add integration test

.github/workflows/integration.yml

@@ -13,7 +13,7 @@ env:
   DATABASE_PASSWORD: TestPassword
   BUCKET_URL: https://ace-minio-1.loris.ca:9000
   BUCKET_NAME: loris-rb-data
-  BUCKET_ACCESS_KEY: lorisadmin
+  BUCKET_ACCESS_KEY: lorisadmin-ro
   BUCKET_SECRET_KEY: Tn=qP3LupmXnMuc
 
 jobs:
@@ -76,6 +76,7 @@ jobs:
         chmod 600 .passwd-s3fs
         echo ${{ env.BUCKET_ACCESS_KEY }}:${{ env.BUCKET_SECRET_KEY }} > .passwd-s3fs
         sudo s3fs ${{ env.BUCKET_NAME }} /data-imaging -o passwd_file=.passwd-s3fs -o url=${{ env.BUCKET_URL }} -o use_path_request_style -o allow_other
+        ls /data-imaging
 
     - name: Run integration tests
-      run: docker compose --file ./test/docker-compose.yml run mri pytest python/tests/integration
+      run: docker compose --file ./test/docker-compose.yml run mri pytest -s python/tests/integration

dicom-archive/database_config_template.py

@@ -1,10 +1,10 @@
 #!/usr/bin/env python
 
 import re
+
+from lib.config_file import CreateVisitInfo, DatabaseConfig, SubjectInfo
 from lib.database import Database
 from lib.imaging import Imaging
-from lib.config_file import CreateVisitInfo, DatabaseConfig, S3Config, SubjectInfo
-
 
 mysql: DatabaseConfig = DatabaseConfig(
     host     = 'DBHOST',
@@ -14,13 +14,13 @@
     port     = 3306,
 )
 
-# This statement can be omitted if the project does not use AWS S3.
-s3: S3Config = S3Config(
-    aws_access_key_id     = 'AWS_ACCESS_KEY_ID',
-    aws_secret_access_key = 'AWS_SECRET_ACCESS_KEY',
-    aws_s3_endpoint_url   = 'AWS_S3_ENDPOINT',
-    aws_s3_bucket_name    = 'AWS_S3_BUCKET_NAME',
-)
+# Uncomment this statement if your project uses AWS S3.
+# s3: S3Config = S3Config(
+#     aws_access_key_id     = 'AWS_ACCESS_KEY_ID',
+#     aws_secret_access_key = 'AWS_SECRET_ACCESS_KEY',
+#     aws_s3_endpoint_url   = 'AWS_S3_ENDPOINT',
+#     aws_s3_bucket_name    = 'AWS_S3_BUCKET_NAME',
+# )
 
 
 def get_subject_info(db: Database, subject_name: str, scanner_id: int | None = None) -> SubjectInfo | None:

install/install_database.sql

@@ -13,11 +13,11 @@ UPDATE Config SET Value = @project
   WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = 'prefix');
 UPDATE Config SET Value = @minc_dir
   WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = 'MINCToolsPath');
-UPDATE Config SET Value = CONCAT('/data/', @project, '/data/')
+UPDATE Config SET Value = CONCAT('/data/', @project, '/')
   WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = 'dataDirBasepath');
-UPDATE Config SET Value = CONCAT('/data/', @project, '/data/')
+UPDATE Config SET Value = CONCAT('/data/', @project, '/')
   WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = 'imagePath');
-UPDATE Config SET Value = CONCAT('/data/', @project, '/data/tarchive/')
+UPDATE Config SET Value = CONCAT('/data/', @project, '/tarchive/')
   WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = 'tarchiveLibraryDir');
 UPDATE Config SET Value = CONCAT('/opt/', @project, '/bin/mri/dicom-archive/get_dicom_info.pl')
   WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = 'get_dicom_info');

python/tests/integration/scripts/test_run_dicom_archive_loader.py

@@ -0,0 +1,18 @@
+import subprocess
+
+
+def test():
+    process = subprocess.run([
+        'run_dicom_archive_loader.py',
+        '--profile', 'database_config.py',
+        '--tarchive_path', '/data/loris/tarchive/DCM_2015-07-07_ImagingUpload-14-30-FoTt1K.tar',
+        # Only one of the DICOM archive path or the upload ID should be specified
+        # '--upload_id', '126',
+    ], capture_output=True)
+
+    print(process.stdout)
+    print(process.stderr)
+    print(process.returncode)
+
+    assert process.returncode == 0
+    assert process.stderr == b''

test/imaging_install_test.sh

@@ -14,16 +14,16 @@ mridir="/opt/loris/bin/mri"
 #############################Create directories########################################
 #######################################################################################
 echo "Creating the data directories"
-  sudo -S su $USER -c "mkdir -m 2770 -p /data/$PROJ/data/"
-  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/trashbin"         #holds mincs that didn't match protocol
-  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/tarchive"         #holds tared dicom-folder
-  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/hrrtarchive"      #holds tared hrrt-folder
-  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/pic"              #holds jpegs generated for the MRI-browser
-  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/logs"             #holds logs from pipeline script
-  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/assembly"         #holds the MINC files
-  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/assembly_bids"    #holds the BIDS files derived from DICOMs
-  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/batch_output"     #contains the result of the SGE (queue)
-  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/data/bids_imports"     #contains imported BIDS studies
+  sudo -S su $USER -c "mkdir -m 2770 -p /data/$PROJ/"
+  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/trashbin"         #holds mincs that didn't match protocol
+  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/tarchive"         #holds tared dicom-folder
+  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/hrrtarchive"      #holds tared hrrt-folder
+  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/pic"              #holds jpegs generated for the MRI-browser
+  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/logs"             #holds logs from pipeline script
+  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/assembly"         #holds the MINC files
+  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/assembly_bids"    #holds the BIDS files derived from DICOMs
+  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/batch_output"     #contains the result of the SGE (queue)
+  sudo -S su $USER -c "mkdir -m 770 -p /data/$PROJ/bids_imports"     #contains imported BIDS studies
   sudo -S su $USER -c "mkdir -m 770 -p $mridir/dicom-archive/.loris_mri"
 echo
 
@@ -71,8 +71,8 @@ sudo usermod -a -G $group $USER
 sudo chgrp $group -R /opt/$PROJ/
 sudo chgrp $group -R /data/$PROJ/
 
-#Setting group ID for all files/dirs under /data/$PROJ/data
-sudo chmod -R g+s /data/$PROJ/data/
+#Setting group ID for all files/dirs under /data/$PROJ/
+sudo chmod -R g+s /data/$PROJ/
 
 # Setting group permissions and group ID for all files/dirs under /data/incoming
 # If the directory was not created earlier, then instructions to do so manually are provided.

test/mri.Dockerfile

@@ -115,3 +115,5 @@ ENV LORIS_MRI=/opt/${PROJECT}/bin/mri
 ENV PYTHONPATH=$PYTHONPATH:/opt/${PROJECT}/bin/mri/python:/opt/${PROJECT}/bin/mri/python/react-series-data-viewer
 ENV BEASTLIB=${MINC_TOOLKIT_DIR}/../share/beast-library-1.1
 ENV MNI_MODELS=${MINC_TOOLKIT_DIR}/../share/icbm152_model_09c
+
+ENTRYPOINT sh -c "replicate_raisinbread_for_mcin_dev_vm.pl /data-imaging /data/loris && $@" --