 minutes I just >> navigated away from the page, so there doesn't seem to be a trace of the >> attempt. >> >> Carolina >> >> On Wed, May 31, 2017 at 3:06 PM, Christine Rogers < >> christine.rogers at mcgill.ca> wrote: >> >>> Hi Carolina, >>> >>> Do you see the file on the server? >>> Also does the database have an entry written to it recording the upload >>> of this file? >>> These two things could help with troubleshooting... >>> C >>> >>> >>> >>> > On May 31, 2017, at 5:15 PM, Carolina Makowski < >>> carolina.mak3 at gmail.com> wrote: >>> > >>> > Hi there, >>> > I have a question about properly setting up the Media Module in LORIS. >>> I am having trouble uploading a file through the front end of the database. >>> > I have gone through the readme in the /modules directory, and have >>> ensured my path in the front end Configuration module matches where the >>> data is expected to come in (i.e. /data/uploads/) and I have ensured >>> /data/uploads has 775 permission and www-data permissions. >>> > >>> > On the front end, the file is uploading and the progress bar reaches >>> 100%, but at this point nothing happens and progress simply stalls there >>> (not sure if a "successfully uploaded" message or something of the like is >>> supposed to appear here). Moving to the Browse tab shows that nothing was >>> uploaded. It is only a 200K file and is well within the upload limits we >>> set for our database. >>> > >>> > I know this is a relatively new module - let me know if something >>> jumps out at you here. Thanks! >>> > >>> > Carolina >>> > _______________________________________________ >>> > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carolina.mak3 at gmail.com Thu Jun 1 21:57:54 2017 From: carolina.mak3 at gmail.com (Carolina Makowski) Date: Thu, 1 Jun 2017 18:57:54 -0700 Subject: [Loris-dev] Fwd: using media module through front end In-Reply-To: References: <49687b198ff64b4dad2ddaee934d01f5@BY2PR0301MB0662.namprd03.prod.outlook.com> Message-ID: Hi Justin, we probably should have posted the final "solution" to this on loris-dev but yes, exactly, we needed to have lorisadmin:www-data ownership, and change permissions on /data/uploads with chmod -R 755. This ended up working for me :) thanks for looking into it, Carolina On Thu, Jun 1, 2017 at 6:54 PM, Justin Kat wrote: > I've never looked at the Media module code but looks like you either need > www-data to be part of lorisadmin or add group write permissions on > /data/uploads > > On Thu, Jun 1, 2017 at 12:59 PM, Carolina Makowski < > carolina.mak3 at gmail.com> wrote: > >> Hi Christine, >> >> Just to provide some more info on the steps I have taken: >> >> 1) Here are the most recent errors I am getting in my loris-error.log >> file: >> >> [Thu Jun 01 09:44:46.935475 2017] [:error] [pid 1786] [client >> 169.228.191.13:62450] PHP Warning: move_uploaded_file(/data/uploa >> ds/DCC0000_baselineyear1arm1_CBCL_test.txt): failed to open stream: >> Permission denied in /var/www/abcd/modules/media/ajax/FileUpload.php on >> line 146, referer: http://169.228.56.161/media/ >> >> [Thu Jun 01 09:44:46.935557 2017] [:error] [pid 1786] [client >> 169.228.191.13:62450] PHP Warning: move_uploaded_file(): Unable to move >> '/tmp/phpCY7laj' to '/data/uploads/DCC0000_baselineyear1arm1_CBCL_test.txt' >> in /var/www/abcd/modules/media/ajax/FileUpload.php on line 146, referer: >> http://169.228.56.161/media/ >> >> It does seem like a permissions issue. Below you will see the permissions >> on my /data/uploads/ directory and my FileUpload.php file in >> /var/www/abcd/modules/media/ajax/ >> >> drwxr-xr-x 2 lorisadmin www-data 4096 Mar 27 10:34 *uploads* >> >> -rwxr-xr-x 1 lorisadmin lorisadmin 8319 Feb 3 10:13 *FileUpload.php* >> >> 2) I also tried to do a "chown lorisadmin:www-data FileUpload.php" to >> match with the ownership of /data/uploads. This also did not work and the >> file is "uploaded 100%" as indicated by the front end but the screen >> freezes at this point, and no file can be found in /data/uploads. >> >> As you can see, I switched to testing out an instrument that had no >> underscores in the name, just to double check this wasn't an issue. Let me >> know if you or anyone else on the team have any other suggestions to fix >> the permissions error. >> >> Thanks, >> Carolina >> >> ---------- Forwarded message ---------- >> From: Carolina Makowski >> Date: Wed, May 31, 2017 at 3:42 PM >> Subject: Re: [Loris-dev] using media module through front end >> To: Christine Rogers >> Cc: "loris-dev at bic.mni.mcgill.ca" >> >> >> Hi Christine, >> Here are the last two warnings pertaining to the upload (there are no >> "true" errors): >> >> [Wed May 31 15:40:23.721871 2017] [:error] [pid 30667] [client >> 137.110.9.195:57908] PHP Warning: move_uploaded_file(/data/uploa >> ds/NDARINV1K3LDK3L_baselineyear1arm1_eprime_data_upload_ABCD >> -nBack-fMRI_run-2016101014 <(201)%20610-1014>2333-EventRelatedInformation.csv): >> failed to open stream: Permission denied in /var/www/abcd/modules/media/ajax/FileUpload.php >> on line 146, referer: http://169.228.56.161/media/ >> >> [Wed May 31 15:40:23.721935 2017] [:error] [pid 30667] [client >> 137.110.9.195:57908] PHP Warning: move_uploaded_file(): Unable to move >> '/tmp/phpNAaV2G' to '/data/uploads/NDARINV1K3LDK3L >> _baselineyear1arm1_eprime_data_upload_ABCD-nBack-fMRI_run- >> 20161010142333-EventRelatedInformation.csv' in >> /var/www/abcd/modules/media/ajax/FileUpload.php on line 146, referer: >> http://169.228.56.161/media/ >> >> >> And here is a screenshot of the front end, where you see the progress bar >> but the "Upload file" button is highlighted blue and the progress bar just >> seems to stall. >> >> Carolina >> >> On Wed, May 31, 2017 at 3:33 PM, Christine Rogers < >> christine.rogers at mcgill.ca> wrote: >> >>> Hi Carolina, >>> Thanks, great to know. >>> What does the Apache error log say? That would be the next thing for >>> the team to know. >>> Cheers, >>> Christine >>> >>> >>> >>> On May 31, 2017, at 6:13 PM, Carolina Makowski >>> wrote: >>> >>> Hi Christine, >>> No, there was no file uploaded onto the server and nothing on the >>> database regarding status of the upload - after about 10 minutes I just >>> navigated away from the page, so there doesn't seem to be a trace of the >>> attempt. >>> >>> Carolina >>> >>> On Wed, May 31, 2017 at 3:06 PM, Christine Rogers < >>> christine.rogers at mcgill.ca> wrote: >>> >>>> Hi Carolina, >>>> >>>> Do you see the file on the server? >>>> Also does the database have an entry written to it recording the upload >>>> of this file? >>>> These two things could help with troubleshooting... >>>> C >>>> >>>> >>>> >>>> > On May 31, 2017, at 5:15 PM, Carolina Makowski < >>>> carolina.mak3 at gmail.com> wrote: >>>> > >>>> > Hi there, >>>> > I have a question about properly setting up the Media Module in >>>> LORIS. I am having trouble uploading a file through the front end of the >>>> database. >>>> > I have gone through the readme in the /modules directory, and have >>>> ensured my path in the front end Configuration module matches where the >>>> data is expected to come in (i.e. /data/uploads/) and I have ensured >>>> /data/uploads has 775 permission and www-data permissions. >>>> > >>>> > On the front end, the file is uploading and the progress bar reaches >>>> 100%, but at this point nothing happens and progress simply stalls there >>>> (not sure if a "successfully uploaded" message or something of the like is >>>> supposed to appear here). Moving to the Browse tab shows that nothing was >>>> uploaded. It is only a 200K file and is well within the upload limits we >>>> set for our database. >>>> > >>>> > I know this is a relatively new module - let me know if something >>>> jumps out at you here. Thanks! >>>> > >>>> > Carolina >>>> > _______________________________________________ >>>> > 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 >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From justinkat at gmail.com Thu Jun 1 21:59:24 2017 From: justinkat at gmail.com (Justin Kat) Date: Thu, 1 Jun 2017 21:59:24 -0400 Subject: [Loris-dev] radiology reviews - error in saving data In-Reply-To: References: Message-ID: Turn on showDatabaseQueries in /var/www/abcd/project/config.xml by setting it to "1", look for the "UPDATE radiology_review SET ...." query upon saving the instrument, log in to MySQL from the command line or otherwise, copy paste that query(you may have to clean up the syntax for the "WHERE CommentID= ..." part), run and see what the error is - most likely a mismatch with your radiology_review table definition vs the update columns, fix or continue debugging and set showDatabaseQueries back to 0 when you're done On Thu, Jun 1, 2017 at 1:16 PM, Carolina Makowski wrote: > Hi LORIS team! > I've started a thread with Christine regarding this but thought I would > bring this to the larger group as well since Christine is heading off on > vacation. > > I am having trouble saving data for a candidate's radiology review, > although I can enter data with no problems through the front end. > > The last error in my loris-error.log is: > > [Thu Jun 01 10:07:32.133258 2017] [:error] [pid 844] [client > 169.228.191.13:62590] Could not execute UPDATE radiology_review SET > `Date_taken`=:set_Date_taken,`Examiner`=:set_Examiner,`Scan_ > done`=:set_Scan_done,`MRI_date`=:set_MRI_date,`MRI_date_ > status`=:set_MRI_date_status,`Review_date`=:set_Review_date, > `Review_date_status`=:set_Review_date_status,`Review_ > results`=:set_Review_results,`abnormal_atypical_ > exclusionary`=:set_abnormal_atypical_exclusionary,` > Incidental_findings`=:set_Incidental_findings,` > Incidental_findings_status`=:set_Incidental_findings_ > status,`Candidate_Age`=:set_Candidate_Age,`Window_Difference`=:set_Window_Difference > WHERE `CommentID`=:where_CommentID. Stack trace#0 > /var/www/abcd/php/libraries/Database.class.inc(391): > Database->_realupdate('radiology_revie...', Array, Array, true)\n#1 > /var/www/abcd/php/libraries/NDB_BVL_Instrument.class.inc(706): > Database->update('radiology_revie...', Array, Array)\n#2 > /var/www/abcd/php/libraries/NDB_BVL_Instrument.class.inc(681): > NDB_BVL_Instrument->_save(Array)\n#3 /var/www/abcd/php/libraries/LorisForm.class.inc(1326): > NDB_BVL_Instrument->_saveValues(Array)\n#4 /var/www/abcd/php/libraries/ > NDB_BVL_Instrument.class.inc(486): LorisForm->process(Array, true)\n#5 > /var/www/abcd/php/libraries/NDB_Caller.class.inc(484): > NDB_BVL_Instrument->save()\n#6 /var/www/abcd/php/libraries/NDB_Caller.class.inc(288): > NDB_Caller->loadInstrument('radiology_revie...', '', > '152475NDARINV1K...', NULL)\n#7 /var/www/abcd/htdocs/main.php(180): > NDB_Caller->load('radiology_revie...', '')\n#8 {main}, referer: > http://169.228.56.161/radiology_review/?commentID= > 152475NDARINV1K3LDK3L112261496267818&sessionID=11&candID=152475 > > > I can confirm that this commentID exists in the flag table and I have an > instrument table for radiology_review. Let me know if one of you might have > some insight into this. > > Thanks a lot! > > Carolina > > _______________________________________________ > 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 carolina.mak3 at gmail.com Thu Jun 1 22:21:39 2017 From: carolina.mak3 at gmail.com (Carolina Makowski) Date: Thu, 1 Jun 2017 19:21:39 -0700 Subject: [Loris-dev] radiology reviews - error in saving data In-Reply-To: References: Message-ID: Excellent, Justin! It worked. Turns out I was missing columns for Candidate_Age and Window_Difference, so I added those to the radiology_review table. Data saved :) thanks a lot! Carolina On Thu, Jun 1, 2017 at 6:59 PM, Justin Kat wrote: > Turn on showDatabaseQueries in /var/www/abcd/project/config.xml by > setting it to "1", look for the "UPDATE radiology_review SET ...." query > upon saving the instrument, log in to MySQL from the command line or > otherwise, copy paste that query(you may have to clean up the syntax for > the "WHERE CommentID= ..." part), run and see what the error is - most > likely a mismatch with your radiology_review table definition vs the update > columns, fix or continue debugging and set showDatabaseQueries back to 0 > when you're done > > On Thu, Jun 1, 2017 at 1:16 PM, Carolina Makowski > wrote: > >> Hi LORIS team! >> I've started a thread with Christine regarding this but thought I would >> bring this to the larger group as well since Christine is heading off on >> vacation. >> >> I am having trouble saving data for a candidate's radiology review, >> although I can enter data with no problems through the front end. >> >> The last error in my loris-error.log is: >> >> [Thu Jun 01 10:07:32.133258 2017] [:error] [pid 844] [client >> 169.228.191.13:62590] Could not execute UPDATE radiology_review SET >> `Date_taken`=:set_Date_taken,`Examiner`=:set_Examiner,`Scan_ >> done`=:set_Scan_done,`MRI_date`=:set_MRI_date,`MRI_date_stat >> us`=:set_MRI_date_status,`Review_date`=:set_Review_date,` >> Review_date_status`=:set_Review_date_status,`Review_results` >> =:set_Review_results,`abnormal_atypical_exclusionary`=:set_ >> abnormal_atypical_exclusionary,`Incidental_findings`=:set_Incidental_ >> findings,`Incidental_findings_status`=:set_Incidental_ >> findings_status,`Candidate_Age`=:set_Candidate_Age,` >> Window_Difference`=:set_Window_Difference WHERE >> `CommentID`=:where_CommentID. Stack trace#0 /var/www/abcd/php/libraries/Database.class.inc(391): >> Database->_realupdate('radiology_revie...', Array, Array, true)\n#1 >> /var/www/abcd/php/libraries/NDB_BVL_Instrument.class.inc(706): >> Database->update('radiology_revie...', Array, Array)\n#2 >> /var/www/abcd/php/libraries/NDB_BVL_Instrument.class.inc(681): >> NDB_BVL_Instrument->_save(Array)\n#3 /var/www/abcd/php/libraries/LorisForm.class.inc(1326): >> NDB_BVL_Instrument->_saveValues(Array)\n#4 /var/www/abcd/php/libraries/ND >> B_BVL_Instrument.class.inc(486): LorisForm->process(Array, true)\n#5 >> /var/www/abcd/php/libraries/NDB_Caller.class.inc(484): >> NDB_BVL_Instrument->save()\n#6 /var/www/abcd/php/libraries/NDB_Caller.class.inc(288): >> NDB_Caller->loadInstrument('radiology_revie...', '', >> '152475NDARINV1K...', NULL)\n#7 /var/www/abcd/htdocs/main.php(180): >> NDB_Caller->load('radiology_revie...', '')\n#8 {main}, referer: >> http://169.228.56.161/radiology_review/?commentID=152475NDAR >> INV1K3LDK3L112261496267818&sessionID=11&candID=152475 >> >> >> I can confirm that this commentID exists in the flag table and I have an >> instrument table for radiology_review. Let me know if one of you might have >> some insight into this. >> >> Thanks a lot! >> >> Carolina >> >> _______________________________________________ >> 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 ganesh.chauhan at cbr.iisc.ac.in Mon Jun 5 05:15:46 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Mon, 5 Jun 2017 14:45:46 +0530 (IST) Subject: [Loris-dev] Adding to "Category Name:" in Document Repository & problems in Candidate Information In-Reply-To: <751487055.14514.1496653210651.JavaMail.zimbra@cbr.iisc.ac.in> References: <751487055.14514.1496653210651.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: <1285337540.14550.1496654146842.JavaMail.zimbra@cbr.iisc.ac.in> Hi, I have two queries: 1. In the "Document Repository" module via the front end I am not able to add anything to the "Category Name:". Even when I add something in the "document_repository_categories" table via MySql it does not reflect in the front end. 2. I also created some additional fields in the "Candidate Information" section. Again the same thing, I cannot save any of the entered values. Many thanks for your help. 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 -- 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 waveflux at gmail.com Mon Jun 5 14:57:00 2017 From: waveflux at gmail.com (Tom Beaudry) Date: Mon, 5 Jun 2017 14:57:00 -0400 Subject: [Loris-dev] PEAR error reporting Message-ID: Hi Guys, What's the new way to do PEAR error reporting in 17.02 / LORISForms? I have an instrument with a score function that contains: //get the saved scores $db =& Database::singleton(); if(PEAR::isError($db)) { return PEAR::raiseError ("Could not connect to database".$db->getMessage()); } What should it be changed to? Thanks! Tom -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.macfarlane2 at mcgill.ca Mon Jun 5 15:01:15 2017 From: david.macfarlane2 at mcgill.ca (David MacFarlane, Mr) Date: Mon, 5 Jun 2017 19:01:15 +0000 Subject: [Loris-dev] PEAR error reporting In-Reply-To: References: Message-ID: It's no longer required. You can just do "Database::singleton()" without the PEAR::isError boilerplate. It'll throw a proper exception instead of returning a PEAR error if there's an exceptional circumstance. - Dave ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Tom Beaudry Sent: June 5, 2017 2:57:00 PM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] PEAR error reporting Hi Guys, What's the new way to do PEAR error reporting in 17.02 / LORISForms? I have an instrument with a score function that contains: //get the saved scores $db =& Database::singleton(); if(PEAR::isError($db)) { return PEAR::raiseError ("Could not connect to database".$db->getMessage()); } What should it be changed to? Thanks! Tom -------------- next part -------------- An HTML attachment was scrubbed... URL: From michael.joseph at sickkids.ca Tue Jun 6 11:31:44 2017 From: michael.joseph at sickkids.ca (Michael Joseph) Date: Tue, 6 Jun 2017 15:31:44 +0000 Subject: [Loris-dev] Imaging Browser Headers and Data Query Tool Message-ID: Hi Loris dev team, I have two queries: 1) I've been uploading images to Loris though the back-end using the dicomTar.pl and tarchiveLoader scripts. I noticed that the headers for each scan in the Imaging Browser module are incomplete. Only the 'Output Type', 'Space', 'Protocol' and 'Inserted Date' fields show up correctly. The 'Voxel Size', 'Echo Time', 'Rep Time', Slice Thick' and 'Number of volumes' all report 0. The rest of the fields are empty. Did I miss a step that populates the headers? 2) I also recently set up the Data Query Tool. For the 'mri_data' instrument, the only filter I get is 'QCComment'. The 'demographics' instrument is working properly. Do you have any ideas why the rest of the filters don't appear? Thank you, 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 iris.rodriguez at cneuro.edu.cu Tue Jun 6 15:43:05 2017 From: iris.rodriguez at cneuro.edu.cu (=?iso-8859-1?Q?Iris_Rodr=EDguez_Gil?=) Date: Tue, 6 Jun 2017 14:43:05 -0500 Subject: [Loris-dev] tarchiveLoader Message-ID: Hi Loris dev team, I'm having problems with the tarchiveLoader script: No Visit label log dir is /data/loris/data/logs and log file is /data/loris/data/logs/TarLoad-12-17-V3ZYsI.log Use of uninitialized value $is_valid in numeric eq (==) at /data/loris/bin/mri/uploadNeuroDB/minc_insertion.pl line 250. DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`loris`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`CenterID`) REFERENCES `psc` (`CenterID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 941. DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`loris`.`mri_scanner`, CONSTRAINT `FK_mri_scanner_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 946. PSCID is: MC0000015 CandID id: 571907 visit_label is: V1 candidate id 571907 => No Visit label Cleaning up temp files: rm -rf /tmp/TarLoad-12-16-0Dtd3H/MC0000015* Can't exec "mail": No such file or directory at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 596. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 597. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 598. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 599. print() on closed filehandle MAIL at /data/loris/bin/mri/uploadNeuroDB/tarchiveLoader line 600. No Mincs inserted. Any suggestions I will be appreciated. Thanks, Iris. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mouna.safi-harb at mail.mcgill.ca Tue Jun 6 14:50:21 2017 From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab) Date: Tue, 6 Jun 2017 18:50:21 +0000 Subject: [Loris-dev] Imaging Browser Headers and Data Query Tool In-Reply-To: References: Message-ID: Hi Michael, I will tackle the first item in your email, and someone else from the Loris team will get back to you on the second. The headers are not showing up because they likely are not populated in the parameter_file table. I think your issue is coming from the MYSQL version you have. I am assuming you have MYSQL 5.7 and as you are inserting scans, you are getting a message as follows: DBD::mysql::db do failed: Data too long for column 'Value' at row 334 at /data/braincode/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 753. This error results in the parameter_file table not populating your entries. A quick fix would be to alter the parameter_file Value column type to go from Text to LongText. You can give it a try and let me know if this solves your issue (I tested it locally and it seems to work), but I need to run this fix by the Loris-MRI group. Once that is done, we will hopefully issue a fix in the next release. - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Michael Joseph Sent: Tuesday, June 6, 2017 11:31:44 AM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] Imaging Browser Headers and Data Query Tool Hi Loris dev team, I have two queries: 1) I've been uploading images to Loris though the back-end using the dicomTar.pl and tarchiveLoader scripts. I noticed that the headers for each scan in the Imaging Browser module are incomplete. Only the 'Output Type', 'Space', 'Protocol' and 'Inserted Date' fields show up correctly. The 'Voxel Size', 'Echo Time', 'Rep Time', Slice Thick' and 'Number of volumes' all report 0. The rest of the fields are empty. Did I miss a step that populates the headers? 2) I also recently set up the Data Query Tool. For the 'mri_data' instrument, the only filter I get is 'QCComment'. The 'demographics' instrument is working properly. Do you have any ideas why the rest of the filters don't appear? Thank you, 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 Tue Jun 6 16:36:06 2017 From: michael.joseph at sickkids.ca (Michael Joseph) Date: Tue, 6 Jun 2017 20:36:06 +0000 Subject: [Loris-dev] Imaging Browser Headers and Data Query Tool In-Reply-To: References: , Message-ID: Hi Mouna, Thank you! That worked. The headers are showing up now. For the 'Number of volumes' field, is that related to time or is it the number of slices taken? It's only being reported for the DTI and fMRI scans. I tried updating CouchDB as I thought the missing headers might be related but this didn't fix that issue. Thanks, Michael ________________________________ From: Mouna Safi-Harab Sent: June 6, 2017 2:50:21 PM To: Michael Joseph; loris-dev at bic.mni.mcgill.ca Subject: Re: Imaging Browser Headers and Data Query Tool Hi Michael, I will tackle the first item in your email, and someone else from the Loris team will get back to you on the second. The headers are not showing up because they likely are not populated in the parameter_file table. I think your issue is coming from the MYSQL version you have. I am assuming you have MYSQL 5.7 and as you are inserting scans, you are getting a message as follows: DBD::mysql::db do failed: Data too long for column 'Value' at row 334 at /data/braincode/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 753. This error results in the parameter_file table not populating your entries. A quick fix would be to alter the parameter_file Value column type to go from Text to LongText. You can give it a try and let me know if this solves your issue (I tested it locally and it seems to work), but I need to run this fix by the Loris-MRI group. Once that is done, we will hopefully issue a fix in the next release. - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Michael Joseph Sent: Tuesday, June 6, 2017 11:31:44 AM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] Imaging Browser Headers and Data Query Tool Hi Loris dev team, I have two queries: 1) I've been uploading images to Loris though the back-end using the dicomTar.pl and tarchiveLoader scripts. I noticed that the headers for each scan in the Imaging Browser module are incomplete. Only the 'Output Type', 'Space', 'Protocol' and 'Inserted Date' fields show up correctly. The 'Voxel Size', 'Echo Time', 'Rep Time', Slice Thick' and 'Number of volumes' all report 0. The rest of the fields are empty. Did I miss a step that populates the headers? 2) I also recently set up the Data Query Tool. For the 'mri_data' instrument, the only filter I get is 'QCComment'. The 'demographics' instrument is working properly. Do you have any ideas why the rest of the filters don't appear? Thank you, 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 mouna.safi-harb at mail.mcgill.ca Thu Jun 8 11:23:24 2017 From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab) Date: Thu, 8 Jun 2017 15:23:24 +0000 Subject: [Loris-dev] Create DCCID and Organizing CIVET outputs In-Reply-To: References: , , , , Message-ID: Hi Michael, Glad our recommendations worked, and the problem is resolved on your end! - Mouna ________________________________ From: Michael Joseph Sent: Thursday, June 1, 2017 10:13:09 AM To: Mouna Safi-Harab; loris-dev at bic.mni.mcgill.ca Subject: Re: Create DCCID and Organizing CIVET outputs Hi Mouna, Thank you for your help and sorry for the delay in getting back to you. I disabled "ONLY_FULL_GROUP_BY mode" in MySQL but I'm still getting a few errors. DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`loris`.`candidate`, CONSTRAINT `FK_candidate_1` FOREIGN KEY (`CenterID`) REFERENCES `psc` (`CenterID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1041. print() on unopened filehandle LOG at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1181. DBD::mysql::db do failed: Cannot add or update a child row: a foreign key constraint fails (`loris`.`session`, CONSTRAINT `FK_session_1` FOREIGN KEY (`CandID`) REFERENCES `candidate` (`CandID`)) at /data/loris/bin/mri/uploadNeuroDB/NeuroDB/MRI.pm line 266. The logs also show that the "CandID does not exist" and "No centerID" In my prod file, I have the following code. The PSCID and visitLabel are retrieved from the dicom header. I've assigned a CandID for testing. } elsif ($patientID =~ /(.*)-([^-]+$)/) { $subjectID{'PSCID'} = NeuroDB::MRI::my_trim($1); $subjectID{'CandID'} = 123456; $subjectID{'visitLabel'} = NeuroDB::MRI::my_trim($2); $subjectID{'createVisitLabel'} = 1; print "PSCID is: " . $subjectID{'PSCID'} . "\nCandID id: " . $subjectID{'CandID'} . "\nvisit_label is: " . $subjectID{'visitLabel'} . "\n"; } Thanks, Michael ________________________________ From: Mouna Safi-Harab Sent: May 9, 2017 2:02:35 PM To: Michael Joseph; loris-dev at bic.mni.mcgill.ca Subject: Re: Create DCCID and Organizing CIVET outputs Hi Michael, Sorry for the delays in getting back to you on this. The LORIS-MRI codebase does the generation of the CandID for you (check the function CreateMRICandidates in tarchive_validation which calls createNewCandID in MRI.pm). The PSCID, however, is not created (LORIS supports multiple ways in which you can create the PSCID, this is usually read from the config.xml file in the LORIS project directory, so it is a bit trickier than creating the CandID). But since your project would have the PSCID_VisitLabel already known and in the DICOM header, and the prod file is made to parse this, I have a workaround for your project needs. In the determineSubjectID() routine in MRIProcessingUtility.pm, after line 241 (on version 17.0.0), you can add a few lines that selects the CandID the pipeline created a step earlier to be used for the execution of the rest of the steps, while relying on your parsed PSCID from the prod file; as follows: # if the candidate was created from the backend, it won't be in the tarchiveInfo, so add it here my $dbh = &NeuroDB::DBI::connect_to_db(@Settings::db); if (!defined($subjectIDsref->{'CandID'}) && $Settings::createCandidates) { my $query = "SELECT CandID FROM candidate WHERE PSCID=?"; my $sth = ${$this->{'dbhr'}}->prepare($query); $sth->execute($subjectIDsref->{'PSCID'}); if ( $sth->rows > 0 ) { $subjectIDsref->{'CandID'} = $sth->fetchrow_array; } } This should allow you to proceed with candidate creation from the backend based on your project assumptions. Please note this is very specific to your project (in particular, due to the fact that you know the PSCID, but not the CandID, while there is a one-to-one correspondence between these two in LORIS). But I believe it addresses your request. Let me know if you have any further questions. - Mouna ________________________________ From: Michael Joseph Sent: Friday, April 28, 2017 12:49:50 PM To: Mouna Safi-Harab; loris-dev at bic.mni.mcgill.ca Subject: Re: Create DCCID and Organizing CIVET outputs Hi Mouna, Thank you for your reply. Your answers certainly help. For our images, the PatientName header is labeled as PSCID-VisitLabel. I've modified the regex in the prod file to parse this out. I didn't want to modify the header to also include a DCCID because there are other groups sharing the images. I was wondering if there's another way to create a DCCID when images are uploaded (similar to how the scanner is registered). The Imaging Uploader GUI isn't as important to us as we'll be relying on the Perl scripts to upload all our images. Thank you for directing me to the DTIPrep directory. It definitely helps as an example for registering processed data. Michael ________________________________ From: Mouna Safi-Harab Sent: April 27, 2017 2:06:58 PM To: Michael Joseph; loris-dev at bic.mni.mcgill.ca Subject: Re: Create DCCID and Organizing CIVET outputs Hi Michael, Here are my answers to your questions: 1) Setting createCandidates to 1 in the prod file does indeed allow for creation of the candidate from the MRI pipeline. You will need to make sure that 1) the PatientName header is anonymized properly in the DICOM files, and 2) getSubjectIDs() function in this prod file is a) splitting the PatientName header information in a way that is consistent with the anonymization and your project DCCID/PSCID/VisitLabel convention, and b) has the $subjectID{'createVisitLabel'} option set to 1 as you will also likely need the MRI pipeline to create the visit for that candidate as well. However, projects using the Imaging Uploader GUI unfortunately does not allow for this option. If you want a way to make it work for now, you can disable the check on Lines 378-395 in NDB_Menu_Filter_imaging_uploader.class.inc (which sole purpose is to check if the CandID is registered in the database). We can look at this from our end, and make sure the option createCandidate is propagated to the Imaging Uploader GUI as well in a seamless manner to the user (will discuss this at our internal meeting). 2) Loris-MRI codebase provides an example of how to insert files from another processing pipeline into the database. Check the DTIPrep/ directory for an example you can follow. Essentially, inserting processed files into LORIS is a two-step process: you will need a 1) wrapper script that "understands" or "knows" how/where the processed files are stored (this step is processing pipeline dependent), and then 2) have that wrapper script call a generic file called uploadNeuroDB/register_processed_data.pl. The register_processed_data.pl file would take in many required arguments, some of which are the full path of the file you are going to register. Other parameters are the acquisition protocol ID. So yes, the"white_matter", "pve", "tal_mask" were initially created to allow for CIVET outputs to be registered with the correct acquisition protocol. Other required parameters are the sourceFileID which would be the ID of the initial file you sent to CIVET for processing. The second step should be processing pipeline independent. I hope the above answers your questions, or at least, gives you a starting point. - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Michael Joseph Sent: Wednesday, April 19, 2017 4:03 PM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] Create DCCID and Organizing CIVET outputs Hi Loris dev community, I have 2 questions: 1) Is there a way to register new candidates into Loris from the back-end without a DCCID? Essentially, I'd like to add candidates and sessions while running the tarchiveLoader script. I noticed that the prod file has a createCandidates variable. Is there anything else that needs to be modified? 2) How are CIVET outputs typically organized in Loris? I noticed that in the mri_scan_type table, there are labels like "white_matter", "pve", "tal_msk". I'm assuming the most of the files from CIVET would get registered using these labels. Also, is there a good way of linking to the htmls from the CIVET QC pipeline? 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. ________________________________ 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 ganesh.chauhan at cbr.iisc.ac.in Thu Jun 8 22:34:02 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Fri, 9 Jun 2017 08:04:02 +0530 (IST) Subject: [Loris-dev] Problems accessing the Examiner page under Clinical Message-ID: <569854594.16584.1496975642780.JavaMail.zimbra@cbr.iisc.ac.in> Hi, I am getting the following error while accessing the Examiner page via the front end. Please can you suggest me how to resolve this. However when I add an examiner via the back end using the mysql database I can do so and they are available for entering data for an instrument. Many thanks for your help. With best regards, Ganesh The following errors occured while attempting to display this page: * Expression #2 of SELECT list is not in GROUP BY clause and contains nonaggregated column 'LORIS.e.examinerID' which is not functionally dependent on columns in GROUP BY clause; this is incompatible with sql_mode=only_full_group_by * Query: SELECT COUNT(*) FROM (SELECT e.full_name as Examiner, e.examinerID as ID, psc.Name as Site, e.radiologist as Radiologist, GROUP_CONCAT(tn.full_name) as Certification FROM examiners e LEFT JOIN psc ON (e.centerID=psc.CenterID) LEFT JOIN certification c ON (c.examinerID=e.examinerID and c.pass = 'certified') LEFT JOIN test_names tn ON (tn.ID = c.testID) WHERE 1=1 GROUP BY e.full_name,psc.Name ORDER BY e.full_name) as tmptable LIMIT 1 * Bind parameters: Array ( ) * Stack Trace: #0 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(716): Database->execute(Object(PDOStatement), Array) #1 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(733): Database->pselect('SELECT COUNT(*)...', Array) #2 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(751): Database->pselectRow('SELECT COUNT(*)...', Array) #3 /var/www/lorisinstall/Loris/php/libraries/NDB_Menu_Filter.class.inc(600): Database->pselectOne('SELECT COUNT(*)...', Array) #4 /var/www/lorisinstall/Loris/php/libraries/NDB_Menu_Filter.class.inc(492): NDB_Menu_Filter->_getNumberPages('SELECT COUNT(*)...') #5 /var/www/lorisinstall/Loris/php/libraries/NDB_Menu_Filter.class.inc(392): NDB_Menu_Filter->_getList() #6 /var/www/lorisinstall/Loris/php/libraries/NDB_Menu_Filter.class.inc(157): NDB_Menu_Filter->_build() #7 /var/www/lorisinstall/Loris/php/libraries/NDB_Caller.class.inc(322): NDB_Menu_Filter->setup() #8 /var/www/lorisinstall/Loris/php/libraries/NDB_Caller.class.inc(187): NDB_Caller->loadMenu(Object(NDB_Menu_Filter_Form_Examiner), '') #9 /var/www/lorisinstall/Loris/htdocs/main.php(180): NDB_Caller->load('examiner', '') #10 {main} -- 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 ganesh.chauhan at cbr.iisc.ac.in Fri Jun 9 21:56:37 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Sat, 10 Jun 2017 07:26:37 +0530 (IST) Subject: [Loris-dev] Candidate information front page trouble Message-ID: <901940539.18151.1497059797024.JavaMail.zimbra@cbr.iisc.ac.in> Dear team Loris, I added additional fields to the "Candidate Information" following the instructions suggested on Loris Wiki ( [ https://github.com/aces/Loris/wiki/Candidate-Parameters | https://github.com/aces/Loris/wiki/Candidate-Parameters ] ). After the addition I have lost the field "Comment" from the front end which appears after " Reason for Caveat Emptor Flag * ". Even the " Reason for Caveat Emptor Flag * " & " Caveat Emptor Flag for Candidate * " are behaving badly. Only after I choose the Null option and then I choose the False option in " Caveat Emptor Flag for Candidate * " I am able to enter values to the new fields I have created and save them. Any suggestions what is happening or what tests I need to run to find the problem. The google drive link to screen shot of my front end is provided below. https://drive.google.com/open?id=0B17moRKGrNolc3d1Unc5RUVTY1k Many thanks for your help. 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 ganesh.chauhan at cbr.iisc.ac.in Tue Jun 13 08:57:31 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Tue, 13 Jun 2017 18:27:31 +0530 (IST) Subject: [Loris-dev] Adding the QuickForm element "radio" for an instrument Message-ID: <998537015.19247.1497358651223.JavaMail.zimbra@cbr.iisc.ac.in> Hi, Is it possible to add the element "radio" from Quickform while developing an instrument using PHP. If so can get a format for doing so. Thanks for your suggestions. 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 dblader.mcin at gmail.com Tue Jun 13 14:55:00 2017 From: dblader.mcin at gmail.com (David Blader) Date: Tue, 13 Jun 2017 14:55:00 -0400 Subject: [Loris-dev] Problems accessing the Examiner page under Clinical In-Reply-To: <569854594.16584.1496975642780.JavaMail.zimbra@cbr.iisc.ac.in> References: <569854594.16584.1496975642780.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: Hi Ganesh, Just to confirm, you are using MySQL version 5.7? If so, we will be issuing a release soon that will address this issue. You should be notified soon after the release is pushed. We apologize for the inconvenience in the mean time. If you are using a different MySQL version, could you please let us know which you are using so we may better investigate the issue? Thank you, David B. On Thu, Jun 8, 2017 at 10:34 PM, Ganesh Chauhan (CBR) < ganesh.chauhan at cbr.iisc.ac.in> wrote: > Hi, > > I am getting the following error while accessing the Examiner page via the > front end. Please can you suggest me how to resolve this. > However when I add an examiner via the back end using the mysql database I > can do so and they are available for entering data for an instrument. > > Many thanks for your help. > > With best regards, > Ganesh > > The following errors occured while attempting to display this page: > > - *Expression #2 of SELECT list is not in GROUP BY clause and contains > nonaggregated column 'LORIS.e.examinerID' which is not functionally > dependent on columns in GROUP BY clause; this is incompatible with > sql_mode=only_full_group_by* > - *Query:* > > SELECT COUNT(*) FROM (SELECT e.full_name as Examiner, e.examinerID as ID, psc.Name as Site, e.radiologist as Radiologist, GROUP_CONCAT(tn.full_name) as Certification > FROM > examiners e LEFT JOIN psc ON > (e.centerID=psc.CenterID) > LEFT JOIN certification c ON > (c.examinerID=e.examinerID and c.pass = 'certified') > LEFT JOIN test_names tn ON (tn.ID = c.testID) WHERE 1=1 GROUP BY e.full_name,psc.Name ORDER BY e.full_name) as tmptable LIMIT 1 > > - *Bind parameters: Array ( )* > - *Stack Trace:* > > #0 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(716): Database->execute(Object(PDOStatement), Array) > #1 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(733): Database->pselect('SELECT COUNT(*)...', Array) > #2 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(751): Database->pselectRow('SELECT COUNT(*)...', Array) > #3 /var/www/lorisinstall/Loris/php/libraries/NDB_Menu_Filter.class.inc(600): Database->pselectOne('SELECT COUNT(*)...', Array) > #4 /var/www/lorisinstall/Loris/php/libraries/NDB_Menu_Filter.class.inc(492): NDB_Menu_Filter->_getNumberPages('SELECT COUNT(*)...') > #5 /var/www/lorisinstall/Loris/php/libraries/NDB_Menu_Filter.class.inc(392): NDB_Menu_Filter->_getList() > #6 /var/www/lorisinstall/Loris/php/libraries/NDB_Menu_Filter.class.inc(157): NDB_Menu_Filter->_build() > #7 /var/www/lorisinstall/Loris/php/libraries/NDB_Caller.class.inc(322): NDB_Menu_Filter->setup() > #8 /var/www/lorisinstall/Loris/php/libraries/NDB_Caller.class.inc(187): NDB_Caller->loadMenu(Object(NDB_Menu_Filter_Form_Examiner), '') > #9 /var/www/lorisinstall/Loris/htdocs/main.php(180): NDB_Caller->load('examiner', '') > #10 {main} > > > > > -- > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.macfarlane2 at mcgill.ca Tue Jun 20 09:59:50 2017 From: david.macfarlane2 at mcgill.ca (David MacFarlane, Mr) Date: Tue, 20 Jun 2017 13:59:50 +0000 Subject: [Loris-dev] Imaging Browser Headers and Data Query Tool In-Reply-To: References: Message-ID: hi Michael, The "mri_data" in the data query tool only shows information for modalities which are inserted and have a scan selected in the imaging browser to avoid showing all the scan types which aren't acquired in your LORIS instance. The QCComment in a session level variable, so it gets inserted regardless. The demographics would be working because it's entirely candidate based and not data-dependant. If you QC some of the scans that you've inserted into LORIS (including choosing "Selected=true" for exactly one scan of each modality that you want to see in the DQT per session), then rerun the CouchDB_MRI_Import script, I believe it should show up in the data query tool. - Dave ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Michael Joseph Sent: June 6, 2017 11:31:44 AM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] Imaging Browser Headers and Data Query Tool Hi Loris dev team, I have two queries: 1) I've been uploading images to Loris though the back-end using the dicomTar.pl and tarchiveLoader scripts. I noticed that the headers for each scan in the Imaging Browser module are incomplete. Only the 'Output Type', 'Space', 'Protocol' and 'Inserted Date' fields show up correctly. The 'Voxel Size', 'Echo Time', 'Rep Time', Slice Thick' and 'Number of volumes' all report 0. The rest of the fields are empty. Did I miss a step that populates the headers? 2) I also recently set up the Data Query Tool. For the 'mri_data' instrument, the only filter I get is 'QCComment'. The 'demographics' instrument is working properly. Do you have any ideas why the rest of the filters don't appear? Thank you, 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 zvirani.mcin at gmail.com Tue Jun 20 11:52:00 2017 From: zvirani.mcin at gmail.com (Zain Virani) Date: Tue, 20 Jun 2017 11:52:00 -0400 Subject: [Loris-dev] Adding the QuickForm element "radio" for an instrument In-Reply-To: <998537015.19247.1497358651223.JavaMail.zimbra@cbr.iisc.ac.in> References: <998537015.19247.1497358651223.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: Hello Ganesh, Radio button implementation with Quickform is in development. We're aiming to have it ready by 17.2. For now, a select element can achieve the same affect, and should be easy to replace once it's released. Thanks, Zain On Tue, Jun 13, 2017 at 8:57 AM, Ganesh Chauhan (CBR) < ganesh.chauhan at cbr.iisc.ac.in> wrote: > Hi, > > Is it possible to add the element "radio" from Quickform while developing > an instrument using PHP. > If so can get a format for doing so. > > Thanks for your suggestions. > > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From istvan.morocz at mcgill.ca Tue Jun 20 12:47:18 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Tue, 20 Jun 2017 12:47:18 -0400 (EDT) Subject: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ? Message-ID: dear LORIS developers, as mentioned before in today's LORIS meeting, our group needs to learn how to import some 42000 old MRI studies in MINC format into LORIS. we learned in the mean time how to create CANDIDATE and VISIT entries in LORIS via its jason API. because there is no API for DICOM upload (and because we may use our own dcm2minc pipeline) we were delighted to hear from Mouna last week that one may go another route and import MINC files actually directly into LORIS - so that subsequently Louis Collins et al will be able to deal with QA and other processing steps. question : can you refer us to weblinks, HOWTOs and any material on using your registerFile.pl script and related environment so we get this MINC upload mechanism working as soon as possible ? 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 Tue Jun 20 13:53:05 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Tue, 20 Jun 2017 23:23:05 +0530 (IST) Subject: [Loris-dev] Adding the QuickForm element "radio" for an instrument In-Reply-To: References: <998537015.19247.1497358651223.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: <1026232566.22691.1497981185425.JavaMail.zimbra@cbr.iisc.ac.in> Dear Zain, Many thanks for your response. Looking forward to the new release. With best regards, Ganesh From: "Zain Virani" To: "Ganesh Chauhan, CBR" Cc: "loris-dev" Sent: Tuesday, June 20, 2017 9:22:00 PM Subject: Re: [Loris-dev] Adding the QuickForm element "radio" for an instrument Hello Ganesh, Radio button implementation with Quickform is in development. We're aiming to have it ready by 17.2. For now, a select element can achieve the same affect, and should be easy to replace once it's released. Thanks, Zain On Tue, Jun 13, 2017 at 8:57 AM, Ganesh Chauhan (CBR) < [ mailto:ganesh.chauhan at cbr.iisc.ac.in | ganesh.chauhan at cbr.iisc.ac.in ] > wrote: Hi, Is it possible to add the element "radio" from Quickform while developing an instrument using PHP. If so can get a format for doing so. Thanks for your suggestions. 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 ] -- 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 michael.joseph at sickkids.ca Wed Jun 21 11:41:09 2017 From: michael.joseph at sickkids.ca (Michael Joseph) Date: Wed, 21 Jun 2017 15:41:09 +0000 Subject: [Loris-dev] Imaging Browser Headers and Data Query Tool In-Reply-To: References: , Message-ID: Thank you Dave, Yes, QCing the scans allowed them to show up in the data query tool. Michael ________________________________ From: David MacFarlane, Mr Sent: June 20, 2017 9:59:50 AM To: Michael Joseph; loris-dev at bic.mni.mcgill.ca Subject: Re: Imaging Browser Headers and Data Query Tool hi Michael, The "mri_data" in the data query tool only shows information for modalities which are inserted and have a scan selected in the imaging browser to avoid showing all the scan types which aren't acquired in your LORIS instance. The QCComment in a session level variable, so it gets inserted regardless. The demographics would be working because it's entirely candidate based and not data-dependant. If you QC some of the scans that you've inserted into LORIS (including choosing "Selected=true" for exactly one scan of each modality that you want to see in the DQT per session), then rerun the CouchDB_MRI_Import script, I believe it should show up in the data query tool. - Dave ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Michael Joseph Sent: June 6, 2017 11:31:44 AM To: loris-dev at bic.mni.mcgill.ca Subject: [Loris-dev] Imaging Browser Headers and Data Query Tool Hi Loris dev team, I have two queries: 1) I've been uploading images to Loris though the back-end using the dicomTar.pl and tarchiveLoader scripts. I noticed that the headers for each scan in the Imaging Browser module are incomplete. Only the 'Output Type', 'Space', 'Protocol' and 'Inserted Date' fields show up correctly. The 'Voxel Size', 'Echo Time', 'Rep Time', Slice Thick' and 'Number of volumes' all report 0. The rest of the fields are empty. Did I miss a step that populates the headers? 2) I also recently set up the Data Query Tool. For the 'mri_data' instrument, the only filter I get is 'QCComment'. The 'demographics' instrument is working properly. Do you have any ideas why the rest of the filters don't appear? Thank you, 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 zvirani.mcin at gmail.com Wed Jun 21 13:35:00 2017 From: zvirani.mcin at gmail.com (Zain Virani) Date: Wed, 21 Jun 2017 13:35:00 -0400 Subject: [Loris-dev] Problems accessing the Examiner page under Clinical In-Reply-To: <569854594.16584.1496975642780.JavaMail.zimbra@cbr.iisc.ac.in> References: <569854594.16584.1496975642780.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: Hello Ganesh, Loris v17.0.5 was just released which should fix the issue you found in the Examiner page. Thanks for your patience, Zain On Thu, Jun 8, 2017 at 10:34 PM, Ganesh Chauhan (CBR) < ganesh.chauhan at cbr.iisc.ac.in> wrote: > Hi, > > I am getting the following error while accessing the Examiner page via the > front end. Please can you suggest me how to resolve this. > However when I add an examiner via the back end using the mysql database I > can do so and they are available for entering data for an instrument. > > Many thanks for your help. > > With best regards, > Ganesh > > The following errors occured while attempting to display this page: > > - *Expression #2 of SELECT list is not in GROUP BY clause and contains > nonaggregated column 'LORIS.e.examinerID' which is not functionally > dependent on columns in GROUP BY clause; this is incompatible with > sql_mode=only_full_group_by* > - *Query:* > > SELECT COUNT(*) FROM (SELECT e.full_name as Examiner, e.examinerID as ID, psc.Name as Site, e.radiologist as Radiologist, GROUP_CONCAT(tn.full_name) as Certification > FROM > examiners e LEFT JOIN psc ON > (e.centerID=psc.CenterID) > LEFT JOIN certification c ON > (c.examinerID=e.examinerID and c.pass = 'certified') > LEFT JOIN test_names tn ON (tn.ID = c.testID) WHERE 1=1 GROUP BY e.full_name,psc.Name ORDER BY e.full_name) as tmptable LIMIT 1 > > - *Bind parameters: Array ( )* > - *Stack Trace:* > > #0 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(716): Database->execute(Object(PDOStatement), Array) > #1 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(733): Database->pselect('SELECT COUNT(*)...', Array) > #2 /var/www/lorisinstall/Loris/php/libraries/Database.class.inc(751): Database->pselectRow('SELECT COUNT(*)...', Array) > #3 /var/www/lorisinstall/Loris/php/libraries/NDB_Menu_Filter.class.inc(600): Database->pselectOne('SELECT COUNT(*)...', Array) > #4 /var/www/lorisinstall/Loris/php/libraries/NDB_Menu_Filter.class.inc(492): NDB_Menu_Filter->_getNumberPages('SELECT COUNT(*)...') > #5 /var/www/lorisinstall/Loris/php/libraries/NDB_Menu_Filter.class.inc(392): NDB_Menu_Filter->_getList() > #6 /var/www/lorisinstall/Loris/php/libraries/NDB_Menu_Filter.class.inc(157): NDB_Menu_Filter->_build() > #7 /var/www/lorisinstall/Loris/php/libraries/NDB_Caller.class.inc(322): NDB_Menu_Filter->setup() > #8 /var/www/lorisinstall/Loris/php/libraries/NDB_Caller.class.inc(187): NDB_Caller->loadMenu(Object(NDB_Menu_Filter_Form_Examiner), '') > #9 /var/www/lorisinstall/Loris/htdocs/main.php(180): NDB_Caller->load('examiner', '') > #10 {main} > > > > > -- > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From david.macfarlane2 at mcgill.ca Wed Jun 21 15:17:41 2017 From: david.macfarlane2 at mcgill.ca (David MacFarlane, Mr) Date: Wed, 21 Jun 2017 19:17:41 +0000 Subject: [Loris-dev] LORIS v17.0.5 Message-ID: Hi all, LORIS v17.0.5 is now released. This release fixes bugs found since v17.0.4 was released. Users of LORIS v17.0.x are strongly encouraged to upgrade in order to receive the two security fixes (and 3 other minor bug fixes). LORIS instances which have a JWTKey setting which does not meet the new key strength requirements will need to change their JWTKey setting in the configuration module in order to continue to use the API. (The new requirements are similar to the LORIS password requirements, except must also be at least 20 characters long since the key is never directly entered by a user.) For the full list of changes, see https://github.com/aces/Loris/releases. - Dave -------------- next part -------------- An HTML attachment was scrubbed... URL: From istvan.morocz at mcgill.ca Thu Jun 22 14:54:05 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Thu, 22 Jun 2017 14:54:05 -0400 (EDT) Subject: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ? In-Reply-To: References: Message-ID: sounds good, dear Mouna - we will give a try this coming tuesday in the afternoon ! thanks for your email ! bye, pisti On Thu, 22 Jun 2017, Mouna Safi-Harab wrote: > Hi Pisti, > I will send a more detailed answer after the long weekend, but for now, the easiest way for you to know how the script functions is > by simply typing at the command line (from where the MRI codebase directory): > registerFile.pl -help > > This applies to almost all .pl scripts we have in the codebase. > > From that, you can see all the arguments and options you have to be able to run the script. But almost inevitably, you will have to > write a wrapper script that is specific to your project and how you want to import the data (with some variable initialisation) that > itself will call the registerFile.pl script. > > Give it a try, and we can talk more after the weekend. > > - Mouna > > On Tue, Jun 20, 2017 at 12:47 PM, Istv?n ?kos M?rocz wrote: > dear LORIS developers, > > as mentioned before in today's LORIS meeting, our group needs to learn > how to import some 42000 old MRI studies in MINC format into LORIS. > > we learned in the mean time how to create CANDIDATE and VISIT entries > in LORIS via its jason API.? because there is no API for DICOM upload > (and because we may use our own dcm2minc pipeline) we were delighted > to hear from Mouna last week that one may go another route and import > MINC files actually directly into LORIS - so that subsequently Louis > Collins et al will be able to deal with QA and other processing steps. > > question : can you refer us to weblinks, HOWTOs and any material on > using your registerFile.pl script and related environment so we get > this MINC upload mechanism working as soon as possible ? > > 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 > ?. > ? `~*-,._.,-*~'`^`'~*-,._.,-*~'`" > > > > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : 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 mouna.safiharab at gmail.com Thu Jun 22 14:48:43 2017 From: mouna.safiharab at gmail.com (Mouna Safi-Harab) Date: Thu, 22 Jun 2017 14:48:43 -0400 Subject: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ? In-Reply-To: References: Message-ID: Hi Pisti, I will send a more detailed answer after the long weekend, but for now, the easiest way for you to know how the script functions is by simply typing at the command line (from where the MRI codebase directory): registerFile.pl -help This applies to almost all .pl scripts we have in the codebase. >From that, you can see all the arguments and options you have to be able to run the script. But almost inevitably, you will have to write a wrapper script that is specific to your project and how you want to import the data (with some variable initialisation) that itself will call the registerFile.pl script. Give it a try, and we can talk more after the weekend. - Mouna On Tue, Jun 20, 2017 at 12:47 PM, Istv?n ?kos M?rocz < istvan.morocz at mcgill.ca> wrote: > dear LORIS developers, > > as mentioned before in today's LORIS meeting, our group needs to learn > how to import some 42000 old MRI studies in MINC format into LORIS. > > we learned in the mean time how to create CANDIDATE and VISIT entries > in LORIS via its jason API. because there is no API for DICOM upload > (and because we may use our own dcm2minc pipeline) we were delighted > to hear from Mouna last week that one may go another route and import > MINC files actually directly into LORIS - so that subsequently Louis > Collins et al will be able to deal with QA and other processing steps. > > question : can you refer us to weblinks, HOWTOs and any material on > using your registerFile.pl script and related environment so we get > this MINC upload mechanism working as soon as possible ? > > 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 gluneau.mcin at gmail.com Mon Jun 26 08:27:58 2017 From: gluneau.mcin at gmail.com (Gregory Luneau) Date: Mon, 26 Jun 2017 08:27:58 -0400 Subject: [Loris-dev] Candidate information front page trouble In-Reply-To: <901940539.18151.1497059797024.JavaMail.zimbra@cbr.iisc.ac.in> References: <901940539.18151.1497059797024.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: Hello Ganesh, can you please provide me with the version of Loris you are running, also the branch you are on. Can you also provide me with the SQL you used to insert the new fields in the candidate information? Any JavaScript errors in the console when on that page? Thank you, Greg On Fri, Jun 9, 2017 at 9:56 PM, Ganesh Chauhan (CBR) < ganesh.chauhan at cbr.iisc.ac.in> wrote: > Dear team Loris, > > I added additional fields to the "Candidate Information" following the > instructions suggested on Loris Wiki (https://github.com/aces/ > Loris/wiki/Candidate-Parameters). After the addition I have lost the > field "Comment" from the front end which appears after "Reason for Caveat > Emptor Flag* ". Even the " Reason for Caveat Emptor Flag* " & " Caveat > Emptor Flag for Candidate* " are behaving badly. Only after I choose the > Null option and then I choose the False option in " Caveat Emptor Flag > for Candidate* " I am able to enter values to the new fields I have > created and save them. > > Any suggestions what is happening or what tests I need to run to find the > problem. The google drive link to screen shot of my front end is provided > below. > https://drive.google.com/open?id=0B17moRKGrNolc3d1Unc5RUVTY1k > > Many thanks for your help. > > 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 istvan.morocz at mcgill.ca Tue Jun 27 13:58:57 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Tue, 27 Jun 2017 13:58:57 -0400 (EDT) Subject: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ? In-Reply-To: References: Message-ID: dear Mouna, one of the key questions for us is if we loose essential information by importing MINC files into LORIS using the registerFile.pl script - as compared to using DCM files via the regular=manual LORIS way. i assume here that we do a 'perfect' job outside LORIS when we convert DCM files to MINC files by using our own scripts. then, we just heard this morning that the next LORIS version this summer will feature a DCM importing API - is that truly the case ? bye, pisti On Thu, 22 Jun 2017, Istv?n ?kos M?rocz wrote: > sounds good, dear Mouna - we will > give a try this coming tuesday in > the afternoon ! thanks for your > email ! bye, pisti > > On Thu, 22 Jun 2017, Mouna Safi-Harab wrote: > >> Hi Pisti, >> I will send a more detailed answer after the long weekend, but for now, the >> easiest way for you to know how the script functions is >> by simply typing at the command line (from where the MRI codebase >> directory): >> registerFile.pl -help >> >> This applies to almost all .pl scripts we have in the codebase. >> >> From that, you can see all the arguments and options you have to be able to >> run the script. But almost inevitably, you will have to >> write a wrapper script that is specific to your project and how you want to >> import the data (with some variable initialisation) that >> itself will call the registerFile.pl script. >> >> Give it a try, and we can talk more after the weekend. >> >> - Mouna >> >> On Tue, Jun 20, 2017 at 12:47 PM, Istv?n ?kos M?rocz >> wrote: >> dear LORIS developers, >> >> as mentioned before in today's LORIS meeting, our group needs to >> learn >> how to import some 42000 old MRI studies in MINC format into LORIS. >> >> we learned in the mean time how to create CANDIDATE and VISIT entries >> in LORIS via its jason API.? because there is no API for DICOM upload >> (and because we may use our own dcm2minc pipeline) we were delighted >> to hear from Mouna last week that one may go another route and import >> MINC files actually directly into LORIS - so that subsequently Louis >> Collins et al will be able to deal with QA and other processing >> steps. >> >> question : can you refer us to weblinks, HOWTOs and any material on >> using your registerFile.pl script and related environment so we get >> this MINC upload mechanism working as soon as possible ? >> >> 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 >> ?. >> ? `~*-,._.,-*~'`^`'~*-,._.,-*~'`" >> >> >> >> > > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ > ' > : 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 samir.das at mcgill.ca Tue Jun 27 16:09:37 2017 From: samir.das at mcgill.ca (Samir Das) Date: Tue, 27 Jun 2017 13:09:37 -0700 Subject: [Loris-dev] Fwd: LORIS Document Repository In-Reply-To: <30266241-3ADA-44AC-9C51-1897BD7E64EB@childmind.org> References: <30266241-3ADA-44AC-9C51-1897BD7E64EB@childmind.org> Message-ID: ---------- 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. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mouna.safi-harb at mail.mcgill.ca Wed Jun 28 10:24:31 2017 From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab) Date: Wed, 28 Jun 2017 14:24:31 +0000 Subject: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ? In-Reply-To: References: , Message-ID: Hi Pisti, When you register a MINC file into the database, you should be able to store whatever MINC header is in the MINC file itself. So if the conversion from DICOM to MINC resulted in some loss, this will be reflected in the database (in other words, the database can only store the extent of what is in the MINC file, and comparing this to a DICOM starting point is dependent on the dcm2mnc conversion, not Loris). Regarding your second question, I know there is a few important things on the API development/improvement roadmap, one of which is uploading DICOMs and launching the pipeline through the API, however, I am not sure that end of summer is the projected completion time. I was under the impression that downloading DICOMs is more feasible by the end of the summer than uploading and inserting through the API, but I could be wrong. Xavier, Dave, and Samir which are on this email list can comment on the API timelines and priorities better than me. - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Istv?n ?kos M?rocz Sent: Tuesday, June 27, 2017 1:58:57 PM To: Mouna Safi-Harab Cc: loris-dev; Jordan Stirling; Sridar Narayanan, Dr. Subject: Re: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ? dear Mouna, one of the key questions for us is if we loose essential information by importing MINC files into LORIS using the registerFile.pl script - as compared to using DCM files via the regular=manual LORIS way. i assume here that we do a 'perfect' job outside LORIS when we convert DCM files to MINC files by using our own scripts. then, we just heard this morning that the next LORIS version this summer will feature a DCM importing API - is that truly the case ? bye, pisti On Thu, 22 Jun 2017, Istv?n ?kos M?rocz wrote: > sounds good, dear Mouna - we will > give a try this coming tuesday in > the afternoon ! thanks for your > email ! bye, pisti > > On Thu, 22 Jun 2017, Mouna Safi-Harab wrote: > >> Hi Pisti, >> I will send a more detailed answer after the long weekend, but for now, the >> easiest way for you to know how the script functions is >> by simply typing at the command line (from where the MRI codebase >> directory): >> registerFile.pl -help >> >> This applies to almost all .pl scripts we have in the codebase. >> >> From that, you can see all the arguments and options you have to be able to >> run the script. But almost inevitably, you will have to >> write a wrapper script that is specific to your project and how you want to >> import the data (with some variable initialisation) that >> itself will call the registerFile.pl script. >> >> Give it a try, and we can talk more after the weekend. >> >> - Mouna >> >> On Tue, Jun 20, 2017 at 12:47 PM, Istv?n ?kos M?rocz >> wrote: >> dear LORIS developers, >> >> as mentioned before in today's LORIS meeting, our group needs to >> learn >> how to import some 42000 old MRI studies in MINC format into LORIS. >> >> we learned in the mean time how to create CANDIDATE and VISIT entries >> in LORIS via its jason API. because there is no API for DICOM upload >> (and because we may use our own dcm2minc pipeline) we were delighted >> to hear from Mouna last week that one may go another route and import >> MINC files actually directly into LORIS - so that subsequently Louis >> Collins et al will be able to deal with QA and other processing >> steps. >> >> question : can you refer us to weblinks, HOWTOs and any material on >> using your registerFile.pl script and related environment so we get >> this MINC upload mechanism working as soon as possible ? >> >> 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 >> . >> `~*-,._.,-*~'`^`'~*-,._.,-*~'`" >> >> >> >> > > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ > ' > : 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 . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" -------------- next part -------------- An HTML attachment was scrubbed... URL: From mouna.safi-harb at mail.mcgill.ca Wed Jun 28 11:54:44 2017 From: mouna.safi-harb at mail.mcgill.ca (Mouna Safi-Harab) Date: Wed, 28 Jun 2017 15:54:44 +0000 Subject: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ? In-Reply-To: <7E01D600-C125-42BF-882B-3D952C9B5AF6@mcgill.ca> References: , <7E01D600-C125-42BF-882B-3D952C9B5AF6@mcgill.ca> Message-ID: Hi Sridar, Yes, I can confirm the script already exists. It is called 'batch_uploads_imageuploader'. It operates on a zip of DICOMs (not on MINCs) without using the imaging uploader GUI. It takes in a standard in (text file) of the entries (i.e. a zip of DICOM scans for a given candidate's MRI session) that need to be inserted into the database. The scans should be placed on the filesystem and the text file would point to them, one at a time, and the above script will read the entries in the file, one line at a time, and process them for you from the backend without using the GUI. Details of how the script is launched and what additional inputs are required can be found here: https://github.com/aces/Loris-MRI/pull/133 We have a meeting today (which I believe is to discuss this). - Mouna ________________________________ From: Sridar Narayanan, Dr. Sent: Wednesday, June 28, 2017 11:43:11 AM To: Mouna Safi-Harab Cc: Istvan Akos Imre Morocz, Dr; Mouna Safi-Harab; loris-dev; Jordan Stirling Subject: Re: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ? Hi Mouna, While the import/upload of DICOMs via the API will be a welcome addition to the LORIS tools, I think the immediate need is for batch upload of MRI files. Samir has indicated that this ability is already available (batch_upload_mri). Could you confirm whether this script operates only on MINC files, or DICOM as well? I think Pisti will need to know the details of how to run this script, as we will be importing tens of thousands of already-acquired MRI data into LORIS for the IPMSA project. Thanks, Sridar On Jun 28, 2017, at 7:24 AM, Mouna Safi-Harab > wrote: Hi Pisti, When you register a MINC file into the database, you should be able to store whatever MINC header is in the MINC file itself. So if the conversion from DICOM to MINC resulted in some loss, this will be reflected in the database (in other words, the database can only store the extent of what is in the MINC file, and comparing this to a DICOM starting point is dependent on the dcm2mnc conversion, not Loris). Regarding your second question, I know there is a few important things on the API development/improvement roadmap, one of which is uploading DICOMs and launching the pipeline through the API, however, I am not sure that end of summer is the projected completion time. I was under the impression that downloading DICOMs is more feasible by the end of the summer than uploading and inserting through the API, but I could be wrong. Xavier, Dave, and Samir which are on this email list can comment on the API timelines and priorities better than me. - Mouna ________________________________ From: loris-dev-bounces at bic.mni.mcgill.ca > on behalf of Istv?n ?kos M?rocz > Sent: Tuesday, June 27, 2017 1:58:57 PM To: Mouna Safi-Harab Cc: loris-dev; Jordan Stirling; Sridar Narayanan, Dr. Subject: Re: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ? dear Mouna, one of the key questions for us is if we loose essential information by importing MINC files into LORIS using the registerFile.pl script - as compared to using DCM files via the regular=manual LORIS way. i assume here that we do a 'perfect' job outside LORIS when we convert DCM files to MINC files by using our own scripts. then, we just heard this morning that the next LORIS version this summer will feature a DCM importing API - is that truly the case ? bye, pisti On Thu, 22 Jun 2017, Istv?n ?kos M?rocz wrote: > sounds good, dear Mouna - we will > give a try this coming tuesday in > the afternoon ! thanks for your > email ! bye, pisti > > On Thu, 22 Jun 2017, Mouna Safi-Harab wrote: > >> Hi Pisti, >> I will send a more detailed answer after the long weekend, but for now, the >> easiest way for you to know how the script functions is >> by simply typing at the command line (from where the MRI codebase >> directory): >> registerFile.pl -help >> >> This applies to almost all .pl scripts we have in the codebase. >> >> From that, you can see all the arguments and options you have to be able to >> run the script. But almost inevitably, you will have to >> write a wrapper script that is specific to your project and how you want to >> import the data (with some variable initialisation) that >> itself will call the registerFile.pl script. >> >> Give it a try, and we can talk more after the weekend. >> >> - Mouna >> >> On Tue, Jun 20, 2017 at 12:47 PM, Istv?n ?kos M?rocz >> > wrote: >> dear LORIS developers, >> >> as mentioned before in today's LORIS meeting, our group needs to >> learn >> how to import some 42000 old MRI studies in MINC format into LORIS. >> >> we learned in the mean time how to create CANDIDATE and VISIT entries >> in LORIS via its jason API. because there is no API for DICOM upload >> (and because we may use our own dcm2minc pipeline) we were delighted >> to hear from Mouna last week that one may go another route and import >> MINC files actually directly into LORIS - so that subsequently Louis >> Collins et al will be able to deal with QA and other processing >> steps. >> >> question : can you refer us to weblinks, HOWTOs and any material on >> using your registerFile.pl script and related environment so we get >> this MINC upload mechanism working as soon as possible ? >> >> 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 >> . >> `~*-,._.,-*~'`^`'~*-,._.,-*~'`" >> >> >> >> > > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ > ' > : 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 . `~*-,._.,-*~'`^`'~*-,._.,-*~'`" -------------- next part -------------- An HTML attachment was scrubbed... URL: From istvan.morocz at mcgill.ca Wed Jun 28 12:07:47 2017 From: istvan.morocz at mcgill.ca (=?ISO-8859-15?Q?Istv=E1n_=C1kos_M=F3rocz?=) Date: Wed, 28 Jun 2017 12:07:47 -0400 (EDT) Subject: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ? In-Reply-To: References: , <7E01D600-C125-42BF-882B-3D952C9B5AF6@mcgill.ca> Message-ID: yes, indeed, we will meet in 90min at NW125 :) thank you for your informative emails, Mouna ! see you soon, bye, pisti On Wed, 28 Jun 2017, Mouna Safi-Harab wrote: > > Hi Sridar, > > > Yes, I can confirm the script already exists. It is called 'batch_uploads_imageuploader'. It operates on a zip of?DICOMs (not > on?MINCs) without using the imaging uploader GUI. It takes in a standard in (text file) of the entries (i.e. a zip of DICOM scans > for a given candidate's MRI session) that need to be inserted into the database. > > The scans should be placed on the filesystem and the text file would point to them, one at a time, and the above script will read > the entries in the file, one line?at a time, and process them for you from the backend without using the GUI. > > > Details of how the script is launched and what additional?inputs are required can be found here: > > https://github.com/aces/Loris-MRI/pull/133 > > > > We have a meeting today (which?I believe is?to discuss this). > > > - Mouna > > ____________________________________________________________________________________________________________________________________ > From: Sridar Narayanan, Dr. > Sent: Wednesday, June 28, 2017 11:43:11 AM > To: Mouna Safi-Harab > Cc: Istvan Akos Imre Morocz, Dr; Mouna Safi-Harab; loris-dev; Jordan Stirling > Subject: Re: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ? ? > Hi Mouna, > While the import/upload of DICOMs via the API will be a welcome addition to the LORIS tools, I think the immediate need is for batch > upload of MRI files. Samir has indicated that this ability is already available (batch_upload_mri). Could you confirm whether this > script operates only on MINC files, or DICOM as well? I think Pisti will need to know the details of how to run this script, as we > will be importing tens of thousands of already-acquired MRI data into LORIS for the IPMSA project. > > Thanks, > > Sridar > > > On Jun 28, 2017, at 7:24 AM, Mouna Safi-Harab wrote: > > Hi Pisti, > > > When you register a MINC file into the database, you should be able to store whatever MINC header is in the MINC file itself. > So if the conversion from DICOM to MINC resulted in some loss, this will be reflected in the database (in other?words, the > database can only store the extent of what is in the MINC file, and comparing this to a DICOM?starting point is dependent on > the dcm2mnc?conversion, not Loris). > > > Regarding your second question, I know there is a few important things on the API development/improvement?roadmap, one of > which?is uploading DICOMs and launching the pipeline through the API, however, I am not sure that end of summer is the > projected completion time. I was under the impression that downloading DICOMs is more feasible by the end of the summer?than > uploading and inserting through the API, but I could be wrong. Xavier, Dave, and Samir which are on this email list?can > comment?on the API?timelines and?priorities better than me.? > > > - Mouna > > ____________________________________________________________________________________________________________________________________ > From: loris-dev-bounces at bic.mni.mcgill.ca on behalf of Istv?n ?kos M?rocz > > Sent: Tuesday, June 27, 2017 1:58:57 PM > To: Mouna Safi-Harab > Cc: loris-dev; Jordan Stirling; Sridar Narayanan, Dr. > Subject: Re: [Loris-dev] importing MINC files into LORIS - registerFile.pl script ? ? > dear Mouna, > > one of the key questions for us is if we loose essential information > by importing MINC files into LORIS using the registerFile.pl script - > as compared to using DCM files via the regular=manual LORIS way.? i > assume here that we do a 'perfect' job outside LORIS when we convert > DCM files to MINC files by using our own scripts. > > then, we just heard this morning that the next LORIS version this > summer will feature a DCM importing API - is that truly the case ? > > bye, pisti > > > On Thu, 22 Jun 2017, Istv?n ?kos M?rocz wrote: > > > sounds good, dear Mouna - we will > > give a try this coming tuesday in > > the afternoon !? thanks for your > > email !? bye, pisti > > > > On Thu, 22 Jun 2017, Mouna Safi-Harab wrote: > > > >> Hi Pisti, > >> I will send a more detailed answer after the long weekend, but for now, the > >> easiest way for you to know how the script functions is > >> by simply typing at the command line (from where the MRI codebase > >> directory): > >> registerFile.pl -help > >> > >> This applies to almost all .pl scripts we have in the codebase. > >> > >> From that, you can see all the arguments and options you have to be able to > >> run the script. But almost inevitably, you will have to > >> write a wrapper script that is specific to your project and how you want to > >> import the data (with some variable initialisation) that > >> itself will call the registerFile.pl script. > >> > >> Give it a try, and we can talk more after the weekend. > >> > >> - Mouna > >> > >> On Tue, Jun 20, 2017 at 12:47 PM, Istv?n ?kos M?rocz > >> wrote: > >>?????? dear LORIS developers, > >> > >>?????? as mentioned before in today's LORIS meeting, our group needs to > >> learn > >>?????? how to import some 42000 old MRI studies in MINC format into LORIS. > >> > >>?????? we learned in the mean time how to create CANDIDATE and VISIT entries > >>?????? in LORIS via its jason API.? because there is no API for DICOM upload > >>?????? (and because we may use our own dcm2minc pipeline) we were delighted > >>?????? to hear from Mouna last week that one may go another route and import > >>?????? MINC files actually directly into LORIS - so that subsequently Louis > >>?????? Collins et al will be able to deal with QA and other processing > >> steps. > >> > >>?????? question : can you refer us to weblinks, HOWTOs and any material on > >>?????? using your registerFile.pl script and related environment so we get > >>?????? this MINC upload mechanism working as soon as possible ? > >> > >>?????? 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 > >>?????? ?. > >>?????? ? `~*-,._.,-*~'`^`'~*-,._.,-*~'`" > >> > >> > >> > >> > > > >? ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ > > ' > > :??????? 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 > ? . > ?? `~*-,._.,-*~'`^`'~*-,._.,-*~'`" > > > > ,-*~'`^`'~*-,._.,-*~'`^`'~*-,._ ' : 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 wangshen.mcin at gmail.com Wed Jun 28 15:22:48 2017 From: wangshen.mcin at gmail.com (Shen Wang) Date: Wed, 28 Jun 2017 15:22:48 -0400 Subject: [Loris-dev] Fwd: LORIS Document Repository In-Reply-To: References: <30266241-3ADA-44AC-9C51-1897BD7E64EB@childmind.org> Message-ID: 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From ganesh.chauhan at cbr.iisc.ac.in Thu Jun 29 00:21:11 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Thu, 29 Jun 2017 09:51:11 +0530 (IST) Subject: [Loris-dev] Fwd: LORIS Document Repository In-Reply-To: References: <30266241-3ADA-44AC-9C51-1897BD7E64EB@childmind.org> Message-ID: <1076585160.28116.1498710071701.JavaMail.zimbra@cbr.iisc.ac.in> 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" 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: ---------- 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 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 https://www.cbr.iisc.ac.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From ganesh.chauhan at cbr.iisc.ac.in Thu Jun 29 01:54:38 2017 From: ganesh.chauhan at cbr.iisc.ac.in (Ganesh Chauhan (CBR)) Date: Thu, 29 Jun 2017 11:24:38 +0530 (IST) Subject: [Loris-dev] Candidate information front page trouble In-Reply-To: References: <901940539.18151.1497059797024.JavaMail.zimbra@cbr.iisc.ac.in> Message-ID: <132902234.28362.1498715678900.JavaMail.zimbra@cbr.iisc.ac.in> Dear Greg, - I am currently using LORIS version 17.0.2. - My MYSQL version is "mysql Ver 14.14 Distrib 5.7.18" - I do not have any JAVA script error showing up on the front end - I do not understand what you meant by "branch you are on" - SQL commands used is as follows: INSERT INTO parameter_type_category (Name, Type) VALUES ('Candidate Parameters','Metavars'); INSERT INTO parameter_type (Name, Type, Description, SourceFrom, Queryable) VALUES ('first_contact', "date", 'Date of first contact (likely by telephone)', 'parameter_candidate', 1); INSERT INTO parameter_type_category_rel (ParameterTypeID, ParameterTypeCategoryID) SELECT pt.ParameterTypeID, ptc.ParameterTypeCategoryID FROM parameter_type_category ptc, parameter_type pt WHERE ptc.Name='Candidate Parameters' AND pt.Name='first_contact'; INSERT INTO parameter_type (Name, Type, Description, SourceFrom, Queryable) VALUES ('first_contact_response', "text", 'Response: first contact', 'parameter_candidate', 1); INSERT INTO parameter_type_category_rel (ParameterTypeID, ParameterTypeCategoryID) SELECT pt.ParameterTypeID, ptc.ParameterTypeCategoryID FROM parameter_type_category ptc, parameter_type pt WHERE ptc.Name='Candidate Parameters' AND pt.Name='first_contact_response'; Many thanks for your help. With best regards, Ganesh From: "Gregory Luneau" To: "Ganesh Chauhan, CBR" Cc: "loris-dev" Sent: Monday, June 26, 2017 5:57:58 PM Subject: Re: [Loris-dev] Candidate information front page trouble Hello Ganesh, can you please provide me with the version of Loris you are running, also the branch you are on. Can you also provide me with the SQL you used to insert the new fields in the candidate information? Any JavaScript errors in the console when on that page? Thank you, Greg On Fri, Jun 9, 2017 at 9:56 PM, Ganesh Chauhan (CBR) < [ mailto:ganesh.chauhan at cbr.iisc.ac.in | ganesh.chauhan at cbr.iisc.ac.in ] > wrote: Dear team Loris, I added additional fields to the "Candidate Information" following the instructions suggested on Loris Wiki ( [ https://github.com/aces/Loris/wiki/Candidate-Parameters | https://github.com/aces/Loris/wiki/Candidate-Parameters ] ). After the addition I have lost the field "Comment" from the front end which appears after " Reason for Caveat Emptor Flag * ". Even the " Reason for Caveat Emptor Flag * " & " Caveat Emptor Flag for Candidate * " are behaving badly. Only after I choose the Null option and then I choose the False option in " Caveat Emptor Flag for Candidate * " I am able to enter values to the new fields I have created and save them. Any suggestions what is happening or what tests I need to run to find the problem. The google drive link to screen shot of my front end is provided below. [ https://drive.google.com/open?id=0B17moRKGrNolc3d1Unc5RUVTY1k | https://drive.google.com/open?id=0B17moRKGrNolc3d1Unc5RUVTY1k ] Many thanks for your help. 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 christine.rogers at mcgill.ca Fri Jun 30 19:30:20 2017 From: christine.rogers at mcgill.ca (Christine Rogers) Date: Fri, 30 Jun 2017 16:30:20 -0700 Subject: [Loris-dev] Document Repository question Message-ID: (Forwarded on behalf of Bonhwang Koo of the Child Mind Institute) > Here?s the message, which the console error typed out: > > 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: > > /document_repository/ajax/addCategory.php 500 (Internal Server Error) > > send @ jquery-1.11.0.min.js:4 > ajax @ jquery-1.11.0.min:js:4 > postCategory @ document_repository_helper.js:89 > dispatch @ jquery-1.11.0.min.js:3 > r.handle @ jquery-1.11.0.min.js:3 > > 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 > f: 646.625.4348 > > 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. > > On 6/30/17, 12:47 PM, "loris-dev-bounces at bic.mni.mcgill.ca on behalf of loris-dev-owner at bic.mni.mcgill.ca" wrote: > > Your request to the Loris-dev mailing list > > Posting of your message titled "Re: [Loris-dev] Fwd: LORIS > Document Repository" > > has been rejected by the list moderator. The moderator gave the > following reason for rejecting your request: > > "Hi Bonhwang, > > Could you please re-send your post? The email you have sent to the > listserv did not come out well with character encoding, I believe. > > Thanks! The Loris team " > > Any questions or comments should be directed to the list administrator > at: > > loris-dev-owner at bic.mni.mcgill.ca > >