From karine.thorn at criugm.qc.ca Mon Nov 5 14:26:40 2018 From: karine.thorn at criugm.qc.ca (Karine Thorn) Date: Mon, 5 Nov 2018 14:26:40 -0500 Subject: [Loris-dev] Request from UGM - MRI synoptic report notifications Message-ID: To whom it may concerns, Could you please do the following changes to the emails addresses that you have for our site (UGM) to inform the concerned team members of the availability of new MRI's synoptic reports ? Please withdraw the following email " joannie1984 at hotmail.com". Add the following emails : joannie.van.houtte.st-gelais at criugm.qc.ca isabelle.bureau at criugm.qc.ca I would like a confirmation that this will be done, Thanks and best regards, Karine Thorn, inf. M. Sc. Professionnelle de recherche Centre de recherche de l?Institut universitaire de g?riatrie de Montr?al CIUSSS du Centre-Sud-de-l??le-de-Montr?al 4565 Queen-Mary Montr?al (Qu?bec) H3W 1W5 T?l?phone :514-340-3540 Poste 3169 ou 3253 Karine.thorn at criugm.qc.ca -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image001.jpg Type: image/jpeg Size: 588395 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: image002.jpg Type: image/jpeg Size: 3240 bytes Desc: not available URL: From aliaarefi1997 at gmail.com Wed Nov 14 07:24:41 2018 From: aliaarefi1997 at gmail.com (Ali Aarefi) Date: Wed, 14 Nov 2018 15:54:41 +0330 Subject: [Loris-dev] one-step insertion pipeline problem Message-ID: *Hello,Dear LORIS dev. team,After running the one-step insertion pipeline on my local LORIS, I've faced a problem.* (executed command : * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* *In my local website > imaging menu tab > image uploader > upload , the detailed log for those uploades shows :* "MRI pipeline not yet executed for this upload." *And the log_batch_imageuploader.txt contains :* Can't locate NeuroDB/DBI.pm in @INC (you may need to install the NeuroDB::DBI module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at ./batch_uploads_imageuploader line 53. BEGIN failed--compilation aborted at ./batch_uploads_imageuploader line 53. *I couldn't find installation instruction for** NeuroDB::DBI** module* *Could anyone help me with this?Best Regards.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From zia.mohades at gmail.com Wed Nov 14 10:31:14 2018 From: zia.mohades at gmail.com (zia mohades) Date: Wed, 14 Nov 2018 10:31:14 -0500 Subject: [Loris-dev] one-step insertion pipeline problem In-Reply-To: References: Message-ID: Hi Ali, Before we start troubleshooting, Please let us know if you have followed Mouna's instructions (detailed below - as per her last email to you). Thank you ---------------------------------------------------------------------------------------------------------------------------------------- *From:* Mouna Safi-Harab *Sent:* Tuesday, August 14, 2018 12:47 PM *To:* Ali Aarefi *Subject:* Re: [Loris-dev] Data insertion problem Hi Ali, I am going to propose a few steps you can look into to try to debug further. Let me know what you get based on the recommendations below. - Try running the command 'source environment' (without the single quotations), BEFORE running the uploadNeuroDB/imaging_upload_file.plcommand. Then type 'echo $PATH' (without single quotations) and let me know what it gives you. In parallel, can you please send me what is inside your 'environment' file which is located in /data/%YOURProject/bin/mri/ directory? - Make sure that the prod file is indeed present in the dicom-archive/.loris_mri/ directory, and is accessible by lorisadmin (or whichever user running the imaging_upload_file.pl). Then open it and make sure there is a line in there like that: @db = ('database_name','database_user', 'database_password', 'database_host'); and make sure all these database information on the line above the way you have them in your prod file are correct (perhaps you can try to connect directly to the mysql host from the command line to make sure this works outside of the scripts). Let me know! ? ? ? On Wed, Nov 14, 2018 at 7:25 AM Ali Aarefi wrote: > > > > > *Hello,Dear LORIS dev. team,After running the one-step insertion pipeline > on my local LORIS, I've faced a problem.* > (executed command : > * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile prod > < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* > > *In my local website > imaging menu tab > image uploader > upload , the > detailed log for those uploades shows :* > "MRI pipeline not yet executed for this upload." > > *And the log_batch_imageuploader.txt contains :* > Can't locate NeuroDB/DBI.pm in @INC (you may need to install the > NeuroDB::DBI module) (@INC contains: /etc/perl > /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 > /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 > /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 > /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at > ./batch_uploads_imageuploader line 53. > BEGIN failed--compilation aborted at ./batch_uploads_imageuploader line 53. > > *I couldn't find installation instruction for** NeuroDB::DBI** module* > > > *Could anyone help me with this?Best Regards.* > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From zia.mohades at gmail.com Wed Nov 14 11:43:04 2018 From: zia.mohades at gmail.com (zia mohades) Date: Wed, 14 Nov 2018 11:43:04 -0500 Subject: [Loris-dev] one-step insertion pipeline problem In-Reply-To: References: Message-ID: Hi Ali, My pleasure. I am glad to hear that your issue is now resolved. Best regards, ? On Wed, Nov 14, 2018 at 11:37 AM Ali Aarefi wrote: > > > > > *Hi Zia,Thanks for your quick response.I should note that the problem was > solved and I could insert a scan to database manually(with > imaging_uplaod_file.pl ), but now I'm > writing a script to use APIs to automate candidate/VisitLabel creation and > data insertion.And also I was answered that mail. The results of Mouna's > instructions are :* > *$ echo $PATH* > > /opt/minc/1.9.16/bin:/opt/minc/1.9.16/pipeline:/opt/minc/1.9.16/bin:/data/last/bin/mri:/data/last/bin/mri/uploadNeuroDB:/data/last/bin/mri/uploadNeuroDB/bin:/data/last/bin/mri/dicom-archive:/opt/minc/1.9.16/bin:/opt/minc/1.9.16/pipeline:/opt/minc/1.9.16/bin:/data/last/bin/mri:/data/last/bin/mri/uploadNeuroDB:/data/last/bin/mri/uploadNeuroDB/bin:/data/last/bin/mri/dicom-archive:/home/ali/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/opt/JetBrains/clion-2018.1.5/bin/:/opt/JetBrains/GoLand-2018.1.5/bin/:/opt/JetBrains/idea-IU-181.5281.24/bin/:/opt/JetBrains/pycharm-2018.1.4/bin/:/opt/JetBrains/WebStorm-181.5281.31/bin/ > > *$ cat environment ( I've added "source /data/last/bin/mri/environment" to > the .bashrc file)* > export > PATH=/opt/minc/1.9.16/bin:/data/last/bin/mri:/data/last/bin/mri/uploadNeuroDB:/data/last/bin/mri/uploadNeuroDB/bin:/data/last/bin/mri/dicom-archive:$PATH > export PERL5LIB=/data/last/bin/mri/uploadNeuroDB:$PERL5LIB > export TMPDIR=/tmp > export LORIS_CONFIG=/data/last/bin/mri/dicom-archive > source /opt/minc/1.9.16/minc-toolkit-config.sh > umask 0002 > > *The prod file is present and has the following file permission(readable > for all users) :* "-rw-r--r-- 1 ali www-data 5.4K Sep 12 18:50 prod" > *and there is a line in my prod file like "*@db = > ('database_name','database_user', 'database_password', 'database_host');" *that > the variables replaced with proper values and I accessed directly to > database with those correct values.* > > > *Thank you.- Ali* > > On Wed, Nov 14, 2018 at 7:01 PM zia mohades wrote: > >> Hi Ali, >> >> Before we start troubleshooting, Please let us know if you have followed >> Mouna's instructions (detailed below - as per her last email to you). >> >> Thank you >> >> >> >> ---------------------------------------------------------------------------------------------------------------------------------------- >> *From:* Mouna Safi-Harab >> *Sent:* Tuesday, August 14, 2018 12:47 PM >> *To:* Ali Aarefi >> *Subject:* Re: [Loris-dev] Data insertion problem >> >> Hi Ali, >> >> >> I am going to propose a few steps you can look into to try to debug >> further. Let me know what you get based on the recommendations below. >> >> >> - Try running the command 'source environment' (without the single quotations), >> BEFORE running the uploadNeuroDB/imaging_upload_file.plcommand. Then >> type 'echo $PATH' (without single quotations) and let me know what it gives >> you. In parallel, can you please send me what is inside your >> 'environment' file which is located in /data/%YOURProject/bin/mri/ >> directory? >> >> - Make sure that the prod file is indeed present in the >> dicom-archive/.loris_mri/ directory, and is accessible by lorisadmin (or >> whichever user running the imaging_upload_file.pl). Then open it and >> make sure there is a line in there like that: >> >> @db = ('database_name','database_user', 'database_password', >> 'database_host'); >> >> and make sure all these database information on the line above the way >> you have them in your prod file are correct (perhaps you can try to connect >> directly to the mysql host from the command line to make sure this works >> outside of the scripts). >> >> >> Let me know! >> >> >> >> ? >> ? >> ? >> >> On Wed, Nov 14, 2018 at 7:25 AM Ali Aarefi >> wrote: >> >>> >>> >>> >>> >>> *Hello,Dear LORIS dev. team,After running the one-step insertion >>> pipeline on my local LORIS, I've faced a problem.* >>> (executed command : >>> * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile prod >>> < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* >>> >>> *In my local website > imaging menu tab > image uploader > upload , the >>> detailed log for those uploades shows :* >>> "MRI pipeline not yet executed for this upload." >>> >>> *And the log_batch_imageuploader.txt contains :* >>> Can't locate NeuroDB/DBI.pm in @INC (you may need to install the >>> NeuroDB::DBI module) (@INC contains: /etc/perl >>> /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 >>> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 >>> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 >>> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at >>> ./batch_uploads_imageuploader line 53. >>> BEGIN failed--compilation aborted at ./batch_uploads_imageuploader line >>> 53. >>> >>> *I couldn't find installation instruction for** NeuroDB::DBI** module* >>> >>> >>> *Could anyone help me with this?Best Regards.* >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: From aliaarefi1997 at gmail.com Wed Nov 14 12:34:10 2018 From: aliaarefi1997 at gmail.com (Ali Aarefi) Date: Wed, 14 Nov 2018 21:04:10 +0330 Subject: [Loris-dev] one-step insertion pipeline problem Message-ID: *Hello,Dear LORIS dev. team,After running the one-step insertion pipeline on my local LORIS, I've faced a problem. (Can't locate NeuroDB/DBI.pm in @INC ...)* *Could anyone help me in inserting a group of data into loris based on following information?* (executed command : * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* *In my local website > imaging menu tab > image uploader > upload , the detailed log for those uploades shows :* "MRI pipeline not yet executed for this upload." *And the log_batch_imageuploader.txt contains :* Can't locate NeuroDB/DBI.pm in @INC (you may need to install the NeuroDB::DBI module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at ./batch_uploads_imageuploader line 53. BEGIN failed--compilation aborted at ./batch_uploads_imageuploader line 53. *I couldn't find installation instruction for** NeuroDB::DBI** module.* *Best Regards.* -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Wed Nov 14 14:47:45 2018 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Wed, 14 Nov 2018 14:47:45 -0500 Subject: [Loris-dev] one-step insertion pipeline problem In-Reply-To: References: Message-ID: Hello, Have you sourced the environment file before trying to run the script? This file always need to be source before running the insertion pipeline. Also, make sure that in the environment file all instances of %PROJECT% have been replaced by your project's name (the one in the /data/ directory). Let me know how it goes, C?cile On Wed, Nov 14, 2018 at 12:34 PM Ali Aarefi wrote: > > > > *Hello,Dear LORIS dev. team,After running the one-step insertion pipeline > on my local LORIS, I've faced a problem. (Can't locate NeuroDB/DBI.pm in > @INC ...)* > > > *Could anyone help me in inserting a group of data into loris based on > following information?* > (executed command : > * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile > prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* > > *In my local website > imaging menu tab > image uploader > upload , the > detailed log for those uploades shows :* > "MRI pipeline not yet executed for this upload." > > *And the log_batch_imageuploader.txt contains :* > Can't locate NeuroDB/DBI.pm in @INC (you may need to install the > NeuroDB::DBI module) (@INC contains: /etc/perl > /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 > /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 > /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 > /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at > ./batch_uploads_imageuploader line 53. > BEGIN failed--compilation aborted at ./batch_uploads_imageuploader line 53. > > *I couldn't find installation instruction for** NeuroDB::DBI** module.* > > *Best Regards.* > _______________________________________________ > Loris-dev mailing list > Loris-dev at bic.mni.mcgill.ca > http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Wed Nov 14 15:02:01 2018 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Wed, 14 Nov 2018 15:02:01 -0500 Subject: [Loris-dev] one-step insertion pipeline problem In-Reply-To: References: Message-ID: Hi again, It seems you were able to run the script imaging_upload_file.pl manually but still have problems running batch_upload_imageuploader. My guess is that the variable $PERL5LIB is not set properly in your environment file so Perl cannot find the LORIS libraries that are under the NeuroDB folder within uploadNeuroDB (imaging_upload_file.pl can since it is located directly in the uploadNeuroDB folder). Here is what you would need to do to fix this: 1) open you environment file and add the following statement if it is not already there (replace %PROJECT% by your project folder name): export PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:$PERL5LIB 2) source the environment file again 3) rerun the pipeline >From now on, all the scripts will be able to access all the LORIS perl libraries under uploadNeuroDB (including NeuroDB:DBI) Hope this helps, C?cile On Wed, Nov 14, 2018 at 2:47 PM Cecile Madjar wrote: > Hello, > > Have you sourced the environment file before trying to run the script? > This file always need to be source before running the insertion pipeline. > > Also, make sure that in the environment file all instances of %PROJECT% > have been replaced by your project's name (the one in the /data/ directory). > > Let me know how it goes, > > C?cile > > > On Wed, Nov 14, 2018 at 12:34 PM Ali Aarefi > wrote: > >> >> >> >> *Hello,Dear LORIS dev. team,After running the one-step insertion pipeline >> on my local LORIS, I've faced a problem. (Can't locate NeuroDB/DBI.pm in >> @INC ...)* >> >> >> *Could anyone help me in inserting a group of data into loris based on >> following information?* >> (executed command : >> * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile >> prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* >> >> *In my local website > imaging menu tab > image uploader > upload , the >> detailed log for those uploades shows :* >> "MRI pipeline not yet executed for this upload." >> >> *And the log_batch_imageuploader.txt contains :* >> Can't locate NeuroDB/DBI.pm in @INC (you may need to install the >> NeuroDB::DBI module) (@INC contains: /etc/perl >> /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 >> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 >> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 >> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at >> ./batch_uploads_imageuploader line 53. >> BEGIN failed--compilation aborted at ./batch_uploads_imageuploader line >> 53. >> >> *I couldn't find installation instruction for** NeuroDB::DBI** module.* >> >> *Best Regards.* >> _______________________________________________ >> Loris-dev mailing list >> Loris-dev at bic.mni.mcgill.ca >> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cecile.madjar at mcin.ca Thu Nov 15 08:50:06 2018 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Thu, 15 Nov 2018 08:50:06 -0500 Subject: [Loris-dev] one-step insertion pipeline problem In-Reply-To: References: Message-ID: Hi Ali, That is strange, it should find the library then. Could you run perl -V and send me the output of that command? (before and after sourcing the environment file) Thanks! C?cile On Thu, Nov 15, 2018 at 8:36 AM Ali Aarefi wrote: > > > > *Hi,Yes, I've sourced the environment file before running > batch_upload_imageuploader script, and there is no remained %PROJECT% in > environment file.The environment file included the PERL5LIB setter line > with correct replacement of %PROJECT%.* > > > > > *The environment file content is attached to this email(Screenshot).But > still the problem is unsolved.Thanks,- Ali* > > On Wed, Nov 14, 2018 at 11:32 PM Cecile Madjar > wrote: > >> Hi again, >> >> It seems you were able to run the script imaging_upload_file.pl manually >> but still have problems running batch_upload_imageuploader. >> >> My guess is that the variable $PERL5LIB is not set properly in your >> environment file so Perl cannot find the LORIS libraries that are under the >> NeuroDB folder within uploadNeuroDB (imaging_upload_file.pl can since it >> is located directly in the uploadNeuroDB folder). >> >> Here is what you would need to do to fix this: >> 1) open you environment file and add the following statement if it is not >> already there (replace %PROJECT% by your project folder name): >> >> export PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:$PERL5LIB >> 2) source the environment file again >> 3) rerun the pipeline >> >> From now on, all the scripts will be able to access all the LORIS perl >> libraries under uploadNeuroDB (including NeuroDB:DBI) >> >> Hope this helps, >> >> C?cile >> >> >> On Wed, Nov 14, 2018 at 2:47 PM Cecile Madjar >> wrote: >> >>> Hello, >>> >>> Have you sourced the environment file before trying to run the script? >>> This file always need to be source before running the insertion pipeline. >>> >>> Also, make sure that in the environment file all instances of %PROJECT% >>> have been replaced by your project's name (the one in the /data/ directory). >>> >>> Let me know how it goes, >>> >>> C?cile >>> >>> >>> On Wed, Nov 14, 2018 at 12:34 PM Ali Aarefi >>> wrote: >>> >>>> >>>> >>>> >>>> *Hello,Dear LORIS dev. team,After running the one-step insertion >>>> pipeline on my local LORIS, I've faced a problem. (Can't locate >>>> NeuroDB/DBI.pm in @INC ...)* >>>> >>>> >>>> *Could anyone help me in inserting a group of data into loris based on >>>> following information?* >>>> (executed command : >>>> * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile >>>> prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* >>>> >>>> *In my local website > imaging menu tab > image uploader > upload , the >>>> detailed log for those uploades shows :* >>>> "MRI pipeline not yet executed for this upload." >>>> >>>> *And the log_batch_imageuploader.txt contains :* >>>> Can't locate NeuroDB/DBI.pm in @INC (you may need to install the >>>> NeuroDB::DBI module) (@INC contains: /etc/perl >>>> /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 >>>> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 >>>> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 >>>> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at >>>> ./batch_uploads_imageuploader line 53. >>>> BEGIN failed--compilation aborted at ./batch_uploads_imageuploader line >>>> 53. >>>> >>>> *I couldn't find installation instruction for** NeuroDB::DBI** module.* >>>> >>>> *Best Regards.* >>>> _______________________________________________ >>>> Loris-dev mailing list >>>> Loris-dev at bic.mni.mcgill.ca >>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>> >>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From aliaarefi1997 at gmail.com Thu Nov 15 08:36:05 2018 From: aliaarefi1997 at gmail.com (Ali Aarefi) Date: Thu, 15 Nov 2018 17:06:05 +0330 Subject: [Loris-dev] one-step insertion pipeline problem In-Reply-To: References: Message-ID: *Hi,Yes, I've sourced the environment file before running batch_upload_imageuploader script, and there is no remained %PROJECT% in environment file.The environment file included the PERL5LIB setter line with correct replacement of %PROJECT%.* *The environment file content is attached to this email(Screenshot).But still the problem is unsolved.Thanks,- Ali* On Wed, Nov 14, 2018 at 11:32 PM Cecile Madjar wrote: > Hi again, > > It seems you were able to run the script imaging_upload_file.pl manually > but still have problems running batch_upload_imageuploader. > > My guess is that the variable $PERL5LIB is not set properly in your > environment file so Perl cannot find the LORIS libraries that are under the > NeuroDB folder within uploadNeuroDB (imaging_upload_file.pl can since it > is located directly in the uploadNeuroDB folder). > > Here is what you would need to do to fix this: > 1) open you environment file and add the following statement if it is not > already there (replace %PROJECT% by your project folder name): > > export PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:$PERL5LIB > 2) source the environment file again > 3) rerun the pipeline > > From now on, all the scripts will be able to access all the LORIS perl > libraries under uploadNeuroDB (including NeuroDB:DBI) > > Hope this helps, > > C?cile > > > On Wed, Nov 14, 2018 at 2:47 PM Cecile Madjar > wrote: > >> Hello, >> >> Have you sourced the environment file before trying to run the script? >> This file always need to be source before running the insertion pipeline. >> >> Also, make sure that in the environment file all instances of %PROJECT% >> have been replaced by your project's name (the one in the /data/ directory). >> >> Let me know how it goes, >> >> C?cile >> >> >> On Wed, Nov 14, 2018 at 12:34 PM Ali Aarefi >> wrote: >> >>> >>> >>> >>> *Hello,Dear LORIS dev. team,After running the one-step insertion >>> pipeline on my local LORIS, I've faced a problem. (Can't locate >>> NeuroDB/DBI.pm in @INC ...)* >>> >>> >>> *Could anyone help me in inserting a group of data into loris based on >>> following information?* >>> (executed command : >>> * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile >>> prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* >>> >>> *In my local website > imaging menu tab > image uploader > upload , the >>> detailed log for those uploades shows :* >>> "MRI pipeline not yet executed for this upload." >>> >>> *And the log_batch_imageuploader.txt contains :* >>> Can't locate NeuroDB/DBI.pm in @INC (you may need to install the >>> NeuroDB::DBI module) (@INC contains: /etc/perl >>> /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 >>> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 >>> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 >>> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at >>> ./batch_uploads_imageuploader line 53. >>> BEGIN failed--compilation aborted at ./batch_uploads_imageuploader line >>> 53. >>> >>> *I couldn't find installation instruction for** NeuroDB::DBI** module.* >>> >>> *Best Regards.* >>> _______________________________________________ >>> Loris-dev mailing list >>> Loris-dev at bic.mni.mcgill.ca >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>> >> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2018-11-15 17-01-31.png Type: image/png Size: 181761 bytes Desc: not available URL: From aliaarefi1997 at gmail.com Mon Nov 19 14:43:21 2018 From: aliaarefi1997 at gmail.com (Ali Aarefi) Date: Mon, 19 Nov 2018 23:13:21 +0330 Subject: [Loris-dev] one-step insertion pipeline problem In-Reply-To: References: Message-ID: Hi C?cile, Thank you for your help. The output of that command (after sourcing the environment file) attached to this email as a text file. The only difference between two outputs of "perl -V" command (before and after sourcing environment file) attached to this email as an image. Please note that : In the attached image : left-side text is output of command after sourcing env. file and right-side text is output of command before sourcing env. file. Best Regards. -Ali On Thu, Nov 15, 2018 at 5:20 PM Cecile Madjar wrote: > Hi Ali, > > That is strange, it should find the library then. Could you run perl -V > and send me the output of that command? (before and after sourcing the > environment file) > > Thanks! > > C?cile > > On Thu, Nov 15, 2018 at 8:36 AM Ali Aarefi > wrote: > >> >> >> >> *Hi,Yes, I've sourced the environment file before running >> batch_upload_imageuploader script, and there is no remained %PROJECT% in >> environment file.The environment file included the PERL5LIB setter line >> with correct replacement of %PROJECT%.* >> >> >> >> >> *The environment file content is attached to this email(Screenshot).But >> still the problem is unsolved.Thanks,- Ali* >> >> On Wed, Nov 14, 2018 at 11:32 PM Cecile Madjar >> wrote: >> >>> Hi again, >>> >>> It seems you were able to run the script imaging_upload_file.pl >>> manually but still have problems running batch_upload_imageuploader. >>> >>> My guess is that the variable $PERL5LIB is not set properly in your >>> environment file so Perl cannot find the LORIS libraries that are under the >>> NeuroDB folder within uploadNeuroDB (imaging_upload_file.pl can since >>> it is located directly in the uploadNeuroDB folder). >>> >>> Here is what you would need to do to fix this: >>> 1) open you environment file and add the following statement if it is >>> not already there (replace %PROJECT% by your project folder name): >>> >>> export PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:$PERL5LIB >>> 2) source the environment file again >>> 3) rerun the pipeline >>> >>> From now on, all the scripts will be able to access all the LORIS perl >>> libraries under uploadNeuroDB (including NeuroDB:DBI) >>> >>> Hope this helps, >>> >>> C?cile >>> >>> >>> On Wed, Nov 14, 2018 at 2:47 PM Cecile Madjar >>> wrote: >>> >>>> Hello, >>>> >>>> Have you sourced the environment file before trying to run the script? >>>> This file always need to be source before running the insertion pipeline. >>>> >>>> Also, make sure that in the environment file all instances of %PROJECT% >>>> have been replaced by your project's name (the one in the /data/ directory). >>>> >>>> Let me know how it goes, >>>> >>>> C?cile >>>> >>>> >>>> On Wed, Nov 14, 2018 at 12:34 PM Ali Aarefi >>>> wrote: >>>> >>>>> >>>>> >>>>> >>>>> *Hello,Dear LORIS dev. team,After running the one-step insertion >>>>> pipeline on my local LORIS, I've faced a problem. (Can't locate >>>>> NeuroDB/DBI.pm in @INC ...)* >>>>> >>>>> >>>>> *Could anyone help me in inserting a group of data into loris based on >>>>> following information?* >>>>> (executed command : >>>>> * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile >>>>> prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* >>>>> >>>>> *In my local website > imaging menu tab > image uploader > upload , >>>>> the detailed log for those uploades shows :* >>>>> "MRI pipeline not yet executed for this upload." >>>>> >>>>> *And the log_batch_imageuploader.txt contains :* >>>>> Can't locate NeuroDB/DBI.pm in @INC (you may need to install the >>>>> NeuroDB::DBI module) (@INC contains: /etc/perl >>>>> /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 >>>>> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 >>>>> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 >>>>> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at >>>>> ./batch_uploads_imageuploader line 53. >>>>> BEGIN failed--compilation aborted at ./batch_uploads_imageuploader >>>>> line 53. >>>>> >>>>> *I couldn't find installation instruction for** NeuroDB::DBI* >>>>> * module.* >>>>> >>>>> *Best Regards.* >>>>> _______________________________________________ >>>>> Loris-dev mailing list >>>>> Loris-dev at bic.mni.mcgill.ca >>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>> >>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: From aliaarefi1997 at gmail.com Mon Nov 19 19:05:09 2018 From: aliaarefi1997 at gmail.com (Ali Aarefi) Date: Tue, 20 Nov 2018 03:35:09 +0330 Subject: [Loris-dev] one-step insertion pipeline problem In-Reply-To: References: Message-ID: Hi, Sorry about that. The output of that command (after sourcing the environment file) attached to this email as a text file. The only difference between two outputs of "perl -V" command (before and after sourcing environment file) attached to this email as an image. Please note that : In the attached image : left-side text is output of command after sourcing env. file and right-side text is output of command before sourcing env. file. Ali [image: Screenshot from 2018-11-19 17-00-32.png] On Mon, Nov 19, 2018 at 11:47 PM Cecile Madjar wrote: > Hi, > > I did not see any attachment to your email. Could you send it again? > > Thank you, > > C?cile > > On Mon, Nov 19, 2018 at 2:43 PM Ali Aarefi > wrote: > >> Hi C?cile, >> >> Thank you for your help. >> The output of that command (after sourcing the environment file) attached >> to this email as a text file. >> The only difference between two outputs of "perl -V" command (before and >> after sourcing environment file) attached to this email as an image. >> Please note that : In the attached image : left-side text is output of >> command after sourcing env. file and right-side text is output of command >> before sourcing env. file. >> >> Best Regards. >> -Ali >> >> On Thu, Nov 15, 2018 at 5:20 PM Cecile Madjar >> wrote: >> >>> Hi Ali, >>> >>> That is strange, it should find the library then. Could you run perl -V >>> and send me the output of that command? (before and after sourcing the >>> environment file) >>> >>> Thanks! >>> >>> C?cile >>> >>> On Thu, Nov 15, 2018 at 8:36 AM Ali Aarefi >>> wrote: >>> >>>> >>>> >>>> >>>> *Hi,Yes, I've sourced the environment file before running >>>> batch_upload_imageuploader script, and there is no remained %PROJECT% in >>>> environment file.The environment file included the PERL5LIB setter line >>>> with correct replacement of %PROJECT%.* >>>> >>>> >>>> >>>> >>>> *The environment file content is attached to this email(Screenshot).But >>>> still the problem is unsolved.Thanks,- Ali* >>>> >>>> On Wed, Nov 14, 2018 at 11:32 PM Cecile Madjar >>>> wrote: >>>> >>>>> Hi again, >>>>> >>>>> It seems you were able to run the script imaging_upload_file.pl >>>>> manually but still have problems running batch_upload_imageuploader. >>>>> >>>>> My guess is that the variable $PERL5LIB is not set properly in your >>>>> environment file so Perl cannot find the LORIS libraries that are under the >>>>> NeuroDB folder within uploadNeuroDB (imaging_upload_file.pl can since >>>>> it is located directly in the uploadNeuroDB folder). >>>>> >>>>> Here is what you would need to do to fix this: >>>>> 1) open you environment file and add the following statement if it is >>>>> not already there (replace %PROJECT% by your project folder name): >>>>> >>>>> export PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:$PERL5LIB >>>>> 2) source the environment file again >>>>> 3) rerun the pipeline >>>>> >>>>> From now on, all the scripts will be able to access all the LORIS perl >>>>> libraries under uploadNeuroDB (including NeuroDB:DBI) >>>>> >>>>> Hope this helps, >>>>> >>>>> C?cile >>>>> >>>>> >>>>> On Wed, Nov 14, 2018 at 2:47 PM Cecile Madjar >>>>> wrote: >>>>> >>>>>> Hello, >>>>>> >>>>>> Have you sourced the environment file before trying to run the >>>>>> script? This file always need to be source before running the insertion >>>>>> pipeline. >>>>>> >>>>>> Also, make sure that in the environment file all instances of >>>>>> %PROJECT% have been replaced by your project's name (the one in the /data/ >>>>>> directory). >>>>>> >>>>>> Let me know how it goes, >>>>>> >>>>>> C?cile >>>>>> >>>>>> >>>>>> On Wed, Nov 14, 2018 at 12:34 PM Ali Aarefi >>>>>> wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> *Hello,Dear LORIS dev. team,After running the one-step insertion >>>>>>> pipeline on my local LORIS, I've faced a problem. (Can't locate >>>>>>> NeuroDB/DBI.pm in @INC ...)* >>>>>>> >>>>>>> >>>>>>> *Could anyone help me in inserting a group of data into loris based >>>>>>> on following information?* >>>>>>> (executed command : >>>>>>> * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile >>>>>>> prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* >>>>>>> >>>>>>> *In my local website > imaging menu tab > image uploader > upload , >>>>>>> the detailed log for those uploades shows :* >>>>>>> "MRI pipeline not yet executed for this upload." >>>>>>> >>>>>>> *And the log_batch_imageuploader.txt contains :* >>>>>>> Can't locate NeuroDB/DBI.pm in @INC (you may need to install the >>>>>>> NeuroDB::DBI module) (@INC contains: /etc/perl >>>>>>> /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 >>>>>>> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 >>>>>>> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 >>>>>>> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at >>>>>>> ./batch_uploads_imageuploader line 53. >>>>>>> BEGIN failed--compilation aborted at ./batch_uploads_imageuploader >>>>>>> line 53. >>>>>>> >>>>>>> *I couldn't find installation instruction for** NeuroDB::DBI* >>>>>>> * module.* >>>>>>> >>>>>>> *Best Regards.* >>>>>>> _______________________________________________ >>>>>>> Loris-dev mailing list >>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>> >>>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2018-11-19 17-00-32.png Type: image/png Size: 192272 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: commandOutput Type: application/octet-stream Size: 11502 bytes Desc: not available URL: From cecile.madjar at mcin.ca Tue Nov 20 09:54:50 2018 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 20 Nov 2018 09:54:50 -0500 Subject: [Loris-dev] one-step insertion pipeline problem In-Reply-To: References: Message-ID: Hi Ali, Note sure I understand completely why Perl cannot find the libraries as the path to uploadNeuroDB seems to be added to the PERL5LIB variable. Could you do a `ls -l /data/last/bin/mri/uploadNeuroDB` and send me the result please? Maybe this is a permission issue? A few other questions: - What is the OS you are using? - What version of Perl are you using? - Which user is used to run batch_upload_imageuploader? Best, On Mon, Nov 19, 2018 at 7:05 PM Ali Aarefi wrote: > Hi, > > Sorry about that. > > The output of that command (after sourcing the environment file) attached > to this email as a text file. > The only difference between two outputs of "perl -V" command (before and > after sourcing environment file) attached to this email as an image. > Please note that : In the attached image : left-side text is output of > command after sourcing env. file and right-side text is output of command > before sourcing env. file. > > Ali > > > [image: Screenshot from 2018-11-19 17-00-32.png] > > On Mon, Nov 19, 2018 at 11:47 PM Cecile Madjar > wrote: > >> Hi, >> >> I did not see any attachment to your email. Could you send it again? >> >> Thank you, >> >> C?cile >> >> On Mon, Nov 19, 2018 at 2:43 PM Ali Aarefi >> wrote: >> >>> Hi C?cile, >>> >>> Thank you for your help. >>> The output of that command (after sourcing the environment file) >>> attached to this email as a text file. >>> The only difference between two outputs of "perl -V" command (before and >>> after sourcing environment file) attached to this email as an image. >>> Please note that : In the attached image : left-side text is output of >>> command after sourcing env. file and right-side text is output of command >>> before sourcing env. file. >>> >>> Best Regards. >>> -Ali >>> >>> On Thu, Nov 15, 2018 at 5:20 PM Cecile Madjar >>> wrote: >>> >>>> Hi Ali, >>>> >>>> That is strange, it should find the library then. Could you run perl -V >>>> and send me the output of that command? (before and after sourcing the >>>> environment file) >>>> >>>> Thanks! >>>> >>>> C?cile >>>> >>>> On Thu, Nov 15, 2018 at 8:36 AM Ali Aarefi >>>> wrote: >>>> >>>>> >>>>> >>>>> >>>>> *Hi,Yes, I've sourced the environment file before running >>>>> batch_upload_imageuploader script, and there is no remained %PROJECT% in >>>>> environment file.The environment file included the PERL5LIB setter line >>>>> with correct replacement of %PROJECT%.* >>>>> >>>>> >>>>> >>>>> >>>>> *The environment file content is attached to this >>>>> email(Screenshot).But still the problem is unsolved.Thanks,- Ali* >>>>> >>>>> On Wed, Nov 14, 2018 at 11:32 PM Cecile Madjar >>>>> wrote: >>>>> >>>>>> Hi again, >>>>>> >>>>>> It seems you were able to run the script imaging_upload_file.pl >>>>>> manually but still have problems running batch_upload_imageuploader. >>>>>> >>>>>> My guess is that the variable $PERL5LIB is not set properly in your >>>>>> environment file so Perl cannot find the LORIS libraries that are under the >>>>>> NeuroDB folder within uploadNeuroDB (imaging_upload_file.pl can >>>>>> since it is located directly in the uploadNeuroDB folder). >>>>>> >>>>>> Here is what you would need to do to fix this: >>>>>> 1) open you environment file and add the following statement if it is >>>>>> not already there (replace %PROJECT% by your project folder name): >>>>>> >>>>>> export PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:$PERL5LIB >>>>>> 2) source the environment file again >>>>>> 3) rerun the pipeline >>>>>> >>>>>> From now on, all the scripts will be able to access all the LORIS >>>>>> perl libraries under uploadNeuroDB (including NeuroDB:DBI) >>>>>> >>>>>> Hope this helps, >>>>>> >>>>>> C?cile >>>>>> >>>>>> >>>>>> On Wed, Nov 14, 2018 at 2:47 PM Cecile Madjar >>>>>> wrote: >>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> Have you sourced the environment file before trying to run the >>>>>>> script? This file always need to be source before running the insertion >>>>>>> pipeline. >>>>>>> >>>>>>> Also, make sure that in the environment file all instances of >>>>>>> %PROJECT% have been replaced by your project's name (the one in the /data/ >>>>>>> directory). >>>>>>> >>>>>>> Let me know how it goes, >>>>>>> >>>>>>> C?cile >>>>>>> >>>>>>> >>>>>>> On Wed, Nov 14, 2018 at 12:34 PM Ali Aarefi >>>>>>> wrote: >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> *Hello,Dear LORIS dev. team,After running the one-step insertion >>>>>>>> pipeline on my local LORIS, I've faced a problem. (Can't locate >>>>>>>> NeuroDB/DBI.pm in @INC ...)* >>>>>>>> >>>>>>>> >>>>>>>> *Could anyone help me in inserting a group of data into loris based >>>>>>>> on following information?* >>>>>>>> (executed command : >>>>>>>> * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile >>>>>>>> prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* >>>>>>>> >>>>>>>> *In my local website > imaging menu tab > image uploader > upload , >>>>>>>> the detailed log for those uploades shows :* >>>>>>>> "MRI pipeline not yet executed for this upload." >>>>>>>> >>>>>>>> *And the log_batch_imageuploader.txt contains :* >>>>>>>> Can't locate NeuroDB/DBI.pm in @INC (you may need to install the >>>>>>>> NeuroDB::DBI module) (@INC contains: /etc/perl >>>>>>>> /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 >>>>>>>> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 >>>>>>>> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 >>>>>>>> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at >>>>>>>> ./batch_uploads_imageuploader line 53. >>>>>>>> BEGIN failed--compilation aborted at ./batch_uploads_imageuploader >>>>>>>> line 53. >>>>>>>> >>>>>>>> *I couldn't find installation instruction for** NeuroDB::DBI* >>>>>>>> * module.* >>>>>>>> >>>>>>>> *Best Regards.* >>>>>>>> _______________________________________________ >>>>>>>> Loris-dev mailing list >>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>> >>>>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2018-11-19 17-00-32.png Type: image/png Size: 192272 bytes Desc: not available URL: From aliaarefi1997 at gmail.com Tue Nov 20 13:47:42 2018 From: aliaarefi1997 at gmail.com (Ali Aarefi) Date: Tue, 20 Nov 2018 22:17:42 +0330 Subject: [Loris-dev] one-step insertion pipeline problem In-Reply-To: References: Message-ID: Hi Cecile, Output of "ls -l /data/last/bin/mri/uploadNeuroDB" command : $ ls -l /data/last/bin/mri/uploadNeuroDB/ total 180 drwxrwx--- 2 ali www-data 4096 Sep 12 17:36 bin -rwxrwx--- 1 ali www-data 9797 Sep 12 17:36 cleanupTarchives.pl -rwxrwx--- 1 ali www-data 4275 Sep 12 17:36 imaging_upload_file_cronjob.pl -rwxrwx--- 1 ali www-data 15606 Sep 12 17:36 imaging_upload_file.pl -rwxrwx--- 1 ali www-data 5590 Sep 12 17:36 mass_nii.pl -rwxrwx--- 1 ali www-data 5229 Sep 12 17:36 mass_pic.pl -rwxrwx--- 1 ali www-data 13867 Sep 12 17:36 minc_deletion.pl -rwxrwx--- 1 ali www-data 24990 Sep 12 17:36 minc_insertion.pl drwxrwx--- 2 ali www-data 4096 Sep 12 17:36 NeuroDB -rwxrwx--- 1 ali www-data 20987 Sep 12 17:36 register_processed_data.pl -rwxrwx--- 1 ali www-data 31065 Sep 12 17:36 tarchiveLoader -rwxrwx--- 1 ali www-data 16232 Sep 12 17:36 tarchive_validation.pl -rwxrwx--- 1 ali www-data 4055 Sep 12 17:36 undoUpload.pl About other questions: - Ubuntu 18.04 - perl5 (revision 5 version 26 subversion 1) - root user Thanks. On Tue, Nov 20, 2018 at 6:25 PM Cecile Madjar wrote: > Hi Ali, > > Note sure I understand completely why Perl cannot find the libraries as > the path to uploadNeuroDB seems to be added to the PERL5LIB variable. > > Could you do a `ls -l /data/last/bin/mri/uploadNeuroDB` and send me the > result please? Maybe this is a permission issue? > > A few other questions: > > - What is the OS you are using? > - What version of Perl are you using? > - Which user is used to run batch_upload_imageuploader? > > Best, > > On Mon, Nov 19, 2018 at 7:05 PM Ali Aarefi > wrote: > >> Hi, >> >> Sorry about that. >> >> The output of that command (after sourcing the environment file) attached >> to this email as a text file. >> The only difference between two outputs of "perl -V" command (before and >> after sourcing environment file) attached to this email as an image. >> Please note that : In the attached image : left-side text is output of >> command after sourcing env. file and right-side text is output of command >> before sourcing env. file. >> >> Ali >> >> >> [image: Screenshot from 2018-11-19 17-00-32.png] >> >> On Mon, Nov 19, 2018 at 11:47 PM Cecile Madjar >> wrote: >> >>> Hi, >>> >>> I did not see any attachment to your email. Could you send it again? >>> >>> Thank you, >>> >>> C?cile >>> >>> On Mon, Nov 19, 2018 at 2:43 PM Ali Aarefi >>> wrote: >>> >>>> Hi C?cile, >>>> >>>> Thank you for your help. >>>> The output of that command (after sourcing the environment file) >>>> attached to this email as a text file. >>>> The only difference between two outputs of "perl -V" command (before >>>> and after sourcing environment file) attached to this email as an image. >>>> Please note that : In the attached image : left-side text is output of >>>> command after sourcing env. file and right-side text is output of command >>>> before sourcing env. file. >>>> >>>> Best Regards. >>>> -Ali >>>> >>>> On Thu, Nov 15, 2018 at 5:20 PM Cecile Madjar >>>> wrote: >>>> >>>>> Hi Ali, >>>>> >>>>> That is strange, it should find the library then. Could you run perl >>>>> -V and send me the output of that command? (before and after sourcing the >>>>> environment file) >>>>> >>>>> Thanks! >>>>> >>>>> C?cile >>>>> >>>>> On Thu, Nov 15, 2018 at 8:36 AM Ali Aarefi >>>>> wrote: >>>>> >>>>>> >>>>>> >>>>>> >>>>>> *Hi,Yes, I've sourced the environment file before running >>>>>> batch_upload_imageuploader script, and there is no remained %PROJECT% in >>>>>> environment file.The environment file included the PERL5LIB setter line >>>>>> with correct replacement of %PROJECT%.* >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> *The environment file content is attached to this >>>>>> email(Screenshot).But still the problem is unsolved.Thanks,- Ali* >>>>>> >>>>>> On Wed, Nov 14, 2018 at 11:32 PM Cecile Madjar >>>>>> wrote: >>>>>> >>>>>>> Hi again, >>>>>>> >>>>>>> It seems you were able to run the script imaging_upload_file.pl >>>>>>> manually but still have problems running batch_upload_imageuploader. >>>>>>> >>>>>>> My guess is that the variable $PERL5LIB is not set properly in your >>>>>>> environment file so Perl cannot find the LORIS libraries that are under the >>>>>>> NeuroDB folder within uploadNeuroDB (imaging_upload_file.pl can >>>>>>> since it is located directly in the uploadNeuroDB folder). >>>>>>> >>>>>>> Here is what you would need to do to fix this: >>>>>>> 1) open you environment file and add the following statement if it >>>>>>> is not already there (replace %PROJECT% by your project folder name): >>>>>>> >>>>>>> export PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:$PERL5LIB >>>>>>> 2) source the environment file again >>>>>>> 3) rerun the pipeline >>>>>>> >>>>>>> From now on, all the scripts will be able to access all the LORIS >>>>>>> perl libraries under uploadNeuroDB (including NeuroDB:DBI) >>>>>>> >>>>>>> Hope this helps, >>>>>>> >>>>>>> C?cile >>>>>>> >>>>>>> >>>>>>> On Wed, Nov 14, 2018 at 2:47 PM Cecile Madjar >>>>>>> wrote: >>>>>>> >>>>>>>> Hello, >>>>>>>> >>>>>>>> Have you sourced the environment file before trying to run the >>>>>>>> script? This file always need to be source before running the insertion >>>>>>>> pipeline. >>>>>>>> >>>>>>>> Also, make sure that in the environment file all instances of >>>>>>>> %PROJECT% have been replaced by your project's name (the one in the /data/ >>>>>>>> directory). >>>>>>>> >>>>>>>> Let me know how it goes, >>>>>>>> >>>>>>>> C?cile >>>>>>>> >>>>>>>> >>>>>>>> On Wed, Nov 14, 2018 at 12:34 PM Ali Aarefi < >>>>>>>> aliaarefi1997 at gmail.com> wrote: >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> *Hello,Dear LORIS dev. team,After running the one-step insertion >>>>>>>>> pipeline on my local LORIS, I've faced a problem. (Can't locate >>>>>>>>> NeuroDB/DBI.pm in @INC ...)* >>>>>>>>> >>>>>>>>> >>>>>>>>> *Could anyone help me in inserting a group of data into loris >>>>>>>>> based on following information?* >>>>>>>>> (executed command : >>>>>>>>> * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile >>>>>>>>> prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* >>>>>>>>> >>>>>>>>> *In my local website > imaging menu tab > image uploader > upload >>>>>>>>> , the detailed log for those uploades shows :* >>>>>>>>> "MRI pipeline not yet executed for this upload." >>>>>>>>> >>>>>>>>> *And the log_batch_imageuploader.txt contains :* >>>>>>>>> Can't locate NeuroDB/DBI.pm in @INC (you may need to install the >>>>>>>>> NeuroDB::DBI module) (@INC contains: /etc/perl >>>>>>>>> /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 >>>>>>>>> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 >>>>>>>>> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 >>>>>>>>> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at >>>>>>>>> ./batch_uploads_imageuploader line 53. >>>>>>>>> BEGIN failed--compilation aborted at ./batch_uploads_imageuploader >>>>>>>>> line 53. >>>>>>>>> >>>>>>>>> *I couldn't find installation instruction for** NeuroDB::DBI* >>>>>>>>> * module.* >>>>>>>>> >>>>>>>>> *Best Regards.* >>>>>>>>> _______________________________________________ >>>>>>>>> Loris-dev mailing list >>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>> >>>>>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2018-11-19 17-00-32.png Type: image/png Size: 192272 bytes Desc: not available URL: From cecile.madjar at mcin.ca Tue Nov 20 14:15:37 2018 From: cecile.madjar at mcin.ca (Cecile Madjar) Date: Tue, 20 Nov 2018 14:15:37 -0500 Subject: [Loris-dev] one-step insertion pipeline problem In-Reply-To: References: Message-ID: Hi Ali, You should not be running the scripts as the root user but as ali (no need to be the root user to run the LORIS imaging scripts). Try out the following steps: 1) log to your VM as ali 2) source your environment file as ali 3) run "batch_upload_imageuploader -h" still as ali Hopefully this will work. Let me know how it goes. Best, C?cile On Tue, Nov 20, 2018 at 1:47 PM Ali Aarefi wrote: > Hi Cecile, > > Output of "ls -l /data/last/bin/mri/uploadNeuroDB" command : > $ ls -l /data/last/bin/mri/uploadNeuroDB/ > total 180 > drwxrwx--- 2 ali www-data 4096 Sep 12 17:36 bin > -rwxrwx--- 1 ali www-data 9797 Sep 12 17:36 cleanupTarchives.pl > -rwxrwx--- 1 ali www-data 4275 Sep 12 17:36 > imaging_upload_file_cronjob.pl > -rwxrwx--- 1 ali www-data 15606 Sep 12 17:36 imaging_upload_file.pl > -rwxrwx--- 1 ali www-data 5590 Sep 12 17:36 mass_nii.pl > -rwxrwx--- 1 ali www-data 5229 Sep 12 17:36 mass_pic.pl > -rwxrwx--- 1 ali www-data 13867 Sep 12 17:36 minc_deletion.pl > -rwxrwx--- 1 ali www-data 24990 Sep 12 17:36 minc_insertion.pl > drwxrwx--- 2 ali www-data 4096 Sep 12 17:36 NeuroDB > -rwxrwx--- 1 ali www-data 20987 Sep 12 17:36 register_processed_data.pl > -rwxrwx--- 1 ali www-data 31065 Sep 12 17:36 tarchiveLoader > -rwxrwx--- 1 ali www-data 16232 Sep 12 17:36 tarchive_validation.pl > -rwxrwx--- 1 ali www-data 4055 Sep 12 17:36 undoUpload.pl > > About other questions: > - Ubuntu 18.04 > - perl5 (revision 5 version 26 subversion 1) > - root user > > Thanks. > > On Tue, Nov 20, 2018 at 6:25 PM Cecile Madjar > wrote: > >> Hi Ali, >> >> Note sure I understand completely why Perl cannot find the libraries as >> the path to uploadNeuroDB seems to be added to the PERL5LIB variable. >> >> Could you do a `ls -l /data/last/bin/mri/uploadNeuroDB` and send me the >> result please? Maybe this is a permission issue? >> >> A few other questions: >> >> - What is the OS you are using? >> - What version of Perl are you using? >> - Which user is used to run batch_upload_imageuploader? >> >> Best, >> >> On Mon, Nov 19, 2018 at 7:05 PM Ali Aarefi >> wrote: >> >>> Hi, >>> >>> Sorry about that. >>> >>> The output of that command (after sourcing the environment file) >>> attached to this email as a text file. >>> The only difference between two outputs of "perl -V" command (before and >>> after sourcing environment file) attached to this email as an image. >>> Please note that : In the attached image : left-side text is output of >>> command after sourcing env. file and right-side text is output of command >>> before sourcing env. file. >>> >>> Ali >>> >>> >>> [image: Screenshot from 2018-11-19 17-00-32.png] >>> >>> On Mon, Nov 19, 2018 at 11:47 PM Cecile Madjar >>> wrote: >>> >>>> Hi, >>>> >>>> I did not see any attachment to your email. Could you send it again? >>>> >>>> Thank you, >>>> >>>> C?cile >>>> >>>> On Mon, Nov 19, 2018 at 2:43 PM Ali Aarefi >>>> wrote: >>>> >>>>> Hi C?cile, >>>>> >>>>> Thank you for your help. >>>>> The output of that command (after sourcing the environment file) >>>>> attached to this email as a text file. >>>>> The only difference between two outputs of "perl -V" command (before >>>>> and after sourcing environment file) attached to this email as an image. >>>>> Please note that : In the attached image : left-side text is output of >>>>> command after sourcing env. file and right-side text is output of command >>>>> before sourcing env. file. >>>>> >>>>> Best Regards. >>>>> -Ali >>>>> >>>>> On Thu, Nov 15, 2018 at 5:20 PM Cecile Madjar >>>>> wrote: >>>>> >>>>>> Hi Ali, >>>>>> >>>>>> That is strange, it should find the library then. Could you run perl >>>>>> -V and send me the output of that command? (before and after sourcing the >>>>>> environment file) >>>>>> >>>>>> Thanks! >>>>>> >>>>>> C?cile >>>>>> >>>>>> On Thu, Nov 15, 2018 at 8:36 AM Ali Aarefi >>>>>> wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> *Hi,Yes, I've sourced the environment file before running >>>>>>> batch_upload_imageuploader script, and there is no remained %PROJECT% in >>>>>>> environment file.The environment file included the PERL5LIB setter line >>>>>>> with correct replacement of %PROJECT%.* >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> *The environment file content is attached to this >>>>>>> email(Screenshot).But still the problem is unsolved.Thanks,- Ali* >>>>>>> >>>>>>> On Wed, Nov 14, 2018 at 11:32 PM Cecile Madjar < >>>>>>> cecile.madjar at mcin.ca> wrote: >>>>>>> >>>>>>>> Hi again, >>>>>>>> >>>>>>>> It seems you were able to run the script imaging_upload_file.pl >>>>>>>> manually but still have problems running batch_upload_imageuploader. >>>>>>>> >>>>>>>> My guess is that the variable $PERL5LIB is not set properly in your >>>>>>>> environment file so Perl cannot find the LORIS libraries that are under the >>>>>>>> NeuroDB folder within uploadNeuroDB (imaging_upload_file.pl can >>>>>>>> since it is located directly in the uploadNeuroDB folder). >>>>>>>> >>>>>>>> Here is what you would need to do to fix this: >>>>>>>> 1) open you environment file and add the following statement if it >>>>>>>> is not already there (replace %PROJECT% by your project folder name): >>>>>>>> >>>>>>>> export PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:$PERL5LIB >>>>>>>> 2) source the environment file again >>>>>>>> 3) rerun the pipeline >>>>>>>> >>>>>>>> From now on, all the scripts will be able to access all the LORIS >>>>>>>> perl libraries under uploadNeuroDB (including NeuroDB:DBI) >>>>>>>> >>>>>>>> Hope this helps, >>>>>>>> >>>>>>>> C?cile >>>>>>>> >>>>>>>> >>>>>>>> On Wed, Nov 14, 2018 at 2:47 PM Cecile Madjar < >>>>>>>> cecile.madjar at mcin.ca> wrote: >>>>>>>> >>>>>>>>> Hello, >>>>>>>>> >>>>>>>>> Have you sourced the environment file before trying to run the >>>>>>>>> script? This file always need to be source before running the insertion >>>>>>>>> pipeline. >>>>>>>>> >>>>>>>>> Also, make sure that in the environment file all instances of >>>>>>>>> %PROJECT% have been replaced by your project's name (the one in the /data/ >>>>>>>>> directory). >>>>>>>>> >>>>>>>>> Let me know how it goes, >>>>>>>>> >>>>>>>>> C?cile >>>>>>>>> >>>>>>>>> >>>>>>>>> On Wed, Nov 14, 2018 at 12:34 PM Ali Aarefi < >>>>>>>>> aliaarefi1997 at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> *Hello,Dear LORIS dev. team,After running the one-step insertion >>>>>>>>>> pipeline on my local LORIS, I've faced a problem. (Can't locate >>>>>>>>>> NeuroDB/DBI.pm in @INC ...)* >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> *Could anyone help me in inserting a group of data into loris >>>>>>>>>> based on following information?* >>>>>>>>>> (executed command : >>>>>>>>>> * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile >>>>>>>>>> prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* >>>>>>>>>> >>>>>>>>>> *In my local website > imaging menu tab > image uploader > upload >>>>>>>>>> , the detailed log for those uploades shows :* >>>>>>>>>> "MRI pipeline not yet executed for this upload." >>>>>>>>>> >>>>>>>>>> *And the log_batch_imageuploader.txt contains :* >>>>>>>>>> Can't locate NeuroDB/DBI.pm in @INC (you may need to install the >>>>>>>>>> NeuroDB::DBI module) (@INC contains: /etc/perl >>>>>>>>>> /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 >>>>>>>>>> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 >>>>>>>>>> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 >>>>>>>>>> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at >>>>>>>>>> ./batch_uploads_imageuploader line 53. >>>>>>>>>> BEGIN failed--compilation aborted at >>>>>>>>>> ./batch_uploads_imageuploader line 53. >>>>>>>>>> >>>>>>>>>> *I couldn't find installation instruction for** NeuroDB::DBI* >>>>>>>>>> * module.* >>>>>>>>>> >>>>>>>>>> *Best Regards.* >>>>>>>>>> _______________________________________________ >>>>>>>>>> Loris-dev mailing list >>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>> >>>>>>>>> -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2018-11-19 17-00-32.png Type: image/png Size: 192272 bytes Desc: not available URL: From aliaarefi1997 at gmail.com Thu Nov 29 05:38:01 2018 From: aliaarefi1997 at gmail.com (Ali Aarefi) Date: Thu, 29 Nov 2018 14:08:01 +0330 Subject: [Loris-dev] one-step insertion pipeline problem In-Reply-To: References: Message-ID: Hi C?cile, I modified that and finally it's done, the script ran successfuly. Thank you so much for your time and consideration. Best Regards, Ali On Wed, Nov 21, 2018 at 6:05 PM Cecile Madjar wrote: > Hi Ali, > > We are making progress. Now the scripts can find NeuroDB::DBI. Always use > the first two steps before running any script in the imaging pipeline and > stay as user ali. > > For the error message, it looks like you don't have qsub installed so you > need to modify the following in the Config module: > > - Under the "Imaging Pipeline" section of the Config module of the > LORIS front-end, there is a configuration setting called "Project batch > management used". Set this config to "No", Save it and then try rerunning > batch_upload_imageuploader. > > Let me know how it goes! > > C?cile > > On Wed, Nov 21, 2018 at 6:00 AM Ali Aarefi > wrote: > >> Hi, >> >> I tried those three steps and attached the output of step 3 to this email >> as "step3". >> >> And also the errors of executing the following command attached as >> "log_batch_imageuploader.txt": >> "/data/last/bin/mri/batch_uploads_imageuploader -profile prod < >> /home/ali/Documents/imageUploader.txt >log_batch_imageuploader.txt 2>&1" >> >> Thanks, >> Ali >> >> On Tue, Nov 20, 2018 at 10:45 PM Cecile Madjar >> wrote: >> >>> Hi Ali, >>> >>> You should not be running the scripts as the root user but as ali (no >>> need to be the root user to run the LORIS imaging scripts). >>> >>> Try out the following steps: >>> 1) log to your VM as ali >>> 2) source your environment file as ali >>> 3) run "batch_upload_imageuploader -h" still as ali >>> >>> Hopefully this will work. Let me know how it goes. >>> >>> Best, >>> >>> C?cile >>> >>> >>> On Tue, Nov 20, 2018 at 1:47 PM Ali Aarefi >>> wrote: >>> >>>> Hi Cecile, >>>> >>>> Output of "ls -l /data/last/bin/mri/uploadNeuroDB" command : >>>> $ ls -l /data/last/bin/mri/uploadNeuroDB/ >>>> total 180 >>>> drwxrwx--- 2 ali www-data 4096 Sep 12 17:36 bin >>>> -rwxrwx--- 1 ali www-data 9797 Sep 12 17:36 cleanupTarchives.pl >>>> -rwxrwx--- 1 ali www-data 4275 Sep 12 17:36 >>>> imaging_upload_file_cronjob.pl >>>> -rwxrwx--- 1 ali www-data 15606 Sep 12 17:36 imaging_upload_file.pl >>>> -rwxrwx--- 1 ali www-data 5590 Sep 12 17:36 mass_nii.pl >>>> -rwxrwx--- 1 ali www-data 5229 Sep 12 17:36 mass_pic.pl >>>> -rwxrwx--- 1 ali www-data 13867 Sep 12 17:36 minc_deletion.pl >>>> -rwxrwx--- 1 ali www-data 24990 Sep 12 17:36 minc_insertion.pl >>>> drwxrwx--- 2 ali www-data 4096 Sep 12 17:36 NeuroDB >>>> -rwxrwx--- 1 ali www-data 20987 Sep 12 17:36 register_processed_data.pl >>>> -rwxrwx--- 1 ali www-data 31065 Sep 12 17:36 tarchiveLoader >>>> -rwxrwx--- 1 ali www-data 16232 Sep 12 17:36 tarchive_validation.pl >>>> -rwxrwx--- 1 ali www-data 4055 Sep 12 17:36 undoUpload.pl >>>> >>>> About other questions: >>>> - Ubuntu 18.04 >>>> - perl5 (revision 5 version 26 subversion 1) >>>> - root user >>>> >>>> Thanks. >>>> >>>> On Tue, Nov 20, 2018 at 6:25 PM Cecile Madjar >>>> wrote: >>>> >>>>> Hi Ali, >>>>> >>>>> Note sure I understand completely why Perl cannot find the libraries >>>>> as the path to uploadNeuroDB seems to be added to the PERL5LIB variable. >>>>> >>>>> Could you do a `ls -l /data/last/bin/mri/uploadNeuroDB` and send me >>>>> the result please? Maybe this is a permission issue? >>>>> >>>>> A few other questions: >>>>> >>>>> - What is the OS you are using? >>>>> - What version of Perl are you using? >>>>> - Which user is used to run batch_upload_imageuploader? >>>>> >>>>> Best, >>>>> >>>>> On Mon, Nov 19, 2018 at 7:05 PM Ali Aarefi >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> Sorry about that. >>>>>> >>>>>> The output of that command (after sourcing the environment file) >>>>>> attached to this email as a text file. >>>>>> The only difference between two outputs of "perl -V" command (before >>>>>> and after sourcing environment file) attached to this email as an image. >>>>>> Please note that : In the attached image : left-side text is output >>>>>> of command after sourcing env. file and right-side text is output of >>>>>> command before sourcing env. file. >>>>>> >>>>>> Ali >>>>>> >>>>>> >>>>>> [image: Screenshot from 2018-11-19 17-00-32.png] >>>>>> >>>>>> On Mon, Nov 19, 2018 at 11:47 PM Cecile Madjar >>>>>> wrote: >>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I did not see any attachment to your email. Could you send it again? >>>>>>> >>>>>>> Thank you, >>>>>>> >>>>>>> C?cile >>>>>>> >>>>>>> On Mon, Nov 19, 2018 at 2:43 PM Ali Aarefi >>>>>>> wrote: >>>>>>> >>>>>>>> Hi C?cile, >>>>>>>> >>>>>>>> Thank you for your help. >>>>>>>> The output of that command (after sourcing the environment file) >>>>>>>> attached to this email as a text file. >>>>>>>> The only difference between two outputs of "perl -V" command >>>>>>>> (before and after sourcing environment file) attached to this email as an >>>>>>>> image. >>>>>>>> Please note that : In the attached image : left-side text is output >>>>>>>> of command after sourcing env. file and right-side text is output of >>>>>>>> command before sourcing env. file. >>>>>>>> >>>>>>>> Best Regards. >>>>>>>> -Ali >>>>>>>> >>>>>>>> On Thu, Nov 15, 2018 at 5:20 PM Cecile Madjar < >>>>>>>> cecile.madjar at mcin.ca> wrote: >>>>>>>> >>>>>>>>> Hi Ali, >>>>>>>>> >>>>>>>>> That is strange, it should find the library then. Could you run >>>>>>>>> perl -V and send me the output of that command? (before and after sourcing >>>>>>>>> the environment file) >>>>>>>>> >>>>>>>>> Thanks! >>>>>>>>> >>>>>>>>> C?cile >>>>>>>>> >>>>>>>>> On Thu, Nov 15, 2018 at 8:36 AM Ali Aarefi < >>>>>>>>> aliaarefi1997 at gmail.com> wrote: >>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> *Hi,Yes, I've sourced the environment file before running >>>>>>>>>> batch_upload_imageuploader script, and there is no remained %PROJECT% in >>>>>>>>>> environment file.The environment file included the PERL5LIB setter line >>>>>>>>>> with correct replacement of %PROJECT%.* >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> *The environment file content is attached to this >>>>>>>>>> email(Screenshot).But still the problem is unsolved.Thanks,- Ali* >>>>>>>>>> >>>>>>>>>> On Wed, Nov 14, 2018 at 11:32 PM Cecile Madjar < >>>>>>>>>> cecile.madjar at mcin.ca> wrote: >>>>>>>>>> >>>>>>>>>>> Hi again, >>>>>>>>>>> >>>>>>>>>>> It seems you were able to run the script imaging_upload_file.pl >>>>>>>>>>> manually but still have problems running batch_upload_imageuploader. >>>>>>>>>>> >>>>>>>>>>> My guess is that the variable $PERL5LIB is not set properly in >>>>>>>>>>> your environment file so Perl cannot find the LORIS libraries that are >>>>>>>>>>> under the NeuroDB folder within uploadNeuroDB ( >>>>>>>>>>> imaging_upload_file.pl can since it is located directly in the >>>>>>>>>>> uploadNeuroDB folder). >>>>>>>>>>> >>>>>>>>>>> Here is what you would need to do to fix this: >>>>>>>>>>> 1) open you environment file and add the following statement if >>>>>>>>>>> it is not already there (replace %PROJECT% by your project folder name): >>>>>>>>>>> >>>>>>>>>>> export PERL5LIB=/data/%PROJECT%/bin/mri/uploadNeuroDB:$PERL5LIB >>>>>>>>>>> 2) source the environment file again >>>>>>>>>>> 3) rerun the pipeline >>>>>>>>>>> >>>>>>>>>>> From now on, all the scripts will be able to access all the >>>>>>>>>>> LORIS perl libraries under uploadNeuroDB (including NeuroDB:DBI) >>>>>>>>>>> >>>>>>>>>>> Hope this helps, >>>>>>>>>>> >>>>>>>>>>> C?cile >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Wed, Nov 14, 2018 at 2:47 PM Cecile Madjar < >>>>>>>>>>> cecile.madjar at mcin.ca> wrote: >>>>>>>>>>> >>>>>>>>>>>> Hello, >>>>>>>>>>>> >>>>>>>>>>>> Have you sourced the environment file before trying to run the >>>>>>>>>>>> script? This file always need to be source before running the insertion >>>>>>>>>>>> pipeline. >>>>>>>>>>>> >>>>>>>>>>>> Also, make sure that in the environment file all instances of >>>>>>>>>>>> %PROJECT% have been replaced by your project's name (the one in the /data/ >>>>>>>>>>>> directory). >>>>>>>>>>>> >>>>>>>>>>>> Let me know how it goes, >>>>>>>>>>>> >>>>>>>>>>>> C?cile >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> On Wed, Nov 14, 2018 at 12:34 PM Ali Aarefi < >>>>>>>>>>>> aliaarefi1997 at gmail.com> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> *Hello,Dear LORIS dev. team,After running the one-step >>>>>>>>>>>>> insertion pipeline on my local LORIS, I've faced a problem. (Can't locate >>>>>>>>>>>>> NeuroDB/DBI.pm in @INC ...)* >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> *Could anyone help me in inserting a group of data into loris >>>>>>>>>>>>> based on following information?* >>>>>>>>>>>>> (executed command : >>>>>>>>>>>>> * cd /data/$PROJ/bin/mri./batch_uploads_imageuploader -profile >>>>>>>>>>>>> prod < MY-imageuploader_list >log_batch_imageuploader.txt 2>&1)* >>>>>>>>>>>>> >>>>>>>>>>>>> *In my local website > imaging menu tab > image uploader > >>>>>>>>>>>>> upload , the detailed log for those uploades shows :* >>>>>>>>>>>>> "MRI pipeline not yet executed for this upload." >>>>>>>>>>>>> >>>>>>>>>>>>> *And the log_batch_imageuploader.txt contains :* >>>>>>>>>>>>> Can't locate NeuroDB/DBI.pm in @INC (you may need to install >>>>>>>>>>>>> the NeuroDB::DBI module) (@INC contains: /etc/perl >>>>>>>>>>>>> /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 >>>>>>>>>>>>> /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 >>>>>>>>>>>>> /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 >>>>>>>>>>>>> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at >>>>>>>>>>>>> ./batch_uploads_imageuploader line 53. >>>>>>>>>>>>> BEGIN failed--compilation aborted at >>>>>>>>>>>>> ./batch_uploads_imageuploader line 53. >>>>>>>>>>>>> >>>>>>>>>>>>> *I couldn't find installation instruction for** NeuroDB::DBI* >>>>>>>>>>>>> * module.* >>>>>>>>>>>>> >>>>>>>>>>>>> *Best Regards.* >>>>>>>>>>>>> _______________________________________________ >>>>>>>>>>>>> Loris-dev mailing list >>>>>>>>>>>>> Loris-dev at bic.mni.mcgill.ca >>>>>>>>>>>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/loris-dev >>>>>>>>>>>>> >>>>>>>>>>>> -------------- next part -------------- An HTML attachment was scrubbed... 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