From cecile.madjar at mcin.ca Mon Feb 1 10:03:38 2021 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Mon, 1 Feb 2021 10:03:38 -0500 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> <0863DD40-4B8E-498C-816E-E28E25A8FCCA@bwh.harvard.edu> Message-ID: Hi Alfredo, This is odd. I cannot reproduce your error when I checkout v23.0.3. How did you do the upgrade? Via a merge of v23.0.3 onto your install or a clean checkout? Thanks, C?cile On Fri, Jan 29, 2021 at 6:19 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Cecile, > > I am now running LORIS-MRI v23.0.3 and LORIS v23.0.2. I am getting the > following output for the same command line: > > Command line > === > perl /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/minc_insertion.pl > -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w > -mincPath > /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc > === > > Output > === > log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is > /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-17-32-M9vqyU.log > Can't locate object method "selectall_array" via package "DBI::db" at > /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm > line 1819. > SELECT ArchiveLocation FROM tarchive WHERE > TarchiveID = ( SELECT TarchiveID > FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? > ) PSCID is: AZH101303 > CandID id: 814099 > visit_label is: 105ms302w48 > PSCID is: AZH101303 > CandID id: 814099 > visit_label is: 105ms302w48 > === > > Log file ( > /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-17-32-M9vqyU.log) > === > ==> Loading file from disk > /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc > > --> mapping DICOM parameter for > /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc > > --> filters out parameters of length > 1000 for > /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc > === > > > I think issue is coming from this line: > > > https://github.com/aces/Loris-MRI/blob/8c7e41549fb10a845caa96f31c8e505ef3adca52/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm#L1819 > > Maybe ?selectall_array? has to be replaced by ?selectall_arrayref?? > > Thank you for all your help. > > Best, > Alfredo. > > > On Jan 29, 2021, at 12:57 PM, Cecile Madjar wrote: > > External Email - Use Caution > > I see. There are significant changes between 22 and 23 on LORIS-MRI > (mainly the ability to set specific MRI protocols based on Visit label, > Projects or subprojects requiring changes to the MRI protocol tables). > However, I do not foresee any major blocker as to proceed to upgrading to > 23.0 for LORIS-MRI. > > Hope this helps, > > C?cile > > On Fri, Jan 29, 2021 at 12:15 PM Sridar Narayanan, Dr. < > sridar.narayanan at mcgill.ca> wrote: > >> Hi Cecile, >> >> I think Alfredo?s plan was to upgrade to 23.0 as soon as the upgrade to >> 22.0 was completed successfully (since a direct upgrade was not possible). >> Since 23.0 appears to fix some bugs in 22.0, when would it be most >> efficient to perform the 22.0 -> 23.0 upgrade? Should Alfredo ensure that >> 22.0 is functional with all patches applied first, to be safe, or will the >> upgrade to 23.0 take care of many of these issues? >> >> Thanks, >> >> Sridar >> >> >> On Jan 29, 2021, at 11:09 AM, Cecile Madjar >> wrote: >> >> Hi Alfredo, >> >> I was able to reproduce your bug on version 22.0 of LORIS-MRI and it was >> maybe present in older versions as well. This was fixed in release 23.0 >> with better logging information. >> >> I just sent a PR with a fix for 22.0 that you can find here: >> https://github.com/aces/Loris-MRI/pull/573/files >> >> >> That should resolve the issue you were having. Let me know how it goes. >> >> Best, >> >> C?cile >> >> On Fri, Jan 29, 2021 at 1:18 AM Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >>> Hi Cecile, >>> >>> I tried the script minc_insertion.pl >>> >>> but it seems that the Candidate should not exist before the execution of >>> the script. Is this the case? This would be problematic in order to upload >>> multiple sequences for a given Candidate. This is the error I am getting: >>> >>> === >>> $ perl minc_insertion.pl >>> >>> -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w >>> -mincPath >>> /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc >>> >>> log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is >>> /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log >>> ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with >>> PSCID=AZH101303 already exists. >>> SELECT ArchiveLocation FROM tarchive WHERE >>> TarchiveID = ( SELECT TarchiveID >>> FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? >>> ) PSCID is: AZH101303 >>> CandID id: 814099 >>> visit_label is: 105ms302w48 >>> PSCID is: AZH101303 >>> CandID id: 814099 >>> visit_label is: 105ms302w48 >>> Spool message is: ERROR: Cannot create candidate (AZH101303, 814099) as >>> a candidate with PSCID=AZH101303 already exists >>> === >>> >>> Best, >>> Alfredo. >>> >>> P.S. The file /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log >>> is not being written. >>> >>> On Jan 26, 2021, at 4:33 PM, Cecile Madjar >>> wrote: >>> >>> External Email - Use Caution >>> >>> Hi, >>> >>> Thank you for the clarification. I think I understand better >>> the confusion. >>> >>> You can insert MINC files without having to insert DICOM files by >>> running the minc_insertion.pl >>> >>> script with the -force option. Basically, the force option will bypass >>> checks to see if there are DICOMs to attach the file to. >>> >>> minc_insertion.pl >>> >>> -profile -mincPath >> your MINC file> -force -create_minc_pics >>> >>> For the NIfTI files alone, because of the nature of that file format (no >>> header information like MINC...), you will have to specify a lot of the >>> information when calling the script imaging_non_minc_insertion.pl >>> >>> (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... >>> Basically all the columns of the files table). It needs to be associated >>> with an upload_id for the logging in the database but the upload_id does >>> not necessarily need to be DICOM files. It could be a zipped archive of all >>> the NIfTI files of the session uploaded for example. Then you would just >>> need to create a little wrapper script to run >>> imaging_non_minc_insertion.pl >>> >>> on the loaded NIfTI files. >>> >>> Does that clarify the steps? >>> >>> Thanks! >>> >>> C?cile >>> >>> On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. < >>> sridar.narayanan at mcgill.ca> wrote: >>> >>>> Hi Cecile, >>>> >>>> Just to clarify, many import issues seem to stem from problems with the >>>> implementation of dcm2mnc used by Loris. These DICOM files can be >>>> successfully converted to MINC and NifTI with other tools, and so we were >>>> wondering if it would be possible to import MRI data into Loris as MINC & >>>> NifTI files *instead of* importing the DICOMs. Alternatively, we could >>>> convert these files to BIDS and import that instead of DICOM. The important >>>> point is whether we can *avoid importing DICOM* for new >>>> scan/participant instances, but import only BIDS or MINC + NiFTI data and >>>> generate a new Loris ID from this. We are not asking about attaching a MINC >>>> or NifTI file to an existing record, which we know can be done (e.g. for >>>> label files associated with the images). >>>> >>>> Thanks, >>>> >>>> Sridar >>>> >>>> >>>> On Jan 25, 2021, at 5:01 PM, Cecile Madjar >>>> wrote: >>>> >>>> Hi Alfredo, >>>> >>>> I am a bit confused by your email. The two perl scripts I mentioned >>>> last week do not require the data to be organized in BIDS to insert them. >>>> Did you look into them? >>>> >>>> Sorry, maybe I am missing something. >>>> >>>> C?cile >>>> >>>> On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo < >>>> AMORALESPINZON at bwh.harvard.edu> wrote: >>>> >>>>> Hi Cecile, >>>>> >>>>> Thank you for your answer. I am sorry I was not enough specific >>>>> regarding what we are looking for. We are actually looking for a solution >>>>> to avoid importing the ?raw? images in minc and nifti images instead of >>>>> DICOM. We are having a lot of issues importing DICOM (~1.700 visits with >>>>> issues) and we want to explore options for uploading the original images >>>>> (e.g., t1) using minc and nifti without them being in BIDS formar. >>>>> >>>>> Do you have scripts for this? >>>>> >>>>> Best, >>>>> Alfredo. >>>>> >>>>> On Jan 19, 2021, at 1:59 PM, Cecile Madjar >>>>> wrote: >>>>> >>>>> External Email - Use Caution >>>>> >>>>> Hi Alfredo, >>>>> >>>>> Very sorry for the late reply. In short, yes, it is possible to do >>>>> both. >>>>> >>>>> It is possible to insert MINC files in LORIS by using the LORIS-MRI >>>>> script called minc_insertion.pl >>>>> in >>>>> the uploadNeuroDB folder. If you run perl minc_insertion.pl >>>>> >>>>> -h; you will see the explanation on how to run the script. >>>>> >>>>> Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI >>>>> script called imaging_non_minc_insertion.pl >>>>> in >>>>> the same uploadNeuroDB folder. Running perl >>>>> imaging_non_minc_insertion.pl >>>>> >>>>> should give you all the information you need in order to run the script. >>>>> >>>>> Hope this helps, >>>>> >>>>> C?cile >>>>> >>>>> On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo < >>>>> AMORALESPINZON at bwh.harvard.edu> wrote: >>>>> >>>>>> Dear LorisDev team, >>>>>> >>>>>> Is is possible to upload nifti and minc files into LORIS, for >>>>>> instance to a given visit, without having the files in BIDS format? >>>>>> >>>>>> Best regards, >>>>>> Alfredo. >>>>>> The information in this e-mail is intended only for the person to >>>>>> whom it is addressed. If you believe this e-mail was sent to you in error >>>>>> and the e-mail contains patient information, please contact the Mass >>>>>> General Brigham Compliance HelpLine at >>>>>> http://www.massgeneralbrigham.org/complianceline >>>>>> >>>>>> . If the e-mail was sent to you in error but does not contain patient >>>>>> information, please contact the sender and properly dispose of the e-mail. >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>>> >>>>> >>>>> The information in this e-mail is intended only for the person to whom >>>>> it is addressed. If you believe this e-mail was sent to you in error and >>>>> the e-mail contains patient information, please contact the Mass General >>>>> Brigham Compliance HelpLine at >>>>> http://www.massgeneralbrigham.org/complianceline >>>>> >>>>> . If the e-mail was sent to you in error but does not contain patient >>>>> information, please contact the sender and properly dispose of the e-mail. >>>>> >>>> >>>> >>> The information in this e-mail is intended only for the person to whom >>> it is addressed. If you believe this e-mail was sent to you in error and >>> the e-mail contains patient information, please contact the Mass General >>> Brigham Compliance HelpLine at >>> http://www.massgeneralbrigham.org/complianceline >>> >>> . If the e-mail was sent to you in error but does not contain patient >>> information, please contact the sender and properly dispose of the e-mail. >>> >> >> > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Mon Feb 1 10:48:44 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 1 Feb 2021 15:48:44 +0000 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> <0863DD40-4B8E-498C-816E-E28E25A8FCCA@bwh.harvard.edu> Message-ID: <8215E6C3-C7CD-4E85-BFA8-02B65C9ECEC9@bwh.harvard.edu> Hi Cecile, I checkout the git tag v23.0.3. Should I update to a newer commit? Let me know if a quick call (Zoom/Google-meet) where I can share my screen would be a good way to check this. Best, Alfredo. On Feb 1, 2021, at 10:03 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, This is odd. I cannot reproduce your error when I checkout v23.0.3. How did you do the upgrade? Via a merge of v23.0.3 onto your install or a clean checkout? Thanks, C?cile On Fri, Jan 29, 2021 at 6:19 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, I am now running LORIS-MRI v23.0.3 and LORIS v23.0.2. I am getting the following output for the same command line: Command line === perl /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/minc_insertion.pl -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w -mincPath /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc === Output === log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-17-32-M9vqyU.log Can't locate object method "selectall_array" via package "DBI::db" at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1819. SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 === Log file (/data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-17-32-M9vqyU.log) === ==> Loading file from disk /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc --> mapping DICOM parameter for /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc --> filters out parameters of length > 1000 for /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc === I think issue is coming from this line: https://github.com/aces/Loris-MRI/blob/8c7e41549fb10a845caa96f31c8e505ef3adca52/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm#L1819 Maybe ?selectall_array? has to be replaced by ?selectall_arrayref?? Thank you for all your help. Best, Alfredo. On Jan 29, 2021, at 12:57 PM, Cecile Madjar > wrote: External Email - Use Caution I see. There are significant changes between 22 and 23 on LORIS-MRI (mainly the ability to set specific MRI protocols based on Visit label, Projects or subprojects requiring changes to the MRI protocol tables). However, I do not foresee any major blocker as to proceed to upgrading to 23.0 for LORIS-MRI. Hope this helps, C?cile On Fri, Jan 29, 2021 at 12:15 PM Sridar Narayanan, Dr. > wrote: Hi Cecile, I think Alfredo?s plan was to upgrade to 23.0 as soon as the upgrade to 22.0 was completed successfully (since a direct upgrade was not possible). Since 23.0 appears to fix some bugs in 22.0, when would it be most efficient to perform the 22.0 -> 23.0 upgrade? Should Alfredo ensure that 22.0 is functional with all patches applied first, to be safe, or will the upgrade to 23.0 take care of many of these issues? Thanks, Sridar On Jan 29, 2021, at 11:09 AM, Cecile Madjar > wrote: Hi Alfredo, I was able to reproduce your bug on version 22.0 of LORIS-MRI and it was maybe present in older versions as well. This was fixed in release 23.0 with better logging information. I just sent a PR with a fix for 22.0 that you can find here: https://github.com/aces/Loris-MRI/pull/573/files That should resolve the issue you were having. Let me know how it goes. Best, C?cile On Fri, Jan 29, 2021 at 1:18 AM Morales Pinzon, Alfredo > wrote: Hi Cecile, I tried the script minc_insertion.pl but it seems that the Candidate should not exist before the execution of the script. Is this the case? This would be problematic in order to upload multiple sequences for a given Candidate. This is the error I am getting: === $ perl minc_insertion.pl -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w -mincPath /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists. SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 Spool message is: ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists === Best, Alfredo. P.S. The file /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log is not being written. On Jan 26, 2021, at 4:33 PM, Cecile Madjar > wrote: External Email - Use Caution Hi, Thank you for the clarification. I think I understand better the confusion. You can insert MINC files without having to insert DICOM files by running the minc_insertion.pl script with the -force option. Basically, the force option will bypass checks to see if there are DICOMs to attach the file to. minc_insertion.pl -profile -mincPath -force -create_minc_pics For the NIfTI files alone, because of the nature of that file format (no header information like MINC...), you will have to specify a lot of the information when calling the script imaging_non_minc_insertion.pl (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... Basically all the columns of the files table). It needs to be associated with an upload_id for the logging in the database but the upload_id does not necessarily need to be DICOM files. It could be a zipped archive of all the NIfTI files of the session uploaded for example. Then you would just need to create a little wrapper script to run imaging_non_minc_insertion.pl on the loaded NIfTI files. Does that clarify the steps? Thanks! C?cile On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. > wrote: Hi Cecile, Just to clarify, many import issues seem to stem from problems with the implementation of dcm2mnc used by Loris. These DICOM files can be successfully converted to MINC and NifTI with other tools, and so we were wondering if it would be possible to import MRI data into Loris as MINC & NifTI files instead of importing the DICOMs. Alternatively, we could convert these files to BIDS and import that instead of DICOM. The important point is whether we can avoid importing DICOM for new scan/participant instances, but import only BIDS or MINC + NiFTI data and generate a new Loris ID from this. We are not asking about attaching a MINC or NifTI file to an existing record, which we know can be done (e.g. for label files associated with the images). Thanks, Sridar On Jan 25, 2021, at 5:01 PM, Cecile Madjar > wrote: Hi Alfredo, I am a bit confused by your email. The two perl scripts I mentioned last week do not require the data to be organized in BIDS to insert them. Did you look into them? Sorry, maybe I am missing something. C?cile On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, Thank you for your answer. I am sorry I was not enough specific regarding what we are looking for. We are actually looking for a solution to avoid importing the ?raw? images in minc and nifti images instead of DICOM. We are having a lot of issues importing DICOM (~1.700 visits with issues) and we want to explore options for uploading the original images (e.g., t1) using minc and nifti without them being in BIDS formar. Do you have scripts for this? Best, Alfredo. On Jan 19, 2021, at 1:59 PM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Very sorry for the late reply. In short, yes, it is possible to do both. It is possible to insert MINC files in LORIS by using the LORIS-MRI script called minc_insertion.pl in the uploadNeuroDB folder. If you run perl minc_insertion.pl -h; you will see the explanation on how to run the script. Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called imaging_non_minc_insertion.pl in the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl should give you all the information you need in order to run the script. Hope this helps, C?cile On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format? Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Mon Feb 1 11:22:48 2021 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Mon, 1 Feb 2021 11:22:48 -0500 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: <8215E6C3-C7CD-4E85-BFA8-02B65C9ECEC9@bwh.harvard.edu> References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> <0863DD40-4B8E-498C-816E-E28E25A8FCCA@bwh.harvard.edu> <8215E6C3-C7CD-4E85-BFA8-02B65C9ECEC9@bwh.harvard.edu> Message-ID: Hi Alfredo, Thank you for the information. Actually, you might just need to reinstall DBI via cpan? A colleague experienced the same issue and reinstalling the library fixed it. Best, C?cile On Mon, Feb 1, 2021 at 10:49 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Cecile, > > I checkout the git tag v23.0.3. Should I update to a newer commit? > > Let me know if a quick call (Zoom/Google-meet) where I can share my > screen would be a good way to check this. > > Best, > Alfredo. > > On Feb 1, 2021, at 10:03 AM, Cecile Madjar wrote: > > External Email - Use Caution > > Hi Alfredo, > > This is odd. I cannot reproduce your error when I checkout v23.0.3. > > How did you do the upgrade? Via a merge of v23.0.3 onto your install or a > clean checkout? > > Thanks, > > C?cile > > On Fri, Jan 29, 2021 at 6:19 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Hi Cecile, >> >> I am now running LORIS-MRI v23.0.3 and LORIS v23.0.2. I am getting the >> following output for the same command line: >> >> Command line >> === >> perl /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/ >> minc_insertion.pl >> >> -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w >> -mincPath >> /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc >> === >> >> Output >> === >> log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is >> /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-17-32-M9vqyU.log >> Can't locate object method "selectall_array" via package "DBI::db" at >> /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm >> line 1819. >> SELECT ArchiveLocation FROM tarchive WHERE >> TarchiveID = ( SELECT TarchiveID >> FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? >> ) PSCID is: AZH101303 >> CandID id: 814099 >> visit_label is: 105ms302w48 >> PSCID is: AZH101303 >> CandID id: 814099 >> visit_label is: 105ms302w48 >> === >> >> Log file ( >> /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-17-32-M9vqyU.log) >> === >> ==> Loading file from disk >> /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc >> >> --> mapping DICOM parameter for >> /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc >> >> --> filters out parameters of length > 1000 for >> /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc >> === >> >> >> I think issue is coming from this line: >> >> >> https://github.com/aces/Loris-MRI/blob/8c7e41549fb10a845caa96f31c8e505ef3adca52/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm#L1819 >> >> >> Maybe ?selectall_array? has to be replaced by ?selectall_arrayref?? >> >> Thank you for all your help. >> >> Best, >> Alfredo. >> >> >> On Jan 29, 2021, at 12:57 PM, Cecile Madjar >> wrote: >> >> External Email - Use Caution >> >> I see. There are significant changes between 22 and 23 on LORIS-MRI >> (mainly the ability to set specific MRI protocols based on Visit label, >> Projects or subprojects requiring changes to the MRI protocol tables). >> However, I do not foresee any major blocker as to proceed to upgrading to >> 23.0 for LORIS-MRI. >> >> Hope this helps, >> >> C?cile >> >> On Fri, Jan 29, 2021 at 12:15 PM Sridar Narayanan, Dr. < >> sridar.narayanan at mcgill.ca> wrote: >> >>> Hi Cecile, >>> >>> I think Alfredo?s plan was to upgrade to 23.0 as soon as the upgrade to >>> 22.0 was completed successfully (since a direct upgrade was not possible). >>> Since 23.0 appears to fix some bugs in 22.0, when would it be most >>> efficient to perform the 22.0 -> 23.0 upgrade? Should Alfredo ensure that >>> 22.0 is functional with all patches applied first, to be safe, or will the >>> upgrade to 23.0 take care of many of these issues? >>> >>> Thanks, >>> >>> Sridar >>> >>> >>> On Jan 29, 2021, at 11:09 AM, Cecile Madjar >>> wrote: >>> >>> Hi Alfredo, >>> >>> I was able to reproduce your bug on version 22.0 of LORIS-MRI and it was >>> maybe present in older versions as well. This was fixed in release 23.0 >>> with better logging information. >>> >>> I just sent a PR with a fix for 22.0 that you can find here: >>> https://github.com/aces/Loris-MRI/pull/573/files >>> >>> >>> That should resolve the issue you were having. Let me know how it goes. >>> >>> Best, >>> >>> C?cile >>> >>> On Fri, Jan 29, 2021 at 1:18 AM Morales Pinzon, Alfredo < >>> AMORALESPINZON at bwh.harvard.edu> wrote: >>> >>>> Hi Cecile, >>>> >>>> I tried the script minc_insertion.pl >>>> >>>> but it seems that the Candidate should not exist before the execution of >>>> the script. Is this the case? This would be problematic in order to upload >>>> multiple sequences for a given Candidate. This is the error I am getting: >>>> >>>> === >>>> $ perl minc_insertion.pl >>>> >>>> -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w >>>> -mincPath >>>> /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc >>>> >>>> log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is >>>> /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log >>>> ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with >>>> PSCID=AZH101303 already exists. >>>> SELECT ArchiveLocation FROM tarchive WHERE >>>> TarchiveID = ( SELECT TarchiveID >>>> FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? >>>> ) PSCID is: AZH101303 >>>> CandID id: 814099 >>>> visit_label is: 105ms302w48 >>>> PSCID is: AZH101303 >>>> CandID id: 814099 >>>> visit_label is: 105ms302w48 >>>> Spool message is: ERROR: Cannot create candidate (AZH101303, 814099) as >>>> a candidate with PSCID=AZH101303 already exists >>>> === >>>> >>>> Best, >>>> Alfredo. >>>> >>>> P.S. The file /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log >>>> is not being written. >>>> >>>> On Jan 26, 2021, at 4:33 PM, Cecile Madjar >>>> wrote: >>>> >>>> External Email - Use Caution >>>> >>>> Hi, >>>> >>>> Thank you for the clarification. I think I understand better >>>> the confusion. >>>> >>>> You can insert MINC files without having to insert DICOM files by >>>> running the minc_insertion.pl >>>> >>>> script with the -force option. Basically, the force option will bypass >>>> checks to see if there are DICOMs to attach the file to. >>>> >>>> minc_insertion.pl >>>> >>>> -profile -mincPath >>> your MINC file> -force -create_minc_pics >>>> >>>> For the NIfTI files alone, because of the nature of that file format >>>> (no header information like MINC...), you will have to specify a lot of the >>>> information when calling the script imaging_non_minc_insertion.pl >>>> >>>> (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... >>>> Basically all the columns of the files table). It needs to be associated >>>> with an upload_id for the logging in the database but the upload_id does >>>> not necessarily need to be DICOM files. It could be a zipped archive of all >>>> the NIfTI files of the session uploaded for example. Then you would just >>>> need to create a little wrapper script to run >>>> imaging_non_minc_insertion.pl >>>> >>>> on the loaded NIfTI files. >>>> >>>> Does that clarify the steps? >>>> >>>> Thanks! >>>> >>>> C?cile >>>> >>>> On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. < >>>> sridar.narayanan at mcgill.ca> wrote: >>>> >>>>> Hi Cecile, >>>>> >>>>> Just to clarify, many import issues seem to stem from problems with >>>>> the implementation of dcm2mnc used by Loris. These DICOM files can be >>>>> successfully converted to MINC and NifTI with other tools, and so we were >>>>> wondering if it would be possible to import MRI data into Loris as MINC & >>>>> NifTI files *instead of* importing the DICOMs. Alternatively, we >>>>> could convert these files to BIDS and import that instead of DICOM. The >>>>> important point is whether we can *avoid importing DICOM* for new >>>>> scan/participant instances, but import only BIDS or MINC + NiFTI data and >>>>> generate a new Loris ID from this. We are not asking about attaching a MINC >>>>> or NifTI file to an existing record, which we know can be done (e.g. for >>>>> label files associated with the images). >>>>> >>>>> Thanks, >>>>> >>>>> Sridar >>>>> >>>>> >>>>> On Jan 25, 2021, at 5:01 PM, Cecile Madjar >>>>> wrote: >>>>> >>>>> Hi Alfredo, >>>>> >>>>> I am a bit confused by your email. The two perl scripts I mentioned >>>>> last week do not require the data to be organized in BIDS to insert them. >>>>> Did you look into them? >>>>> >>>>> Sorry, maybe I am missing something. >>>>> >>>>> C?cile >>>>> >>>>> On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo < >>>>> AMORALESPINZON at bwh.harvard.edu> wrote: >>>>> >>>>>> Hi Cecile, >>>>>> >>>>>> Thank you for your answer. I am sorry I was not enough specific >>>>>> regarding what we are looking for. We are actually looking for a solution >>>>>> to avoid importing the ?raw? images in minc and nifti images instead of >>>>>> DICOM. We are having a lot of issues importing DICOM (~1.700 visits with >>>>>> issues) and we want to explore options for uploading the original images >>>>>> (e.g., t1) using minc and nifti without them being in BIDS formar. >>>>>> >>>>>> Do you have scripts for this? >>>>>> >>>>>> Best, >>>>>> Alfredo. >>>>>> >>>>>> On Jan 19, 2021, at 1:59 PM, Cecile Madjar >>>>>> wrote: >>>>>> >>>>>> External Email - Use Caution >>>>>> >>>>>> Hi Alfredo, >>>>>> >>>>>> Very sorry for the late reply. In short, yes, it is possible to do >>>>>> both. >>>>>> >>>>>> It is possible to insert MINC files in LORIS by using the LORIS-MRI >>>>>> script called minc_insertion.pl >>>>>> in >>>>>> the uploadNeuroDB folder. If you run perl minc_insertion.pl >>>>>> >>>>>> -h; you will see the explanation on how to run the script. >>>>>> >>>>>> Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI >>>>>> script called imaging_non_minc_insertion.pl >>>>>> in >>>>>> the same uploadNeuroDB folder. Running perl >>>>>> imaging_non_minc_insertion.pl >>>>>> >>>>>> should give you all the information you need in order to run the script. >>>>>> >>>>>> Hope this helps, >>>>>> >>>>>> C?cile >>>>>> >>>>>> On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo < >>>>>> AMORALESPINZON at bwh.harvard.edu> wrote: >>>>>> >>>>>>> Dear LorisDev team, >>>>>>> >>>>>>> Is is possible to upload nifti and minc files into LORIS, for >>>>>>> instance to a given visit, without having the files in BIDS format? >>>>>>> >>>>>>> Best regards, >>>>>>> Alfredo. >>>>>>> The information in this e-mail is intended only for the person to >>>>>>> whom it is addressed. If you believe this e-mail was sent to you in error >>>>>>> and the e-mail contains patient information, please contact the Mass >>>>>>> General Brigham Compliance HelpLine at >>>>>>> http://www.massgeneralbrigham.org/complianceline >>>>>>> >>>>>>> . If the e-mail was sent to you in error but does not contain patient >>>>>>> information, please contact the sender and properly dispose of the e-mail. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>>> >>>>>> >>>>>> The information in this e-mail is intended only for the person to >>>>>> whom it is addressed. If you believe this e-mail was sent to you in error >>>>>> and the e-mail contains patient information, please contact the Mass >>>>>> General Brigham Compliance HelpLine at >>>>>> http://www.massgeneralbrigham.org/complianceline >>>>>> >>>>>> . If the e-mail was sent to you in error but does not contain patient >>>>>> information, please contact the sender and properly dispose of the e-mail. >>>>>> >>>>> >>>>> >>>> The information in this e-mail is intended only for the person to whom >>>> it is addressed. If you believe this e-mail was sent to you in error and >>>> the e-mail contains patient information, please contact the Mass General >>>> Brigham Compliance HelpLine at >>>> http://www.massgeneralbrigham.org/complianceline >>>> >>>> . If the e-mail was sent to you in error but does not contain patient >>>> information, please contact the sender and properly dispose of the e-mail. >>>> >>> >>> >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.org/complianceline >> >> . If the e-mail was sent to you in error but does not contain patient >> information, please contact the sender and properly dispose of the e-mail. >> > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Mon Feb 1 23:01:09 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Tue, 2 Feb 2021 04:01:09 +0000 Subject: [Loris-dev] LORIS - Upload nifti and minc In-Reply-To: References: <4232C92C-2E56-460D-89F0-9FF528151CFB@bwh.harvard.edu> <38FAFB94-9EE0-4E22-9B32-C3BB83408A55@mcgill.ca> <0863DD40-4B8E-498C-816E-E28E25A8FCCA@bwh.harvard.edu> <8215E6C3-C7CD-4E85-BFA8-02B65C9ECEC9@bwh.harvard.edu> Message-ID: <540D865A-4ABC-4676-9DD3-63ABEC67594B@bwh.harvard.edu> Hi Cecile, After upgrading, I don?t have the same error anymore. Now I?m facing some issues with duplicated SeriesInstanceUID which I can check on my side. Thank you for all your help! By the way, I ended up installing DBI 1.643, the version 1.632, which seems to be the default for Ubuntu 16.04.4 Xenial, doesn?t include the function selectall_array. Best, Alfredo. On Feb 1, 2021, at 11:22 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Thank you for the information. Actually, you might just need to reinstall DBI via cpan? A colleague experienced the same issue and reinstalling the library fixed it. Best, C?cile On Mon, Feb 1, 2021 at 10:49 AM Morales Pinzon, Alfredo > wrote: Hi Cecile, I checkout the git tag v23.0.3. Should I update to a newer commit? Let me know if a quick call (Zoom/Google-meet) where I can share my screen would be a good way to check this. Best, Alfredo. On Feb 1, 2021, at 10:03 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, This is odd. I cannot reproduce your error when I checkout v23.0.3. How did you do the upgrade? Via a merge of v23.0.3 onto your install or a clean checkout? Thanks, C?cile On Fri, Jan 29, 2021 at 6:19 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, I am now running LORIS-MRI v23.0.3 and LORIS v23.0.2. I am getting the following output for the same command line: Command line === perl /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/minc_insertion.pl -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w -mincPath /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc === Output === log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-17-32-M9vqyU.log Can't locate object method "selectall_array" via package "DBI::db" at /data_/ipmsa/loris_data/IPMSA/bin/mri/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm line 1819. SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 === Log file (/data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-17-32-M9vqyU.log) === ==> Loading file from disk /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc --> mapping DICOM parameter for /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc --> filters out parameters of length > 1000 for /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc === I think issue is coming from this line: https://github.com/aces/Loris-MRI/blob/8c7e41549fb10a845caa96f31c8e505ef3adca52/uploadNeuroDB/NeuroDB/MRIProcessingUtility.pm#L1819 Maybe ?selectall_array? has to be replaced by ?selectall_arrayref?? Thank you for all your help. Best, Alfredo. On Jan 29, 2021, at 12:57 PM, Cecile Madjar > wrote: External Email - Use Caution I see. There are significant changes between 22 and 23 on LORIS-MRI (mainly the ability to set specific MRI protocols based on Visit label, Projects or subprojects requiring changes to the MRI protocol tables). However, I do not foresee any major blocker as to proceed to upgrading to 23.0 for LORIS-MRI. Hope this helps, C?cile On Fri, Jan 29, 2021 at 12:15 PM Sridar Narayanan, Dr. > wrote: Hi Cecile, I think Alfredo?s plan was to upgrade to 23.0 as soon as the upgrade to 22.0 was completed successfully (since a direct upgrade was not possible). Since 23.0 appears to fix some bugs in 22.0, when would it be most efficient to perform the 22.0 -> 23.0 upgrade? Should Alfredo ensure that 22.0 is functional with all patches applied first, to be safe, or will the upgrade to 23.0 take care of many of these issues? Thanks, Sridar On Jan 29, 2021, at 11:09 AM, Cecile Madjar > wrote: Hi Alfredo, I was able to reproduce your bug on version 22.0 of LORIS-MRI and it was maybe present in older versions as well. This was fixed in release 23.0 with better logging information. I just sent a PR with a fix for 22.0 that you can find here: https://github.com/aces/Loris-MRI/pull/573/files That should resolve the issue you were having. Let me know how it goes. Best, C?cile On Fri, Jan 29, 2021 at 1:18 AM Morales Pinzon, Alfredo > wrote: Hi Cecile, I tried the script minc_insertion.pl but it seems that the Candidate should not exist before the execution of the script. Is this the case? This would be problematic in order to upload multiple sequences for a given Candidate. This is the error I am getting: === $ perl minc_insertion.pl -profile prod -force -verbose -create_minc_pics -acquisition_protocol t2w -mincPath /home/bic/moralf/testInsertionMncAdvance/AZH101303_814099_105ms302w48/azh101303_814099_105ms302w48_20130507_123330/azh101303_814099_105ms302w48_20130507_123330_6e1_mri.mnc log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists. SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 Spool message is: ERROR: Cannot create candidate (AZH101303, 814099) as a candidate with PSCID=AZH101303 already exists === Best, Alfredo. P.S. The file /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-0-27-M2gjUd.log is not being written. On Jan 26, 2021, at 4:33 PM, Cecile Madjar > wrote: External Email - Use Caution Hi, Thank you for the clarification. I think I understand better the confusion. You can insert MINC files without having to insert DICOM files by running the minc_insertion.pl script with the -force option. Basically, the force option will bypass checks to see if there are DICOMs to attach the file to. minc_insertion.pl -profile -mincPath -force -create_minc_pics For the NIfTI files alone, because of the nature of that file format (no header information like MINC...), you will have to specify a lot of the information when calling the script imaging_non_minc_insertion.pl (output_type, scan_type, date_acquired, scanner_id, coordinate_space etc... Basically all the columns of the files table). It needs to be associated with an upload_id for the logging in the database but the upload_id does not necessarily need to be DICOM files. It could be a zipped archive of all the NIfTI files of the session uploaded for example. Then you would just need to create a little wrapper script to run imaging_non_minc_insertion.pl on the loaded NIfTI files. Does that clarify the steps? Thanks! C?cile On Mon, Jan 25, 2021 at 5:16 PM Sridar Narayanan, Dr. > wrote: Hi Cecile, Just to clarify, many import issues seem to stem from problems with the implementation of dcm2mnc used by Loris. These DICOM files can be successfully converted to MINC and NifTI with other tools, and so we were wondering if it would be possible to import MRI data into Loris as MINC & NifTI files instead of importing the DICOMs. Alternatively, we could convert these files to BIDS and import that instead of DICOM. The important point is whether we can avoid importing DICOM for new scan/participant instances, but import only BIDS or MINC + NiFTI data and generate a new Loris ID from this. We are not asking about attaching a MINC or NifTI file to an existing record, which we know can be done (e.g. for label files associated with the images). Thanks, Sridar On Jan 25, 2021, at 5:01 PM, Cecile Madjar > wrote: Hi Alfredo, I am a bit confused by your email. The two perl scripts I mentioned last week do not require the data to be organized in BIDS to insert them. Did you look into them? Sorry, maybe I am missing something. C?cile On Mon, Jan 25, 2021 at 3:45 PM Morales Pinzon, Alfredo > wrote: Hi Cecile, Thank you for your answer. I am sorry I was not enough specific regarding what we are looking for. We are actually looking for a solution to avoid importing the ?raw? images in minc and nifti images instead of DICOM. We are having a lot of issues importing DICOM (~1.700 visits with issues) and we want to explore options for uploading the original images (e.g., t1) using minc and nifti without them being in BIDS formar. Do you have scripts for this? Best, Alfredo. On Jan 19, 2021, at 1:59 PM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Very sorry for the late reply. In short, yes, it is possible to do both. It is possible to insert MINC files in LORIS by using the LORIS-MRI script called minc_insertion.pl in the uploadNeuroDB folder. If you run perl minc_insertion.pl -h; you will see the explanation on how to run the script. Regarding NIfTI files that are not in BIDS, you can use the LORIS-MRI script called imaging_non_minc_insertion.pl in the same uploadNeuroDB folder. Running perl imaging_non_minc_insertion.pl should give you all the information you need in order to run the script. Hope this helps, C?cile On Thu, Jan 14, 2021 at 3:28 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, Is is possible to upload nifti and minc files into LORIS, for instance to a given visit, without having the files in BIDS format? Best regards, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From zia.mohades at mcin.ca Tue Feb 2 09:49:47 2021 From: zia.mohades at mcin.ca (Zia Mohades) Date: Tue, 2 Feb 2021 09:49:47 -0500 Subject: [Loris-dev] Issues with landing page, data query and BrainBrowser In-Reply-To: References: <09C35758-DB2A-41D9-B5B6-94FB0095B4F5@bwh.harvard.edu> Message-ID: Hi Alfredo, Please let me know if your issue has been resolved. Thank you On Mon, Jan 25, 2021 at 8:35 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear Zia, > > The issue is when loading the landing page once a user had logged in into > LORIS. The systems remains unresponsive until the graph is loaded. I am > moving to the last version of LORIS right now, I will inform if the issues > persists in the latests version. > > Thank you. > > Alfredo. > > On Jan 7, 2021, at 3:34 PM, Zia Mohades wrote: > > External Email - Use Caution > > Hello, > > Regarding your first question. As Dave mentioned we haven't experienced > any issues with loading when we click on the link/site under the graph. We > did however noticed some formatting issues which should be fixed in the new > version of LORIS but nothing related to the loading functionality. > > > Thank you > > > On Wed, Jan 6, 2021 at 12:51 PM Dave MacFarlane > wrote: > >> On Wed, Jan 6, 2021 at 12:30 PM Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >>> Dear LorisDev team, >>> >>> We are experiencing the following issues in Loris. Could you please help >>> me or guide me on how address them. >>> >>> 1. After login into LORIS, the webpage does not allow the user to go to >>> any link until the graph under "Study Progression" is created. This is >>> taking more than one minute to load. I guess this is because we have >>> hundreds of centers. Is it possible to remove the graph from the landing >>> page? (See attachment) >>> >>> >> I don't believe it should take that long even with a large number of >> sites. I'll let someone from CCNA handle this part of the question since >> they also have hundreds of sites and might have more insight.. >> >> >>> >>> 2. When using the Data Query Tool the front-end crashes with error 500. >>> >>> This is what I can see in the loris-error.log >>> >>> === >>> [Wed Jan 06 12:23:31.920274 2021] [php7:error] [pid 12100] [client >>> 216.15.126.108:56023 >>> ] >>> PHP Fatal error: Uncaught ConfigurationException: NDB_Factory::CouchDB() >>> requires all parameters to be supplied. in >>> /var/www/loris/php/libraries/NDB_Factory.class.inc:297\nStack trace:\n#0 >>> /var/www/loris/modules/dataquery/php/dataquery.class.inc(59): >>> NDB_Factory->couchDB('%COUCH_DATABASE...', '%COUCH_HOSTNAME...', 0, >>> '%COUCH_USERNAME...', '%COUCH_PASSWORD...')\n#1 >>> /var/www/loris/php/libraries/NDB_Form.class.inc(188): >>> LORIS\\dataquery\\Dataquery->setup()\n#2 >>> /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171): >>> NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#3 >>> /var/www/loris/src/Middleware/PageDecorationMiddleware.php(49): >>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), >>> Object(LORIS\\dataquery\\Dataquery))\n#4 >>> /var/www/loris/php/libraries/NDB_Page.class.inc(659): >>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), >>> Object(LORIS\\dataquery\\Dataquery))\n#5 >>> /var/www/loris/php/libraries/Module.class.inc(341): >>> NDB_Page->process(Object(Zend\\ in >>> /var/www/loris/php/libraries/NDB_Factory.class.inc on line 297, referer: >>> >>> https://ipmsa-loris.bic.mni.mcgill.ca/imaging_browser/viewSession/?sessionID=85935 >>> >>> === >>> >>> >> The DQT currently requires a CouchDB backend with the data imported into >> it. It looks like the CouchDB hostname/database/username/ password/etc >> aren't set up. The Configurations section of the file >> modules/dataquery/README.md should have more information about the setup >> required. Is the `` tag in project/config.xml setup as described >> in step 3 of that document? >> >> >>> >>> 3. In the statistics section (Reports -> Statistics) I can see the >>> following message at the bottom of the page: >>> >>> === >>> Oops >>> >>> It seems like the scan type selected does not have a corresponding >>> column in the mri_parameter_form table in the database. >>> In order to display the statistics for the scan type, make sure the >>> mri_parameter_form table contains a column in the exact format >>> SCANTYPE_Scan_done >>> === >>> >>> >> The statistics page using an instrument named "mri_parameter_form" to >> determine numbers for the scan done. For each scan type in the >> mri_scan_types table* it expects there to be a column named >> "SCANTYPE_Scan_Done" to use for reporting statistics. I believe there's >> somewhere in the MRI documentation that goes into more depth but I'm not >> entirely sure where, maybe Cecile can chime in.. >> >> In the loris-error.log a see a large list of the following messages: >>> >>> === >>> [Wed Jan 06 12:26:24.730900 2021] [php7:notice] [pid 25824] [client >>> 216.15.126.108:56738 >>> ] >>> PHP Notice: Undefined index: Female in >>> /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line >>> 137, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ >>> >>> [Wed Jan 06 12:26:24.730935 2021] [php7:notice] [pid 25824] [client >>> 216.15.126.108:56738 >>> ] >>> PHP Notice: Undefined index: OLYMPUS_CLINICAL_SCREENING in >>> /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line >>> 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ >>> >>> [Wed Jan 06 12:26:24.730944 2021] [php7:notice] [pid 25824] [client >>> 216.15.126.108:56738 >>> ] >>> PHP Notice: Undefined index: Male in >>> /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line >>> 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ >>> >>> === >>> >>> >> What version of LORIS is this? I think the notices are unrelated and >> probably harmless but should still be fixed if they haven't been yet. >> >> >>> 4. I am not able to visualiza any image. A message ?LOADING ?? appears >>> but nothing happens. >>> Looking at the loris-error.log I can see that the path to the images is >>> missing a ?/? >>> >>> === >>> PHP Warning: readfile(/data_/ipmsa/loris_data/IPMSA/dataassembly/343633/baseline/mri/native/IPMSA_343633_baseline_flair_001.mnc): >>> failed to open stream: No such file or directory in >>> /var/www/loris/modules/brainbrowser/ajax/image.php on line 56, referer: >>> https://ipmsa-loris.bic.mni.mcgill.ca/brainbrowser/?minc_id=[112603 >>> >>> ] >>> === >>> >>> Do you know where can this missing ?/? should be set? >>> >>> >> It looks like that code is using the imagePath configuration variable >> which should have a trailing /. It should be the configuration option >> labeled "Path to images for display in Imaging Browser (e.g. >> /data/$project/data/)" in the Configuration module frontend. >> >> - Dave >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Wed Feb 3 13:11:13 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Wed, 3 Feb 2021 18:11:13 +0000 Subject: [Loris-dev] Insertion error Message-ID: <38656469-51A3-4D94-8480-F3F89E7EF7EC@bwh.harvard.edu> Dear LorisDev team. I have an insertion error in LORIS where a scan of subject was added to a different subject. I reviewed the scripts I am using and the logs from my scripts and from LORIS, and everything looks fine except the minc files that were created in LORIS. The error surfaced when I was trying to upload a minc file to a subject. LORIS was replying with the following message: === log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-20-14-uvzbWX.log --> ERROR: there is already a file registered in the files table with SeriesUID='1.2.840.113619.2.25.4.2418272.1367947481.424' and EchoTime='0.081816'. The already registered file is 'assembly/240720/105ms302w48/mri/native/IPMSA_240720_105ms302w48_t2w_001.mnc' SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 === Based on that error, I looked at the provenance of the file "assembly/240720/105ms302w48/mri/native/IPMSA_240720_105ms302w48_t2w_001.mnc". I extracted the header for that file and found that indeed it has the same "SeriesInstanceUID" === $ mincheader /data_/ipmsa/loris_data/IPMSA/data/assembly/240720/105ms302w48/mri/native/IPMSA_240720_105ms302w48_t2w_001.mnc | grep 0x0020:el_0x000e dicom_0x0020:el_0x000e = "1.2.840.113619.2.25.4.2418272.1367947481.424" ; === Then I found for the tarfile associated with that the visit for that minc file: === SELECT DicomArchiveID, PatientID, PatientName, PatientDoB, PatientSex, neurodbCenterName, CenterName, LastUpdate, DateAcquired, DateFirstArchived, DateLastArchived, AcquisitionCount, NonDicomFileCount, DicomFileCount, md5sumDicomOnly, md5sumArchive, CreatingUser, sumTypeVersion, tarTypeVersion, SourceLocation, ArchiveLocation, ScannerManufacturer, ScannerModel, ScannerSerialNumber, ScannerSoftwareVersion, SessionID, uploadAttempt, CreateInfo, TarchiveID, DateSent, PendingTransfer -> FROM tarchive -> WHERE SessionID IN ( SELECT ID FROM session WHERE CandID=240720 AND Visit_label='105ms302w48') \G; *************************** 1. row *************************** DicomArchiveID: 1.3.12.2.1107.5.2.30.26523.30000014071913412629600000031 PatientID: 105MS301_272-CAA-1_ccc_272-903_105MS302-w48 PatientName: BAG272302_240720_105ms302w48 PatientDoB: 1980-10-12 PatientSex: Anonymized neurodbCenterName: NULL CenterName: Anonymized LastUpdate: NULL DateAcquired: 2014-07-19 DateFirstArchived: 2020-11-24 07:56:13 DateLastArchived: 2020-11-24 07:56:13 AcquisitionCount: 5 NonDicomFileCount: 0 DicomFileCount: 300 md5sumDicomOnly: 7d9e2c2e653de5586b30ad6125115441 ImagingUpload-7-24-6mxg7z.tar md5sumArchive: 6d50ab9ebd4d2174eb961be7298b536f DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar CreatingUser: lorisadmin sumTypeVersion: 1 tarTypeVersion: 1 SourceLocation: /tmp/ImagingUpload-7-24-6mxg7z ArchiveLocation: 2014/DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar ScannerManufacturer: SIEMENS ScannerModel: Avanto ScannerSerialNumber: 26523 ScannerSoftwareVersion: syngo MR B15 SessionID: 116004 uploadAttempt: 0 CreateInfo: * Taken from dir : /tmp/ImagingUpload-7-24-6mxg7z * Archive target location : /data_/ipmsa/loris_data/IPMSA/data/tarchive/DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar * Name of creating host : 132.216.133.49 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2020-11-24 07:54:05 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 7d9e2c2e653de5586b30ad6125115441 ImagingUpload-7-24-6mxg7z.tar * md5sum for DICOM tarball gzipped : d9b420f7495ab7f5bad5ddcf0f198963 ImagingUpload-7-24-6mxg7z.tar.gz * md5sum for complete archive : 6d50ab9ebd4d2174eb961be7298b536f DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar TarchiveID: 35280 DateSent: NULL PendingTransfer: 0 1 row in set (0.00 sec) === The tar file is the following: /data_/ipmsa/loris_data/IPMSA/data/tarchive/2014/DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar The "SeriesInstanceUID" for the t2w dicoms is "1.3.12.2.1107.5.2.30.26523.2014071919365885482743202.0.0.0" which different as the one reported in the minc file! What could be happening here? The only thing I think might play a role here is that I was uploading 7.500 visits for one study, running 15 insertions in parallel. Maybe some temporary files were overwritten by processes running in parallel? Please advice on how to deal with this issue, and how to validate/verify the integrity of the files that have been uploaded so far (~30.000 visits). Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Thu Feb 4 08:50:16 2021 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Thu, 4 Feb 2021 08:50:16 -0500 Subject: [Loris-dev] Insertion error In-Reply-To: <38656469-51A3-4D94-8480-F3F89E7EF7EC@bwh.harvard.edu> References: <38656469-51A3-4D94-8480-F3F89E7EF7EC@bwh.harvard.edu> Message-ID: Hi Alfredo, Regarding your query of the tarchive tables, instead of querying based on the SessionID of the MINC file, it would be best to query based on the TarchiveID of the MINC file. The TarchiveID in the tarchive table is linked to the field TarchiveSource of the files table. (There could be multiple DICOM archives associated to a SessionID while TarchiveID is unique.) Separately, could you try running the two queries below? One will compare the Study Instance UID between the MINC file and the DICOM archive stored in the database tables and the other will do the same for PatientName. I think that will help spotting the weird case you are seeing above. Note: they will take time to run given the amount of data you have. One thing that could maybe make them run faster is if you grep the ParameterType ID for patient_name and study_instance_uid in the parameter_type table and give it directly to the query instead of joining the parameter_file and parameter_type table. *Comparison of the patient_name:* SELECT t.TarchiveID, f.File, pf.Value FROM files f JOIN parameter_file pf USING (FileID) JOIN parameter_type pt USING (ParameterTypeID) JOIN tarchive t ON (f.TarchiveSource=t.TarchiveID) WHERE pt.Name='patient_name' AND t.PatientName!=pf.Value; *Comparison of the Study Instance UID:*SELECT t.TarchiveID, f.File, pf.Value FROM files f JOIN parameter_file pf USING (FileID) JOIN parameter_type pt USING (ParameterTypeID) JOIN tarchive t ON (f.TarchiveSource=t.TarchiveID) WHERE pt.Name='study_instance_uid' AND t.DicomArchiveID!=pf.Value; Let me know how it goes. C?cile On Wed, Feb 3, 2021 at 1:11 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team. > > I have an insertion error in LORIS where a scan of subject was added to a > different subject. I reviewed the scripts I am using and the logs from my > scripts and from LORIS, and everything looks fine except the minc files > that were created in LORIS. > > The error surfaced when I was trying to upload a minc file to a subject. > LORIS was replying with the following message: > > === > log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is > /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-20-14-uvzbWX.log > > --> ERROR: there is already a file registered in the files table with > SeriesUID='1.2.840.113619.2.25.4.2418272.1367947481.424' and > EchoTime='0.081816'. > The already registered file is > 'assembly/240720/105ms302w48/mri/native/IPMSA_240720_105ms302w48_t2w_001.mnc' > SELECT ArchiveLocation FROM tarchive WHERE > TarchiveID = ( SELECT TarchiveID > FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? > ) PSCID is: AZH101303 > CandID id: 814099 > visit_label is: 105ms302w48 > PSCID is: AZH101303 > CandID id: 814099 > visit_label is: 105ms302w48 > === > > Based on that error, I looked at the provenance of the file > "assembly/240720/105ms302w48/mri/native/IPMSA_240720_105ms302w48_t2w_001.mnc". > I extracted the header for that file and found that indeed it has the same > "SeriesInstanceUID" > > === > $ mincheader > /data_/ipmsa/loris_data/IPMSA/data/assembly/240720/105ms302w48/mri/native/IPMSA_240720_105ms302w48_t2w_001.mnc > | grep 0x0020:el_0x000e > dicom_0x0020:el_0x000e = "1.2.840.113619.2.25.4.2418272.1367947481.424" ; > === > > Then I found for the tarfile associated with that the visit for that minc > file: > > === > SELECT DicomArchiveID, PatientID, PatientName, PatientDoB, PatientSex, > neurodbCenterName, CenterName, LastUpdate, DateAcquired, DateFirstArchived, > DateLastArchived, AcquisitionCount, NonDicomFileCount, DicomFileCount, > md5sumDicomOnly, md5sumArchive, CreatingUser, sumTypeVersion, > tarTypeVersion, SourceLocation, ArchiveLocation, ScannerManufacturer, > ScannerModel, ScannerSerialNumber, ScannerSoftwareVersion, SessionID, > uploadAttempt, CreateInfo, TarchiveID, DateSent, PendingTransfer > -> FROM tarchive > -> WHERE SessionID IN ( SELECT ID FROM session WHERE CandID=240720 AND > Visit_label='105ms302w48') \G; > *************************** 1. row *************************** > DicomArchiveID: > 1.3.12.2.1107.5.2.30.26523.30000014071913412629600000031 > PatientID: 105MS301_272-CAA-1_ccc_272-903_105MS302-w48 > PatientName: BAG272302_240720_105ms302w48 > PatientDoB: 1980-10-12 > PatientSex: Anonymized > neurodbCenterName: NULL > CenterName: Anonymized > LastUpdate: NULL > DateAcquired: 2014-07-19 > DateFirstArchived: 2020-11-24 07:56:13 > DateLastArchived: 2020-11-24 07:56:13 > AcquisitionCount: 5 > NonDicomFileCount: 0 > DicomFileCount: 300 > md5sumDicomOnly: 7d9e2c2e653de5586b30ad6125115441 > ImagingUpload-7-24-6mxg7z.tar > > md5sumArchive: 6d50ab9ebd4d2174eb961be7298b536f > DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar > > CreatingUser: lorisadmin > sumTypeVersion: 1 > tarTypeVersion: 1 > SourceLocation: /tmp/ImagingUpload-7-24-6mxg7z > ArchiveLocation: 2014/DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar > ScannerManufacturer: SIEMENS > ScannerModel: Avanto > ScannerSerialNumber: 26523 > ScannerSoftwareVersion: syngo MR B15 > SessionID: 116004 > uploadAttempt: 0 > CreateInfo: > * Taken from dir : /tmp/ImagingUpload-7-24-6mxg7z > * Archive target location : > /data_/ipmsa/loris_data/IPMSA/data/tarchive/DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar > * Name of creating host : 132.216.133.49 > * Name of host OS : Linux > * Created by user : lorisadmin > * Archived on : 2020-11-24 07:54:05 > * dicomSummary version : 1 > * dicomTar version : 1 > * md5sum for DICOM tarball : 7d9e2c2e653de5586b30ad6125115441 > ImagingUpload-7-24-6mxg7z.tar > * md5sum for DICOM tarball gzipped : d9b420f7495ab7f5bad5ddcf0f198963 > ImagingUpload-7-24-6mxg7z.tar.gz > * md5sum for complete archive : 6d50ab9ebd4d2174eb961be7298b536f > DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar > > TarchiveID: 35280 > DateSent: NULL > PendingTransfer: 0 > 1 row in set (0.00 sec) > === > > The tar file is the following: > /data_/ipmsa/loris_data/IPMSA/data/tarchive/2014/DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar > The "SeriesInstanceUID" for the t2w dicoms is > "1.3.12.2.1107.5.2.30.26523.2014071919365885482743202.0.0.0" which > different as the one reported in the minc file! > > What could be happening here? The only thing I think might play a role > here is that I was uploading 7.500 visits for one study, running 15 > insertions in parallel. Maybe some temporary files were overwritten by > processes running in parallel? > > Please advice on how to deal with this issue, and how to validate/verify > the integrity of the files that have been uploaded so far (~30.000 visits). > > Best, > Alfredo. > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Thu Feb 4 12:45:21 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Thu, 4 Feb 2021 17:45:21 +0000 Subject: [Loris-dev] Insertion error In-Reply-To: References: <38656469-51A3-4D94-8480-F3F89E7EF7EC@bwh.harvard.edu> Message-ID: <8A4B4BD5-865C-4BAF-A3DE-008CEF413D88@bwh.harvard.edu> Hi Cecile, Thank you for your answer. I did the query using the files table, I?m getting the same TarchiveID. I will send the results of the query in a separate email. In summary, we have 335 images with different StudyInstanceID, and 265 with different PatientName. The case we are looking at is in those results. What would you suggest to fix this and to avoid it for future insertions? Best, Alfredo. On Feb 4, 2021, at 8:50 AM, Cecile Madjar > wrote: External Email - Use Caution Hi Alfredo, Regarding your query of the tarchive tables, instead of querying based on the SessionID of the MINC file, it would be best to query based on the TarchiveID of the MINC file. The TarchiveID in the tarchive table is linked to the field TarchiveSource of the files table. (There could be multiple DICOM archives associated to a SessionID while TarchiveID is unique.) Separately, could you try running the two queries below? One will compare the Study Instance UID between the MINC file and the DICOM archive stored in the database tables and the other will do the same for PatientName. I think that will help spotting the weird case you are seeing above. Note: they will take time to run given the amount of data you have. One thing that could maybe make them run faster is if you grep the ParameterType ID for patient_name and study_instance_uid in the parameter_type table and give it directly to the query instead of joining the parameter_file and parameter_type table. Comparison of the patient_name: SELECT t.TarchiveID, f.File, pf.Value FROM files f JOIN parameter_file pf USING (FileID) JOIN parameter_type pt USING (ParameterTypeID) JOIN tarchive t ON (f.TarchiveSource=t.TarchiveID) WHERE pt.Name='patient_name' AND t.PatientName!=pf.Value; Comparison of the Study Instance UID: SELECT t.TarchiveID, f.File, pf.Value FROM files f JOIN parameter_file pf USING (FileID) JOIN parameter_type pt USING (ParameterTypeID) JOIN tarchive t ON (f.TarchiveSource=t.TarchiveID) WHERE pt.Name='study_instance_uid' AND t.DicomArchiveID!=pf.Value; Let me know how it goes. C?cile On Wed, Feb 3, 2021 at 1:11 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team. I have an insertion error in LORIS where a scan of subject was added to a different subject. I reviewed the scripts I am using and the logs from my scripts and from LORIS, and everything looks fine except the minc files that were created in LORIS. The error surfaced when I was trying to upload a minc file to a subject. LORIS was replying with the following message: === log dir is /data_/ipmsa/loris_data/IPMSA/data/logs and log file is /data_/ipmsa/loris_data/IPMSA/data/logs/TarLoad-20-14-uvzbWX.log --> ERROR: there is already a file registered in the files table with SeriesUID='1.2.840.113619.2.25.4.2418272.1367947481.424' and EchoTime='0.081816'. The already registered file is 'assembly/240720/105ms302w48/mri/native/IPMSA_240720_105ms302w48_t2w_001.mnc' SELECT ArchiveLocation FROM tarchive WHERE TarchiveID = ( SELECT TarchiveID FROM tarchive_series WHERE SeriesUID=? AND EchoTime=? ) PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 PSCID is: AZH101303 CandID id: 814099 visit_label is: 105ms302w48 === Based on that error, I looked at the provenance of the file "assembly/240720/105ms302w48/mri/native/IPMSA_240720_105ms302w48_t2w_001.mnc". I extracted the header for that file and found that indeed it has the same "SeriesInstanceUID" === $ mincheader /data_/ipmsa/loris_data/IPMSA/data/assembly/240720/105ms302w48/mri/native/IPMSA_240720_105ms302w48_t2w_001.mnc | grep 0x0020:el_0x000e dicom_0x0020:el_0x000e = "1.2.840.113619.2.25.4.2418272.1367947481.424" ; === Then I found for the tarfile associated with that the visit for that minc file: === SELECT DicomArchiveID, PatientID, PatientName, PatientDoB, PatientSex, neurodbCenterName, CenterName, LastUpdate, DateAcquired, DateFirstArchived, DateLastArchived, AcquisitionCount, NonDicomFileCount, DicomFileCount, md5sumDicomOnly, md5sumArchive, CreatingUser, sumTypeVersion, tarTypeVersion, SourceLocation, ArchiveLocation, ScannerManufacturer, ScannerModel, ScannerSerialNumber, ScannerSoftwareVersion, SessionID, uploadAttempt, CreateInfo, TarchiveID, DateSent, PendingTransfer -> FROM tarchive -> WHERE SessionID IN ( SELECT ID FROM session WHERE CandID=240720 AND Visit_label='105ms302w48') \G; *************************** 1. row *************************** DicomArchiveID: 1.3.12.2.1107.5.2.30.26523.30000014071913412629600000031 PatientID: 105MS301_272-CAA-1_ccc_272-903_105MS302-w48 PatientName: BAG272302_240720_105ms302w48 PatientDoB: 1980-10-12 PatientSex: Anonymized neurodbCenterName: NULL CenterName: Anonymized LastUpdate: NULL DateAcquired: 2014-07-19 DateFirstArchived: 2020-11-24 07:56:13 DateLastArchived: 2020-11-24 07:56:13 AcquisitionCount: 5 NonDicomFileCount: 0 DicomFileCount: 300 md5sumDicomOnly: 7d9e2c2e653de5586b30ad6125115441 ImagingUpload-7-24-6mxg7z.tar md5sumArchive: 6d50ab9ebd4d2174eb961be7298b536f DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar CreatingUser: lorisadmin sumTypeVersion: 1 tarTypeVersion: 1 SourceLocation: /tmp/ImagingUpload-7-24-6mxg7z ArchiveLocation: 2014/DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar ScannerManufacturer: SIEMENS ScannerModel: Avanto ScannerSerialNumber: 26523 ScannerSoftwareVersion: syngo MR B15 SessionID: 116004 uploadAttempt: 0 CreateInfo: * Taken from dir : /tmp/ImagingUpload-7-24-6mxg7z * Archive target location : /data_/ipmsa/loris_data/IPMSA/data/tarchive/DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar * Name of creating host : 132.216.133.49 * Name of host OS : Linux * Created by user : lorisadmin * Archived on : 2020-11-24 07:54:05 * dicomSummary version : 1 * dicomTar version : 1 * md5sum for DICOM tarball : 7d9e2c2e653de5586b30ad6125115441 ImagingUpload-7-24-6mxg7z.tar * md5sum for DICOM tarball gzipped : d9b420f7495ab7f5bad5ddcf0f198963 ImagingUpload-7-24-6mxg7z.tar.gz * md5sum for complete archive : 6d50ab9ebd4d2174eb961be7298b536f DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar TarchiveID: 35280 DateSent: NULL PendingTransfer: 0 1 row in set (0.00 sec) === The tar file is the following: /data_/ipmsa/loris_data/IPMSA/data/tarchive/2014/DCM_2014-07-19_ImagingUpload-7-24-6mxg7z.tar The "SeriesInstanceUID" for the t2w dicoms is "1.3.12.2.1107.5.2.30.26523.2014071919365885482743202.0.0.0" which different as the one reported in the minc file! What could be happening here? The only thing I think might play a role here is that I was uploading 7.500 visits for one study, running 15 insertions in parallel. Maybe some temporary files were overwritten by processes running in parallel? Please advice on how to deal with this issue, and how to validate/verify the integrity of the files that have been uploaded so far (~30.000 visits). Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Thu Feb 4 13:00:43 2021 From: waveflux at gmail.com (Tom Beaudry) Date: Thu, 4 Feb 2021 13:00:43 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error Message-ID: Hey Guys, I decided to upgrade LORIS v22 to v23 and I ran into this apache error when i navigate to the homepage in my web browser: [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] [client 172.16.253.6:62122] PHP Warning: session_start(): Setting option 'cookie_samesite' failed in /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] [client 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: Class 'Laminas\\Diactoros\\ServerRequestFactory'* not found in /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in /var/www/loris/htdocs/index.php on line 35 It seems that the server request is failing: $serverrequest = \Laminas\Diactoros\ServerRequestFactory::fromGlobals(); 36 Any help would be greatly appreciated! Tom -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Thu Feb 4 13:13:09 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Thu, 4 Feb 2021 13:13:09 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hi Tom, You need to re-run " composer install " to solve this issue. Good Luck. Best Shen On Thu, 4 Feb 2021 at 13:01, Tom Beaudry wrote: > Hey Guys, > > I decided to upgrade LORIS v22 to v23 and I ran into this apache error > when i navigate to the homepage in my web browser: > > [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] [client > 172.16.253.6:62122] PHP Warning: session_start(): Setting option > 'cookie_samesite' failed in > /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 > > [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] [client > 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: Class > 'Laminas\\Diactoros\\ServerRequestFactory'* not found in > /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in > /var/www/loris/htdocs/index.php on line 35 > > > It seems that the server request is failing: > > $serverrequest = \Laminas\Diactoros\ServerRequestFactory::fromGlobals(); > 36 > > Any help would be greatly appreciated! > Tom > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Thu Feb 4 13:29:44 2021 From: waveflux at gmail.com (Tom Beaudry) Date: Thu, 4 Feb 2021 13:29:44 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hi Shen, Thanks for the answer: Composer install gives me the following error: [lorisadmin at loris loris]$ composer install PHP Deprecated: Required parameter $ignoreFilters follows optional parameter $packageName in phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on line 97 Deprecated: Required parameter $ignoreFilters follows optional parameter $packageName in phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on line 97 Deprecation Notice: Required parameter $path follows optional parameter $schema in phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 Deprecation Notice: Required parameter $path follows optional parameter $schema in phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 [ErrorException] Trying to access array offset on value of type null Best, Tom On Thu, Feb 4, 2021 at 1:13 PM Shen Wang wrote: > Hi Tom, > You need to re-run " composer install " to solve this issue. > Good Luck. > Best > Shen > > On Thu, 4 Feb 2021 at 13:01, Tom Beaudry wrote: > >> Hey Guys, >> >> I decided to upgrade LORIS v22 to v23 and I ran into this apache error >> when i navigate to the homepage in my web browser: >> >> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] [client >> 172.16.253.6:62122] PHP Warning: session_start(): Setting option >> 'cookie_samesite' failed in >> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >> >> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] [client >> 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: Class >> 'Laminas\\Diactoros\\ServerRequestFactory'* not found in >> /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in >> /var/www/loris/htdocs/index.php on line 35 >> >> >> It seems that the server request is failing: >> >> $serverrequest = \Laminas\Diactoros\ServerRequestFactory::fromGlobals(); >> 36 >> >> Any help would be greatly appreciated! >> Tom >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Thu Feb 4 13:40:17 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Thu, 4 Feb 2021 13:40:17 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hi Tom, You are welcome. I think that you need to remove all the vendor files. Try step 1: "make clean" (delete all the vendor and node_modules) step 2: "make" ( run composer install and npm install ...) If it still can't work, could you tell me which PHP version are you using? Best Shen On Thu, 4 Feb 2021 at 13:29, Tom Beaudry wrote: > Hi Shen, > > Thanks for the answer: Composer install gives me the following error: > > [lorisadmin at loris loris]$ composer install > PHP Deprecated: Required parameter $ignoreFilters follows optional > parameter $packageName in > phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on > line 97 > > Deprecated: Required parameter $ignoreFilters follows optional parameter > $packageName in > phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on > line 97 > Deprecation Notice: Required parameter $path follows optional parameter > $schema in > phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 > Deprecation Notice: Required parameter $path follows optional parameter > $schema in > phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 > > > [ErrorException] > Trying to access array offset on value of type null > > Best, > Tom > > > On Thu, Feb 4, 2021 at 1:13 PM Shen Wang wrote: > >> Hi Tom, >> You need to re-run " composer install " to solve this issue. >> Good Luck. >> Best >> Shen >> >> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry wrote: >> >>> Hey Guys, >>> >>> I decided to upgrade LORIS v22 to v23 and I ran into this apache error >>> when i navigate to the homepage in my web browser: >>> >>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] [client >>> 172.16.253.6:62122] PHP Warning: session_start(): Setting option >>> 'cookie_samesite' failed in >>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>> >>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] [client >>> 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: Class >>> 'Laminas\\Diactoros\\ServerRequestFactory'* not found in >>> /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in >>> /var/www/loris/htdocs/index.php on line 35 >>> >>> >>> It seems that the server request is failing: >>> >>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory::fromGlobals(); >>> 36 >>> >>> Any help would be greatly appreciated! >>> Tom >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Thu Feb 4 13:49:49 2021 From: waveflux at gmail.com (Tom Beaudry) Date: Thu, 4 Feb 2021 13:49:49 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hey Shen, Unfortunately it didn't work. Here's the output: https://pastebin.com/raw/ZQjPuAG1 I'm using php8. Thanks, Tom On Thu, Feb 4, 2021 at 1:40 PM Shen Wang wrote: > Hi Tom, > You are welcome. I think that you need to remove all the vendor files. > Try step 1: "make clean" (delete all the vendor and node_modules) > step 2: "make" ( run composer install and npm install > ...) > If it still can't work, could you tell me which PHP version are you using? > Best > Shen > > On Thu, 4 Feb 2021 at 13:29, Tom Beaudry wrote: > >> Hi Shen, >> >> Thanks for the answer: Composer install gives me the following error: >> >> [lorisadmin at loris loris]$ composer install >> PHP Deprecated: Required parameter $ignoreFilters follows optional >> parameter $packageName in >> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >> line 97 >> >> Deprecated: Required parameter $ignoreFilters follows optional parameter >> $packageName in >> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >> line 97 >> Deprecation Notice: Required parameter $path follows optional parameter >> $schema in >> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >> Deprecation Notice: Required parameter $path follows optional parameter >> $schema in >> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >> >> >> [ErrorException] >> Trying to access array offset on value of type null >> >> Best, >> Tom >> >> >> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang wrote: >> >>> Hi Tom, >>> You need to re-run " composer install " to solve this issue. >>> Good Luck. >>> Best >>> Shen >>> >>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry wrote: >>> >>>> Hey Guys, >>>> >>>> I decided to upgrade LORIS v22 to v23 and I ran into this apache error >>>> when i navigate to the homepage in my web browser: >>>> >>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] [client >>>> 172.16.253.6:62122] PHP Warning: session_start(): Setting option >>>> 'cookie_samesite' failed in >>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>> >>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] [client >>>> 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: Class >>>> 'Laminas\\Diactoros\\ServerRequestFactory'* not found in >>>> /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in >>>> /var/www/loris/htdocs/index.php on line 35 >>>> >>>> >>>> It seems that the server request is failing: >>>> >>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory::fromGlobals >>>> (); >>>> 36 >>>> >>>> Any help would be greatly appreciated! >>>> Tom >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Thu Feb 4 14:00:58 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Thu, 4 Feb 2021 14:00:58 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hi Tom, We don't support PHP 8 with Loris yet. We are working on it. For the 23.0-release, you have to use PHP 7.3 or 7.4. Best Shen On Thu, 4 Feb 2021 at 13:50, Tom Beaudry wrote: > Hey Shen, > > Unfortunately it didn't work. Here's the output: > https://pastebin.com/raw/ZQjPuAG1 > > I'm using php8. > > Thanks, > Tom > > On Thu, Feb 4, 2021 at 1:40 PM Shen Wang wrote: > >> Hi Tom, >> You are welcome. I think that you need to remove all the vendor files. >> Try step 1: "make clean" (delete all the vendor and node_modules) >> step 2: "make" ( run composer install and npm install >> ...) >> If it still can't work, could you tell me which PHP version are you using? >> Best >> Shen >> >> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry wrote: >> >>> Hi Shen, >>> >>> Thanks for the answer: Composer install gives me the following error: >>> >>> [lorisadmin at loris loris]$ composer install >>> PHP Deprecated: Required parameter $ignoreFilters follows optional >>> parameter $packageName in >>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>> line 97 >>> >>> Deprecated: Required parameter $ignoreFilters follows optional parameter >>> $packageName in >>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>> line 97 >>> Deprecation Notice: Required parameter $path follows optional parameter >>> $schema in >>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>> Deprecation Notice: Required parameter $path follows optional parameter >>> $schema in >>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>> >>> >>> [ErrorException] >>> Trying to access array offset on value of type null >>> >>> Best, >>> Tom >>> >>> >>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang >>> wrote: >>> >>>> Hi Tom, >>>> You need to re-run " composer install " to solve this issue. >>>> Good Luck. >>>> Best >>>> Shen >>>> >>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry wrote: >>>> >>>>> Hey Guys, >>>>> >>>>> I decided to upgrade LORIS v22 to v23 and I ran into this apache error >>>>> when i navigate to the homepage in my web browser: >>>>> >>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] [client >>>>> 172.16.253.6:62122] PHP Warning: session_start(): Setting option >>>>> 'cookie_samesite' failed in >>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>> >>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] [client >>>>> 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: Class >>>>> 'Laminas\\Diactoros\\ServerRequestFactory'* not found in >>>>> /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in >>>>> /var/www/loris/htdocs/index.php on line 35 >>>>> >>>>> >>>>> It seems that the server request is failing: >>>>> >>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory::fromGlobals >>>>> (); >>>>> 36 >>>>> >>>>> Any help would be greatly appreciated! >>>>> Tom >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> >>>> >>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Thu Feb 4 15:05:23 2021 From: waveflux at gmail.com (Tom Beaudry) Date: Thu, 4 Feb 2021 15:05:23 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hey Shen, I downgraded to php 7.4 and get the same results. What can i try next? Tom On Thu, Feb 4, 2021 at 2:01 PM Shen Wang wrote: > Hi Tom, > We don't support PHP 8 with Loris yet. We are working on it. For the > 23.0-release, you have to use PHP 7.3 or 7.4. > Best > Shen > > On Thu, 4 Feb 2021 at 13:50, Tom Beaudry wrote: > >> Hey Shen, >> >> Unfortunately it didn't work. Here's the output: >> https://pastebin.com/raw/ZQjPuAG1 >> >> I'm using php8. >> >> Thanks, >> Tom >> >> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang wrote: >> >>> Hi Tom, >>> You are welcome. I think that you need to remove all the vendor files. >>> Try step 1: "make clean" (delete all the vendor and node_modules) >>> step 2: "make" ( run composer install and npm install >>> ...) >>> If it still can't work, could you tell me which PHP version are >>> you using? >>> Best >>> Shen >>> >>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry wrote: >>> >>>> Hi Shen, >>>> >>>> Thanks for the answer: Composer install gives me the following error: >>>> >>>> [lorisadmin at loris loris]$ composer install >>>> PHP Deprecated: Required parameter $ignoreFilters follows optional >>>> parameter $packageName in >>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>> line 97 >>>> >>>> Deprecated: Required parameter $ignoreFilters follows optional >>>> parameter $packageName in >>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>> line 97 >>>> Deprecation Notice: Required parameter $path follows optional parameter >>>> $schema in >>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>> Deprecation Notice: Required parameter $path follows optional parameter >>>> $schema in >>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>> >>>> >>>> [ErrorException] >>>> Trying to access array offset on value of type null >>>> >>>> Best, >>>> Tom >>>> >>>> >>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang >>>> wrote: >>>> >>>>> Hi Tom, >>>>> You need to re-run " composer install " to solve this issue. >>>>> Good Luck. >>>>> Best >>>>> Shen >>>>> >>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry wrote: >>>>> >>>>>> Hey Guys, >>>>>> >>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this apache >>>>>> error when i navigate to the homepage in my web browser: >>>>>> >>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] [client >>>>>> 172.16.253.6:62122] PHP Warning: session_start(): Setting option >>>>>> 'cookie_samesite' failed in >>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>> >>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] [client >>>>>> 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: Class >>>>>> 'Laminas\\Diactoros\\ServerRequestFactory'* not found in >>>>>> /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in >>>>>> /var/www/loris/htdocs/index.php on line 35 >>>>>> >>>>>> >>>>>> It seems that the server request is failing: >>>>>> >>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory::fromGlobals >>>>>> (); >>>>>> 36 >>>>>> >>>>>> Any help would be greatly appreciated! >>>>>> Tom >>>>>> _______________________________________________ >>>>>> Loris-dev mailing list >>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>> >>>>> >>>>> >>>>> -- >>>>> Shen Wang >>>>> Loris Developer >>>>> Montreal Neurological Institute >>>>> McGill University >>>>> >>>>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Thu Feb 4 15:36:49 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Thu, 4 Feb 2021 15:36:49 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hi Tom, If you got same error like "Deprecated: Required parameter $ignoreFilters follows optional parameter $packageName " , It seems like you are still using PHP 8. After downgraded to PHP 7.4, you need to install PHP 7.4 dependencies as well. Try these steps : 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml php7.4-json php7.4-mbstring php7.4-gd php-ast 2. sudo apt-get install -y composer 3. sudo apt-get install -y libapache2-mod-php7.4 4. sudo a2dismod php8.0 5. sudo a2enmod php7.4 6. sudo service apache2 restart 7, make clean 8, make Good luck. Best Shen On Thu, 4 Feb 2021 at 15:05, Tom Beaudry wrote: > Hey Shen, > > I downgraded to php 7.4 and get the same results. > > What can i try next? > Tom > > On Thu, Feb 4, 2021 at 2:01 PM Shen Wang wrote: > >> Hi Tom, >> We don't support PHP 8 with Loris yet. We are working on it. For the >> 23.0-release, you have to use PHP 7.3 or 7.4. >> Best >> Shen >> >> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry wrote: >> >>> Hey Shen, >>> >>> Unfortunately it didn't work. Here's the output: >>> https://pastebin.com/raw/ZQjPuAG1 >>> >>> I'm using php8. >>> >>> Thanks, >>> Tom >>> >>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang >>> wrote: >>> >>>> Hi Tom, >>>> You are welcome. I think that you need to remove all the vendor files. >>>> Try step 1: "make clean" (delete all the vendor and node_modules) >>>> step 2: "make" ( run composer install and npm >>>> install ...) >>>> If it still can't work, could you tell me which PHP version are >>>> you using? >>>> Best >>>> Shen >>>> >>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry wrote: >>>> >>>>> Hi Shen, >>>>> >>>>> Thanks for the answer: Composer install gives me the following error: >>>>> >>>>> [lorisadmin at loris loris]$ composer install >>>>> PHP Deprecated: Required parameter $ignoreFilters follows optional >>>>> parameter $packageName in >>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>> line 97 >>>>> >>>>> Deprecated: Required parameter $ignoreFilters follows optional >>>>> parameter $packageName in >>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>> line 97 >>>>> Deprecation Notice: Required parameter $path follows optional >>>>> parameter $schema in >>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>> Deprecation Notice: Required parameter $path follows optional >>>>> parameter $schema in >>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>> >>>>> >>>>> [ErrorException] >>>>> Trying to access array offset on value of type null >>>>> >>>>> Best, >>>>> Tom >>>>> >>>>> >>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang >>>>> wrote: >>>>> >>>>>> Hi Tom, >>>>>> You need to re-run " composer install " to solve this issue. >>>>>> Good Luck. >>>>>> Best >>>>>> Shen >>>>>> >>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry wrote: >>>>>> >>>>>>> Hey Guys, >>>>>>> >>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this apache >>>>>>> error when i navigate to the homepage in my web browser: >>>>>>> >>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] [client >>>>>>> 172.16.253.6:62122] PHP Warning: session_start(): Setting option >>>>>>> 'cookie_samesite' failed in >>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>> >>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] [client >>>>>>> 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: Class >>>>>>> 'Laminas\\Diactoros\\ServerRequestFactory'* not found in >>>>>>> /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in >>>>>>> /var/www/loris/htdocs/index.php on line 35 >>>>>>> >>>>>>> >>>>>>> It seems that the server request is failing: >>>>>>> >>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory:: >>>>>>> fromGlobals(); >>>>>>> 36 >>>>>>> >>>>>>> Any help would be greatly appreciated! >>>>>>> Tom >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Shen Wang >>>>>> Loris Developer >>>>>> Montreal Neurological Institute >>>>>> McGill University >>>>>> >>>>>> >>>> >>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Thu Feb 4 15:45:59 2021 From: waveflux at gmail.com (Tom Beaudry) Date: Thu, 4 Feb 2021 15:45:59 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hi Shen, My productions server is CentOS. If i check what version of php i'm using: [lorisadmin at loris loris]$ rpm -qa | grep php php-json-7.4.15-1.el7.remi.x86_64 php-pear-1.10.12-5.el7.remi.noarch php-7.4.15-1.el7.remi.x86_64 php-devel-7.4.15-1.el7.remi.x86_64 php-sodium-7.4.15-1.el7.remi.x86_64 php-fedora-autoloader-1.0.1-2.el7.noarch php-fpm-7.4.15-1.el7.remi.x86_64 php-gd-7.4.15-1.el7.remi.x86_64 php-cli-7.4.15-1.el7.remi.x86_64 php-pdo-7.4.15-1.el7.remi.x86_64 php-mysqlnd-7.4.15-1.el7.remi.x86_64 php-bcmath-7.4.15-1.el7.remi.x86_64 php-xml-7.4.15-1.el7.remi.x86_64 php-mbstring-7.4.15-1.el7.remi.x86_64 oniguruma5php-6.9.6-1.el7.remi.x86_64 php-common-7.4.15-1.el7.remi.x86_64 php-process-7.4.15-1.el7.remi.x86_64 php-pecl-mcrypt-1.0.4-1.el7.remi.7.4.x86_64 They are all showing up as 7.4. Thanks! Tom On Thu, Feb 4, 2021 at 3:37 PM Shen Wang wrote: > Hi Tom, > If you got same error like "Deprecated: Required parameter $ignoreFilters > follows optional parameter $packageName " , > It seems like you are still using PHP 8. After downgraded to PHP 7.4, you > need to install PHP 7.4 dependencies as well. > Try these steps : > > 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml php7.4-json > php7.4-mbstring php7.4-gd php-ast > 2. sudo apt-get install -y composer > 3. sudo apt-get install -y libapache2-mod-php7.4 > 4. sudo a2dismod php8.0 > 5. sudo a2enmod php7.4 > 6. sudo service apache2 restart > > 7, make clean > 8, make > Good luck. > Best > Shen > > > On Thu, 4 Feb 2021 at 15:05, Tom Beaudry wrote: > >> Hey Shen, >> >> I downgraded to php 7.4 and get the same results. >> >> What can i try next? >> Tom >> >> On Thu, Feb 4, 2021 at 2:01 PM Shen Wang wrote: >> >>> Hi Tom, >>> We don't support PHP 8 with Loris yet. We are working on it. For the >>> 23.0-release, you have to use PHP 7.3 or 7.4. >>> Best >>> Shen >>> >>> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry wrote: >>> >>>> Hey Shen, >>>> >>>> Unfortunately it didn't work. Here's the output: >>>> https://pastebin.com/raw/ZQjPuAG1 >>>> >>>> I'm using php8. >>>> >>>> Thanks, >>>> Tom >>>> >>>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang >>>> wrote: >>>> >>>>> Hi Tom, >>>>> You are welcome. I think that you need to remove all the vendor files. >>>>> Try step 1: "make clean" (delete all the vendor and node_modules) >>>>> step 2: "make" ( run composer install and npm >>>>> install ...) >>>>> If it still can't work, could you tell me which PHP version are >>>>> you using? >>>>> Best >>>>> Shen >>>>> >>>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry wrote: >>>>> >>>>>> Hi Shen, >>>>>> >>>>>> Thanks for the answer: Composer install gives me the following error: >>>>>> >>>>>> [lorisadmin at loris loris]$ composer install >>>>>> PHP Deprecated: Required parameter $ignoreFilters follows optional >>>>>> parameter $packageName in >>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>> line 97 >>>>>> >>>>>> Deprecated: Required parameter $ignoreFilters follows optional >>>>>> parameter $packageName in >>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>> line 97 >>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>> parameter $schema in >>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>> parameter $schema in >>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>>> >>>>>> >>>>>> [ErrorException] >>>>>> Trying to access array offset on value of type null >>>>>> >>>>>> Best, >>>>>> Tom >>>>>> >>>>>> >>>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang >>>>>> wrote: >>>>>> >>>>>>> Hi Tom, >>>>>>> You need to re-run " composer install " to solve this issue. >>>>>>> Good Luck. >>>>>>> Best >>>>>>> Shen >>>>>>> >>>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry wrote: >>>>>>> >>>>>>>> Hey Guys, >>>>>>>> >>>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this apache >>>>>>>> error when i navigate to the homepage in my web browser: >>>>>>>> >>>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] [client >>>>>>>> 172.16.253.6:62122] PHP Warning: session_start(): Setting option >>>>>>>> 'cookie_samesite' failed in >>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>>> >>>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] [client >>>>>>>> 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: Class >>>>>>>> 'Laminas\\Diactoros\\ServerRequestFactory'* not found in >>>>>>>> /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in >>>>>>>> /var/www/loris/htdocs/index.php on line 35 >>>>>>>> >>>>>>>> >>>>>>>> It seems that the server request is failing: >>>>>>>> >>>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory:: >>>>>>>> fromGlobals(); >>>>>>>> 36 >>>>>>>> >>>>>>>> Any help would be greatly appreciated! >>>>>>>> Tom >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Shen Wang >>>>>>> Loris Developer >>>>>>> Montreal Neurological Institute >>>>>>> McGill University >>>>>>> >>>>>>> >>>>> >>>>> -- >>>>> Shen Wang >>>>> Loris Developer >>>>> Montreal Neurological Institute >>>>> McGill University >>>>> >>>>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Thu Feb 4 15:55:14 2021 From: waveflux at gmail.com (Tom Beaudry) Date: Thu, 4 Feb 2021 15:55:14 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hey Shen, I checked the apache log and the error is different now: [Thu Feb 04 15:54:16.131158 2021] [php7:warn] [pid 5215] [client 172.16.253.6:62349] PHP Warning: require_once(/var/www/loris/htdocs/../vendor/autoload.php): failed to open stream: No such file or directory in /var/www/loris/htdocs/index.php on line 18 [Thu Feb 04 15:54:16.131215 2021] [php7:error] [pid 5215] [client 172.16.253.6:62349] PHP Fatal error: require_once(): Failed opening required '/var/www/loris/htdocs/../vendor/autoload.php' (include_path='.:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries') in /var/www/loris/htdocs/index.php on line 18 I'm not sure if that helps figure out what's wrong. Thanks again! Tom On Thu, Feb 4, 2021 at 3:45 PM Tom Beaudry wrote: > Hi Shen, > > My productions server is CentOS. > > If i check what version of php i'm using: > > [lorisadmin at loris loris]$ rpm -qa | grep php > php-json-7.4.15-1.el7.remi.x86_64 > php-pear-1.10.12-5.el7.remi.noarch > php-7.4.15-1.el7.remi.x86_64 > php-devel-7.4.15-1.el7.remi.x86_64 > php-sodium-7.4.15-1.el7.remi.x86_64 > php-fedora-autoloader-1.0.1-2.el7.noarch > php-fpm-7.4.15-1.el7.remi.x86_64 > php-gd-7.4.15-1.el7.remi.x86_64 > php-cli-7.4.15-1.el7.remi.x86_64 > php-pdo-7.4.15-1.el7.remi.x86_64 > php-mysqlnd-7.4.15-1.el7.remi.x86_64 > php-bcmath-7.4.15-1.el7.remi.x86_64 > php-xml-7.4.15-1.el7.remi.x86_64 > php-mbstring-7.4.15-1.el7.remi.x86_64 > oniguruma5php-6.9.6-1.el7.remi.x86_64 > php-common-7.4.15-1.el7.remi.x86_64 > php-process-7.4.15-1.el7.remi.x86_64 > php-pecl-mcrypt-1.0.4-1.el7.remi.7.4.x86_64 > > They are all showing up as 7.4. > > Thanks! > Tom > > On Thu, Feb 4, 2021 at 3:37 PM Shen Wang wrote: > >> Hi Tom, >> If you got same error like "Deprecated: Required parameter >> $ignoreFilters follows optional parameter $packageName " , >> It seems like you are still using PHP 8. After downgraded to PHP 7.4, >> you need to install PHP 7.4 dependencies as well. >> Try these steps : >> >> 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml php7.4-json >> php7.4-mbstring php7.4-gd php-ast >> 2. sudo apt-get install -y composer >> 3. sudo apt-get install -y libapache2-mod-php7.4 >> 4. sudo a2dismod php8.0 >> 5. sudo a2enmod php7.4 >> 6. sudo service apache2 restart >> >> 7, make clean >> 8, make >> Good luck. >> Best >> Shen >> >> >> On Thu, 4 Feb 2021 at 15:05, Tom Beaudry wrote: >> >>> Hey Shen, >>> >>> I downgraded to php 7.4 and get the same results. >>> >>> What can i try next? >>> Tom >>> >>> On Thu, Feb 4, 2021 at 2:01 PM Shen Wang >>> wrote: >>> >>>> Hi Tom, >>>> We don't support PHP 8 with Loris yet. We are working on it. For the >>>> 23.0-release, you have to use PHP 7.3 or 7.4. >>>> Best >>>> Shen >>>> >>>> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry wrote: >>>> >>>>> Hey Shen, >>>>> >>>>> Unfortunately it didn't work. Here's the output: >>>>> https://pastebin.com/raw/ZQjPuAG1 >>>>> >>>>> I'm using php8. >>>>> >>>>> Thanks, >>>>> Tom >>>>> >>>>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang >>>>> wrote: >>>>> >>>>>> Hi Tom, >>>>>> You are welcome. I think that you need to remove all the vendor >>>>>> files. >>>>>> Try step 1: "make clean" (delete all the vendor and node_modules) >>>>>> step 2: "make" ( run composer install and npm >>>>>> install ...) >>>>>> If it still can't work, could you tell me which PHP version are >>>>>> you using? >>>>>> Best >>>>>> Shen >>>>>> >>>>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry wrote: >>>>>> >>>>>>> Hi Shen, >>>>>>> >>>>>>> Thanks for the answer: Composer install gives me the following >>>>>>> error: >>>>>>> >>>>>>> [lorisadmin at loris loris]$ composer install >>>>>>> PHP Deprecated: Required parameter $ignoreFilters follows optional >>>>>>> parameter $packageName in >>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>> line 97 >>>>>>> >>>>>>> Deprecated: Required parameter $ignoreFilters follows optional >>>>>>> parameter $packageName in >>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>> line 97 >>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>> parameter $schema in >>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>> parameter $schema in >>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>>>> >>>>>>> >>>>>>> [ErrorException] >>>>>>> Trying to access array offset on value of type null >>>>>>> >>>>>>> Best, >>>>>>> Tom >>>>>>> >>>>>>> >>>>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Tom, >>>>>>>> You need to re-run " composer install " to solve this issue. >>>>>>>> Good Luck. >>>>>>>> Best >>>>>>>> Shen >>>>>>>> >>>>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hey Guys, >>>>>>>>> >>>>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this apache >>>>>>>>> error when i navigate to the homepage in my web browser: >>>>>>>>> >>>>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] [client >>>>>>>>> 172.16.253.6:62122] PHP Warning: session_start(): Setting option >>>>>>>>> 'cookie_samesite' failed in >>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>>>> >>>>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] [client >>>>>>>>> 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: Class >>>>>>>>> 'Laminas\\Diactoros\\ServerRequestFactory'* not found in >>>>>>>>> /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in >>>>>>>>> /var/www/loris/htdocs/index.php on line 35 >>>>>>>>> >>>>>>>>> >>>>>>>>> It seems that the server request is failing: >>>>>>>>> >>>>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory:: >>>>>>>>> fromGlobals(); >>>>>>>>> 36 >>>>>>>>> >>>>>>>>> Any help would be greatly appreciated! >>>>>>>>> Tom >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Shen Wang >>>>>>>> Loris Developer >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University >>>>>>>> >>>>>>>> >>>>>> >>>>>> -- >>>>>> Shen Wang >>>>>> Loris Developer >>>>>> Montreal Neurological Institute >>>>>> McGill University >>>>>> >>>>>> >>>> >>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Thu Feb 4 16:04:24 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Thu, 4 Feb 2021 16:04:24 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hi Tom, It is very helpful, it means you need to do "composer install" again. if it not works for you then try these steps for Centos. sudo yum-config-manager --disable remi-php80 sudo yum-config-manager --enable remi-php74 sudo systemctl restart httpd sudo systemctl status httpd /var/www/loris/htdocs$ echo "" >> test.php Using test.php to check your PHP version in your brower. Best Shen On Thu, 4 Feb 2021 at 15:55, Tom Beaudry wrote: > Hey Shen, > > I checked the apache log and the error is different now: > > [Thu Feb 04 15:54:16.131158 2021] [php7:warn] [pid 5215] [client > 172.16.253.6:62349] PHP Warning: > require_once(/var/www/loris/htdocs/../vendor/autoload.php): failed to open > stream: No such file or directory in /var/www/loris/htdocs/index.php on > line 18 > [Thu Feb 04 15:54:16.131215 2021] [php7:error] [pid 5215] [client > 172.16.253.6:62349] PHP Fatal error: require_once(): Failed opening > required '/var/www/loris/htdocs/../vendor/autoload.php' > (include_path='.:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries') > in /var/www/loris/htdocs/index.php on line 18 > > I'm not sure if that helps figure out what's wrong. > > Thanks again! > Tom > > On Thu, Feb 4, 2021 at 3:45 PM Tom Beaudry wrote: > >> Hi Shen, >> >> My productions server is CentOS. >> >> If i check what version of php i'm using: >> >> [lorisadmin at loris loris]$ rpm -qa | grep php >> php-json-7.4.15-1.el7.remi.x86_64 >> php-pear-1.10.12-5.el7.remi.noarch >> php-7.4.15-1.el7.remi.x86_64 >> php-devel-7.4.15-1.el7.remi.x86_64 >> php-sodium-7.4.15-1.el7.remi.x86_64 >> php-fedora-autoloader-1.0.1-2.el7.noarch >> php-fpm-7.4.15-1.el7.remi.x86_64 >> php-gd-7.4.15-1.el7.remi.x86_64 >> php-cli-7.4.15-1.el7.remi.x86_64 >> php-pdo-7.4.15-1.el7.remi.x86_64 >> php-mysqlnd-7.4.15-1.el7.remi.x86_64 >> php-bcmath-7.4.15-1.el7.remi.x86_64 >> php-xml-7.4.15-1.el7.remi.x86_64 >> php-mbstring-7.4.15-1.el7.remi.x86_64 >> oniguruma5php-6.9.6-1.el7.remi.x86_64 >> php-common-7.4.15-1.el7.remi.x86_64 >> php-process-7.4.15-1.el7.remi.x86_64 >> php-pecl-mcrypt-1.0.4-1.el7.remi.7.4.x86_64 >> >> They are all showing up as 7.4. >> >> Thanks! >> Tom >> >> On Thu, Feb 4, 2021 at 3:37 PM Shen Wang wrote: >> >>> Hi Tom, >>> If you got same error like "Deprecated: Required parameter >>> $ignoreFilters follows optional parameter $packageName " , >>> It seems like you are still using PHP 8. After downgraded to PHP 7.4, >>> you need to install PHP 7.4 dependencies as well. >>> Try these steps : >>> >>> 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml >>> php7.4-json php7.4-mbstring php7.4-gd php-ast >>> 2. sudo apt-get install -y composer >>> 3. sudo apt-get install -y libapache2-mod-php7.4 >>> 4. sudo a2dismod php8.0 >>> 5. sudo a2enmod php7.4 >>> 6. sudo service apache2 restart >>> >>> 7, make clean >>> 8, make >>> Good luck. >>> Best >>> Shen >>> >>> >>> On Thu, 4 Feb 2021 at 15:05, Tom Beaudry wrote: >>> >>>> Hey Shen, >>>> >>>> I downgraded to php 7.4 and get the same results. >>>> >>>> What can i try next? >>>> Tom >>>> >>>> On Thu, Feb 4, 2021 at 2:01 PM Shen Wang >>>> wrote: >>>> >>>>> Hi Tom, >>>>> We don't support PHP 8 with Loris yet. We are working on it. For the >>>>> 23.0-release, you have to use PHP 7.3 or 7.4. >>>>> Best >>>>> Shen >>>>> >>>>> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry wrote: >>>>> >>>>>> Hey Shen, >>>>>> >>>>>> Unfortunately it didn't work. Here's the output: >>>>>> https://pastebin.com/raw/ZQjPuAG1 >>>>>> >>>>>> I'm using php8. >>>>>> >>>>>> Thanks, >>>>>> Tom >>>>>> >>>>>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang >>>>>> wrote: >>>>>> >>>>>>> Hi Tom, >>>>>>> You are welcome. I think that you need to remove all the vendor >>>>>>> files. >>>>>>> Try step 1: "make clean" (delete all the vendor and node_modules >>>>>>> ) >>>>>>> step 2: "make" ( run composer install and npm >>>>>>> install ...) >>>>>>> If it still can't work, could you tell me which PHP version are >>>>>>> you using? >>>>>>> Best >>>>>>> Shen >>>>>>> >>>>>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry wrote: >>>>>>> >>>>>>>> Hi Shen, >>>>>>>> >>>>>>>> Thanks for the answer: Composer install gives me the following >>>>>>>> error: >>>>>>>> >>>>>>>> [lorisadmin at loris loris]$ composer install >>>>>>>> PHP Deprecated: Required parameter $ignoreFilters follows optional >>>>>>>> parameter $packageName in >>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>> line 97 >>>>>>>> >>>>>>>> Deprecated: Required parameter $ignoreFilters follows optional >>>>>>>> parameter $packageName in >>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>> line 97 >>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>> parameter $schema in >>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>> parameter $schema in >>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>>>>> >>>>>>>> >>>>>>>> [ErrorException] >>>>>>>> Trying to access array offset on value of type null >>>>>>>> >>>>>>>> Best, >>>>>>>> Tom >>>>>>>> >>>>>>>> >>>>>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi Tom, >>>>>>>>> You need to re-run " composer install " to solve this issue. >>>>>>>>> Good Luck. >>>>>>>>> Best >>>>>>>>> Shen >>>>>>>>> >>>>>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hey Guys, >>>>>>>>>> >>>>>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this apache >>>>>>>>>> error when i navigate to the homepage in my web browser: >>>>>>>>>> >>>>>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] [client >>>>>>>>>> 172.16.253.6:62122] PHP Warning: session_start(): Setting >>>>>>>>>> option 'cookie_samesite' failed in >>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>>>>> >>>>>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] [client >>>>>>>>>> 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: Class >>>>>>>>>> 'Laminas\\Diactoros\\ServerRequestFactory'* not found in >>>>>>>>>> /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in >>>>>>>>>> /var/www/loris/htdocs/index.php on line 35 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> It seems that the server request is failing: >>>>>>>>>> >>>>>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory:: >>>>>>>>>> fromGlobals(); >>>>>>>>>> 36 >>>>>>>>>> >>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>> Tom >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Shen Wang >>>>>>>>> Loris Developer >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University >>>>>>>>> >>>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Shen Wang >>>>>>> Loris Developer >>>>>>> Montreal Neurological Institute >>>>>>> McGill University >>>>>>> >>>>>>> >>>>> >>>>> -- >>>>> Shen Wang >>>>> Loris Developer >>>>> Montreal Neurological Institute >>>>> McGill University >>>>> >>>>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Thu Feb 4 16:27:37 2021 From: waveflux at gmail.com (Tom Beaudry) Date: Thu, 4 Feb 2021 16:27:37 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hey Shen, I followed your instructions and can confirm i'm using php 7.4: https://docs.google.com/document/d/1QppFZ8MtKoMRltiIQidFDslfVwriuS9cpfuZN49nOZ8/edit?usp=sharing composer install still fails: [ErrorException] Trying to access array offset on value of type null Thanks! Tom On Thu, Feb 4, 2021 at 4:04 PM Shen Wang wrote: > Hi Tom, > It is very helpful, it means you need to do "composer install" again. > if it not works for you then try these steps for Centos. > sudo yum-config-manager --disable remi-php80 > sudo yum-config-manager --enable remi-php74 > sudo systemctl restart httpd sudo systemctl status httpd > /var/www/loris/htdocs$ echo "" >> test.php > Using test.php to check your PHP version in your brower. > Best > Shen > > > > > > On Thu, 4 Feb 2021 at 15:55, Tom Beaudry wrote: > >> Hey Shen, >> >> I checked the apache log and the error is different now: >> >> [Thu Feb 04 15:54:16.131158 2021] [php7:warn] [pid 5215] [client >> 172.16.253.6:62349] PHP Warning: >> require_once(/var/www/loris/htdocs/../vendor/autoload.php): failed to open >> stream: No such file or directory in /var/www/loris/htdocs/index.php on >> line 18 >> [Thu Feb 04 15:54:16.131215 2021] [php7:error] [pid 5215] [client >> 172.16.253.6:62349] PHP Fatal error: require_once(): Failed opening >> required '/var/www/loris/htdocs/../vendor/autoload.php' >> (include_path='.:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries') >> in /var/www/loris/htdocs/index.php on line 18 >> >> I'm not sure if that helps figure out what's wrong. >> >> Thanks again! >> Tom >> >> On Thu, Feb 4, 2021 at 3:45 PM Tom Beaudry wrote: >> >>> Hi Shen, >>> >>> My productions server is CentOS. >>> >>> If i check what version of php i'm using: >>> >>> [lorisadmin at loris loris]$ rpm -qa | grep php >>> php-json-7.4.15-1.el7.remi.x86_64 >>> php-pear-1.10.12-5.el7.remi.noarch >>> php-7.4.15-1.el7.remi.x86_64 >>> php-devel-7.4.15-1.el7.remi.x86_64 >>> php-sodium-7.4.15-1.el7.remi.x86_64 >>> php-fedora-autoloader-1.0.1-2.el7.noarch >>> php-fpm-7.4.15-1.el7.remi.x86_64 >>> php-gd-7.4.15-1.el7.remi.x86_64 >>> php-cli-7.4.15-1.el7.remi.x86_64 >>> php-pdo-7.4.15-1.el7.remi.x86_64 >>> php-mysqlnd-7.4.15-1.el7.remi.x86_64 >>> php-bcmath-7.4.15-1.el7.remi.x86_64 >>> php-xml-7.4.15-1.el7.remi.x86_64 >>> php-mbstring-7.4.15-1.el7.remi.x86_64 >>> oniguruma5php-6.9.6-1.el7.remi.x86_64 >>> php-common-7.4.15-1.el7.remi.x86_64 >>> php-process-7.4.15-1.el7.remi.x86_64 >>> php-pecl-mcrypt-1.0.4-1.el7.remi.7.4.x86_64 >>> >>> They are all showing up as 7.4. >>> >>> Thanks! >>> Tom >>> >>> On Thu, Feb 4, 2021 at 3:37 PM Shen Wang >>> wrote: >>> >>>> Hi Tom, >>>> If you got same error like "Deprecated: Required parameter >>>> $ignoreFilters follows optional parameter $packageName " , >>>> It seems like you are still using PHP 8. After downgraded to PHP 7.4, >>>> you need to install PHP 7.4 dependencies as well. >>>> Try these steps : >>>> >>>> 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml >>>> php7.4-json php7.4-mbstring php7.4-gd php-ast >>>> 2. sudo apt-get install -y composer >>>> 3. sudo apt-get install -y libapache2-mod-php7.4 >>>> 4. sudo a2dismod php8.0 >>>> 5. sudo a2enmod php7.4 >>>> 6. sudo service apache2 restart >>>> >>>> 7, make clean >>>> 8, make >>>> Good luck. >>>> Best >>>> Shen >>>> >>>> >>>> On Thu, 4 Feb 2021 at 15:05, Tom Beaudry wrote: >>>> >>>>> Hey Shen, >>>>> >>>>> I downgraded to php 7.4 and get the same results. >>>>> >>>>> What can i try next? >>>>> Tom >>>>> >>>>> On Thu, Feb 4, 2021 at 2:01 PM Shen Wang >>>>> wrote: >>>>> >>>>>> Hi Tom, >>>>>> We don't support PHP 8 with Loris yet. We are working on it. For the >>>>>> 23.0-release, you have to use PHP 7.3 or 7.4. >>>>>> Best >>>>>> Shen >>>>>> >>>>>> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry wrote: >>>>>> >>>>>>> Hey Shen, >>>>>>> >>>>>>> Unfortunately it didn't work. Here's the output: >>>>>>> https://pastebin.com/raw/ZQjPuAG1 >>>>>>> >>>>>>> I'm using php8. >>>>>>> >>>>>>> Thanks, >>>>>>> Tom >>>>>>> >>>>>>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Tom, >>>>>>>> You are welcome. I think that you need to remove all the vendor >>>>>>>> files. >>>>>>>> Try step 1: "make clean" (delete all the vendor and >>>>>>>> node_modules) >>>>>>>> step 2: "make" ( run composer install and npm >>>>>>>> install ...) >>>>>>>> If it still can't work, could you tell me which PHP version are >>>>>>>> you using? >>>>>>>> Best >>>>>>>> Shen >>>>>>>> >>>>>>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi Shen, >>>>>>>>> >>>>>>>>> Thanks for the answer: Composer install gives me the following >>>>>>>>> error: >>>>>>>>> >>>>>>>>> [lorisadmin at loris loris]$ composer install >>>>>>>>> PHP Deprecated: Required parameter $ignoreFilters follows >>>>>>>>> optional parameter $packageName in >>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>> line 97 >>>>>>>>> >>>>>>>>> Deprecated: Required parameter $ignoreFilters follows optional >>>>>>>>> parameter $packageName in >>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>> line 97 >>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>> parameter $schema in >>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>> parameter $schema in >>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>>>>>> >>>>>>>>> >>>>>>>>> [ErrorException] >>>>>>>>> Trying to access array offset on value of type null >>>>>>>>> >>>>>>>>> Best, >>>>>>>>> Tom >>>>>>>>> >>>>>>>>> >>>>>>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hi Tom, >>>>>>>>>> You need to re-run " composer install " to solve this issue. >>>>>>>>>> Good Luck. >>>>>>>>>> Best >>>>>>>>>> Shen >>>>>>>>>> >>>>>>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Hey Guys, >>>>>>>>>>> >>>>>>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this apache >>>>>>>>>>> error when i navigate to the homepage in my web browser: >>>>>>>>>>> >>>>>>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] [client >>>>>>>>>>> 172.16.253.6:62122] PHP Warning: session_start(): Setting >>>>>>>>>>> option 'cookie_samesite' failed in >>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>>>>>> >>>>>>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] >>>>>>>>>>> [client 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: >>>>>>>>>>> Class 'Laminas\\Diactoros\\ServerRequestFactory'* not found in >>>>>>>>>>> /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in >>>>>>>>>>> /var/www/loris/htdocs/index.php on line 35 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> It seems that the server request is failing: >>>>>>>>>>> >>>>>>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory:: >>>>>>>>>>> fromGlobals(); >>>>>>>>>>> 36 >>>>>>>>>>> >>>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>>> Tom >>>>>>>>>>> _______________________________________________ >>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Shen Wang >>>>>>>>>> Loris Developer >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University >>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Shen Wang >>>>>>>> Loris Developer >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University >>>>>>>> >>>>>>>> >>>>>> >>>>>> -- >>>>>> Shen Wang >>>>>> Loris Developer >>>>>> Montreal Neurological Institute >>>>>> McGill University >>>>>> >>>>>> >>>> >>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Thu Feb 4 16:39:21 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Thu, 4 Feb 2021 16:39:21 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hi Tom, Try "composer self-update --snapshot" or "composer self-update --stable". Please let me know the result. Best Shen On Thu, 4 Feb 2021 at 16:27, Tom Beaudry wrote: > Hey Shen, > > I followed your instructions and can confirm i'm using php 7.4: > https://docs.google.com/document/d/1QppFZ8MtKoMRltiIQidFDslfVwriuS9cpfuZN49nOZ8/edit?usp=sharing > > composer install still fails: > > [ErrorException] > Trying to access array offset on value of type null > > Thanks! > Tom > > On Thu, Feb 4, 2021 at 4:04 PM Shen Wang wrote: > >> Hi Tom, >> It is very helpful, it means you need to do "composer install" again. >> if it not works for you then try these steps for Centos. >> sudo yum-config-manager --disable remi-php80 >> sudo yum-config-manager --enable remi-php74 >> sudo systemctl restart httpd sudo systemctl status httpd >> /var/www/loris/htdocs$ echo "" >> test.php >> Using test.php to check your PHP version in your brower. >> Best >> Shen >> >> >> >> >> >> On Thu, 4 Feb 2021 at 15:55, Tom Beaudry wrote: >> >>> Hey Shen, >>> >>> I checked the apache log and the error is different now: >>> >>> [Thu Feb 04 15:54:16.131158 2021] [php7:warn] [pid 5215] [client >>> 172.16.253.6:62349] PHP Warning: >>> require_once(/var/www/loris/htdocs/../vendor/autoload.php): failed to open >>> stream: No such file or directory in /var/www/loris/htdocs/index.php on >>> line 18 >>> [Thu Feb 04 15:54:16.131215 2021] [php7:error] [pid 5215] [client >>> 172.16.253.6:62349] PHP Fatal error: require_once(): Failed opening >>> required '/var/www/loris/htdocs/../vendor/autoload.php' >>> (include_path='.:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries') >>> in /var/www/loris/htdocs/index.php on line 18 >>> >>> I'm not sure if that helps figure out what's wrong. >>> >>> Thanks again! >>> Tom >>> >>> On Thu, Feb 4, 2021 at 3:45 PM Tom Beaudry wrote: >>> >>>> Hi Shen, >>>> >>>> My productions server is CentOS. >>>> >>>> If i check what version of php i'm using: >>>> >>>> [lorisadmin at loris loris]$ rpm -qa | grep php >>>> php-json-7.4.15-1.el7.remi.x86_64 >>>> php-pear-1.10.12-5.el7.remi.noarch >>>> php-7.4.15-1.el7.remi.x86_64 >>>> php-devel-7.4.15-1.el7.remi.x86_64 >>>> php-sodium-7.4.15-1.el7.remi.x86_64 >>>> php-fedora-autoloader-1.0.1-2.el7.noarch >>>> php-fpm-7.4.15-1.el7.remi.x86_64 >>>> php-gd-7.4.15-1.el7.remi.x86_64 >>>> php-cli-7.4.15-1.el7.remi.x86_64 >>>> php-pdo-7.4.15-1.el7.remi.x86_64 >>>> php-mysqlnd-7.4.15-1.el7.remi.x86_64 >>>> php-bcmath-7.4.15-1.el7.remi.x86_64 >>>> php-xml-7.4.15-1.el7.remi.x86_64 >>>> php-mbstring-7.4.15-1.el7.remi.x86_64 >>>> oniguruma5php-6.9.6-1.el7.remi.x86_64 >>>> php-common-7.4.15-1.el7.remi.x86_64 >>>> php-process-7.4.15-1.el7.remi.x86_64 >>>> php-pecl-mcrypt-1.0.4-1.el7.remi.7.4.x86_64 >>>> >>>> They are all showing up as 7.4. >>>> >>>> Thanks! >>>> Tom >>>> >>>> On Thu, Feb 4, 2021 at 3:37 PM Shen Wang >>>> wrote: >>>> >>>>> Hi Tom, >>>>> If you got same error like "Deprecated: Required parameter >>>>> $ignoreFilters follows optional parameter $packageName " , >>>>> It seems like you are still using PHP 8. After downgraded to PHP 7.4, >>>>> you need to install PHP 7.4 dependencies as well. >>>>> Try these steps : >>>>> >>>>> 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml >>>>> php7.4-json php7.4-mbstring php7.4-gd php-ast >>>>> 2. sudo apt-get install -y composer >>>>> 3. sudo apt-get install -y libapache2-mod-php7.4 >>>>> 4. sudo a2dismod php8.0 >>>>> 5. sudo a2enmod php7.4 >>>>> 6. sudo service apache2 restart >>>>> >>>>> 7, make clean >>>>> 8, make >>>>> Good luck. >>>>> Best >>>>> Shen >>>>> >>>>> >>>>> On Thu, 4 Feb 2021 at 15:05, Tom Beaudry wrote: >>>>> >>>>>> Hey Shen, >>>>>> >>>>>> I downgraded to php 7.4 and get the same results. >>>>>> >>>>>> What can i try next? >>>>>> Tom >>>>>> >>>>>> On Thu, Feb 4, 2021 at 2:01 PM Shen Wang >>>>>> wrote: >>>>>> >>>>>>> Hi Tom, >>>>>>> We don't support PHP 8 with Loris yet. We are working on it. For >>>>>>> the 23.0-release, you have to use PHP 7.3 or 7.4. >>>>>>> Best >>>>>>> Shen >>>>>>> >>>>>>> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry wrote: >>>>>>> >>>>>>>> Hey Shen, >>>>>>>> >>>>>>>> Unfortunately it didn't work. Here's the output: >>>>>>>> https://pastebin.com/raw/ZQjPuAG1 >>>>>>>> >>>>>>>> I'm using php8. >>>>>>>> >>>>>>>> Thanks, >>>>>>>> Tom >>>>>>>> >>>>>>>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi Tom, >>>>>>>>> You are welcome. I think that you need to remove all the vendor >>>>>>>>> files. >>>>>>>>> Try step 1: "make clean" (delete all the vendor and >>>>>>>>> node_modules) >>>>>>>>> step 2: "make" ( run composer install and npm >>>>>>>>> install ...) >>>>>>>>> If it still can't work, could you tell me which PHP version are >>>>>>>>> you using? >>>>>>>>> Best >>>>>>>>> Shen >>>>>>>>> >>>>>>>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hi Shen, >>>>>>>>>> >>>>>>>>>> Thanks for the answer: Composer install gives me the following >>>>>>>>>> error: >>>>>>>>>> >>>>>>>>>> [lorisadmin at loris loris]$ composer install >>>>>>>>>> PHP Deprecated: Required parameter $ignoreFilters follows >>>>>>>>>> optional parameter $packageName in >>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>> line 97 >>>>>>>>>> >>>>>>>>>> Deprecated: Required parameter $ignoreFilters follows optional >>>>>>>>>> parameter $packageName in >>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>> line 97 >>>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>>> parameter $schema in >>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>>> parameter $schema in >>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> [ErrorException] >>>>>>>>>> Trying to access array offset on value of type null >>>>>>>>>> >>>>>>>>>> Best, >>>>>>>>>> Tom >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Tom, >>>>>>>>>>> You need to re-run " composer install " to solve this issue. >>>>>>>>>>> Good Luck. >>>>>>>>>>> Best >>>>>>>>>>> Shen >>>>>>>>>>> >>>>>>>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hey Guys, >>>>>>>>>>>> >>>>>>>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this >>>>>>>>>>>> apache error when i navigate to the homepage in my web browser: >>>>>>>>>>>> >>>>>>>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] >>>>>>>>>>>> [client 172.16.253.6:62122] PHP Warning: session_start(): >>>>>>>>>>>> Setting option 'cookie_samesite' failed in >>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>>>>>>> >>>>>>>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] >>>>>>>>>>>> [client 172.16.253.6:62122] PHP Fatal error*: Uncaught Error: >>>>>>>>>>>> Class 'Laminas\\Diactoros\\ServerRequestFactory'* not found in >>>>>>>>>>>> /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n thrown in >>>>>>>>>>>> /var/www/loris/htdocs/index.php on line 35 >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> It seems that the server request is failing: >>>>>>>>>>>> >>>>>>>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory:: >>>>>>>>>>>> fromGlobals(); >>>>>>>>>>>> 36 >>>>>>>>>>>> >>>>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>>>> Tom >>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Shen Wang >>>>>>>>>>> Loris Developer >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Shen Wang >>>>>>>>> Loris Developer >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University >>>>>>>>> >>>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Shen Wang >>>>>>> Loris Developer >>>>>>> Montreal Neurological Institute >>>>>>> McGill University >>>>>>> >>>>>>> >>>>> >>>>> -- >>>>> Shen Wang >>>>> Loris Developer >>>>> Montreal Neurological Institute >>>>> McGill University >>>>> >>>>> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Thu Feb 4 18:00:09 2021 From: waveflux at gmail.com (Tom Beaudry) Date: Thu, 4 Feb 2021 18:00:09 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hey Shen, Sadly it's the same error. Tom On Thu, Feb 4, 2021 at 4:39 PM Shen Wang wrote: > Hi Tom, > Try "composer self-update --snapshot" or "composer self-update --stable". > Please let me know the result. > Best > Shen > > On Thu, 4 Feb 2021 at 16:27, Tom Beaudry wrote: > >> Hey Shen, >> >> I followed your instructions and can confirm i'm using php 7.4: >> https://docs.google.com/document/d/1QppFZ8MtKoMRltiIQidFDslfVwriuS9cpfuZN49nOZ8/edit?usp=sharing >> >> composer install still fails: >> >> [ErrorException] >> Trying to access array offset on value of type null >> >> Thanks! >> Tom >> >> On Thu, Feb 4, 2021 at 4:04 PM Shen Wang wrote: >> >>> Hi Tom, >>> It is very helpful, it means you need to do "composer install" again. >>> if it not works for you then try these steps for Centos. >>> sudo yum-config-manager --disable remi-php80 >>> sudo yum-config-manager --enable remi-php74 >>> sudo systemctl restart httpd sudo systemctl status httpd >>> /var/www/loris/htdocs$ echo "" >> test.php >>> Using test.php to check your PHP version in your brower. >>> Best >>> Shen >>> >>> >>> >>> >>> >>> On Thu, 4 Feb 2021 at 15:55, Tom Beaudry wrote: >>> >>>> Hey Shen, >>>> >>>> I checked the apache log and the error is different now: >>>> >>>> [Thu Feb 04 15:54:16.131158 2021] [php7:warn] [pid 5215] [client >>>> 172.16.253.6:62349] PHP Warning: >>>> require_once(/var/www/loris/htdocs/../vendor/autoload.php): failed to open >>>> stream: No such file or directory in /var/www/loris/htdocs/index.php on >>>> line 18 >>>> [Thu Feb 04 15:54:16.131215 2021] [php7:error] [pid 5215] [client >>>> 172.16.253.6:62349] PHP Fatal error: require_once(): Failed opening >>>> required '/var/www/loris/htdocs/../vendor/autoload.php' >>>> (include_path='.:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries') >>>> in /var/www/loris/htdocs/index.php on line 18 >>>> >>>> I'm not sure if that helps figure out what's wrong. >>>> >>>> Thanks again! >>>> Tom >>>> >>>> On Thu, Feb 4, 2021 at 3:45 PM Tom Beaudry wrote: >>>> >>>>> Hi Shen, >>>>> >>>>> My productions server is CentOS. >>>>> >>>>> If i check what version of php i'm using: >>>>> >>>>> [lorisadmin at loris loris]$ rpm -qa | grep php >>>>> php-json-7.4.15-1.el7.remi.x86_64 >>>>> php-pear-1.10.12-5.el7.remi.noarch >>>>> php-7.4.15-1.el7.remi.x86_64 >>>>> php-devel-7.4.15-1.el7.remi.x86_64 >>>>> php-sodium-7.4.15-1.el7.remi.x86_64 >>>>> php-fedora-autoloader-1.0.1-2.el7.noarch >>>>> php-fpm-7.4.15-1.el7.remi.x86_64 >>>>> php-gd-7.4.15-1.el7.remi.x86_64 >>>>> php-cli-7.4.15-1.el7.remi.x86_64 >>>>> php-pdo-7.4.15-1.el7.remi.x86_64 >>>>> php-mysqlnd-7.4.15-1.el7.remi.x86_64 >>>>> php-bcmath-7.4.15-1.el7.remi.x86_64 >>>>> php-xml-7.4.15-1.el7.remi.x86_64 >>>>> php-mbstring-7.4.15-1.el7.remi.x86_64 >>>>> oniguruma5php-6.9.6-1.el7.remi.x86_64 >>>>> php-common-7.4.15-1.el7.remi.x86_64 >>>>> php-process-7.4.15-1.el7.remi.x86_64 >>>>> php-pecl-mcrypt-1.0.4-1.el7.remi.7.4.x86_64 >>>>> >>>>> They are all showing up as 7.4. >>>>> >>>>> Thanks! >>>>> Tom >>>>> >>>>> On Thu, Feb 4, 2021 at 3:37 PM Shen Wang >>>>> wrote: >>>>> >>>>>> Hi Tom, >>>>>> If you got same error like "Deprecated: Required parameter >>>>>> $ignoreFilters follows optional parameter $packageName " , >>>>>> It seems like you are still using PHP 8. After downgraded to PHP >>>>>> 7.4, you need to install PHP 7.4 dependencies as well. >>>>>> Try these steps : >>>>>> >>>>>> 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml >>>>>> php7.4-json php7.4-mbstring php7.4-gd php-ast >>>>>> 2. sudo apt-get install -y composer >>>>>> 3. sudo apt-get install -y libapache2-mod-php7.4 >>>>>> 4. sudo a2dismod php8.0 >>>>>> 5. sudo a2enmod php7.4 >>>>>> 6. sudo service apache2 restart >>>>>> >>>>>> 7, make clean >>>>>> 8, make >>>>>> Good luck. >>>>>> Best >>>>>> Shen >>>>>> >>>>>> >>>>>> On Thu, 4 Feb 2021 at 15:05, Tom Beaudry wrote: >>>>>> >>>>>>> Hey Shen, >>>>>>> >>>>>>> I downgraded to php 7.4 and get the same results. >>>>>>> >>>>>>> What can i try next? >>>>>>> Tom >>>>>>> >>>>>>> On Thu, Feb 4, 2021 at 2:01 PM Shen Wang >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Tom, >>>>>>>> We don't support PHP 8 with Loris yet. We are working on it. For >>>>>>>> the 23.0-release, you have to use PHP 7.3 or 7.4. >>>>>>>> Best >>>>>>>> Shen >>>>>>>> >>>>>>>> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hey Shen, >>>>>>>>> >>>>>>>>> Unfortunately it didn't work. Here's the output: >>>>>>>>> https://pastebin.com/raw/ZQjPuAG1 >>>>>>>>> >>>>>>>>> I'm using php8. >>>>>>>>> >>>>>>>>> Thanks, >>>>>>>>> Tom >>>>>>>>> >>>>>>>>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hi Tom, >>>>>>>>>> You are welcome. I think that you need to remove all the vendor >>>>>>>>>> files. >>>>>>>>>> Try step 1: "make clean" (delete all the vendor and >>>>>>>>>> node_modules) >>>>>>>>>> step 2: "make" ( run composer install and npm >>>>>>>>>> install ...) >>>>>>>>>> If it still can't work, could you tell me which PHP version are >>>>>>>>>> you using? >>>>>>>>>> Best >>>>>>>>>> Shen >>>>>>>>>> >>>>>>>>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Shen, >>>>>>>>>>> >>>>>>>>>>> Thanks for the answer: Composer install gives me the following >>>>>>>>>>> error: >>>>>>>>>>> >>>>>>>>>>> [lorisadmin at loris loris]$ composer install >>>>>>>>>>> PHP Deprecated: Required parameter $ignoreFilters follows >>>>>>>>>>> optional parameter $packageName in >>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>> line 97 >>>>>>>>>>> >>>>>>>>>>> Deprecated: Required parameter $ignoreFilters follows optional >>>>>>>>>>> parameter $packageName in >>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>> line 97 >>>>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>>>> parameter $schema in >>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>>>> parameter $schema in >>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> [ErrorException] >>>>>>>>>>> Trying to access array offset on value of type null >>>>>>>>>>> >>>>>>>>>>> Best, >>>>>>>>>>> Tom >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang < >>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi Tom, >>>>>>>>>>>> You need to re-run " composer install " to solve this issue. >>>>>>>>>>>> Good Luck. >>>>>>>>>>>> Best >>>>>>>>>>>> Shen >>>>>>>>>>>> >>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry >>>>>>>>>>>> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hey Guys, >>>>>>>>>>>>> >>>>>>>>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this >>>>>>>>>>>>> apache error when i navigate to the homepage in my web browser: >>>>>>>>>>>>> >>>>>>>>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] >>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Warning: session_start(): >>>>>>>>>>>>> Setting option 'cookie_samesite' failed in >>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>>>>>>>> >>>>>>>>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] >>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Fatal error*: Uncaught >>>>>>>>>>>>> Error: Class 'Laminas\\Diactoros\\ServerRequestFactory'* not >>>>>>>>>>>>> found in /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n >>>>>>>>>>>>> thrown in /var/www/loris/htdocs/index.php on line 35 >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> It seems that the server request is failing: >>>>>>>>>>>>> >>>>>>>>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory:: >>>>>>>>>>>>> fromGlobals(); >>>>>>>>>>>>> 36 >>>>>>>>>>>>> >>>>>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>>>>> Tom >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> Shen Wang >>>>>>>>>>>> Loris Developer >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Shen Wang >>>>>>>>>> Loris Developer >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University >>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Shen Wang >>>>>>>> Loris Developer >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University >>>>>>>> >>>>>>>> >>>>>> >>>>>> -- >>>>>> Shen Wang >>>>>> Loris Developer >>>>>> Montreal Neurological Institute >>>>>> McGill University >>>>>> >>>>>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Fri Feb 5 10:19:11 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Fri, 5 Feb 2021 10:19:11 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: What version of composer are you using? Composer 2 (which was backwards incompatible) came out at around the same time as LORIS 23. If you're using composer 2 you can try `composer self-update 1.10.17` to downgrade and then try the composer install again. On Thu, Feb 4, 2021 at 6:00 PM Tom Beaudry wrote: > Hey Shen, > > Sadly it's the same error. > > Tom > > On Thu, Feb 4, 2021 at 4:39 PM Shen Wang wrote: > >> Hi Tom, >> Try "composer self-update --snapshot" or "composer self-update --stable". >> Please let me know the result. >> Best >> Shen >> >> On Thu, 4 Feb 2021 at 16:27, Tom Beaudry wrote: >> >>> Hey Shen, >>> >>> I followed your instructions and can confirm i'm using php 7.4: >>> https://docs.google.com/document/d/1QppFZ8MtKoMRltiIQidFDslfVwriuS9cpfuZN49nOZ8/edit?usp=sharing >>> >>> composer install still fails: >>> >>> [ErrorException] >>> Trying to access array offset on value of type null >>> >>> Thanks! >>> Tom >>> >>> On Thu, Feb 4, 2021 at 4:04 PM Shen Wang >>> wrote: >>> >>>> Hi Tom, >>>> It is very helpful, it means you need to do "composer install" again. >>>> if it not works for you then try these steps for Centos. >>>> sudo yum-config-manager --disable remi-php80 >>>> sudo yum-config-manager --enable remi-php74 >>>> sudo systemctl restart httpd sudo systemctl status httpd >>>> /var/www/loris/htdocs$ echo "" >> test.php >>>> Using test.php to check your PHP version in your brower. >>>> Best >>>> Shen >>>> >>>> >>>> >>>> >>>> >>>> On Thu, 4 Feb 2021 at 15:55, Tom Beaudry wrote: >>>> >>>>> Hey Shen, >>>>> >>>>> I checked the apache log and the error is different now: >>>>> >>>>> [Thu Feb 04 15:54:16.131158 2021] [php7:warn] [pid 5215] [client >>>>> 172.16.253.6:62349] PHP Warning: >>>>> require_once(/var/www/loris/htdocs/../vendor/autoload.php): failed to open >>>>> stream: No such file or directory in /var/www/loris/htdocs/index.php on >>>>> line 18 >>>>> [Thu Feb 04 15:54:16.131215 2021] [php7:error] [pid 5215] [client >>>>> 172.16.253.6:62349] PHP Fatal error: require_once(): Failed opening >>>>> required '/var/www/loris/htdocs/../vendor/autoload.php' >>>>> (include_path='.:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries') >>>>> in /var/www/loris/htdocs/index.php on line 18 >>>>> >>>>> I'm not sure if that helps figure out what's wrong. >>>>> >>>>> Thanks again! >>>>> Tom >>>>> >>>>> On Thu, Feb 4, 2021 at 3:45 PM Tom Beaudry wrote: >>>>> >>>>>> Hi Shen, >>>>>> >>>>>> My productions server is CentOS. >>>>>> >>>>>> If i check what version of php i'm using: >>>>>> >>>>>> [lorisadmin at loris loris]$ rpm -qa | grep php >>>>>> php-json-7.4.15-1.el7.remi.x86_64 >>>>>> php-pear-1.10.12-5.el7.remi.noarch >>>>>> php-7.4.15-1.el7.remi.x86_64 >>>>>> php-devel-7.4.15-1.el7.remi.x86_64 >>>>>> php-sodium-7.4.15-1.el7.remi.x86_64 >>>>>> php-fedora-autoloader-1.0.1-2.el7.noarch >>>>>> php-fpm-7.4.15-1.el7.remi.x86_64 >>>>>> php-gd-7.4.15-1.el7.remi.x86_64 >>>>>> php-cli-7.4.15-1.el7.remi.x86_64 >>>>>> php-pdo-7.4.15-1.el7.remi.x86_64 >>>>>> php-mysqlnd-7.4.15-1.el7.remi.x86_64 >>>>>> php-bcmath-7.4.15-1.el7.remi.x86_64 >>>>>> php-xml-7.4.15-1.el7.remi.x86_64 >>>>>> php-mbstring-7.4.15-1.el7.remi.x86_64 >>>>>> oniguruma5php-6.9.6-1.el7.remi.x86_64 >>>>>> php-common-7.4.15-1.el7.remi.x86_64 >>>>>> php-process-7.4.15-1.el7.remi.x86_64 >>>>>> php-pecl-mcrypt-1.0.4-1.el7.remi.7.4.x86_64 >>>>>> >>>>>> They are all showing up as 7.4. >>>>>> >>>>>> Thanks! >>>>>> Tom >>>>>> >>>>>> On Thu, Feb 4, 2021 at 3:37 PM Shen Wang >>>>>> wrote: >>>>>> >>>>>>> Hi Tom, >>>>>>> If you got same error like "Deprecated: Required parameter >>>>>>> $ignoreFilters follows optional parameter $packageName " , >>>>>>> It seems like you are still using PHP 8. After downgraded to PHP >>>>>>> 7.4, you need to install PHP 7.4 dependencies as well. >>>>>>> Try these steps : >>>>>>> >>>>>>> 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml >>>>>>> php7.4-json php7.4-mbstring php7.4-gd php-ast >>>>>>> 2. sudo apt-get install -y composer >>>>>>> 3. sudo apt-get install -y libapache2-mod-php7.4 >>>>>>> 4. sudo a2dismod php8.0 >>>>>>> 5. sudo a2enmod php7.4 >>>>>>> 6. sudo service apache2 restart >>>>>>> >>>>>>> 7, make clean >>>>>>> 8, make >>>>>>> Good luck. >>>>>>> Best >>>>>>> Shen >>>>>>> >>>>>>> >>>>>>> On Thu, 4 Feb 2021 at 15:05, Tom Beaudry wrote: >>>>>>> >>>>>>>> Hey Shen, >>>>>>>> >>>>>>>> I downgraded to php 7.4 and get the same results. >>>>>>>> >>>>>>>> What can i try next? >>>>>>>> Tom >>>>>>>> >>>>>>>> On Thu, Feb 4, 2021 at 2:01 PM Shen Wang >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi Tom, >>>>>>>>> We don't support PHP 8 with Loris yet. We are working on it. For >>>>>>>>> the 23.0-release, you have to use PHP 7.3 or 7.4. >>>>>>>>> Best >>>>>>>>> Shen >>>>>>>>> >>>>>>>>> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hey Shen, >>>>>>>>>> >>>>>>>>>> Unfortunately it didn't work. Here's the output: >>>>>>>>>> https://pastebin.com/raw/ZQjPuAG1 >>>>>>>>>> >>>>>>>>>> I'm using php8. >>>>>>>>>> >>>>>>>>>> Thanks, >>>>>>>>>> Tom >>>>>>>>>> >>>>>>>>>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Tom, >>>>>>>>>>> You are welcome. I think that you need to remove all the vendor >>>>>>>>>>> files. >>>>>>>>>>> Try step 1: "make clean" (delete all the vendor and >>>>>>>>>>> node_modules) >>>>>>>>>>> step 2: "make" ( run composer install and npm >>>>>>>>>>> install ...) >>>>>>>>>>> If it still can't work, could you tell me which PHP version are >>>>>>>>>>> you using? >>>>>>>>>>> Best >>>>>>>>>>> Shen >>>>>>>>>>> >>>>>>>>>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi Shen, >>>>>>>>>>>> >>>>>>>>>>>> Thanks for the answer: Composer install gives me the following >>>>>>>>>>>> error: >>>>>>>>>>>> >>>>>>>>>>>> [lorisadmin at loris loris]$ composer install >>>>>>>>>>>> PHP Deprecated: Required parameter $ignoreFilters follows >>>>>>>>>>>> optional parameter $packageName in >>>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>>> line 97 >>>>>>>>>>>> >>>>>>>>>>>> Deprecated: Required parameter $ignoreFilters follows optional >>>>>>>>>>>> parameter $packageName in >>>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>>> line 97 >>>>>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>>>>> parameter $schema in >>>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>>>>> parameter $schema in >>>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> [ErrorException] >>>>>>>>>>>> Trying to access array offset on value of type null >>>>>>>>>>>> >>>>>>>>>>>> Best, >>>>>>>>>>>> Tom >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang < >>>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Tom, >>>>>>>>>>>>> You need to re-run " composer install " to solve this issue. >>>>>>>>>>>>> Good Luck. >>>>>>>>>>>>> Best >>>>>>>>>>>>> Shen >>>>>>>>>>>>> >>>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry >>>>>>>>>>>>> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hey Guys, >>>>>>>>>>>>>> >>>>>>>>>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this >>>>>>>>>>>>>> apache error when i navigate to the homepage in my web browser: >>>>>>>>>>>>>> >>>>>>>>>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] >>>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Warning: session_start(): >>>>>>>>>>>>>> Setting option 'cookie_samesite' failed in >>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>>>>>>>>> >>>>>>>>>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] >>>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Fatal error*: Uncaught >>>>>>>>>>>>>> Error: Class 'Laminas\\Diactoros\\ServerRequestFactory'* not >>>>>>>>>>>>>> found in /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n >>>>>>>>>>>>>> thrown in /var/www/loris/htdocs/index.php on line 35 >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> It seems that the server request is failing: >>>>>>>>>>>>>> >>>>>>>>>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory:: >>>>>>>>>>>>>> fromGlobals(); >>>>>>>>>>>>>> 36 >>>>>>>>>>>>>> >>>>>>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>>>>>> Tom >>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Shen Wang >>>>>>>>>>> Loris Developer >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Shen Wang >>>>>>>>> Loris Developer >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University >>>>>>>>> >>>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Shen Wang >>>>>>> Loris Developer >>>>>>> Montreal Neurological Institute >>>>>>> McGill University >>>>>>> >>>>>>> >>>> >>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> >> >> -- >> Shen Wang >> Loris Developer >> Montreal Neurological Institute >> McGill University >> >> _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Mon Feb 8 09:47:18 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 8 Feb 2021 14:47:18 +0000 Subject: [Loris-dev] Issues with landing page, data query and BrainBrowser In-Reply-To: References: <09C35758-DB2A-41D9-B5B6-94FB0095B4F5@bwh.harvard.edu> Message-ID: <73864227-1FB0-4E7B-A0DB-074C23197C1B@bwh.harvard.edu> Hi Zia, The issue persists, see the times in the attached image (site_recruitment | jquery | 3.4 min). I am now running LORIS v23. How can we check what is happening? We can a have a Zoom call where I can share my screen if needed. Regards, Alfredo. [cid:9491381B-A96A-43E2-93CC-CED1300E544D] On Feb 2, 2021, at 9:49 AM, Zia Mohades > wrote: External Email - Use Caution Hi Alfredo, Please let me know if your issue has been resolved. Thank you On Mon, Jan 25, 2021 at 8:35 AM Morales Pinzon, Alfredo > wrote: Dear Zia, The issue is when loading the landing page once a user had logged in into LORIS. The systems remains unresponsive until the graph is loaded. I am moving to the last version of LORIS right now, I will inform if the issues persists in the latests version. Thank you. Alfredo. On Jan 7, 2021, at 3:34 PM, Zia Mohades > wrote: External Email - Use Caution Hello, Regarding your first question. As Dave mentioned we haven't experienced any issues with loading when we click on the link/site under the graph. We did however noticed some formatting issues which should be fixed in the new version of LORIS but nothing related to the loading functionality. Thank you On Wed, Jan 6, 2021 at 12:51 PM Dave MacFarlane > wrote: On Wed, Jan 6, 2021 at 12:30 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev team, We are experiencing the following issues in Loris. Could you please help me or guide me on how address them. 1. After login into LORIS, the webpage does not allow the user to go to any link until the graph under "Study Progression" is created. This is taking more than one minute to load. I guess this is because we have hundreds of centers. Is it possible to remove the graph from the landing page? (See attachment) I don't believe it should take that long even with a large number of sites. I'll let someone from CCNA handle this part of the question since they also have hundreds of sites and might have more insight.. 2. When using the Data Query Tool the front-end crashes with error 500. This is what I can see in the loris-error.log === [Wed Jan 06 12:23:31.920274 2021] [php7:error] [pid 12100] [client 216.15.126.108:56023] PHP Fatal error: Uncaught ConfigurationException: NDB_Factory::CouchDB() requires all parameters to be supplied. in /var/www/loris/php/libraries/NDB_Factory.class.inc:297\nStack trace:\n#0 /var/www/loris/modules/dataquery/php/dataquery.class.inc(59): NDB_Factory->couchDB('%COUCH_DATABASE...', '%COUCH_HOSTNAME...', 0, '%COUCH_USERNAME...', '%COUCH_PASSWORD...')\n#1 /var/www/loris/php/libraries/NDB_Form.class.inc(188): LORIS\\dataquery\\Dataquery->setup()\n#2 /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171): NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#3 /var/www/loris/src/Middleware/PageDecorationMiddleware.php(49): LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), Object(LORIS\\dataquery\\Dataquery))\n#4 /var/www/loris/php/libraries/NDB_Page.class.inc(659): LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), Object(LORIS\\dataquery\\Dataquery))\n#5 /var/www/loris/php/libraries/Module.class.inc(341): NDB_Page->process(Object(Zend\\ in /var/www/loris/php/libraries/NDB_Factory.class.inc on line 297, referer: https://ipmsa-loris.bic.mni.mcgill.ca/imaging_browser/viewSession/?sessionID=85935 === The DQT currently requires a CouchDB backend with the data imported into it. It looks like the CouchDB hostname/database/username/ password/etc aren't set up. The Configurations section of the file modules/dataquery/README.md should have more information about the setup required. Is the `` tag in project/config.xml setup as described in step 3 of that document? 3. In the statistics section (Reports -> Statistics) I can see the following message at the bottom of the page: === Oops It seems like the scan type selected does not have a corresponding column in the mri_parameter_form table in the database. In order to display the statistics for the scan type, make sure the mri_parameter_form table contains a column in the exact format SCANTYPE_Scan_done === The statistics page using an instrument named "mri_parameter_form" to determine numbers for the scan done. For each scan type in the mri_scan_types table* it expects there to be a column named "SCANTYPE_Scan_Done" to use for reporting statistics. I believe there's somewhere in the MRI documentation that goes into more depth but I'm not entirely sure where, maybe Cecile can chime in.. In the loris-error.log a see a large list of the following messages: === [Wed Jan 06 12:26:24.730900 2021] [php7:notice] [pid 25824] [client 216.15.126.108:56738] PHP Notice: Undefined index: Female in /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line 137, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ [Wed Jan 06 12:26:24.730935 2021] [php7:notice] [pid 25824] [client 216.15.126.108:56738] PHP Notice: Undefined index: OLYMPUS_CLINICAL_SCREENING in /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ [Wed Jan 06 12:26:24.730944 2021] [php7:notice] [pid 25824] [client 216.15.126.108:56738] PHP Notice: Undefined index: Male in /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ === What version of LORIS is this? I think the notices are unrelated and probably harmless but should still be fixed if they haven't been yet. 4. I am not able to visualiza any image. A message ?LOADING ?? appears but nothing happens. Looking at the loris-error.log I can see that the path to the images is missing a ?/? === PHP Warning: readfile(/data_/ipmsa/loris_data/IPMSA/dataassembly/343633/baseline/mri/native/IPMSA_343633_baseline_flair_001.mnc): failed to open stream: No such file or directory in /var/www/loris/modules/brainbrowser/ajax/image.php on line 56, referer: https://ipmsa-loris.bic.mni.mcgill.ca/brainbrowser/?minc_id=[112603] === Do you know where can this missing ?/? should be set? It looks like that code is using the imagePath configuration variable which should have a trailing /. It should be the configuration option labeled "Path to images for display in Imaging Browser (e.g. /data/$project/data/)" in the Configuration module frontend. - Dave _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: LORIS loading times 2021-02-08 at 9.44.57 AM.png Type: image/png Size: 312041 bytes Desc: LORIS loading times 2021-02-08 at 9.44.57 AM.png URL: From zia.mohades at mcin.ca Mon Feb 8 10:00:52 2021 From: zia.mohades at mcin.ca (Zia Mohades) Date: Mon, 8 Feb 2021 10:00:52 -0500 Subject: [Loris-dev] Issues with landing page, data query and BrainBrowser In-Reply-To: <73864227-1FB0-4E7B-A0DB-074C23197C1B@bwh.harvard.edu> References: <09C35758-DB2A-41D9-B5B6-94FB0095B4F5@bwh.harvard.edu> <73864227-1FB0-4E7B-A0DB-074C23197C1B@bwh.harvard.edu> Message-ID: Hi Alfredo, Sorry to hear that you're still experiencing this issue. Since haven't experienced this in my Project, I'll let others (perhaps Rida or Dave) to help you with this. On Mon, Feb 8, 2021 at 9:47 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Zia, > > The issue persists, see the times in the attached image (site_recruitment > | jquery | 3.4 min). I am now running LORIS v23. > > How can we check what is happening? We can a have a Zoom call where I can > share my screen if needed. > > Regards, > Alfredo. > > > > On Feb 2, 2021, at 9:49 AM, Zia Mohades wrote: > > External Email - Use Caution > > Hi Alfredo, > > Please let me know if your issue has been resolved. > > Thank you > > > On Mon, Jan 25, 2021 at 8:35 AM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Dear Zia, >> >> The issue is when loading the landing page once a user had logged in into >> LORIS. The systems remains unresponsive until the graph is loaded. I am >> moving to the last version of LORIS right now, I will inform if the issues >> persists in the latests version. >> >> Thank you. >> >> Alfredo. >> >> On Jan 7, 2021, at 3:34 PM, Zia Mohades wrote: >> >> External Email - Use Caution >> >> Hello, >> >> Regarding your first question. As Dave mentioned we haven't experienced >> any issues with loading when we click on the link/site under the graph. We >> did however noticed some formatting issues which should be fixed in the new >> version of LORIS but nothing related to the loading functionality. >> >> >> Thank you >> >> >> On Wed, Jan 6, 2021 at 12:51 PM Dave MacFarlane >> wrote: >> >>> On Wed, Jan 6, 2021 at 12:30 PM Morales Pinzon, Alfredo < >>> AMORALESPINZON at bwh.harvard.edu> wrote: >>> >>>> Dear LorisDev team, >>>> >>>> We are experiencing the following issues in Loris. Could you please >>>> help me or guide me on how address them. >>>> >>>> 1. After login into LORIS, the webpage does not allow the user to go to >>>> any link until the graph under "Study Progression" is created. This is >>>> taking more than one minute to load. I guess this is because we have >>>> hundreds of centers. Is it possible to remove the graph from the landing >>>> page? (See attachment) >>>> >>>> >>> I don't believe it should take that long even with a large number of >>> sites. I'll let someone from CCNA handle this part of the question since >>> they also have hundreds of sites and might have more insight.. >>> >>> >>>> >>>> 2. When using the Data Query Tool the front-end crashes with error 500. >>>> >>>> This is what I can see in the loris-error.log >>>> >>>> === >>>> [Wed Jan 06 12:23:31.920274 2021] [php7:error] [pid 12100] [client >>>> 216.15.126.108:56023 >>>> ] >>>> PHP Fatal error: Uncaught ConfigurationException: NDB_Factory::CouchDB() >>>> requires all parameters to be supplied. in >>>> /var/www/loris/php/libraries/NDB_Factory.class.inc:297\nStack trace:\n#0 >>>> /var/www/loris/modules/dataquery/php/dataquery.class.inc(59): >>>> NDB_Factory->couchDB('%COUCH_DATABASE...', '%COUCH_HOSTNAME...', 0, >>>> '%COUCH_USERNAME...', '%COUCH_PASSWORD...')\n#1 >>>> /var/www/loris/php/libraries/NDB_Form.class.inc(188): >>>> LORIS\\dataquery\\Dataquery->setup()\n#2 >>>> /var/www/loris/src/Middleware/UserPageDecorationMiddleware.php(171): >>>> NDB_Form->handle(Object(Zend\\Diactoros\\ServerRequest))\n#3 >>>> /var/www/loris/src/Middleware/PageDecorationMiddleware.php(49): >>>> LORIS\\Middleware\\UserPageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), >>>> Object(LORIS\\dataquery\\Dataquery))\n#4 >>>> /var/www/loris/php/libraries/NDB_Page.class.inc(659): >>>> LORIS\\Middleware\\PageDecorationMiddleware->process(Object(Zend\\Diactoros\\ServerRequest), >>>> Object(LORIS\\dataquery\\Dataquery))\n#5 >>>> /var/www/loris/php/libraries/Module.class.inc(341): >>>> NDB_Page->process(Object(Zend\\ in >>>> /var/www/loris/php/libraries/NDB_Factory.class.inc on line 297, referer: >>>> >>>> https://ipmsa-loris.bic.mni.mcgill.ca/imaging_browser/viewSession/?sessionID=85935 >>>> >>>> === >>>> >>>> >>> The DQT currently requires a CouchDB backend with the data imported into >>> it. It looks like the CouchDB hostname/database/username/ password/etc >>> aren't set up. The Configurations section of the file >>> modules/dataquery/README.md should have more information about the setup >>> required. Is the `` tag in project/config.xml setup as described >>> in step 3 of that document? >>> >>> >>>> >>>> 3. In the statistics section (Reports -> Statistics) I can see the >>>> following message at the bottom of the page: >>>> >>>> === >>>> Oops >>>> >>>> It seems like the scan type selected does not have a corresponding >>>> column in the mri_parameter_form table in the database. >>>> In order to display the statistics for the scan type, make sure the >>>> mri_parameter_form table contains a column in the exact format >>>> SCANTYPE_Scan_done >>>> === >>>> >>>> >>> The statistics page using an instrument named "mri_parameter_form" to >>> determine numbers for the scan done. For each scan type in the >>> mri_scan_types table* it expects there to be a column named >>> "SCANTYPE_Scan_Done" to use for reporting statistics. I believe there's >>> somewhere in the MRI documentation that goes into more depth but I'm not >>> entirely sure where, maybe Cecile can chime in.. >>> >>> In the loris-error.log a see a large list of the following messages: >>>> >>>> === >>>> [Wed Jan 06 12:26:24.730900 2021] [php7:notice] [pid 25824] [client >>>> 216.15.126.108:56738 >>>> ] >>>> PHP Notice: Undefined index: Female in >>>> /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line >>>> 137, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ >>>> >>>> [Wed Jan 06 12:26:24.730935 2021] [php7:notice] [pid 25824] [client >>>> 216.15.126.108:56738 >>>> ] >>>> PHP Notice: Undefined index: OLYMPUS_CLINICAL_SCREENING in >>>> /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line >>>> 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ >>>> >>>> [Wed Jan 06 12:26:24.730944 2021] [php7:notice] [pid 25824] [client >>>> 216.15.126.108:56738 >>>> ] >>>> PHP Notice: Undefined index: Male in >>>> /var/www/loris/modules/statistics/php/stats_demographic.class.inc on line >>>> 133, referer: https://ipmsa-loris.bic.mni.mcgill.ca/statistics/ >>>> >>>> === >>>> >>>> >>> What version of LORIS is this? I think the notices are unrelated and >>> probably harmless but should still be fixed if they haven't been yet. >>> >>> >>>> 4. I am not able to visualiza any image. A message ?LOADING ?? appears >>>> but nothing happens. >>>> Looking at the loris-error.log I can see that the path to the images is >>>> missing a ?/? >>>> >>>> === >>>> PHP Warning: readfile(/data_/ipmsa/loris_data/IPMSA/dataassembly/343633/baseline/mri/native/IPMSA_343633_baseline_flair_001.mnc): >>>> failed to open stream: No such file or directory in >>>> /var/www/loris/modules/brainbrowser/ajax/image.php on line 56, referer: >>>> https://ipmsa-loris.bic.mni.mcgill.ca/brainbrowser/?minc_id=[112603 >>>> >>>> ] >>>> === >>>> >>>> Do you know where can this missing ?/? should be set? >>>> >>>> >>> It looks like that code is using the imagePath configuration variable >>> which should have a trailing /. It should be the configuration option >>> labeled "Path to images for display in Imaging Browser (e.g. >>> /data/$project/data/)" in the Configuration module frontend. >>> >>> - Dave >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.org/complianceline >> >> . If the e-mail was sent to you in error but does not contain patient >> information, please contact the sender and properly dispose of the e-mail. >> > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: LORIS loading times 2021-02-08 at 9.44.57 AM.png Type: image/png Size: 312041 bytes Desc: not available URL: From waveflux at gmail.com Mon Feb 8 12:49:37 2021 From: waveflux at gmail.com (Tom Beaudry) Date: Mon, 8 Feb 2021 12:49:37 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hi DAve and Shen, I wasn't able to rollback my version of composer so it made me realize it was corrupt, so i removed composer, reinstalled it and rolled back to the version you suggest. Now i can do composer insall with no problem, and make clean & make work without errors. The only error i'm left with now when i visit the main page is: [Mon Feb 08 12:47:27.785383 2021] [php7:error] [pid 7082] [client 172.16.253.8:54598] PHP Fatal error: Uncaught --> Smarty: unable to write file /var/www/loris/smarty/templates_c/wrt6021792fbfb5b4_53411590 <-- \n thrown in /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_runtime_writefile.php on line 60 Thanks! Tom [Mon Feb 08 12:47:27.785383 2021] [php7:error] [pid 7082] [client 172.16.253.8:54598] PHP Fatal error: Uncaught --> Smarty: unable to write file /var/www/loris/smarty/templates_c/wrt6021792fbfb5b4_53411590 <-- \n thrown in /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_runtime_writefile.php on line 60 On Fri, Feb 5, 2021 at 10:19 AM Dave MacFarlane wrote: > What version of composer are you using? > > Composer 2 (which was backwards incompatible) came out at around the same > time as LORIS 23. > > If you're using composer 2 you can try `composer self-update 1.10.17` to > downgrade and then try the > composer install again. > > On Thu, Feb 4, 2021 at 6:00 PM Tom Beaudry wrote: > >> Hey Shen, >> >> Sadly it's the same error. >> >> Tom >> >> On Thu, Feb 4, 2021 at 4:39 PM Shen Wang wrote: >> >>> Hi Tom, >>> Try "composer self-update --snapshot" or "composer self-update >>> --stable". >>> Please let me know the result. >>> Best >>> Shen >>> >>> On Thu, 4 Feb 2021 at 16:27, Tom Beaudry wrote: >>> >>>> Hey Shen, >>>> >>>> I followed your instructions and can confirm i'm using php 7.4: >>>> https://docs.google.com/document/d/1QppFZ8MtKoMRltiIQidFDslfVwriuS9cpfuZN49nOZ8/edit?usp=sharing >>>> >>>> composer install still fails: >>>> >>>> [ErrorException] >>>> Trying to access array offset on value of type null >>>> >>>> Thanks! >>>> Tom >>>> >>>> On Thu, Feb 4, 2021 at 4:04 PM Shen Wang >>>> wrote: >>>> >>>>> Hi Tom, >>>>> It is very helpful, it means you need to do "composer install" again. >>>>> if it not works for you then try these steps for Centos. >>>>> sudo yum-config-manager --disable remi-php80 >>>>> sudo yum-config-manager --enable remi-php74 >>>>> sudo systemctl restart httpd sudo systemctl status httpd >>>>> /var/www/loris/htdocs$ echo "" >> test.php >>>>> Using test.php to check your PHP version in your brower. >>>>> Best >>>>> Shen >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> On Thu, 4 Feb 2021 at 15:55, Tom Beaudry wrote: >>>>> >>>>>> Hey Shen, >>>>>> >>>>>> I checked the apache log and the error is different now: >>>>>> >>>>>> [Thu Feb 04 15:54:16.131158 2021] [php7:warn] [pid 5215] [client >>>>>> 172.16.253.6:62349] PHP Warning: >>>>>> require_once(/var/www/loris/htdocs/../vendor/autoload.php): failed to open >>>>>> stream: No such file or directory in /var/www/loris/htdocs/index.php on >>>>>> line 18 >>>>>> [Thu Feb 04 15:54:16.131215 2021] [php7:error] [pid 5215] [client >>>>>> 172.16.253.6:62349] PHP Fatal error: require_once(): Failed opening >>>>>> required '/var/www/loris/htdocs/../vendor/autoload.php' >>>>>> (include_path='.:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries') >>>>>> in /var/www/loris/htdocs/index.php on line 18 >>>>>> >>>>>> I'm not sure if that helps figure out what's wrong. >>>>>> >>>>>> Thanks again! >>>>>> Tom >>>>>> >>>>>> On Thu, Feb 4, 2021 at 3:45 PM Tom Beaudry >>>>>> wrote: >>>>>> >>>>>>> Hi Shen, >>>>>>> >>>>>>> My productions server is CentOS. >>>>>>> >>>>>>> If i check what version of php i'm using: >>>>>>> >>>>>>> [lorisadmin at loris loris]$ rpm -qa | grep php >>>>>>> php-json-7.4.15-1.el7.remi.x86_64 >>>>>>> php-pear-1.10.12-5.el7.remi.noarch >>>>>>> php-7.4.15-1.el7.remi.x86_64 >>>>>>> php-devel-7.4.15-1.el7.remi.x86_64 >>>>>>> php-sodium-7.4.15-1.el7.remi.x86_64 >>>>>>> php-fedora-autoloader-1.0.1-2.el7.noarch >>>>>>> php-fpm-7.4.15-1.el7.remi.x86_64 >>>>>>> php-gd-7.4.15-1.el7.remi.x86_64 >>>>>>> php-cli-7.4.15-1.el7.remi.x86_64 >>>>>>> php-pdo-7.4.15-1.el7.remi.x86_64 >>>>>>> php-mysqlnd-7.4.15-1.el7.remi.x86_64 >>>>>>> php-bcmath-7.4.15-1.el7.remi.x86_64 >>>>>>> php-xml-7.4.15-1.el7.remi.x86_64 >>>>>>> php-mbstring-7.4.15-1.el7.remi.x86_64 >>>>>>> oniguruma5php-6.9.6-1.el7.remi.x86_64 >>>>>>> php-common-7.4.15-1.el7.remi.x86_64 >>>>>>> php-process-7.4.15-1.el7.remi.x86_64 >>>>>>> php-pecl-mcrypt-1.0.4-1.el7.remi.7.4.x86_64 >>>>>>> >>>>>>> They are all showing up as 7.4. >>>>>>> >>>>>>> Thanks! >>>>>>> Tom >>>>>>> >>>>>>> On Thu, Feb 4, 2021 at 3:37 PM Shen Wang >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Tom, >>>>>>>> If you got same error like "Deprecated: Required parameter >>>>>>>> $ignoreFilters follows optional parameter $packageName " , >>>>>>>> It seems like you are still using PHP 8. After downgraded to PHP >>>>>>>> 7.4, you need to install PHP 7.4 dependencies as well. >>>>>>>> Try these steps : >>>>>>>> >>>>>>>> 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml >>>>>>>> php7.4-json php7.4-mbstring php7.4-gd php-ast >>>>>>>> 2. sudo apt-get install -y composer >>>>>>>> 3. sudo apt-get install -y libapache2-mod-php7.4 >>>>>>>> 4. sudo a2dismod php8.0 >>>>>>>> 5. sudo a2enmod php7.4 >>>>>>>> 6. sudo service apache2 restart >>>>>>>> >>>>>>>> 7, make clean >>>>>>>> 8, make >>>>>>>> Good luck. >>>>>>>> Best >>>>>>>> Shen >>>>>>>> >>>>>>>> >>>>>>>> On Thu, 4 Feb 2021 at 15:05, Tom Beaudry >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hey Shen, >>>>>>>>> >>>>>>>>> I downgraded to php 7.4 and get the same results. >>>>>>>>> >>>>>>>>> What can i try next? >>>>>>>>> Tom >>>>>>>>> >>>>>>>>> On Thu, Feb 4, 2021 at 2:01 PM Shen Wang >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hi Tom, >>>>>>>>>> We don't support PHP 8 with Loris yet. We are working on it. For >>>>>>>>>> the 23.0-release, you have to use PHP 7.3 or 7.4. >>>>>>>>>> Best >>>>>>>>>> Shen >>>>>>>>>> >>>>>>>>>> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Hey Shen, >>>>>>>>>>> >>>>>>>>>>> Unfortunately it didn't work. Here's the output: >>>>>>>>>>> https://pastebin.com/raw/ZQjPuAG1 >>>>>>>>>>> >>>>>>>>>>> I'm using php8. >>>>>>>>>>> >>>>>>>>>>> Thanks, >>>>>>>>>>> Tom >>>>>>>>>>> >>>>>>>>>>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang < >>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi Tom, >>>>>>>>>>>> You are welcome. I think that you need to remove all the vendor >>>>>>>>>>>> files. >>>>>>>>>>>> Try step 1: "make clean" (delete all the vendor and >>>>>>>>>>>> node_modules) >>>>>>>>>>>> step 2: "make" ( run composer install and >>>>>>>>>>>> npm install ...) >>>>>>>>>>>> If it still can't work, could you tell me which PHP version are >>>>>>>>>>>> you using? >>>>>>>>>>>> Best >>>>>>>>>>>> Shen >>>>>>>>>>>> >>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry >>>>>>>>>>>> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Shen, >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks for the answer: Composer install gives me the >>>>>>>>>>>>> following error: >>>>>>>>>>>>> >>>>>>>>>>>>> [lorisadmin at loris loris]$ composer install >>>>>>>>>>>>> PHP Deprecated: Required parameter $ignoreFilters follows >>>>>>>>>>>>> optional parameter $packageName in >>>>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>>>> line 97 >>>>>>>>>>>>> >>>>>>>>>>>>> Deprecated: Required parameter $ignoreFilters follows optional >>>>>>>>>>>>> parameter $packageName in >>>>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>>>> line 97 >>>>>>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>>>>>> parameter $schema in >>>>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>>>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>>>>>> parameter $schema in >>>>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> [ErrorException] >>>>>>>>>>>>> Trying to access array offset on value of type null >>>>>>>>>>>>> >>>>>>>>>>>>> Best, >>>>>>>>>>>>> Tom >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang < >>>>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Tom, >>>>>>>>>>>>>> You need to re-run " composer install " to solve this issue. >>>>>>>>>>>>>> Good Luck. >>>>>>>>>>>>>> Best >>>>>>>>>>>>>> Shen >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry >>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hey Guys, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this >>>>>>>>>>>>>>> apache error when i navigate to the homepage in my web browser: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] >>>>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Warning: session_start(): >>>>>>>>>>>>>>> Setting option 'cookie_samesite' failed in >>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] >>>>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Fatal error*: Uncaught >>>>>>>>>>>>>>> Error: Class 'Laminas\\Diactoros\\ServerRequestFactory'* >>>>>>>>>>>>>>> not found in /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n >>>>>>>>>>>>>>> thrown in /var/www/loris/htdocs/index.php on line 35 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> It seems that the server request is failing: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory:: >>>>>>>>>>>>>>> fromGlobals(); >>>>>>>>>>>>>>> 36 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>>>>>>> Tom >>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> Shen Wang >>>>>>>>>>>> Loris Developer >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Shen Wang >>>>>>>>>> Loris Developer >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University >>>>>>>>>> >>>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Shen Wang >>>>>>>> Loris Developer >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University >>>>>>>> >>>>>>>> >>>>> >>>>> -- >>>>> Shen Wang >>>>> Loris Developer >>>>> Montreal Neurological Institute >>>>> McGill University >>>>> >>>>> >>> >>> -- >>> Shen Wang >>> Loris Developer >>> Montreal Neurological Institute >>> McGill University >>> >>> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Mon Feb 8 13:06:46 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 8 Feb 2021 18:06:46 +0000 Subject: [Loris-dev] 500 after login Message-ID: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> Dear LorisDev, I am getting a 500 error after login into LORIS. This is what I can see in the logs: === [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client 216.15.126.108:61071] PHP Fatal error: Uncaught TypeError: Return value of User::getFullname() must be of the type string, null returned in /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 /var/www/loris/modules/dashboard/php/module.class.inc(118): User->getFullname()\n#1 /var/www/loris/modules/dashboard/php/module.class.inc(57): LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), Object(NDB_Config), Object(User))\n#2 /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 /var/www/loris/php/libraries/Module.class.inc(275): LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), 'dashboard', '', '', 'dashboard')\n#4 /var/www/loris/php/libraries/Module.class.inc(342): Module->loadPage('dashboard')\n#5 /var/www/loris/src/Middleware/ResponseGenerator.php(50): Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 /var/www/loris/src/Middleware/AuthMiddleware.php(63): LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se in /var/www/loris/php/libraries/User.class.inc on line 236 === Perhaps it is an issue with the name of the user? I created hundreds of users for batch insertion of candidates and visits for previous versions of LORIS that required insertion of Candidates and Visits by users belonging to a given center. This is an entry in the users table without the hashed password: === *************************** 850. row *************************** ID: 850 UserID: 723-DKC-1_dataman Password: NULL Real_name: NULL First_name: NULL Last_name: NULL Degree: NULL Position_title: NULL Institution: NULL Department: NULL Address: NULL City: NULL State: NULL Zip_code: NULL Country: NULL Phone: NULL Fax: NULL Email: 723-DKC-1_dataman at ipmsa.com Privilege: 0 PSCPI: N DBAccess: Active: Y Password_hash: /REMOVED/ Password_expiry: 2035-01-01 Pending_approval: N Doc_Repo_Notifications: N language_preference: NULL active_from: NULL active_to: NULL === Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Mon Feb 8 13:11:54 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 8 Feb 2021 18:11:54 +0000 Subject: [Loris-dev] "error": "You can`t create candidates visit for that site" Message-ID: <2CF75546-8107-4F65-8E4B-E2D3717DA555@bwh.harvard.edu> Dear LorisDev team, After upgrading to Loris 23 I am not able to insert Visits using the APIs. I updated the payload for the creation of visits but I?m getting the following error: === { "error": "You can`t create candidates visit for that site" } === This is my request and payload: === https://ipmsa-loris.bic.mni.mcgill.ca/api/v0.0.3//candidates/559153/w024 { "CandID": "559153", "Visit": "w024", "Site": "111-RWA-1", "Battery": "Experimental", "Project": ?REMOVED" } === The user accessing this end-point was only created for that specific site. Additionally, I don?t see any logs in apache. Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Mon Feb 8 13:16:39 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Mon, 8 Feb 2021 13:16:39 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hi To I am so glad to hear that you had fixed the composer issue. "chmod 770 smarty/templates_c" It will fix the problem. Best Shen On Mon, 8 Feb 2021 at 12:49, Tom Beaudry wrote: > Hi DAve and Shen, > > I wasn't able to rollback my version of composer so it made me realize it > was corrupt, so i removed composer, reinstalled it and rolled back to the > version you suggest. Now i can do composer insall with no problem, and > make clean & make work without errors. > > The only error i'm left with now when i visit the main page is: > > [Mon Feb 08 12:47:27.785383 2021] [php7:error] [pid 7082] [client > 172.16.253.8:54598] PHP Fatal error: Uncaught --> Smarty: unable to > write file /var/www/loris/smarty/templates_c/wrt6021792fbfb5b4_53411590 <-- > \n thrown in > /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_runtime_writefile.php > on line 60 > > Thanks! > Tom > > [Mon Feb 08 12:47:27.785383 2021] [php7:error] [pid 7082] [client > 172.16.253.8:54598] PHP Fatal error: Uncaught --> Smarty: unable to > write file /var/www/loris/smarty/templates_c/wrt6021792fbfb5b4_53411590 <-- > \n thrown in > /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_runtime_writefile.php > on line 60 > > On Fri, Feb 5, 2021 at 10:19 AM Dave MacFarlane > wrote: > >> What version of composer are you using? >> >> Composer 2 (which was backwards incompatible) came out at around the same >> time as LORIS 23. >> >> If you're using composer 2 you can try `composer self-update 1.10.17` to >> downgrade and then try the >> composer install again. >> >> On Thu, Feb 4, 2021 at 6:00 PM Tom Beaudry wrote: >> >>> Hey Shen, >>> >>> Sadly it's the same error. >>> >>> Tom >>> >>> On Thu, Feb 4, 2021 at 4:39 PM Shen Wang >>> wrote: >>> >>>> Hi Tom, >>>> Try "composer self-update --snapshot" or "composer self-update >>>> --stable". >>>> Please let me know the result. >>>> Best >>>> Shen >>>> >>>> On Thu, 4 Feb 2021 at 16:27, Tom Beaudry wrote: >>>> >>>>> Hey Shen, >>>>> >>>>> I followed your instructions and can confirm i'm using php 7.4: >>>>> https://docs.google.com/document/d/1QppFZ8MtKoMRltiIQidFDslfVwriuS9cpfuZN49nOZ8/edit?usp=sharing >>>>> >>>>> composer install still fails: >>>>> >>>>> [ErrorException] >>>>> Trying to access array offset on value of type null >>>>> >>>>> Thanks! >>>>> Tom >>>>> >>>>> On Thu, Feb 4, 2021 at 4:04 PM Shen Wang >>>>> wrote: >>>>> >>>>>> Hi Tom, >>>>>> It is very helpful, it means you need to do "composer install" >>>>>> again. >>>>>> if it not works for you then try these steps for Centos. >>>>>> sudo yum-config-manager --disable remi-php80 >>>>>> sudo yum-config-manager --enable remi-php74 >>>>>> sudo systemctl restart httpd sudo systemctl status httpd >>>>>> /var/www/loris/htdocs$ echo "" >> test.php >>>>>> Using test.php to check your PHP version in your brower. >>>>>> Best >>>>>> Shen >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Thu, 4 Feb 2021 at 15:55, Tom Beaudry wrote: >>>>>> >>>>>>> Hey Shen, >>>>>>> >>>>>>> I checked the apache log and the error is different now: >>>>>>> >>>>>>> [Thu Feb 04 15:54:16.131158 2021] [php7:warn] [pid 5215] [client >>>>>>> 172.16.253.6:62349] PHP Warning: >>>>>>> require_once(/var/www/loris/htdocs/../vendor/autoload.php): failed to open >>>>>>> stream: No such file or directory in /var/www/loris/htdocs/index.php on >>>>>>> line 18 >>>>>>> [Thu Feb 04 15:54:16.131215 2021] [php7:error] [pid 5215] [client >>>>>>> 172.16.253.6:62349] PHP Fatal error: require_once(): Failed >>>>>>> opening required '/var/www/loris/htdocs/../vendor/autoload.php' >>>>>>> (include_path='.:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries') >>>>>>> in /var/www/loris/htdocs/index.php on line 18 >>>>>>> >>>>>>> I'm not sure if that helps figure out what's wrong. >>>>>>> >>>>>>> Thanks again! >>>>>>> Tom >>>>>>> >>>>>>> On Thu, Feb 4, 2021 at 3:45 PM Tom Beaudry >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Shen, >>>>>>>> >>>>>>>> My productions server is CentOS. >>>>>>>> >>>>>>>> If i check what version of php i'm using: >>>>>>>> >>>>>>>> [lorisadmin at loris loris]$ rpm -qa | grep php >>>>>>>> php-json-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-pear-1.10.12-5.el7.remi.noarch >>>>>>>> php-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-devel-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-sodium-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-fedora-autoloader-1.0.1-2.el7.noarch >>>>>>>> php-fpm-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-gd-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-cli-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-pdo-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-mysqlnd-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-bcmath-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-xml-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-mbstring-7.4.15-1.el7.remi.x86_64 >>>>>>>> oniguruma5php-6.9.6-1.el7.remi.x86_64 >>>>>>>> php-common-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-process-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-pecl-mcrypt-1.0.4-1.el7.remi.7.4.x86_64 >>>>>>>> >>>>>>>> They are all showing up as 7.4. >>>>>>>> >>>>>>>> Thanks! >>>>>>>> Tom >>>>>>>> >>>>>>>> On Thu, Feb 4, 2021 at 3:37 PM Shen Wang >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi Tom, >>>>>>>>> If you got same error like "Deprecated: Required parameter >>>>>>>>> $ignoreFilters follows optional parameter $packageName " , >>>>>>>>> It seems like you are still using PHP 8. After downgraded to PHP >>>>>>>>> 7.4, you need to install PHP 7.4 dependencies as well. >>>>>>>>> Try these steps : >>>>>>>>> >>>>>>>>> 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml >>>>>>>>> php7.4-json php7.4-mbstring php7.4-gd php-ast >>>>>>>>> 2. sudo apt-get install -y composer >>>>>>>>> 3. sudo apt-get install -y libapache2-mod-php7.4 >>>>>>>>> 4. sudo a2dismod php8.0 >>>>>>>>> 5. sudo a2enmod php7.4 >>>>>>>>> 6. sudo service apache2 restart >>>>>>>>> >>>>>>>>> 7, make clean >>>>>>>>> 8, make >>>>>>>>> Good luck. >>>>>>>>> Best >>>>>>>>> Shen >>>>>>>>> >>>>>>>>> >>>>>>>>> On Thu, 4 Feb 2021 at 15:05, Tom Beaudry >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hey Shen, >>>>>>>>>> >>>>>>>>>> I downgraded to php 7.4 and get the same results. >>>>>>>>>> >>>>>>>>>> What can i try next? >>>>>>>>>> Tom >>>>>>>>>> >>>>>>>>>> On Thu, Feb 4, 2021 at 2:01 PM Shen Wang >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Tom, >>>>>>>>>>> We don't support PHP 8 with Loris yet. We are working on it. >>>>>>>>>>> For the 23.0-release, you have to use PHP 7.3 or 7.4. >>>>>>>>>>> Best >>>>>>>>>>> Shen >>>>>>>>>>> >>>>>>>>>>> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hey Shen, >>>>>>>>>>>> >>>>>>>>>>>> Unfortunately it didn't work. Here's the output: >>>>>>>>>>>> https://pastebin.com/raw/ZQjPuAG1 >>>>>>>>>>>> >>>>>>>>>>>> I'm using php8. >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Tom >>>>>>>>>>>> >>>>>>>>>>>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang < >>>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Tom, >>>>>>>>>>>>> You are welcome. I think that you need to remove all the >>>>>>>>>>>>> vendor files. >>>>>>>>>>>>> Try step 1: "make clean" (delete all the vendor and >>>>>>>>>>>>> node_modules) >>>>>>>>>>>>> step 2: "make" ( run composer install and >>>>>>>>>>>>> npm install ...) >>>>>>>>>>>>> If it still can't work, could you tell me which PHP version >>>>>>>>>>>>> are you using? >>>>>>>>>>>>> Best >>>>>>>>>>>>> Shen >>>>>>>>>>>>> >>>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry >>>>>>>>>>>>> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Shen, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks for the answer: Composer install gives me the >>>>>>>>>>>>>> following error: >>>>>>>>>>>>>> >>>>>>>>>>>>>> [lorisadmin at loris loris]$ composer install >>>>>>>>>>>>>> PHP Deprecated: Required parameter $ignoreFilters follows >>>>>>>>>>>>>> optional parameter $packageName in >>>>>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>>>>> line 97 >>>>>>>>>>>>>> >>>>>>>>>>>>>> Deprecated: Required parameter $ignoreFilters follows >>>>>>>>>>>>>> optional parameter $packageName in >>>>>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>>>>> line 97 >>>>>>>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>>>>>>> parameter $schema in >>>>>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>>>>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>>>>>>> parameter $schema in >>>>>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> [ErrorException] >>>>>>>>>>>>>> Trying to access array offset on value of type null >>>>>>>>>>>>>> >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> Tom >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang < >>>>>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Tom, >>>>>>>>>>>>>>> You need to re-run " composer install " to solve this issue. >>>>>>>>>>>>>>> Good Luck. >>>>>>>>>>>>>>> Best >>>>>>>>>>>>>>> Shen >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry >>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hey Guys, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this >>>>>>>>>>>>>>>> apache error when i navigate to the homepage in my web browser: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] >>>>>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Warning: session_start(): >>>>>>>>>>>>>>>> Setting option 'cookie_samesite' failed in >>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] >>>>>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Fatal error*: Uncaught >>>>>>>>>>>>>>>> Error: Class 'Laminas\\Diactoros\\ServerRequestFactory'* >>>>>>>>>>>>>>>> not found in /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n >>>>>>>>>>>>>>>> thrown in /var/www/loris/htdocs/index.php on line 35 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> It seems that the server request is failing: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory:: >>>>>>>>>>>>>>>> fromGlobals(); >>>>>>>>>>>>>>>> 36 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>>>>>>>> Tom >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Shen Wang >>>>>>>>>>> Loris Developer >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Shen Wang >>>>>>>>> Loris Developer >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University >>>>>>>>> >>>>>>>>> >>>>>> >>>>>> -- >>>>>> Shen Wang >>>>>> Loris Developer >>>>>> Montreal Neurological Institute >>>>>> McGill University >>>>>> >>>>>> >>>> >>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Mon Feb 8 13:17:43 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Mon, 8 Feb 2021 13:17:43 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: My first thoughts for reasons that error might come up are: Does the directory /var/www/loris/smarty/templates_c/ exist and is writable by your web server? If so, are all the directories leading up to it executable by your web server? Is the drive full? On Mon, Feb 8, 2021 at 12:49 PM Tom Beaudry wrote: > Hi DAve and Shen, > > I wasn't able to rollback my version of composer so it made me realize it > was corrupt, so i removed composer, reinstalled it and rolled back to the > version you suggest. Now i can do composer insall with no problem, and > make clean & make work without errors. > > The only error i'm left with now when i visit the main page is: > > [Mon Feb 08 12:47:27.785383 2021] [php7:error] [pid 7082] [client > 172.16.253.8:54598] PHP Fatal error: Uncaught --> Smarty: unable to > write file /var/www/loris/smarty/templates_c/wrt6021792fbfb5b4_53411590 <-- > \n thrown in > /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_runtime_writefile.php > on line 60 > > Thanks! > Tom > > [Mon Feb 08 12:47:27.785383 2021] [php7:error] [pid 7082] [client > 172.16.253.8:54598] PHP Fatal error: Uncaught --> Smarty: unable to > write file /var/www/loris/smarty/templates_c/wrt6021792fbfb5b4_53411590 <-- > \n thrown in > /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_runtime_writefile.php > on line 60 > > On Fri, Feb 5, 2021 at 10:19 AM Dave MacFarlane > wrote: > >> What version of composer are you using? >> >> Composer 2 (which was backwards incompatible) came out at around the same >> time as LORIS 23. >> >> If you're using composer 2 you can try `composer self-update 1.10.17` to >> downgrade and then try the >> composer install again. >> >> On Thu, Feb 4, 2021 at 6:00 PM Tom Beaudry wrote: >> >>> Hey Shen, >>> >>> Sadly it's the same error. >>> >>> Tom >>> >>> On Thu, Feb 4, 2021 at 4:39 PM Shen Wang >>> wrote: >>> >>>> Hi Tom, >>>> Try "composer self-update --snapshot" or "composer self-update >>>> --stable". >>>> Please let me know the result. >>>> Best >>>> Shen >>>> >>>> On Thu, 4 Feb 2021 at 16:27, Tom Beaudry wrote: >>>> >>>>> Hey Shen, >>>>> >>>>> I followed your instructions and can confirm i'm using php 7.4: >>>>> https://docs.google.com/document/d/1QppFZ8MtKoMRltiIQidFDslfVwriuS9cpfuZN49nOZ8/edit?usp=sharing >>>>> >>>>> composer install still fails: >>>>> >>>>> [ErrorException] >>>>> Trying to access array offset on value of type null >>>>> >>>>> Thanks! >>>>> Tom >>>>> >>>>> On Thu, Feb 4, 2021 at 4:04 PM Shen Wang >>>>> wrote: >>>>> >>>>>> Hi Tom, >>>>>> It is very helpful, it means you need to do "composer install" >>>>>> again. >>>>>> if it not works for you then try these steps for Centos. >>>>>> sudo yum-config-manager --disable remi-php80 >>>>>> sudo yum-config-manager --enable remi-php74 >>>>>> sudo systemctl restart httpd sudo systemctl status httpd >>>>>> /var/www/loris/htdocs$ echo "" >> test.php >>>>>> Using test.php to check your PHP version in your brower. >>>>>> Best >>>>>> Shen >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On Thu, 4 Feb 2021 at 15:55, Tom Beaudry wrote: >>>>>> >>>>>>> Hey Shen, >>>>>>> >>>>>>> I checked the apache log and the error is different now: >>>>>>> >>>>>>> [Thu Feb 04 15:54:16.131158 2021] [php7:warn] [pid 5215] [client >>>>>>> 172.16.253.6:62349] PHP Warning: >>>>>>> require_once(/var/www/loris/htdocs/../vendor/autoload.php): failed to open >>>>>>> stream: No such file or directory in /var/www/loris/htdocs/index.php on >>>>>>> line 18 >>>>>>> [Thu Feb 04 15:54:16.131215 2021] [php7:error] [pid 5215] [client >>>>>>> 172.16.253.6:62349] PHP Fatal error: require_once(): Failed >>>>>>> opening required '/var/www/loris/htdocs/../vendor/autoload.php' >>>>>>> (include_path='.:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries') >>>>>>> in /var/www/loris/htdocs/index.php on line 18 >>>>>>> >>>>>>> I'm not sure if that helps figure out what's wrong. >>>>>>> >>>>>>> Thanks again! >>>>>>> Tom >>>>>>> >>>>>>> On Thu, Feb 4, 2021 at 3:45 PM Tom Beaudry >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Shen, >>>>>>>> >>>>>>>> My productions server is CentOS. >>>>>>>> >>>>>>>> If i check what version of php i'm using: >>>>>>>> >>>>>>>> [lorisadmin at loris loris]$ rpm -qa | grep php >>>>>>>> php-json-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-pear-1.10.12-5.el7.remi.noarch >>>>>>>> php-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-devel-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-sodium-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-fedora-autoloader-1.0.1-2.el7.noarch >>>>>>>> php-fpm-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-gd-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-cli-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-pdo-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-mysqlnd-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-bcmath-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-xml-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-mbstring-7.4.15-1.el7.remi.x86_64 >>>>>>>> oniguruma5php-6.9.6-1.el7.remi.x86_64 >>>>>>>> php-common-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-process-7.4.15-1.el7.remi.x86_64 >>>>>>>> php-pecl-mcrypt-1.0.4-1.el7.remi.7.4.x86_64 >>>>>>>> >>>>>>>> They are all showing up as 7.4. >>>>>>>> >>>>>>>> Thanks! >>>>>>>> Tom >>>>>>>> >>>>>>>> On Thu, Feb 4, 2021 at 3:37 PM Shen Wang >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi Tom, >>>>>>>>> If you got same error like "Deprecated: Required parameter >>>>>>>>> $ignoreFilters follows optional parameter $packageName " , >>>>>>>>> It seems like you are still using PHP 8. After downgraded to PHP >>>>>>>>> 7.4, you need to install PHP 7.4 dependencies as well. >>>>>>>>> Try these steps : >>>>>>>>> >>>>>>>>> 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml >>>>>>>>> php7.4-json php7.4-mbstring php7.4-gd php-ast >>>>>>>>> 2. sudo apt-get install -y composer >>>>>>>>> 3. sudo apt-get install -y libapache2-mod-php7.4 >>>>>>>>> 4. sudo a2dismod php8.0 >>>>>>>>> 5. sudo a2enmod php7.4 >>>>>>>>> 6. sudo service apache2 restart >>>>>>>>> >>>>>>>>> 7, make clean >>>>>>>>> 8, make >>>>>>>>> Good luck. >>>>>>>>> Best >>>>>>>>> Shen >>>>>>>>> >>>>>>>>> >>>>>>>>> On Thu, 4 Feb 2021 at 15:05, Tom Beaudry >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hey Shen, >>>>>>>>>> >>>>>>>>>> I downgraded to php 7.4 and get the same results. >>>>>>>>>> >>>>>>>>>> What can i try next? >>>>>>>>>> Tom >>>>>>>>>> >>>>>>>>>> On Thu, Feb 4, 2021 at 2:01 PM Shen Wang >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Tom, >>>>>>>>>>> We don't support PHP 8 with Loris yet. We are working on it. >>>>>>>>>>> For the 23.0-release, you have to use PHP 7.3 or 7.4. >>>>>>>>>>> Best >>>>>>>>>>> Shen >>>>>>>>>>> >>>>>>>>>>> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hey Shen, >>>>>>>>>>>> >>>>>>>>>>>> Unfortunately it didn't work. Here's the output: >>>>>>>>>>>> https://pastebin.com/raw/ZQjPuAG1 >>>>>>>>>>>> >>>>>>>>>>>> I'm using php8. >>>>>>>>>>>> >>>>>>>>>>>> Thanks, >>>>>>>>>>>> Tom >>>>>>>>>>>> >>>>>>>>>>>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang < >>>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Tom, >>>>>>>>>>>>> You are welcome. I think that you need to remove all the >>>>>>>>>>>>> vendor files. >>>>>>>>>>>>> Try step 1: "make clean" (delete all the vendor and >>>>>>>>>>>>> node_modules) >>>>>>>>>>>>> step 2: "make" ( run composer install and >>>>>>>>>>>>> npm install ...) >>>>>>>>>>>>> If it still can't work, could you tell me which PHP version >>>>>>>>>>>>> are you using? >>>>>>>>>>>>> Best >>>>>>>>>>>>> Shen >>>>>>>>>>>>> >>>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry >>>>>>>>>>>>> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Shen, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks for the answer: Composer install gives me the >>>>>>>>>>>>>> following error: >>>>>>>>>>>>>> >>>>>>>>>>>>>> [lorisadmin at loris loris]$ composer install >>>>>>>>>>>>>> PHP Deprecated: Required parameter $ignoreFilters follows >>>>>>>>>>>>>> optional parameter $packageName in >>>>>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>>>>> line 97 >>>>>>>>>>>>>> >>>>>>>>>>>>>> Deprecated: Required parameter $ignoreFilters follows >>>>>>>>>>>>>> optional parameter $packageName in >>>>>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>>>>> line 97 >>>>>>>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>>>>>>> parameter $schema in >>>>>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>>>>>>>>>>> Deprecation Notice: Required parameter $path follows optional >>>>>>>>>>>>>> parameter $schema in >>>>>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> [ErrorException] >>>>>>>>>>>>>> Trying to access array offset on value of type null >>>>>>>>>>>>>> >>>>>>>>>>>>>> Best, >>>>>>>>>>>>>> Tom >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang < >>>>>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Tom, >>>>>>>>>>>>>>> You need to re-run " composer install " to solve this issue. >>>>>>>>>>>>>>> Good Luck. >>>>>>>>>>>>>>> Best >>>>>>>>>>>>>>> Shen >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry >>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hey Guys, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this >>>>>>>>>>>>>>>> apache error when i navigate to the homepage in my web browser: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] >>>>>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Warning: session_start(): >>>>>>>>>>>>>>>> Setting option 'cookie_samesite' failed in >>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] >>>>>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Fatal error*: Uncaught >>>>>>>>>>>>>>>> Error: Class 'Laminas\\Diactoros\\ServerRequestFactory'* >>>>>>>>>>>>>>>> not found in /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n >>>>>>>>>>>>>>>> thrown in /var/www/loris/htdocs/index.php on line 35 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> It seems that the server request is failing: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory:: >>>>>>>>>>>>>>>> fromGlobals(); >>>>>>>>>>>>>>>> 36 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>>>>>>>> Tom >>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Shen Wang >>>>>>>>>>> Loris Developer >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Shen Wang >>>>>>>>> Loris Developer >>>>>>>>> Montreal Neurological Institute >>>>>>>>> McGill University >>>>>>>>> >>>>>>>>> >>>>>> >>>>>> -- >>>>>> Shen Wang >>>>>> Loris Developer >>>>>> Montreal Neurological Institute >>>>>> McGill University >>>>>> >>>>>> >>>> >>>> -- >>>> Shen Wang >>>> Loris Developer >>>> Montreal Neurological Institute >>>> McGill University >>>> >>>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Mon Feb 8 13:24:14 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Mon, 8 Feb 2021 13:24:14 -0500 Subject: [Loris-dev] 500 after login In-Reply-To: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> References: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> Message-ID: I don't think the Real_name field should be null. It's used for the name to display in the menu at the top of LORIS. (In my local database the column is non-nullable, but it seems that the default schema allows null.. I think the fact that it allowed you to insert a null value is a minor bug.) - Dave On Mon, Feb 8, 2021 at 1:07 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev, > > I am getting a 500 error after login into LORIS. This is what I can see in > the logs: > > === > [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client > 216.15.126.108:61071] PHP Fatal error: Uncaught TypeError: Return value > of User::getFullname() must be of the type string, null returned in > /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 > /var/www/loris/modules/dashboard/php/module.class.inc(118): > User->getFullname()\n#1 > /var/www/loris/modules/dashboard/php/module.class.inc(57): > LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), > Object(NDB_Config), Object(User))\n#2 > /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): > LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 > /var/www/loris/php/libraries/Module.class.inc(275): > LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), > 'dashboard', '', '', 'dashboard')\n#4 > /var/www/loris/php/libraries/Module.class.inc(342): > Module->loadPage('dashboard')\n#5 > /var/www/loris/src/Middleware/ResponseGenerator.php(50): > Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 > /var/www/loris/src/Middleware/AuthMiddleware.php(63): > LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se > in /var/www/loris/php/libraries/User.class.inc on line 236 > === > > Perhaps it is an issue with the name of the user? I created hundreds of > users for batch insertion of candidates and visits for previous versions of > LORIS that required insertion of Candidates and Visits by users belonging > to a given center. > > This is an entry in the users table without the hashed password: > > === > *************************** 850. row *************************** > ID: 850 > UserID: 723-DKC-1_dataman > Password: NULL > Real_name: NULL > First_name: NULL > Last_name: NULL > Degree: NULL > Position_title: NULL > Institution: NULL > Department: NULL > Address: NULL > City: NULL > State: NULL > Zip_code: NULL > Country: NULL > Phone: NULL > Fax: NULL > Email: 723-DKC-1_dataman at ipmsa.com > <723-DKC-1_dataman at ipmsa.com> > Privilege: 0 > PSCPI: N > DBAccess: > Active: Y > Password_hash: /REMOVED/ > Password_expiry: 2035-01-01 > Pending_approval: N > Doc_Repo_Notifications: N > language_preference: NULL > active_from: NULL > active_to: NULL > === > > Best, > Alfredo. > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From wangshen.mcin at gmail.com Mon Feb 8 13:35:23 2021 From: wangshen.mcin at gmail.com (Shen Wang) Date: Mon, 8 Feb 2021 13:35:23 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hi Tom, Your drive is not full. "make clean" did " rm -f smarty/templates_c/* | rm -rf node_modules| rm -rf vendor | rm -fr package-lock.json " . "make" will rebuild node_modules and re-run composer etc. So you need to make smarty and template_c manually. Sorry to forget tell you early. mkdir -p ../smarty/templates_c # Setting 770 permissions for templates_c sudo chmod 770 ../smarty/templates_c On Mon, 8 Feb 2021 at 13:17, Dave MacFarlane wrote: > My first thoughts for reasons that error might come up are: Does the > directory /var/www/loris/smarty/templates_c/ exist and is writable by your > web server? If so, are all the directories leading up to it executable by > your web server? Is the drive full? > > > > On Mon, Feb 8, 2021 at 12:49 PM Tom Beaudry wrote: > >> Hi DAve and Shen, >> >> I wasn't able to rollback my version of composer so it made me realize it >> was corrupt, so i removed composer, reinstalled it and rolled back to the >> version you suggest. Now i can do composer insall with no problem, and >> make clean & make work without errors. >> >> The only error i'm left with now when i visit the main page is: >> >> [Mon Feb 08 12:47:27.785383 2021] [php7:error] [pid 7082] [client >> 172.16.253.8:54598] PHP Fatal error: Uncaught --> Smarty: unable to >> write file /var/www/loris/smarty/templates_c/wrt6021792fbfb5b4_53411590 <-- >> \n thrown in >> /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_runtime_writefile.php >> on line 60 >> >> Thanks! >> Tom >> >> [Mon Feb 08 12:47:27.785383 2021] [php7:error] [pid 7082] [client >> 172.16.253.8:54598] PHP Fatal error: Uncaught --> Smarty: unable to >> write file /var/www/loris/smarty/templates_c/wrt6021792fbfb5b4_53411590 <-- >> \n thrown in >> /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_runtime_writefile.php >> on line 60 >> >> On Fri, Feb 5, 2021 at 10:19 AM Dave MacFarlane >> wrote: >> >>> What version of composer are you using? >>> >>> Composer 2 (which was backwards incompatible) came out at around the >>> same time as LORIS 23. >>> >>> If you're using composer 2 you can try `composer self-update 1.10.17` >>> to downgrade and then try the >>> composer install again. >>> >>> On Thu, Feb 4, 2021 at 6:00 PM Tom Beaudry wrote: >>> >>>> Hey Shen, >>>> >>>> Sadly it's the same error. >>>> >>>> Tom >>>> >>>> On Thu, Feb 4, 2021 at 4:39 PM Shen Wang >>>> wrote: >>>> >>>>> Hi Tom, >>>>> Try "composer self-update --snapshot" or "composer self-update >>>>> --stable". >>>>> Please let me know the result. >>>>> Best >>>>> Shen >>>>> >>>>> On Thu, 4 Feb 2021 at 16:27, Tom Beaudry wrote: >>>>> >>>>>> Hey Shen, >>>>>> >>>>>> I followed your instructions and can confirm i'm using php 7.4: >>>>>> https://docs.google.com/document/d/1QppFZ8MtKoMRltiIQidFDslfVwriuS9cpfuZN49nOZ8/edit?usp=sharing >>>>>> >>>>>> composer install still fails: >>>>>> >>>>>> [ErrorException] >>>>>> Trying to access array offset on value of type null >>>>>> >>>>>> Thanks! >>>>>> Tom >>>>>> >>>>>> On Thu, Feb 4, 2021 at 4:04 PM Shen Wang >>>>>> wrote: >>>>>> >>>>>>> Hi Tom, >>>>>>> It is very helpful, it means you need to do "composer install" >>>>>>> again. >>>>>>> if it not works for you then try these steps for Centos. >>>>>>> sudo yum-config-manager --disable remi-php80 >>>>>>> sudo yum-config-manager --enable remi-php74 >>>>>>> sudo systemctl restart httpd sudo systemctl status httpd >>>>>>> /var/www/loris/htdocs$ echo "" >> test.php >>>>>>> Using test.php to check your PHP version in your brower. >>>>>>> Best >>>>>>> Shen >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> On Thu, 4 Feb 2021 at 15:55, Tom Beaudry wrote: >>>>>>> >>>>>>>> Hey Shen, >>>>>>>> >>>>>>>> I checked the apache log and the error is different now: >>>>>>>> >>>>>>>> [Thu Feb 04 15:54:16.131158 2021] [php7:warn] [pid 5215] [client >>>>>>>> 172.16.253.6:62349] PHP Warning: >>>>>>>> require_once(/var/www/loris/htdocs/../vendor/autoload.php): failed to open >>>>>>>> stream: No such file or directory in /var/www/loris/htdocs/index.php on >>>>>>>> line 18 >>>>>>>> [Thu Feb 04 15:54:16.131215 2021] [php7:error] [pid 5215] [client >>>>>>>> 172.16.253.6:62349] PHP Fatal error: require_once(): Failed >>>>>>>> opening required '/var/www/loris/htdocs/../vendor/autoload.php' >>>>>>>> (include_path='.:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries') >>>>>>>> in /var/www/loris/htdocs/index.php on line 18 >>>>>>>> >>>>>>>> I'm not sure if that helps figure out what's wrong. >>>>>>>> >>>>>>>> Thanks again! >>>>>>>> Tom >>>>>>>> >>>>>>>> On Thu, Feb 4, 2021 at 3:45 PM Tom Beaudry >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hi Shen, >>>>>>>>> >>>>>>>>> My productions server is CentOS. >>>>>>>>> >>>>>>>>> If i check what version of php i'm using: >>>>>>>>> >>>>>>>>> [lorisadmin at loris loris]$ rpm -qa | grep php >>>>>>>>> php-json-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-pear-1.10.12-5.el7.remi.noarch >>>>>>>>> php-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-devel-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-sodium-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-fedora-autoloader-1.0.1-2.el7.noarch >>>>>>>>> php-fpm-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-gd-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-cli-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-pdo-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-mysqlnd-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-bcmath-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-xml-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-mbstring-7.4.15-1.el7.remi.x86_64 >>>>>>>>> oniguruma5php-6.9.6-1.el7.remi.x86_64 >>>>>>>>> php-common-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-process-7.4.15-1.el7.remi.x86_64 >>>>>>>>> php-pecl-mcrypt-1.0.4-1.el7.remi.7.4.x86_64 >>>>>>>>> >>>>>>>>> They are all showing up as 7.4. >>>>>>>>> >>>>>>>>> Thanks! >>>>>>>>> Tom >>>>>>>>> >>>>>>>>> On Thu, Feb 4, 2021 at 3:37 PM Shen Wang >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hi Tom, >>>>>>>>>> If you got same error like "Deprecated: Required parameter >>>>>>>>>> $ignoreFilters follows optional parameter $packageName " , >>>>>>>>>> It seems like you are still using PHP 8. After downgraded to PHP >>>>>>>>>> 7.4, you need to install PHP 7.4 dependencies as well. >>>>>>>>>> Try these steps : >>>>>>>>>> >>>>>>>>>> 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml >>>>>>>>>> php7.4-json php7.4-mbstring php7.4-gd php-ast >>>>>>>>>> 2. sudo apt-get install -y composer >>>>>>>>>> 3. sudo apt-get install -y libapache2-mod-php7.4 >>>>>>>>>> 4. sudo a2dismod php8.0 >>>>>>>>>> 5. sudo a2enmod php7.4 >>>>>>>>>> 6. sudo service apache2 restart >>>>>>>>>> >>>>>>>>>> 7, make clean >>>>>>>>>> 8, make >>>>>>>>>> Good luck. >>>>>>>>>> Best >>>>>>>>>> Shen >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Thu, 4 Feb 2021 at 15:05, Tom Beaudry >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Hey Shen, >>>>>>>>>>> >>>>>>>>>>> I downgraded to php 7.4 and get the same results. >>>>>>>>>>> >>>>>>>>>>> What can i try next? >>>>>>>>>>> Tom >>>>>>>>>>> >>>>>>>>>>> On Thu, Feb 4, 2021 at 2:01 PM Shen Wang < >>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hi Tom, >>>>>>>>>>>> We don't support PHP 8 with Loris yet. We are working on it. >>>>>>>>>>>> For the 23.0-release, you have to use PHP 7.3 or 7.4. >>>>>>>>>>>> Best >>>>>>>>>>>> Shen >>>>>>>>>>>> >>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry >>>>>>>>>>>> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hey Shen, >>>>>>>>>>>>> >>>>>>>>>>>>> Unfortunately it didn't work. Here's the output: >>>>>>>>>>>>> https://pastebin.com/raw/ZQjPuAG1 >>>>>>>>>>>>> >>>>>>>>>>>>> I'm using php8. >>>>>>>>>>>>> >>>>>>>>>>>>> Thanks, >>>>>>>>>>>>> Tom >>>>>>>>>>>>> >>>>>>>>>>>>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang < >>>>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Tom, >>>>>>>>>>>>>> You are welcome. I think that you need to remove all the >>>>>>>>>>>>>> vendor files. >>>>>>>>>>>>>> Try step 1: "make clean" (delete all the vendor and >>>>>>>>>>>>>> node_modules) >>>>>>>>>>>>>> step 2: "make" ( run composer install and >>>>>>>>>>>>>> npm install ...) >>>>>>>>>>>>>> If it still can't work, could you tell me which PHP version >>>>>>>>>>>>>> are you using? >>>>>>>>>>>>>> Best >>>>>>>>>>>>>> Shen >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry >>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Shen, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Thanks for the answer: Composer install gives me the >>>>>>>>>>>>>>> following error: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [lorisadmin at loris loris]$ composer install >>>>>>>>>>>>>>> PHP Deprecated: Required parameter $ignoreFilters follows >>>>>>>>>>>>>>> optional parameter $packageName in >>>>>>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>>>>>> line 97 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Deprecated: Required parameter $ignoreFilters follows >>>>>>>>>>>>>>> optional parameter $packageName in >>>>>>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>>>>>> line 97 >>>>>>>>>>>>>>> Deprecation Notice: Required parameter $path follows >>>>>>>>>>>>>>> optional parameter $schema in >>>>>>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>>>>>>>>>>>> Deprecation Notice: Required parameter $path follows >>>>>>>>>>>>>>> optional parameter $schema in >>>>>>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [ErrorException] >>>>>>>>>>>>>>> Trying to access array offset on value of type null >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>> Tom >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang < >>>>>>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Tom, >>>>>>>>>>>>>>>> You need to re-run " composer install " to solve this issue. >>>>>>>>>>>>>>>> Good Luck. >>>>>>>>>>>>>>>> Best >>>>>>>>>>>>>>>> Shen >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry < >>>>>>>>>>>>>>>> waveflux at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hey Guys, >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this >>>>>>>>>>>>>>>>> apache error when i navigate to the homepage in my web browser: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] >>>>>>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Warning: >>>>>>>>>>>>>>>>> session_start(): Setting option 'cookie_samesite' failed in >>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] >>>>>>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Fatal error*: Uncaught >>>>>>>>>>>>>>>>> Error: Class 'Laminas\\Diactoros\\ServerRequestFactory'* >>>>>>>>>>>>>>>>> not found in /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n >>>>>>>>>>>>>>>>> thrown in /var/www/loris/htdocs/index.php on line 35 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> It seems that the server request is failing: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory:: >>>>>>>>>>>>>>>>> fromGlobals(); >>>>>>>>>>>>>>>>> 36 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>>>>>>>>> Tom >>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>> McGill University >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> -- >>>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>> McGill University >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> -- >>>>>>>>>>>> Shen Wang >>>>>>>>>>>> Loris Developer >>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>> McGill University >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> Shen Wang >>>>>>>>>> Loris Developer >>>>>>>>>> Montreal Neurological Institute >>>>>>>>>> McGill University >>>>>>>>>> >>>>>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Shen Wang >>>>>>> Loris Developer >>>>>>> Montreal Neurological Institute >>>>>>> McGill University >>>>>>> >>>>>>> >>>>> >>>>> -- >>>>> Shen Wang >>>>> Loris Developer >>>>> Montreal Neurological Institute >>>>> McGill University >>>>> >>>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> -- Shen Wang Loris Developer Montreal Neurological Institute McGill University -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Mon Feb 8 14:04:36 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Mon, 8 Feb 2021 14:04:36 -0500 Subject: [Loris-dev] "error": "You can`t create candidates visit for that site" In-Reply-To: <2CF75546-8107-4F65-8E4B-E2D3717DA555@bwh.harvard.edu> References: <2CF75546-8107-4F65-8E4B-E2D3717DA555@bwh.harvard.edu> Message-ID: That error indicates that the user making the request does not have a site affiliation with the site that it's attempting to create a visit for. Try ensuring that the user has access to 111-RWA-1 under "Sites" in the user_accounts page and trying the API request again. On Mon, Feb 8, 2021 at 1:12 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev team, > > After upgrading to Loris 23 I am not able to insert Visits using the APIs. > I updated the payload for the creation of visits but I?m getting the > following error: > > === > { > "error": "You can`t create candidates visit for that site" > } > === > > This is my request and payload: > > === > https://ipmsa-loris.bic.mni.mcgill.ca/api/v0.0.3//candidates/559153/w024 > > { > "CandID": "559153", > "Visit": "w024", > "Site": "111-RWA-1", > "Battery": "Experimental", > "Project": ?REMOVED" > } > === > > The user accessing this end-point was only created for that specific site. > Additionally, I don?t see any logs in apache. > > Best, > Alfredo. > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Mon Feb 8 14:33:26 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Mon, 8 Feb 2021 19:33:26 +0000 Subject: [Loris-dev] 500 after login In-Reply-To: References: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> Message-ID: <44A13251-016E-438B-8264-26F9D37BE8C1@bwh.harvard.edu> Hi Dave, What is your suggestion to fix this? Best, Alfredo. On Feb 8, 2021, at 1:24 PM, Dave MacFarlane > wrote: External Email - Use Caution I don't think the Real_name field should be null. It's used for the name to display in the menu at the top of LORIS. (In my local database the column is non-nullable, but it seems that the default schema allows null.. I think the fact that it allowed you to insert a null value is a minor bug.) - Dave On Mon, Feb 8, 2021 at 1:07 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev, I am getting a 500 error after login into LORIS. This is what I can see in the logs: === [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client 216.15.126.108:61071] PHP Fatal error: Uncaught TypeError: Return value of User::getFullname() must be of the type string, null returned in /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 /var/www/loris/modules/dashboard/php/module.class.inc(118): User->getFullname()\n#1 /var/www/loris/modules/dashboard/php/module.class.inc(57): LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), Object(NDB_Config), Object(User))\n#2 /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 /var/www/loris/php/libraries/Module.class.inc(275): LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), 'dashboard', '', '', 'dashboard')\n#4 /var/www/loris/php/libraries/Module.class.inc(342): Module->loadPage('dashboard')\n#5 /var/www/loris/src/Middleware/ResponseGenerator.php(50): Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 /var/www/loris/src/Middleware/AuthMiddleware.php(63): LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se in /var/www/loris/php/libraries/User.class.inc on line 236 === Perhaps it is an issue with the name of the user? I created hundreds of users for batch insertion of candidates and visits for previous versions of LORIS that required insertion of Candidates and Visits by users belonging to a given center. This is an entry in the users table without the hashed password: === *************************** 850. row *************************** ID: 850 UserID: 723-DKC-1_dataman Password: NULL Real_name: NULL First_name: NULL Last_name: NULL Degree: NULL Position_title: NULL Institution: NULL Department: NULL Address: NULL City: NULL State: NULL Zip_code: NULL Country: NULL Phone: NULL Fax: NULL Email: 723-DKC-1_dataman at ipmsa.com Privilege: 0 PSCPI: N DBAccess: Active: Y Password_hash: /REMOVED/ Password_expiry: 2035-01-01 Pending_approval: N Doc_Repo_Notifications: N language_preference: NULL active_from: NULL active_to: NULL === Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Mon Feb 8 14:37:09 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Mon, 8 Feb 2021 14:37:09 -0500 Subject: [Loris-dev] 500 after login In-Reply-To: <44A13251-016E-438B-8264-26F9D37BE8C1@bwh.harvard.edu> References: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> <44A13251-016E-438B-8264-26F9D37BE8C1@bwh.harvard.edu> Message-ID: Set the "Real_name" field in the user table for that user to a value other than null (and maybe ensure no other users have null real names while you're at it.. they would have the same problem logging in). I think that any string value should fix the error that you posted. On Mon, Feb 8, 2021 at 2:33 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Dave, > > What is your suggestion to fix this? > > Best, > Alfredo. > > On Feb 8, 2021, at 1:24 PM, Dave MacFarlane > wrote: > > External Email - Use Caution > > I don't think the Real_name field should be null. It's used for the name > to display in the menu at the top of LORIS. > > (In my local database the column is non-nullable, but it seems that the > default schema allows null.. I think the fact that it allowed you to insert > a null value is a minor bug.) > > - Dave > > > On Mon, Feb 8, 2021 at 1:07 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Dear LorisDev, >> >> I am getting a 500 error after login into LORIS. This is what I can see >> in the logs: >> >> === >> [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client >> 216.15.126.108:61071 >> ] >> PHP Fatal error: Uncaught TypeError: Return value of User::getFullname() >> must be of the type string, null returned in >> /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 >> /var/www/loris/modules/dashboard/php/module.class.inc(118): >> User->getFullname()\n#1 >> /var/www/loris/modules/dashboard/php/module.class.inc(57): >> LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), >> Object(NDB_Config), Object(User))\n#2 >> /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): >> LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 >> /var/www/loris/php/libraries/Module.class.inc(275): >> LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), >> 'dashboard', '', '', 'dashboard')\n#4 >> /var/www/loris/php/libraries/Module.class.inc(342): >> Module->loadPage('dashboard')\n#5 >> /var/www/loris/src/Middleware/ResponseGenerator.php(50): >> Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 >> /var/www/loris/src/Middleware/AuthMiddleware.php(63): >> LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se >> in /var/www/loris/php/libraries/User.class.inc on line 236 >> === >> >> Perhaps it is an issue with the name of the user? I created hundreds of >> users for batch insertion of candidates and visits for previous versions of >> LORIS that required insertion of Candidates and Visits by users belonging >> to a given center. >> >> This is an entry in the users table without the hashed password: >> >> === >> *************************** 850. row *************************** >> ID: 850 >> UserID: 723-DKC-1_dataman >> Password: NULL >> Real_name: NULL >> First_name: NULL >> Last_name: NULL >> Degree: NULL >> Position_title: NULL >> Institution: NULL >> Department: NULL >> Address: NULL >> City: NULL >> State: NULL >> Zip_code: NULL >> Country: NULL >> Phone: NULL >> Fax: NULL >> Email: 723-DKC-1_dataman at ipmsa.com >> <723-DKC-1_dataman at ipmsa.com> >> Privilege: 0 >> PSCPI: N >> DBAccess: >> Active: Y >> Password_hash: /REMOVED/ >> Password_expiry: 2035-01-01 >> Pending_approval: N >> Doc_Repo_Notifications: N >> language_preference: NULL >> active_from: NULL >> active_to: NULL >> === >> >> Best, >> Alfredo. >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.org/complianceline >> >> . If the e-mail was sent to you in error but does not contain patient >> information, please contact the sender and properly dispose of the e-mail. >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From waveflux at gmail.com Mon Feb 8 15:13:56 2021 From: waveflux at gmail.com (Tom Beaudry) Date: Mon, 8 Feb 2021 15:13:56 -0500 Subject: [Loris-dev] upgrading LORIS v22 - v23 error In-Reply-To: References: Message-ID: Hey Shen, What you suggested worked! Although i had to do a chmod 777 on the smart/template_c directory. Thanks again! Tom On Mon, Feb 8, 2021 at 1:35 PM Shen Wang wrote: > Hi Tom, > Your drive is not full. > "make clean" did " rm -f smarty/templates_c/* | rm -rf node_modules| rm > -rf vendor | rm -fr package-lock.json " . > "make" will rebuild node_modules and re-run composer etc. > So you need to make smarty and template_c manually. Sorry to forget tell > you early. > mkdir -p ../smarty/templates_c # Setting 770 permissions for templates_c > sudo chmod 770 ../smarty/templates_c > > > > > > On Mon, 8 Feb 2021 at 13:17, Dave MacFarlane > wrote: > >> My first thoughts for reasons that error might come up are: Does the >> directory /var/www/loris/smarty/templates_c/ exist and is writable by your >> web server? If so, are all the directories leading up to it executable by >> your web server? Is the drive full? >> >> >> >> On Mon, Feb 8, 2021 at 12:49 PM Tom Beaudry wrote: >> >>> Hi DAve and Shen, >>> >>> I wasn't able to rollback my version of composer so it made me realize >>> it was corrupt, so i removed composer, reinstalled it and rolled back to >>> the version you suggest. Now i can do composer insall with no problem, and >>> make clean & make work without errors. >>> >>> The only error i'm left with now when i visit the main page is: >>> >>> [Mon Feb 08 12:47:27.785383 2021] [php7:error] [pid 7082] [client >>> 172.16.253.8:54598] PHP Fatal error: Uncaught --> Smarty: unable to >>> write file /var/www/loris/smarty/templates_c/wrt6021792fbfb5b4_53411590 <-- >>> \n thrown in >>> /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_runtime_writefile.php >>> on line 60 >>> >>> Thanks! >>> Tom >>> >>> [Mon Feb 08 12:47:27.785383 2021] [php7:error] [pid 7082] [client >>> 172.16.253.8:54598] PHP Fatal error: Uncaught --> Smarty: unable to >>> write file /var/www/loris/smarty/templates_c/wrt6021792fbfb5b4_53411590 <-- >>> \n thrown in >>> /var/www/loris/vendor/smarty/smarty/libs/sysplugins/smarty_internal_runtime_writefile.php >>> on line 60 >>> >>> On Fri, Feb 5, 2021 at 10:19 AM Dave MacFarlane >>> wrote: >>> >>>> What version of composer are you using? >>>> >>>> Composer 2 (which was backwards incompatible) came out at around the >>>> same time as LORIS 23. >>>> >>>> If you're using composer 2 you can try `composer self-update 1.10.17` >>>> to downgrade and then try the >>>> composer install again. >>>> >>>> On Thu, Feb 4, 2021 at 6:00 PM Tom Beaudry wrote: >>>> >>>>> Hey Shen, >>>>> >>>>> Sadly it's the same error. >>>>> >>>>> Tom >>>>> >>>>> On Thu, Feb 4, 2021 at 4:39 PM Shen Wang >>>>> wrote: >>>>> >>>>>> Hi Tom, >>>>>> Try "composer self-update --snapshot" or "composer self-update >>>>>> --stable". >>>>>> Please let me know the result. >>>>>> Best >>>>>> Shen >>>>>> >>>>>> On Thu, 4 Feb 2021 at 16:27, Tom Beaudry wrote: >>>>>> >>>>>>> Hey Shen, >>>>>>> >>>>>>> I followed your instructions and can confirm i'm using php 7.4: >>>>>>> https://docs.google.com/document/d/1QppFZ8MtKoMRltiIQidFDslfVwriuS9cpfuZN49nOZ8/edit?usp=sharing >>>>>>> >>>>>>> composer install still fails: >>>>>>> >>>>>>> [ErrorException] >>>>>>> Trying to access array offset on value of type null >>>>>>> >>>>>>> Thanks! >>>>>>> Tom >>>>>>> >>>>>>> On Thu, Feb 4, 2021 at 4:04 PM Shen Wang >>>>>>> wrote: >>>>>>> >>>>>>>> Hi Tom, >>>>>>>> It is very helpful, it means you need to do "composer install" >>>>>>>> again. >>>>>>>> if it not works for you then try these steps for Centos. >>>>>>>> sudo yum-config-manager --disable remi-php80 >>>>>>>> sudo yum-config-manager --enable remi-php74 >>>>>>>> sudo systemctl restart httpd sudo systemctl status httpd >>>>>>>> /var/www/loris/htdocs$ echo "" >> test.php >>>>>>>> Using test.php to check your PHP version in your brower. >>>>>>>> Best >>>>>>>> Shen >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Thu, 4 Feb 2021 at 15:55, Tom Beaudry >>>>>>>> wrote: >>>>>>>> >>>>>>>>> Hey Shen, >>>>>>>>> >>>>>>>>> I checked the apache log and the error is different now: >>>>>>>>> >>>>>>>>> [Thu Feb 04 15:54:16.131158 2021] [php7:warn] [pid 5215] [client >>>>>>>>> 172.16.253.6:62349] PHP Warning: >>>>>>>>> require_once(/var/www/loris/htdocs/../vendor/autoload.php): failed to open >>>>>>>>> stream: No such file or directory in /var/www/loris/htdocs/index.php on >>>>>>>>> line 18 >>>>>>>>> [Thu Feb 04 15:54:16.131215 2021] [php7:error] [pid 5215] [client >>>>>>>>> 172.16.253.6:62349] PHP Fatal error: require_once(): Failed >>>>>>>>> opening required '/var/www/loris/htdocs/../vendor/autoload.php' >>>>>>>>> (include_path='.:/usr/share/php:/var/www/loris/project/libraries:/var/www/loris/php/libraries') >>>>>>>>> in /var/www/loris/htdocs/index.php on line 18 >>>>>>>>> >>>>>>>>> I'm not sure if that helps figure out what's wrong. >>>>>>>>> >>>>>>>>> Thanks again! >>>>>>>>> Tom >>>>>>>>> >>>>>>>>> On Thu, Feb 4, 2021 at 3:45 PM Tom Beaudry >>>>>>>>> wrote: >>>>>>>>> >>>>>>>>>> Hi Shen, >>>>>>>>>> >>>>>>>>>> My productions server is CentOS. >>>>>>>>>> >>>>>>>>>> If i check what version of php i'm using: >>>>>>>>>> >>>>>>>>>> [lorisadmin at loris loris]$ rpm -qa | grep php >>>>>>>>>> php-json-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-pear-1.10.12-5.el7.remi.noarch >>>>>>>>>> php-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-devel-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-sodium-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-fedora-autoloader-1.0.1-2.el7.noarch >>>>>>>>>> php-fpm-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-gd-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-cli-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-pdo-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-mysqlnd-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-bcmath-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-xml-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-mbstring-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> oniguruma5php-6.9.6-1.el7.remi.x86_64 >>>>>>>>>> php-common-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-process-7.4.15-1.el7.remi.x86_64 >>>>>>>>>> php-pecl-mcrypt-1.0.4-1.el7.remi.7.4.x86_64 >>>>>>>>>> >>>>>>>>>> They are all showing up as 7.4. >>>>>>>>>> >>>>>>>>>> Thanks! >>>>>>>>>> Tom >>>>>>>>>> >>>>>>>>>> On Thu, Feb 4, 2021 at 3:37 PM Shen Wang >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Hi Tom, >>>>>>>>>>> If you got same error like "Deprecated: Required parameter >>>>>>>>>>> $ignoreFilters follows optional parameter $packageName " , >>>>>>>>>>> It seems like you are still using PHP 8. After downgraded to >>>>>>>>>>> PHP 7.4, you need to install PHP 7.4 dependencies as well. >>>>>>>>>>> Try these steps : >>>>>>>>>>> >>>>>>>>>>> 1. sudo apt-get install -y php7.4 php7.4-mysql php7.4-xml >>>>>>>>>>> php7.4-json php7.4-mbstring php7.4-gd php-ast >>>>>>>>>>> 2. sudo apt-get install -y composer >>>>>>>>>>> 3. sudo apt-get install -y libapache2-mod-php7.4 >>>>>>>>>>> 4. sudo a2dismod php8.0 >>>>>>>>>>> 5. sudo a2enmod php7.4 >>>>>>>>>>> 6. sudo service apache2 restart >>>>>>>>>>> >>>>>>>>>>> 7, make clean >>>>>>>>>>> 8, make >>>>>>>>>>> Good luck. >>>>>>>>>>> Best >>>>>>>>>>> Shen >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Thu, 4 Feb 2021 at 15:05, Tom Beaudry >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hey Shen, >>>>>>>>>>>> >>>>>>>>>>>> I downgraded to php 7.4 and get the same results. >>>>>>>>>>>> >>>>>>>>>>>> What can i try next? >>>>>>>>>>>> Tom >>>>>>>>>>>> >>>>>>>>>>>> On Thu, Feb 4, 2021 at 2:01 PM Shen Wang < >>>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> Hi Tom, >>>>>>>>>>>>> We don't support PHP 8 with Loris yet. We are working on it. >>>>>>>>>>>>> For the 23.0-release, you have to use PHP 7.3 or 7.4. >>>>>>>>>>>>> Best >>>>>>>>>>>>> Shen >>>>>>>>>>>>> >>>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:50, Tom Beaudry >>>>>>>>>>>>> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hey Shen, >>>>>>>>>>>>>> >>>>>>>>>>>>>> Unfortunately it didn't work. Here's the output: >>>>>>>>>>>>>> https://pastebin.com/raw/ZQjPuAG1 >>>>>>>>>>>>>> >>>>>>>>>>>>>> I'm using php8. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Thanks, >>>>>>>>>>>>>> Tom >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Thu, Feb 4, 2021 at 1:40 PM Shen Wang < >>>>>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi Tom, >>>>>>>>>>>>>>> You are welcome. I think that you need to remove all the >>>>>>>>>>>>>>> vendor files. >>>>>>>>>>>>>>> Try step 1: "make clean" (delete all the vendor and >>>>>>>>>>>>>>> node_modules) >>>>>>>>>>>>>>> step 2: "make" ( run composer install and >>>>>>>>>>>>>>> npm install ...) >>>>>>>>>>>>>>> If it still can't work, could you tell me which PHP version >>>>>>>>>>>>>>> are you using? >>>>>>>>>>>>>>> Best >>>>>>>>>>>>>>> Shen >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:29, Tom Beaudry >>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Hi Shen, >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Thanks for the answer: Composer install gives me the >>>>>>>>>>>>>>>> following error: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [lorisadmin at loris loris]$ composer install >>>>>>>>>>>>>>>> PHP Deprecated: Required parameter $ignoreFilters follows >>>>>>>>>>>>>>>> optional parameter $packageName in >>>>>>>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>>>>>>> line 97 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Deprecated: Required parameter $ignoreFilters follows >>>>>>>>>>>>>>>> optional parameter $packageName in >>>>>>>>>>>>>>>> phar:///usr/local/bin/composer/src/Composer/Command/ArchiveCommand.php on >>>>>>>>>>>>>>>> line 97 >>>>>>>>>>>>>>>> Deprecation Notice: Required parameter $path follows >>>>>>>>>>>>>>>> optional parameter $schema in >>>>>>>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:53 >>>>>>>>>>>>>>>> Deprecation Notice: Required parameter $path follows >>>>>>>>>>>>>>>> optional parameter $schema in >>>>>>>>>>>>>>>> phar:///usr/local/bin/composer/vendor/justinrainbow/json-schema/src/JsonSchema/Constraints/UndefinedConstraint.php:97 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> [ErrorException] >>>>>>>>>>>>>>>> Trying to access array offset on value of type null >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Best, >>>>>>>>>>>>>>>> Tom >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Thu, Feb 4, 2021 at 1:13 PM Shen Wang < >>>>>>>>>>>>>>>> wangshen.mcin at gmail.com> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Hi Tom, >>>>>>>>>>>>>>>>> You need to re-run " composer install " to solve this >>>>>>>>>>>>>>>>> issue. >>>>>>>>>>>>>>>>> Good Luck. >>>>>>>>>>>>>>>>> Best >>>>>>>>>>>>>>>>> Shen >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Thu, 4 Feb 2021 at 13:01, Tom Beaudry < >>>>>>>>>>>>>>>>> waveflux at gmail.com> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Hey Guys, >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> I decided to upgrade LORIS v22 to v23 and I ran into this >>>>>>>>>>>>>>>>>> apache error when i navigate to the homepage in my web browser: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [Thu Feb 04 12:52:22.608901 2021] [php7:warn] [pid 5215] >>>>>>>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Warning: >>>>>>>>>>>>>>>>>> session_start(): Setting option 'cookie_samesite' failed in >>>>>>>>>>>>>>>>>> /var/www/loris/php/libraries/NDB_Client.class.inc on line 147 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> [Thu Feb 04 12:52:22.610434 2021] [php7:error] [pid 5215] >>>>>>>>>>>>>>>>>> [client 172.16.253.6:62122] PHP Fatal error*: Uncaught >>>>>>>>>>>>>>>>>> Error: Class 'Laminas\\Diactoros\\ServerRequestFactory'* >>>>>>>>>>>>>>>>>> not found in /var/www/loris/htdocs/index.php:35\nStack trace:\n#0 {main}\n >>>>>>>>>>>>>>>>>> thrown in /var/www/loris/htdocs/index.php on line 35 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> It seems that the server request is failing: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> $serverrequest = \Laminas\Diactoros\ServerRequestFactory >>>>>>>>>>>>>>>>>> ::fromGlobals(); >>>>>>>>>>>>>>>>>> 36 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Any help would be greatly appreciated! >>>>>>>>>>>>>>>>>> Tom >>>>>>>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>>>> McGill University >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>>>> McGill University >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> -- >>>>>>>>>>>>> Shen Wang >>>>>>>>>>>>> Loris Developer >>>>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>>>> McGill University >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Shen Wang >>>>>>>>>>> Loris Developer >>>>>>>>>>> Montreal Neurological Institute >>>>>>>>>>> McGill University >>>>>>>>>>> >>>>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Shen Wang >>>>>>>> Loris Developer >>>>>>>> Montreal Neurological Institute >>>>>>>> McGill University >>>>>>>> >>>>>>>> >>>>>> >>>>>> -- >>>>>> Shen Wang >>>>>> Loris Developer >>>>>> Montreal Neurological Institute >>>>>> McGill University >>>>>> >>>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> > > -- > Shen Wang > Loris Developer > Montreal Neurological Institute > McGill University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sridar.narayanan at mcgill.ca Mon Feb 8 15:31:42 2021 From: sridar.narayanan at mcgill.ca (Sridar Narayanan, Dr.) Date: Mon, 8 Feb 2021 20:31:42 +0000 Subject: [Loris-dev] 500 after login In-Reply-To: References: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> <44A13251-016E-438B-8264-26F9D37BE8C1@bwh.harvard.edu> Message-ID: Hi Dave, While requiring comprehensive site uploader data makes sense in the context of a prospective study where the sites are actually uploading data directly, it doesn?t make much sense when data is being uploaded centrally, either prospectively or retrospectively as in our case. Is there an option to specify a single, centralized uploader for all sites? Thanks, Sridar On Feb 8, 2021, at 2:37 PM, Dave MacFarlane > wrote: Set the "Real_name" field in the user table for that user to a value other than null (and maybe ensure no other users have null real names while you're at it.. they would have the same problem logging in). I think that any string value should fix the error that you posted. On Mon, Feb 8, 2021 at 2:33 PM Morales Pinzon, Alfredo > wrote: Hi Dave, What is your suggestion to fix this? Best, Alfredo. On Feb 8, 2021, at 1:24 PM, Dave MacFarlane > wrote: External Email - Use Caution I don't think the Real_name field should be null. It's used for the name to display in the menu at the top of LORIS. (In my local database the column is non-nullable, but it seems that the default schema allows null.. I think the fact that it allowed you to insert a null value is a minor bug.) - Dave On Mon, Feb 8, 2021 at 1:07 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev, I am getting a 500 error after login into LORIS. This is what I can see in the logs: === [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client 216.15.126.108:61071] PHP Fatal error: Uncaught TypeError: Return value of User::getFullname() must be of the type string, null returned in /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 /var/www/loris/modules/dashboard/php/module.class.inc(118): User->getFullname()\n#1 /var/www/loris/modules/dashboard/php/module.class.inc(57): LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), Object(NDB_Config), Object(User))\n#2 /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 /var/www/loris/php/libraries/Module.class.inc(275): LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), 'dashboard', '', '', 'dashboard')\n#4 /var/www/loris/php/libraries/Module.class.inc(342): Module->loadPage('dashboard')\n#5 /var/www/loris/src/Middleware/ResponseGenerator.php(50): Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 /var/www/loris/src/Middleware/AuthMiddleware.php(63): LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se in /var/www/loris/php/libraries/User.class.inc on line 236 === Perhaps it is an issue with the name of the user? I created hundreds of users for batch insertion of candidates and visits for previous versions of LORIS that required insertion of Candidates and Visits by users belonging to a given center. This is an entry in the users table without the hashed password: === *************************** 850. row *************************** ID: 850 UserID: 723-DKC-1_dataman Password: NULL Real_name: NULL First_name: NULL Last_name: NULL Degree: NULL Position_title: NULL Institution: NULL Department: NULL Address: NULL City: NULL State: NULL Zip_code: NULL Country: NULL Phone: NULL Fax: NULL Email: 723-DKC-1_dataman at ipmsa.com Privilege: 0 PSCPI: N DBAccess: Active: Y Password_hash: /REMOVED/ Password_expiry: 2035-01-01 Pending_approval: N Doc_Repo_Notifications: N language_preference: NULL active_from: NULL active_to: NULL === Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Mon Feb 8 16:02:37 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Mon, 8 Feb 2021 16:02:37 -0500 Subject: [Loris-dev] 500 after login In-Reply-To: References: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> <44A13251-016E-438B-8264-26F9D37BE8C1@bwh.harvard.edu> Message-ID: Hi Sridar, Users in LORIS may be affiliated with multiple sites at once. If there's a single uploader the easiest is just to ensure that the account used for uploading is affiliated with all the sites in LORIS by selecting them all in the multi-select in the user management page. (Clicking on the first one, then scrolling down and clicking the last one while holding shift should select them all in most web browsers.) - Dave On Mon, Feb 8, 2021 at 3:31 PM Sridar Narayanan, Dr. < sridar.narayanan at mcgill.ca> wrote: > Hi Dave, > > While requiring comprehensive site uploader data makes sense in the > context of a prospective study where the sites are actually uploading data > directly, it doesn?t make much sense when data is being uploaded centrally, > either prospectively or retrospectively as in our case. Is there an option > to specify a single, centralized uploader for all sites? > > Thanks, > > Sridar > > > On Feb 8, 2021, at 2:37 PM, Dave MacFarlane > wrote: > > Set the "Real_name" field in the user table for that user to a value other > than null (and maybe ensure no other users have null real names while > you're at it.. they would have the same problem logging in). I think that > any string value should fix the error that you posted. > > On Mon, Feb 8, 2021 at 2:33 PM Morales Pinzon, Alfredo < > AMORALESPINZON at bwh.harvard.edu> wrote: > >> Hi Dave, >> >> What is your suggestion to fix this? >> >> Best, >> Alfredo. >> >> On Feb 8, 2021, at 1:24 PM, Dave MacFarlane >> wrote: >> >> External Email - Use Caution >> >> I don't think the Real_name field should be null. It's used for the name >> to display in the menu at the top of LORIS. >> >> (In my local database the column is non-nullable, but it seems that the >> default schema allows null.. I think the fact that it allowed you to insert >> a null value is a minor bug.) >> >> - Dave >> >> >> On Mon, Feb 8, 2021 at 1:07 PM Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >>> Dear LorisDev, >>> >>> I am getting a 500 error after login into LORIS. This is what I can see >>> in the logs: >>> >>> === >>> [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client >>> 216.15.126.108:61071 >>> ] >>> PHP Fatal error: Uncaught TypeError: Return value of User::getFullname() >>> must be of the type string, null returned in >>> /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 >>> /var/www/loris/modules/dashboard/php/module.class.inc(118): >>> User->getFullname()\n#1 >>> /var/www/loris/modules/dashboard/php/module.class.inc(57): >>> LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), >>> Object(NDB_Config), Object(User))\n#2 >>> /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): >>> LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 >>> /var/www/loris/php/libraries/Module.class.inc(275): >>> LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), >>> 'dashboard', '', '', 'dashboard')\n#4 >>> /var/www/loris/php/libraries/Module.class.inc(342): >>> Module->loadPage('dashboard')\n#5 >>> /var/www/loris/src/Middleware/ResponseGenerator.php(50): >>> Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 >>> /var/www/loris/src/Middleware/AuthMiddleware.php(63): >>> LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se >>> in /var/www/loris/php/libraries/User.class.inc on line 236 >>> === >>> >>> Perhaps it is an issue with the name of the user? I created hundreds of >>> users for batch insertion of candidates and visits for previous versions of >>> LORIS that required insertion of Candidates and Visits by users belonging >>> to a given center. >>> >>> This is an entry in the users table without the hashed password: >>> >>> === >>> *************************** 850. row *************************** >>> ID: 850 >>> UserID: 723-DKC-1_dataman >>> Password: NULL >>> Real_name: NULL >>> First_name: NULL >>> Last_name: NULL >>> Degree: NULL >>> Position_title: NULL >>> Institution: NULL >>> Department: NULL >>> Address: NULL >>> City: NULL >>> State: NULL >>> Zip_code: NULL >>> Country: NULL >>> Phone: NULL >>> Fax: NULL >>> Email: 723-DKC-1_dataman at ipmsa.com >>> <723-DKC-1_dataman at ipmsa.com> >>> Privilege: 0 >>> PSCPI: N >>> DBAccess: >>> Active: Y >>> Password_hash: /REMOVED/ >>> Password_expiry: 2035-01-01 >>> Pending_approval: N >>> Doc_Repo_Notifications: N >>> language_preference: NULL >>> active_from: NULL >>> active_to: NULL >>> === >>> >>> Best, >>> Alfredo. >>> The information in this e-mail is intended only for the person to whom >>> it is addressed. If you believe this e-mail was sent to you in error and >>> the e-mail contains patient information, please contact the Mass General >>> Brigham Compliance HelpLine at >>> http://www.massgeneralbrigham.org/complianceline >>> >>> . If the e-mail was sent to you in error but does not contain patient >>> information, please contact the sender and properly dispose of the e-mail. >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> >> >> The information in this e-mail is intended only for the person to whom it >> is addressed. If you believe this e-mail was sent to you in error and the >> e-mail contains patient information, please contact the Mass General >> Brigham Compliance HelpLine at >> http://www.massgeneralbrigham.org/complianceline . If the e-mail was >> sent to you in error but does not contain patient information, please >> contact the sender and properly dispose of the e-mail. >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Tue Feb 9 23:04:35 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Wed, 10 Feb 2021 04:04:35 +0000 Subject: [Loris-dev] 500 after login In-Reply-To: References: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> <44A13251-016E-438B-8264-26F9D37BE8C1@bwh.harvard.edu> Message-ID: <49C01922-ACA8-401F-9151-741CC101FCB0@bwh.harvard.edu> Hi Dave, I am trying to give add more sites for a user but I?m getting the error in the image attached. I tried in a different user and I got the same error. This is the error log in loris-error.log: === [Tue Feb 09 22:59:18.026223 2021] [php7:notice] [pid 21147] [client 216.15.126.108:59451] PHP Notice: Undefined index: active_to in /var/www/loris/modules/user_accounts/php/edit_user.class.inc on line 1259, referer: https://ipmsa-loris.bic.mni.mcgill.ca/user_accounts/edit_user/alfredouser === Any ideas? Best, Alfredo,. [cid:7BDF9833-5229-43CB-8521-F3C56E016DAF] On Feb 8, 2021, at 4:02 PM, Dave MacFarlane > wrote: External Email - Use Caution Hi Sridar, Users in LORIS may be affiliated with multiple sites at once. If there's a single uploader the easiest is just to ensure that the account used for uploading is affiliated with all the sites in LORIS by selecting them all in the multi-select in the user management page. (Clicking on the first one, then scrolling down and clicking the last one while holding shift should select them all in most web browsers.) - Dave On Mon, Feb 8, 2021 at 3:31 PM Sridar Narayanan, Dr. > wrote: Hi Dave, While requiring comprehensive site uploader data makes sense in the context of a prospective study where the sites are actually uploading data directly, it doesn?t make much sense when data is being uploaded centrally, either prospectively or retrospectively as in our case. Is there an option to specify a single, centralized uploader for all sites? Thanks, Sridar On Feb 8, 2021, at 2:37 PM, Dave MacFarlane > wrote: Set the "Real_name" field in the user table for that user to a value other than null (and maybe ensure no other users have null real names while you're at it.. they would have the same problem logging in). I think that any string value should fix the error that you posted. On Mon, Feb 8, 2021 at 2:33 PM Morales Pinzon, Alfredo > wrote: Hi Dave, What is your suggestion to fix this? Best, Alfredo. On Feb 8, 2021, at 1:24 PM, Dave MacFarlane > wrote: External Email - Use Caution I don't think the Real_name field should be null. It's used for the name to display in the menu at the top of LORIS. (In my local database the column is non-nullable, but it seems that the default schema allows null.. I think the fact that it allowed you to insert a null value is a minor bug.) - Dave On Mon, Feb 8, 2021 at 1:07 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev, I am getting a 500 error after login into LORIS. This is what I can see in the logs: === [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client 216.15.126.108:61071] PHP Fatal error: Uncaught TypeError: Return value of User::getFullname() must be of the type string, null returned in /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 /var/www/loris/modules/dashboard/php/module.class.inc(118): User->getFullname()\n#1 /var/www/loris/modules/dashboard/php/module.class.inc(57): LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), Object(NDB_Config), Object(User))\n#2 /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 /var/www/loris/php/libraries/Module.class.inc(275): LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), 'dashboard', '', '', 'dashboard')\n#4 /var/www/loris/php/libraries/Module.class.inc(342): Module->loadPage('dashboard')\n#5 /var/www/loris/src/Middleware/ResponseGenerator.php(50): Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 /var/www/loris/src/Middleware/AuthMiddleware.php(63): LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se in /var/www/loris/php/libraries/User.class.inc on line 236 === Perhaps it is an issue with the name of the user? I created hundreds of users for batch insertion of candidates and visits for previous versions of LORIS that required insertion of Candidates and Visits by users belonging to a given center. This is an entry in the users table without the hashed password: === *************************** 850. row *************************** ID: 850 UserID: 723-DKC-1_dataman Password: NULL Real_name: NULL First_name: NULL Last_name: NULL Degree: NULL Position_title: NULL Institution: NULL Department: NULL Address: NULL City: NULL State: NULL Zip_code: NULL Country: NULL Phone: NULL Fax: NULL Email: 723-DKC-1_dataman at ipmsa.com Privilege: 0 PSCPI: N DBAccess: Active: Y Password_hash: /REMOVED/ Password_expiry: 2035-01-01 Pending_approval: N Doc_Repo_Notifications: N language_preference: NULL active_from: NULL active_to: NULL === Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2021-02-09 at 11.00.44 PM.png Type: image/png Size: 13960 bytes Desc: Screen Shot 2021-02-09 at 11.00.44 PM.png URL: From AMORALESPINZON at BWH.HARVARD.EDU Fri Feb 12 13:11:24 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Fri, 12 Feb 2021 18:11:24 +0000 Subject: [Loris-dev] 500 after login In-Reply-To: <49C01922-ACA8-401F-9151-741CC101FCB0@bwh.harvard.edu> References: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> <44A13251-016E-438B-8264-26F9D37BE8C1@bwh.harvard.edu> <49C01922-ACA8-401F-9151-741CC101FCB0@bwh.harvard.edu> Message-ID: <1FD15049-8A61-4486-9B24-0572B324FBB9@bwh.harvard.edu> Dear LorisDev, I added all the sites for a user and gave all the permissions to that user, but still I cannot use the end-point ?PUT /api/v0.0.3/candidates/{candidate}/{visitlabel}? with the following payload: === { "CandID": "559153", "Visit": "w024", "Site": "111-RWA-1", "Battery": "Experimental", "Project": "ADVANCE_ATTAIN" } === I am getting the following response: === { "error": "You can`t create candidates visit for that site" } === I don?t see any errors in apache. Any ideas? Best, Alfredo. On Feb 9, 2021, at 11:04 PM, Morales Pinzon, Alfredo > wrote: External Email - Use Caution Hi Dave, I am trying to give add more sites for a user but I?m getting the error in the image attached. I tried in a different user and I got the same error. This is the error log in loris-error.log: === [Tue Feb 09 22:59:18.026223 2021] [php7:notice] [pid 21147] [client 216.15.126.108:59451] PHP Notice: Undefined index: active_to in /var/www/loris/modules/user_accounts/php/edit_user.class.inc on line 1259, referer: https://ipmsa-loris.bic.mni.mcgill.ca/user_accounts/edit_user/alfredouser === Any ideas? Best, Alfredo,. On Feb 8, 2021, at 4:02 PM, Dave MacFarlane > wrote: External Email - Use Caution Hi Sridar, Users in LORIS may be affiliated with multiple sites at once. If there's a single uploader the easiest is just to ensure that the account used for uploading is affiliated with all the sites in LORIS by selecting them all in the multi-select in the user management page. (Clicking on the first one, then scrolling down and clicking the last one while holding shift should select them all in most web browsers.) - Dave On Mon, Feb 8, 2021 at 3:31 PM Sridar Narayanan, Dr. > wrote: Hi Dave, While requiring comprehensive site uploader data makes sense in the context of a prospective study where the sites are actually uploading data directly, it doesn?t make much sense when data is being uploaded centrally, either prospectively or retrospectively as in our case. Is there an option to specify a single, centralized uploader for all sites? Thanks, Sridar On Feb 8, 2021, at 2:37 PM, Dave MacFarlane > wrote: Set the "Real_name" field in the user table for that user to a value other than null (and maybe ensure no other users have null real names while you're at it.. they would have the same problem logging in). I think that any string value should fix the error that you posted. On Mon, Feb 8, 2021 at 2:33 PM Morales Pinzon, Alfredo > wrote: Hi Dave, What is your suggestion to fix this? Best, Alfredo. On Feb 8, 2021, at 1:24 PM, Dave MacFarlane > wrote: External Email - Use Caution I don't think the Real_name field should be null. It's used for the name to display in the menu at the top of LORIS. (In my local database the column is non-nullable, but it seems that the default schema allows null.. I think the fact that it allowed you to insert a null value is a minor bug.) - Dave On Mon, Feb 8, 2021 at 1:07 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev, I am getting a 500 error after login into LORIS. This is what I can see in the logs: === [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client 216.15.126.108:61071] PHP Fatal error: Uncaught TypeError: Return value of User::getFullname() must be of the type string, null returned in /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 /var/www/loris/modules/dashboard/php/module.class.inc(118): User->getFullname()\n#1 /var/www/loris/modules/dashboard/php/module.class.inc(57): LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), Object(NDB_Config), Object(User))\n#2 /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 /var/www/loris/php/libraries/Module.class.inc(275): LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), 'dashboard', '', '', 'dashboard')\n#4 /var/www/loris/php/libraries/Module.class.inc(342): Module->loadPage('dashboard')\n#5 /var/www/loris/src/Middleware/ResponseGenerator.php(50): Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 /var/www/loris/src/Middleware/AuthMiddleware.php(63): LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se in /var/www/loris/php/libraries/User.class.inc on line 236 === Perhaps it is an issue with the name of the user? I created hundreds of users for batch insertion of candidates and visits for previous versions of LORIS that required insertion of Candidates and Visits by users belonging to a given center. This is an entry in the users table without the hashed password: === *************************** 850. row *************************** ID: 850 UserID: 723-DKC-1_dataman Password: NULL Real_name: NULL First_name: NULL Last_name: NULL Degree: NULL Position_title: NULL Institution: NULL Department: NULL Address: NULL City: NULL State: NULL Zip_code: NULL Country: NULL Phone: NULL Fax: NULL Email: 723-DKC-1_dataman at ipmsa.com Privilege: 0 PSCPI: N DBAccess: Active: Y Password_hash: /REMOVED/ Password_expiry: 2035-01-01 Pending_approval: N Doc_Repo_Notifications: N language_preference: NULL active_from: NULL active_to: NULL === Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://secure-web.cisco.com/1-zL4DlVdDgIpuP-wmX2G-_BmTOEoFKnRRdZt9lD0LaePFAD5YNdPkfKUs2HN3qJbIDG6ENFBb5A1eA5UrlUr8mIeZTxSKQoxNlr5INLM454I7Pt1yZ5NeChKafwZ4ofTxasbruAKIKuoyCewU2N79yOuXpOh8u2HMDTW23OLP_KP5XdVthRSNY4opuKoWoI791SsnNNzh0MruQqFELfEAaKQ5JY0F-i51qEWUhIHD7buHnWpE-XwMDoxW5tAzkStaaoqzRYXnrSlP2Ff3z8iGQ/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Fri Feb 12 15:59:08 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Fri, 12 Feb 2021 15:59:08 -0500 Subject: [Loris-dev] 500 after login In-Reply-To: <1FD15049-8A61-4486-9B24-0572B324FBB9@bwh.harvard.edu> References: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> <44A13251-016E-438B-8264-26F9D37BE8C1@bwh.harvard.edu> <49C01922-ACA8-401F-9151-741CC101FCB0@bwh.harvard.edu> <1FD15049-8A61-4486-9B24-0572B324FBB9@bwh.harvard.edu> Message-ID: Hi Alfredo, The only place in the code I see that error message is in modules/api/php/endpoints/candidate/visit/visit.class.inc. The code around it is: $centerid = array_search($visitinfo['Site'], \Utility::getSiteList()); if (!in_array($centerid, $user->getCenterIDs())) { return new \LORIS\Http\Response\JSON\Forbidden( 'You can`t create candidates visit for that site' ); } I don't see any way it would be possible to trigger that error if you've given the user all sites. If you have a dev or staging server where you could add debugging statements could you (inside of the if statement) put: var_dump($user->getCenterIDs()); var_dump($centerid); var_dump($visitinfo); var_dump(\Utility::getSiteList()); I think that would cover all the variables that have any affect on the condition in order to trace where it's going wrong.. On Fri, Feb 12, 2021 at 1:11 PM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Dear LorisDev, > > I added all the sites for a user and gave all the permissions to that > user, but still I cannot use the end-point ?PUT > /api/v0.0.3/candidates/{candidate}/{visitlabel}? with the following payload: > > === > { > "CandID": "559153", > "Visit": "w024", > "Site": "111-RWA-1", > "Battery": "Experimental", > "Project": "ADVANCE_ATTAIN" > } > === > > I am getting the following response: > > === > { > "error": "You can`t create candidates visit for that site" > } > === > > I don?t see any errors in apache. > Any ideas? > > Best, > Alfredo. > > On Feb 9, 2021, at 11:04 PM, Morales Pinzon, Alfredo < > AMORALESPINZON at BWH.HARVARD.EDU> wrote: > > External Email - Use Caution > > Hi Dave, > > I am trying to give add more sites for a user but I?m getting the error in > the image attached. I tried in a different user and I got the same error. > This is the error log in loris-error.log: > > === > [Tue Feb 09 22:59:18.026223 2021] [php7:notice] [pid 21147] [client > 216.15.126.108:59451] PHP Notice: Undefined index: active_to in > /var/www/loris/modules/user_accounts/php/edit_user.class.inc on line 1259, > referer: > https://ipmsa-loris.bic.mni.mcgill.ca/user_accounts/edit_user/alfredouser > > === > > Any ideas? > > Best, > Alfredo,. > > > > On Feb 8, 2021, at 4:02 PM, Dave MacFarlane > wrote: > > External Email - Use Caution > > Hi Sridar, > > Users in LORIS may be affiliated with multiple sites at once. If there's a > single uploader the easiest is just to ensure that the account used for > uploading is affiliated with all the sites in LORIS by selecting them all > in the multi-select in the user management page. (Clicking on the first > one, then scrolling down and clicking the last one while holding shift > should select them all in most web browsers.) > > - Dave > > On Mon, Feb 8, 2021 at 3:31 PM Sridar Narayanan, Dr. < > sridar.narayanan at mcgill.ca> wrote: > >> Hi Dave, >> >> While requiring comprehensive site uploader data makes sense in the >> context of a prospective study where the sites are actually uploading data >> directly, it doesn?t make much sense when data is being uploaded centrally, >> either prospectively or retrospectively as in our case. Is there an option >> to specify a single, centralized uploader for all sites? >> >> Thanks, >> >> Sridar >> >> >> On Feb 8, 2021, at 2:37 PM, Dave MacFarlane >> wrote: >> >> Set the "Real_name" field in the user table for that user to a value >> other than null (and maybe ensure no other users have null real names while >> you're at it.. they would have the same problem logging in). I think that >> any string value should fix the error that you posted. >> >> On Mon, Feb 8, 2021 at 2:33 PM Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >>> Hi Dave, >>> >>> What is your suggestion to fix this? >>> >>> Best, >>> Alfredo. >>> >>> On Feb 8, 2021, at 1:24 PM, Dave MacFarlane >>> wrote: >>> >>> External Email - Use Caution >>> >>> I don't think the Real_name field should be null. It's used for the name >>> to display in the menu at the top of LORIS. >>> >>> (In my local database the column is non-nullable, but it seems that the >>> default schema allows null.. I think the fact that it allowed you to insert >>> a null value is a minor bug.) >>> >>> - Dave >>> >>> >>> On Mon, Feb 8, 2021 at 1:07 PM Morales Pinzon, Alfredo < >>> AMORALESPINZON at bwh.harvard.edu> wrote: >>> >>>> Dear LorisDev, >>>> >>>> I am getting a 500 error after login into LORIS. This is what I can see >>>> in the logs: >>>> >>>> === >>>> [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client >>>> 216.15.126.108:61071 >>>> ] >>>> PHP Fatal error: Uncaught TypeError: Return value of User::getFullname() >>>> must be of the type string, null returned in >>>> /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 >>>> /var/www/loris/modules/dashboard/php/module.class.inc(118): >>>> User->getFullname()\n#1 >>>> /var/www/loris/modules/dashboard/php/module.class.inc(57): >>>> LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), >>>> Object(NDB_Config), Object(User))\n#2 >>>> /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): >>>> LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 >>>> /var/www/loris/php/libraries/Module.class.inc(275): >>>> LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), >>>> 'dashboard', '', '', 'dashboard')\n#4 >>>> /var/www/loris/php/libraries/Module.class.inc(342): >>>> Module->loadPage('dashboard')\n#5 >>>> /var/www/loris/src/Middleware/ResponseGenerator.php(50): >>>> Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 >>>> /var/www/loris/src/Middleware/AuthMiddleware.php(63): >>>> LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se >>>> in /var/www/loris/php/libraries/User.class.inc on line 236 >>>> === >>>> >>>> Perhaps it is an issue with the name of the user? I created hundreds of >>>> users for batch insertion of candidates and visits for previous versions of >>>> LORIS that required insertion of Candidates and Visits by users belonging >>>> to a given center. >>>> >>>> This is an entry in the users table without the hashed password: >>>> >>>> === >>>> *************************** 850. row *************************** >>>> ID: 850 >>>> UserID: 723-DKC-1_dataman >>>> Password: NULL >>>> Real_name: NULL >>>> First_name: NULL >>>> Last_name: NULL >>>> Degree: NULL >>>> Position_title: NULL >>>> Institution: NULL >>>> Department: NULL >>>> Address: NULL >>>> City: NULL >>>> State: NULL >>>> Zip_code: NULL >>>> Country: NULL >>>> Phone: NULL >>>> Fax: NULL >>>> Email: 723-DKC-1_dataman at ipmsa.com >>>> <723-DKC-1_dataman at ipmsa.com> >>>> Privilege: 0 >>>> PSCPI: N >>>> DBAccess: >>>> Active: Y >>>> Password_hash: /REMOVED/ >>>> Password_expiry: 2035-01-01 >>>> Pending_approval: N >>>> Doc_Repo_Notifications: N >>>> language_preference: NULL >>>> active_from: NULL >>>> active_to: NULL >>>> === >>>> >>>> Best, >>>> Alfredo. >>>> The information in this e-mail is intended only for the person to whom >>>> it is addressed. If you believe this e-mail was sent to you in error and >>>> the e-mail contains patient information, please contact the Mass General >>>> Brigham Compliance HelpLine at >>>> http://www.massgeneralbrigham.org/complianceline >>>> >>>> . If the e-mail was sent to you in error but does not contain patient >>>> information, please contact the sender and properly dispose of the e-mail. >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is addressed. If you believe this e-mail was sent to you in error and >>> the e-mail contains patient information, please contact the Mass General >>> Brigham Compliance HelpLine at >>> http://www.massgeneralbrigham.org/complianceline >>> >>> . If the e-mail was sent to you in error but does not contain patient >>> information, please contact the sender and properly dispose of the e-mail. >>> >> >> > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > > https://secure-web.cisco.com/1-zL4DlVdDgIpuP-wmX2G-_BmTOEoFKnRRdZt9lD0LaePFAD5YNdPkfKUs2HN3qJbIDG6ENFBb5A1eA5UrlUr8mIeZTxSKQoxNlr5INLM454I7Pt1yZ5NeChKafwZ4ofTxasbruAKIKuoyCewU2N79yOuXpOh8u2HMDTW23OLP_KP5XdVthRSNY4opuKoWoI791SsnNNzh0MruQqFELfEAaKQ5JY0F-i51qEWUhIHD7buHnWpE-XwMDoxW5tAzkStaaoqzRYXnrSlP2Ff3z8iGQ/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev > > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Fri Feb 12 18:30:04 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Fri, 12 Feb 2021 23:30:04 +0000 Subject: [Loris-dev] 500 after login In-Reply-To: References: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> <44A13251-016E-438B-8264-26F9D37BE8C1@bwh.harvard.edu> <49C01922-ACA8-401F-9151-741CC101FCB0@bwh.harvard.edu> <1FD15049-8A61-4486-9B24-0572B324FBB9@bwh.harvard.edu> Message-ID: <49A6DCEA-2199-425C-8543-B2C4991C7B7B@bwh.harvard.edu> Hi Dave, I had to add the ?Permission -> Roles -> Data entry? to the user. I have hundreds of users that were creating visits previously without this permission. I?m moving my scripts to use single user for the creation of candidates and visits. Thank you. Best, Alfredo. On Feb 12, 2021, at 3:59 PM, Dave MacFarlane > wrote: External Email - Use Caution Hi Alfredo, The only place in the code I see that error message is in modules/api/php/endpoints/candidate/visit/visit.class.inc. The code around it is: $centerid = array_search($visitinfo['Site'], \Utility::getSiteList()); if (!in_array($centerid, $user->getCenterIDs())) { return new \LORIS\Http\Response\JSON\Forbidden( 'You can`t create candidates visit for that site' ); } I don't see any way it would be possible to trigger that error if you've given the user all sites. If you have a dev or staging server where you could add debugging statements could you (inside of the if statement) put: var_dump($user->getCenterIDs()); var_dump($centerid); var_dump($visitinfo); var_dump(\Utility::getSiteList()); I think that would cover all the variables that have any affect on the condition in order to trace where it's going wrong.. On Fri, Feb 12, 2021 at 1:11 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev, I added all the sites for a user and gave all the permissions to that user, but still I cannot use the end-point ?PUT /api/v0.0.3/candidates/{candidate}/{visitlabel}? with the following payload: === { "CandID": "559153", "Visit": "w024", "Site": "111-RWA-1", "Battery": "Experimental", "Project": "ADVANCE_ATTAIN" } === I am getting the following response: === { "error": "You can`t create candidates visit for that site" } === I don?t see any errors in apache. Any ideas? Best, Alfredo. On Feb 9, 2021, at 11:04 PM, Morales Pinzon, Alfredo > wrote: External Email - Use Caution Hi Dave, I am trying to give add more sites for a user but I?m getting the error in the image attached. I tried in a different user and I got the same error. This is the error log in loris-error.log: === [Tue Feb 09 22:59:18.026223 2021] [php7:notice] [pid 21147] [client 216.15.126.108:59451] PHP Notice: Undefined index: active_to in /var/www/loris/modules/user_accounts/php/edit_user.class.inc on line 1259, referer: https://ipmsa-loris.bic.mni.mcgill.ca/user_accounts/edit_user/alfredouser === Any ideas? Best, Alfredo,. On Feb 8, 2021, at 4:02 PM, Dave MacFarlane > wrote: External Email - Use Caution Hi Sridar, Users in LORIS may be affiliated with multiple sites at once. If there's a single uploader the easiest is just to ensure that the account used for uploading is affiliated with all the sites in LORIS by selecting them all in the multi-select in the user management page. (Clicking on the first one, then scrolling down and clicking the last one while holding shift should select them all in most web browsers.) - Dave On Mon, Feb 8, 2021 at 3:31 PM Sridar Narayanan, Dr. > wrote: Hi Dave, While requiring comprehensive site uploader data makes sense in the context of a prospective study where the sites are actually uploading data directly, it doesn?t make much sense when data is being uploaded centrally, either prospectively or retrospectively as in our case. Is there an option to specify a single, centralized uploader for all sites? Thanks, Sridar On Feb 8, 2021, at 2:37 PM, Dave MacFarlane > wrote: Set the "Real_name" field in the user table for that user to a value other than null (and maybe ensure no other users have null real names while you're at it.. they would have the same problem logging in). I think that any string value should fix the error that you posted. On Mon, Feb 8, 2021 at 2:33 PM Morales Pinzon, Alfredo > wrote: Hi Dave, What is your suggestion to fix this? Best, Alfredo. On Feb 8, 2021, at 1:24 PM, Dave MacFarlane > wrote: External Email - Use Caution I don't think the Real_name field should be null. It's used for the name to display in the menu at the top of LORIS. (In my local database the column is non-nullable, but it seems that the default schema allows null.. I think the fact that it allowed you to insert a null value is a minor bug.) - Dave On Mon, Feb 8, 2021 at 1:07 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev, I am getting a 500 error after login into LORIS. This is what I can see in the logs: === [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client 216.15.126.108:61071] PHP Fatal error: Uncaught TypeError: Return value of User::getFullname() must be of the type string, null returned in /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 /var/www/loris/modules/dashboard/php/module.class.inc(118): User->getFullname()\n#1 /var/www/loris/modules/dashboard/php/module.class.inc(57): LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), Object(NDB_Config), Object(User))\n#2 /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 /var/www/loris/php/libraries/Module.class.inc(275): LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), 'dashboard', '', '', 'dashboard')\n#4 /var/www/loris/php/libraries/Module.class.inc(342): Module->loadPage('dashboard')\n#5 /var/www/loris/src/Middleware/ResponseGenerator.php(50): Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 /var/www/loris/src/Middleware/AuthMiddleware.php(63): LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se in /var/www/loris/php/libraries/User.class.inc on line 236 === Perhaps it is an issue with the name of the user? I created hundreds of users for batch insertion of candidates and visits for previous versions of LORIS that required insertion of Candidates and Visits by users belonging to a given center. This is an entry in the users table without the hashed password: === *************************** 850. row *************************** ID: 850 UserID: 723-DKC-1_dataman Password: NULL Real_name: NULL First_name: NULL Last_name: NULL Degree: NULL Position_title: NULL Institution: NULL Department: NULL Address: NULL City: NULL State: NULL Zip_code: NULL Country: NULL Phone: NULL Fax: NULL Email: 723-DKC-1_dataman at ipmsa.com Privilege: 0 PSCPI: N DBAccess: Active: Y Password_hash: /REMOVED/ Password_expiry: 2035-01-01 Pending_approval: N Doc_Repo_Notifications: N language_preference: NULL active_from: NULL active_to: NULL === Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://secure-web.cisco.com/1-zL4DlVdDgIpuP-wmX2G-_BmTOEoFKnRRdZt9lD0LaePFAD5YNdPkfKUs2HN3qJbIDG6ENFBb5A1eA5UrlUr8mIeZTxSKQoxNlr5INLM454I7Pt1yZ5NeChKafwZ4ofTxasbruAKIKuoyCewU2N79yOuXpOh8u2HMDTW23OLP_KP5XdVthRSNY4opuKoWoI791SsnNNzh0MruQqFELfEAaKQ5JY0F-i51qEWUhIHD7buHnWpE-XwMDoxW5tAzkStaaoqzRYXnrSlP2Ff3z8iGQ/https%3A%2F%2Fmailman.bic.mni.mcgill.ca%2Fmailman%2Flistinfo%2Floris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Sat Feb 13 11:28:59 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Sat, 13 Feb 2021 16:28:59 +0000 Subject: [Loris-dev] 500 after login In-Reply-To: <49C01922-ACA8-401F-9151-741CC101FCB0@bwh.harvard.edu> References: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> <44A13251-016E-438B-8264-26F9D37BE8C1@bwh.harvard.edu> <49C01922-ACA8-401F-9151-741CC101FCB0@bwh.harvard.edu> Message-ID: Hi Dave, I am still having issues editing a user permissions in the front-end. The changes I am doing for one specific user are not saved and I don?t receive any message/error. Let me know what is the best way for me help on this. Best, Alfredo. On Feb 9, 2021, at 11:04 PM, Morales Pinzon, Alfredo > wrote: Hi Dave, I am trying to give add more sites for a user but I?m getting the error in the image attached. I tried in a different user and I got the same error. This is the error log in loris-error.log: === [Tue Feb 09 22:59:18.026223 2021] [php7:notice] [pid 21147] [client 216.15.126.108:59451] PHP Notice: Undefined index: active_to in /var/www/loris/modules/user_accounts/php/edit_user.class.inc on line 1259, referer: https://ipmsa-loris.bic.mni.mcgill.ca/user_accounts/edit_user/alfredouser === Any ideas? Best, Alfredo,. On Feb 8, 2021, at 4:02 PM, Dave MacFarlane > wrote: External Email - Use Caution Hi Sridar, Users in LORIS may be affiliated with multiple sites at once. If there's a single uploader the easiest is just to ensure that the account used for uploading is affiliated with all the sites in LORIS by selecting them all in the multi-select in the user management page. (Clicking on the first one, then scrolling down and clicking the last one while holding shift should select them all in most web browsers.) - Dave On Mon, Feb 8, 2021 at 3:31 PM Sridar Narayanan, Dr. > wrote: Hi Dave, While requiring comprehensive site uploader data makes sense in the context of a prospective study where the sites are actually uploading data directly, it doesn?t make much sense when data is being uploaded centrally, either prospectively or retrospectively as in our case. Is there an option to specify a single, centralized uploader for all sites? Thanks, Sridar On Feb 8, 2021, at 2:37 PM, Dave MacFarlane > wrote: Set the "Real_name" field in the user table for that user to a value other than null (and maybe ensure no other users have null real names while you're at it.. they would have the same problem logging in). I think that any string value should fix the error that you posted. On Mon, Feb 8, 2021 at 2:33 PM Morales Pinzon, Alfredo > wrote: Hi Dave, What is your suggestion to fix this? Best, Alfredo. On Feb 8, 2021, at 1:24 PM, Dave MacFarlane > wrote: External Email - Use Caution I don't think the Real_name field should be null. It's used for the name to display in the menu at the top of LORIS. (In my local database the column is non-nullable, but it seems that the default schema allows null.. I think the fact that it allowed you to insert a null value is a minor bug.) - Dave On Mon, Feb 8, 2021 at 1:07 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev, I am getting a 500 error after login into LORIS. This is what I can see in the logs: === [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client 216.15.126.108:61071] PHP Fatal error: Uncaught TypeError: Return value of User::getFullname() must be of the type string, null returned in /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 /var/www/loris/modules/dashboard/php/module.class.inc(118): User->getFullname()\n#1 /var/www/loris/modules/dashboard/php/module.class.inc(57): LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), Object(NDB_Config), Object(User))\n#2 /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 /var/www/loris/php/libraries/Module.class.inc(275): LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), 'dashboard', '', '', 'dashboard')\n#4 /var/www/loris/php/libraries/Module.class.inc(342): Module->loadPage('dashboard')\n#5 /var/www/loris/src/Middleware/ResponseGenerator.php(50): Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 /var/www/loris/src/Middleware/AuthMiddleware.php(63): LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se in /var/www/loris/php/libraries/User.class.inc on line 236 === Perhaps it is an issue with the name of the user? I created hundreds of users for batch insertion of candidates and visits for previous versions of LORIS that required insertion of Candidates and Visits by users belonging to a given center. This is an entry in the users table without the hashed password: === *************************** 850. row *************************** ID: 850 UserID: 723-DKC-1_dataman Password: NULL Real_name: NULL First_name: NULL Last_name: NULL Degree: NULL Position_title: NULL Institution: NULL Department: NULL Address: NULL City: NULL State: NULL Zip_code: NULL Country: NULL Phone: NULL Fax: NULL Email: 723-DKC-1_dataman at ipmsa.com Privilege: 0 PSCPI: N DBAccess: Active: Y Password_hash: /REMOVED/ Password_expiry: 2035-01-01 Pending_approval: N Doc_Repo_Notifications: N language_preference: NULL active_from: NULL active_to: NULL === Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: From dave.macfarlane at mcin.ca Thu Feb 18 16:53:33 2021 From: dave.macfarlane at mcin.ca (Dave MacFarlane) Date: Thu, 18 Feb 2021 16:53:33 -0500 Subject: [Loris-dev] 500 after login In-Reply-To: References: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> <44A13251-016E-438B-8264-26F9D37BE8C1@bwh.harvard.edu> <49C01922-ACA8-401F-9151-741CC101FCB0@bwh.harvard.edu> Message-ID: Hi Alfred, It might be best to debug this interactively. Is there a time you'd be available for a Zoom call to go over your problems? - Dave On Sat, Feb 13, 2021 at 11:29 AM Morales Pinzon, Alfredo < AMORALESPINZON at bwh.harvard.edu> wrote: > Hi Dave, > > I am still having issues editing a user permissions in the front-end. The > changes I am doing for one specific user are not saved and I don?t receive > any message/error. > > Let me know what is the best way for me help on this. > > Best, > Alfredo. > > > On Feb 9, 2021, at 11:04 PM, Morales Pinzon, Alfredo < > AMORALESPINZON at BWH.HARVARD.EDU> wrote: > > Hi Dave, > > I am trying to give add more sites for a user but I?m getting the error in > the image attached. I tried in a different user and I got the same error. > This is the error log in loris-error.log: > > === > [Tue Feb 09 22:59:18.026223 2021] [php7:notice] [pid 21147] [client > 216.15.126.108:59451] PHP Notice: Undefined index: active_to in > /var/www/loris/modules/user_accounts/php/edit_user.class.inc on line 1259, > referer: > https://ipmsa-loris.bic.mni.mcgill.ca/user_accounts/edit_user/alfredouser > === > > Any ideas? > > Best, > Alfredo,. > > > > On Feb 8, 2021, at 4:02 PM, Dave MacFarlane > wrote: > > External Email - Use Caution > > Hi Sridar, > > Users in LORIS may be affiliated with multiple sites at once. If there's a > single uploader the easiest is just to ensure that the account used for > uploading is affiliated with all the sites in LORIS by selecting them all > in the multi-select in the user management page. (Clicking on the first > one, then scrolling down and clicking the last one while holding shift > should select them all in most web browsers.) > > - Dave > > On Mon, Feb 8, 2021 at 3:31 PM Sridar Narayanan, Dr. < > sridar.narayanan at mcgill.ca> wrote: > >> Hi Dave, >> >> While requiring comprehensive site uploader data makes sense in the >> context of a prospective study where the sites are actually uploading data >> directly, it doesn?t make much sense when data is being uploaded centrally, >> either prospectively or retrospectively as in our case. Is there an option >> to specify a single, centralized uploader for all sites? >> >> Thanks, >> >> Sridar >> >> >> On Feb 8, 2021, at 2:37 PM, Dave MacFarlane >> wrote: >> >> Set the "Real_name" field in the user table for that user to a value >> other than null (and maybe ensure no other users have null real names while >> you're at it.. they would have the same problem logging in). I think that >> any string value should fix the error that you posted. >> >> On Mon, Feb 8, 2021 at 2:33 PM Morales Pinzon, Alfredo < >> AMORALESPINZON at bwh.harvard.edu> wrote: >> >>> Hi Dave, >>> >>> What is your suggestion to fix this? >>> >>> Best, >>> Alfredo. >>> >>> On Feb 8, 2021, at 1:24 PM, Dave MacFarlane >>> wrote: >>> >>> External Email - Use Caution >>> >>> I don't think the Real_name field should be null. It's used for the name >>> to display in the menu at the top of LORIS. >>> >>> (In my local database the column is non-nullable, but it seems that the >>> default schema allows null.. I think the fact that it allowed you to insert >>> a null value is a minor bug.) >>> >>> - Dave >>> >>> >>> On Mon, Feb 8, 2021 at 1:07 PM Morales Pinzon, Alfredo < >>> AMORALESPINZON at bwh.harvard.edu> wrote: >>> >>>> Dear LorisDev, >>>> >>>> I am getting a 500 error after login into LORIS. This is what I can see >>>> in the logs: >>>> >>>> === >>>> [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client >>>> 216.15.126.108:61071 >>>> ] >>>> PHP Fatal error: Uncaught TypeError: Return value of User::getFullname() >>>> must be of the type string, null returned in >>>> /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 >>>> /var/www/loris/modules/dashboard/php/module.class.inc(118): >>>> User->getFullname()\n#1 >>>> /var/www/loris/modules/dashboard/php/module.class.inc(57): >>>> LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), >>>> Object(NDB_Config), Object(User))\n#2 >>>> /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): >>>> LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 >>>> /var/www/loris/php/libraries/Module.class.inc(275): >>>> LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), >>>> 'dashboard', '', '', 'dashboard')\n#4 >>>> /var/www/loris/php/libraries/Module.class.inc(342): >>>> Module->loadPage('dashboard')\n#5 >>>> /var/www/loris/src/Middleware/ResponseGenerator.php(50): >>>> Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 >>>> /var/www/loris/src/Middleware/AuthMiddleware.php(63): >>>> LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se >>>> in /var/www/loris/php/libraries/User.class.inc on line 236 >>>> === >>>> >>>> Perhaps it is an issue with the name of the user? I created hundreds of >>>> users for batch insertion of candidates and visits for previous versions of >>>> LORIS that required insertion of Candidates and Visits by users belonging >>>> to a given center. >>>> >>>> This is an entry in the users table without the hashed password: >>>> >>>> === >>>> *************************** 850. row *************************** >>>> ID: 850 >>>> UserID: 723-DKC-1_dataman >>>> Password: NULL >>>> Real_name: NULL >>>> First_name: NULL >>>> Last_name: NULL >>>> Degree: NULL >>>> Position_title: NULL >>>> Institution: NULL >>>> Department: NULL >>>> Address: NULL >>>> City: NULL >>>> State: NULL >>>> Zip_code: NULL >>>> Country: NULL >>>> Phone: NULL >>>> Fax: NULL >>>> Email: 723-DKC-1_dataman at ipmsa.com >>>> <723-DKC-1_dataman at ipmsa.com> >>>> Privilege: 0 >>>> PSCPI: N >>>> DBAccess: >>>> Active: Y >>>> Password_hash: /REMOVED/ >>>> Password_expiry: 2035-01-01 >>>> Pending_approval: N >>>> Doc_Repo_Notifications: N >>>> language_preference: NULL >>>> active_from: NULL >>>> active_to: NULL >>>> === >>>> >>>> Best, >>>> Alfredo. >>>> The information in this e-mail is intended only for the person to whom >>>> it is addressed. If you believe this e-mail was sent to you in error and >>>> the e-mail contains patient information, please contact the Mass General >>>> Brigham Compliance HelpLine at >>>> http://www.massgeneralbrigham.org/complianceline >>>> >>>> . If the e-mail was sent to you in error but does not contain patient >>>> information, please contact the sender and properly dispose of the e-mail. >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> >>> >>> The information in this e-mail is intended only for the person to whom >>> it is addressed. If you believe this e-mail was sent to you in error and >>> the e-mail contains patient information, please contact the Mass General >>> Brigham Compliance HelpLine at >>> http://www.massgeneralbrigham.org/complianceline >>> >>> . If the e-mail was sent to you in error but does not contain patient >>> information, please contact the sender and properly dispose of the e-mail. >>> >> >> > > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent > to you in error but does not contain patient information, please contact > the sender and properly dispose of the e-mail. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From AMORALESPINZON at BWH.HARVARD.EDU Fri Feb 19 08:38:32 2021 From: AMORALESPINZON at BWH.HARVARD.EDU (Morales Pinzon, Alfredo) Date: Fri, 19 Feb 2021 13:38:32 +0000 Subject: [Loris-dev] 500 after login In-Reply-To: References: <8F46C74A-55E7-48AE-B38F-1DEF9936251D@bwh.harvard.edu> <44A13251-016E-438B-8264-26F9D37BE8C1@bwh.harvard.edu> <49C01922-ACA8-401F-9151-741CC101FCB0@bwh.harvard.edu> Message-ID: <2357E537-D3C3-4812-99C5-763BA5F2EB83@bwh.harvard.edu> Hi Dave, Thank you for your answer. Any time today after 11am, let me know. Best, Alfredo. On Feb 18, 2021, at 4:53 PM, Dave MacFarlane > wrote: External Email - Use Caution Hi Alfred, It might be best to debug this interactively. Is there a time you'd be available for a Zoom call to go over your problems? - Dave On Sat, Feb 13, 2021 at 11:29 AM Morales Pinzon, Alfredo > wrote: Hi Dave, I am still having issues editing a user permissions in the front-end. The changes I am doing for one specific user are not saved and I don?t receive any message/error. Let me know what is the best way for me help on this. Best, Alfredo. On Feb 9, 2021, at 11:04 PM, Morales Pinzon, Alfredo > wrote: Hi Dave, I am trying to give add more sites for a user but I?m getting the error in the image attached. I tried in a different user and I got the same error. This is the error log in loris-error.log: === [Tue Feb 09 22:59:18.026223 2021] [php7:notice] [pid 21147] [client 216.15.126.108:59451] PHP Notice: Undefined index: active_to in /var/www/loris/modules/user_accounts/php/edit_user.class.inc on line 1259, referer: https://ipmsa-loris.bic.mni.mcgill.ca/user_accounts/edit_user/alfredouser === Any ideas? Best, Alfredo,. On Feb 8, 2021, at 4:02 PM, Dave MacFarlane > wrote: External Email - Use Caution Hi Sridar, Users in LORIS may be affiliated with multiple sites at once. If there's a single uploader the easiest is just to ensure that the account used for uploading is affiliated with all the sites in LORIS by selecting them all in the multi-select in the user management page. (Clicking on the first one, then scrolling down and clicking the last one while holding shift should select them all in most web browsers.) - Dave On Mon, Feb 8, 2021 at 3:31 PM Sridar Narayanan, Dr. > wrote: Hi Dave, While requiring comprehensive site uploader data makes sense in the context of a prospective study where the sites are actually uploading data directly, it doesn?t make much sense when data is being uploaded centrally, either prospectively or retrospectively as in our case. Is there an option to specify a single, centralized uploader for all sites? Thanks, Sridar On Feb 8, 2021, at 2:37 PM, Dave MacFarlane > wrote: Set the "Real_name" field in the user table for that user to a value other than null (and maybe ensure no other users have null real names while you're at it.. they would have the same problem logging in). I think that any string value should fix the error that you posted. On Mon, Feb 8, 2021 at 2:33 PM Morales Pinzon, Alfredo > wrote: Hi Dave, What is your suggestion to fix this? Best, Alfredo. On Feb 8, 2021, at 1:24 PM, Dave MacFarlane > wrote: External Email - Use Caution I don't think the Real_name field should be null. It's used for the name to display in the menu at the top of LORIS. (In my local database the column is non-nullable, but it seems that the default schema allows null.. I think the fact that it allowed you to insert a null value is a minor bug.) - Dave On Mon, Feb 8, 2021 at 1:07 PM Morales Pinzon, Alfredo > wrote: Dear LorisDev, I am getting a 500 error after login into LORIS. This is what I can see in the logs: === [Mon Feb 08 12:57:54.559522 2021] [php7:error] [pid 8074] [client 216.15.126.108:61071] PHP Fatal error: Uncaught TypeError: Return value of User::getFullname() must be of the type string, null returned in /var/www/loris/php/libraries/User.class.inc:236\nStack trace:\n#0 /var/www/loris/modules/dashboard/php/module.class.inc(118): User->getFullname()\n#1 /var/www/loris/modules/dashboard/php/module.class.inc(57): LORIS\\dashboard\\Module->_getWelcomeWidget(Object(Database), Object(NDB_Config), Object(User))\n#2 /var/www/loris/modules/dashboard/php/dashboard.class.inc(75): LORIS\\dashboard\\Module->getWidgets('dashboard', Object(User), Array)\n#3 /var/www/loris/php/libraries/Module.class.inc(275): LORIS\\dashboard\\Dashboard->__construct(Object(LORIS\\dashboard\\Module), 'dashboard', '', '', 'dashboard')\n#4 /var/www/loris/php/libraries/Module.class.inc(342): Module->loadPage('dashboard')\n#5 /var/www/loris/src/Middleware/ResponseGenerator.php(50): Module->handle(Object(Laminas\\Diactoros\\ServerRequest))\n#6 /var/www/loris/src/Middleware/AuthMiddleware.php(63): LORIS\\Middleware\\ResponseGenerator->process(Object(Laminas\\Diactoros\\Se in /var/www/loris/php/libraries/User.class.inc on line 236 === Perhaps it is an issue with the name of the user? I created hundreds of users for batch insertion of candidates and visits for previous versions of LORIS that required insertion of Candidates and Visits by users belonging to a given center. This is an entry in the users table without the hashed password: === *************************** 850. row *************************** ID: 850 UserID: 723-DKC-1_dataman Password: NULL Real_name: NULL First_name: NULL Last_name: NULL Degree: NULL Position_title: NULL Institution: NULL Department: NULL Address: NULL City: NULL State: NULL Zip_code: NULL Country: NULL Phone: NULL Fax: NULL Email: 723-DKC-1_dataman at ipmsa.com Privilege: 0 PSCPI: N DBAccess: Active: Y Password_hash: /REMOVED/ Password_expiry: 2035-01-01 Pending_approval: N Doc_Repo_Notifications: N language_preference: NULL active_from: NULL active_to: NULL === Best, Alfredo. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. _______________________________________________ Loris-dev mailing list Loris-dev at bic.mni.mcgill.ca https://mailman.bic.mni.mcgill.ca/mailman/listinfo/loris-dev The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -------------- next part -------------- An HTML attachment was scrubbed... URL: