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Move batch_upload_imageuploader.pl and batch_upload_tarchive.pl out of the root directory #1362

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Move batch_upload_imageuploader.pl and batch_upload_tarchive.pl out of the root directory #1362

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2 changes: 1 addition & 1 deletion install/templates/environment_template
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Expand Up @@ -6,7 +6,7 @@ source ${MINC_TOOLKIT_DIR}/minc-toolkit-config.sh
umask 0002

# export PATH, PERL5LIB, TMPDIR and LORIS_CONFIG variables
export PATH=/opt/${PROJECT}/bin/mri:/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/uploadNeuroDB/bin:/opt/${PROJECT}/bin/mri/dicom-archive:/opt/${PROJECT}/bin/mri/python/scripts:/opt/${PROJECT}/bin/mri/tools:${MINC_TOOLKIT_DIR}/bin:/usr/local/bin/tpcclib:$PATH
export PATH=/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/uploadNeuroDB/bin:/opt/${PROJECT}/bin/mri/dicom-archive:/opt/${PROJECT}/bin/mri/python/scripts:/opt/${PROJECT}/bin/mri/tools:${MINC_TOOLKIT_DIR}/bin:/usr/local/bin/tpcclib:$PATH
export PERL5LIB=/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/dicom-archive:$PERL5LIB
export TMPDIR=/tmp
export LORIS_CONFIG=/opt/${PROJECT}/bin/mri/config
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2 changes: 1 addition & 1 deletion test/mri.Dockerfile
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Expand Up @@ -86,7 +86,7 @@ RUN bash ./test/imaging_install_test.sh $DATABASE_NAME $DATABASE_USER $DATABASE_
# Setup the LORIS-MRI environment variables
ENV PROJECT=loris
ENV MINC_TOOLKIT_DIR=/opt/minc/1.9.18
ENV PATH=/opt/${PROJECT}/bin/mri:/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/uploadNeuroDB/bin:/opt/${PROJECT}/bin/mri/dicom-archive:/opt/${PROJECT}/bin/mri/python/scripts:/opt/${PROJECT}/bin/mri/tools:${MINC_TOOLKIT_DIR}/bin:/usr/local/bin/tpcclib:$PATH
ENV PATH=/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/uploadNeuroDB/bin:/opt/${PROJECT}/bin/mri/dicom-archive:/opt/${PROJECT}/bin/mri/python/scripts:/opt/${PROJECT}/bin/mri/tools:${MINC_TOOLKIT_DIR}/bin:/usr/local/bin/tpcclib:$PATH
ENV PERL5LIB=/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/dicom-archive:$PERL5LIB
ENV TMPDIR=/tmp
ENV LORIS_CONFIG=/opt/${PROJECT}/bin/mri/config
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4 changes: 2 additions & 2 deletions tools/mass_perldoc_md_creation.pl
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Expand Up @@ -58,8 +58,6 @@ =head1 AUTHORS
'DTIPrep/DTI/DTI.pm',
'DTIPrep/DTIPrepRegister.pl',
'DTIPrep/DTIPrep_pipeline.pl',
'batch_uploads_imageuploader.pl',
'batch_uploads_tarchive.pl',
'dicom-archive/DICOM/DCMSUM.pm',
'dicom-archive/DICOM/DICOM.pm',
'dicom-archive/DICOM/Element.pm',
Expand Down Expand Up @@ -114,6 +112,8 @@ =head1 AUTHORS
'uploadNeuroDB/NeuroDB/UnexpectedValueException.pm',
'uploadNeuroDB/bin/concat_mri.pl',
'uploadNeuroDB/bin/mincpik.pl',
'uploadNeuroDB/batch_uploads_imageuploader.pl',
'uploadNeuroDB/batch_uploads_tarchive.pl',
'uploadNeuroDB/imaging_non_minc_insertion.pl',
'uploadNeuroDB/imaging_upload_file.pl',
'uploadNeuroDB/imaging_upload_file_cronjob.pl',
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2 changes: 1 addition & 1 deletion tools/petupload_cron_prod
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Expand Up @@ -75,5 +75,5 @@ fi
mv ${tmpDir}tmp.txt ${uploadList} &&
echo "#### BATCH UPLOAD IMAGING ####" >&2 &&
source ${lorisMRIDir}environment &&
perl ${lorisMRIDir}batch_uploads_imageuploader.pl -profile prod < ${uploadList} &&
batch_uploads_imageuploader.pl -profile prod < ${uploadList} &&
echo "Successfully executed batch_uploads_imageuploader." >&2
0 batch_uploads_imageuploader.pl → uploadNeuroDB/batch_uploads_imageuploader.pl
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0 batch_uploads_tarchive.pl → uploadNeuroDB/batch_uploads_tarchive.pl
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