test (#1187)

.github/workflows/integration.yml

@@ -0,0 +1,60 @@
+name: Integration tests
+
+on:
+  pull_request:
+  push:
+    branches:
+    - 'main'
+    - '*-release'
+
+jobs:
+  docker:
+    name: Docker
+    runs-on: ubuntu-latest
+    steps:
+    - name: Check out LORIS-MRI
+      uses: actions/checkout@v4
+
+    - name: Clone the LORIS core repository
+      run: git clone https://github.com/aces/Loris.git /tmp/Loris
+
+    - name: Import database files 
+      run: |
+        mkdir -p ./test/database
+        mkdir -p ./test/database/SQL
+        mkdir -p ./test/database/raisinbread/RB_files
+        mkdir -p ./test/database/raisinbread/instruments/instrument_sql
+        mkdir -p ./test/database/test/test_instrument
+        cp -r /tmp/Loris/SQL/* ./test/database/SQL
+        cp -r ./test/RB_SQL/* ./test/database/raisinbread/RB_files
+        cp -r -n /tmp/Loris/raisinbread/RB_files/* ./test/database/raisinbread/RB_files
+        cp -r /tmp/Loris/raisinbread/instruments/instrument_sql/* ./test/database/raisinbread/instruments/instrument_sql
+        cp -r /tmp/Loris/test/test_instrument/testtest.sql ./test/database/test/test_instrument/testtest.sql
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+
+    - name: Build Docker database image
+      uses: docker/build-push-action@v6
+      with:
+        context: .
+        file: ./test/db.Dockerfile
+        build-args: |
+          BASE_DIR=/app/
+        tags: loris-db
+        load: true
+        cache-from: type=gha,scope=loris-db
+        cache-to: type=gha,scope=loris-db
+
+    - name: Build Docker MRI image
+      uses: docker/build-push-action@v6
+      with:
+        context: .
+        file: ./test/mri.Dockerfile
+        tags: loris-mri
+        load: true
+        cache-from: type=gha,scope=loris-mri
+        cache-to: type=gha,scope=loris-mri
+
+    - name: Run integration tests
+      run: docker compose --file ./test/docker-compose.yml run mri pytest python/tests/integration

.github/workflows/stale.yml

@@ -11,8 +11,8 @@ on:
 
 jobs:
   stale:
-
     runs-on: ubuntu-latest
+
     permissions:
       issues: write
       pull-requests: write
@@ -24,6 +24,6 @@ jobs:
         stale-issue-message: 'This issue is stale because it has been open 1 year with no activity.  Remove stale label or comment or this will be closed in 3 months.'
         stale-pr-message: 'This PR is stale because it has been open 45 days with no activity. Remove stale label or comment or this will be closed in 20 days.'
         days-before-issue-stale: 365 # ~1 year
-        days-before-issue-close: 90 # ~3 months   
+        days-before-issue-close: 90 # ~3 months
         days-before-pr-stale: 90 # ~3 months
         days-before-pr-close: 45 # ~1.5 month

install/imaging_install.sh

@@ -268,12 +268,5 @@ fi
 ###### Update the Database table, Config, with the user values #######
 ######################################################################
 echo "Populating database configuration entries for the Imaging Pipeline and LORIS-MRI code and images Path:"
-mysql $mysqldb -h$mysqlhost --user=$mysqluser --password="$mysqlpass" -A -e "UPDATE Config SET Value='/data/$PROJ/data/' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='dataDirBasepath')"
-mysql $mysqldb -h$mysqlhost --user=$mysqluser --password="$mysqlpass" -A -e "UPDATE Config SET Value='/data/$PROJ/data/' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='imagePath')"
-mysql $mysqldb -h$mysqlhost --user=$mysqluser --password="$mysqlpass" -A -e "UPDATE Config SET Value='$PROJ' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='prefix')"
-mysql $mysqldb -h$mysqlhost --user=$mysqluser --password="$mysqlpass" -A -e "UPDATE Config SET Value='$email' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='mail_user')"
-mysql $mysqldb -h$mysqlhost --user=$mysqluser --password="$mysqlpass" -A -e "UPDATE Config SET Value='/opt/$PROJ/bin/mri/dicom-archive/get_dicom_info.pl' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='get_dicom_info')"
-mysql $mysqldb -h$mysqlhost --user=$mysqluser --password="$mysqlpass" -A -e "UPDATE Config SET Value='/data/$PROJ/data/tarchive/' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='tarchiveLibraryDir')"
-mysql $mysqldb -h$mysqlhost --user=$mysqluser --password="$mysqlpass" -A -e "UPDATE Config SET Value='/opt/$PROJ/bin/mri/' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='MRICodePath')"
-mysql $mysqldb -h$mysqlhost --user=$mysqluser --password="$mysqlpass" -A -e "UPDATE Config SET Value='$MINC_TOOLKIT_DIR' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='MINCToolsPath')"
-echo
+mysql $mysqldb -h$mysqlhost --user=$mysqluser --password="$mysqlpass" -A -e \
+	"SET @email := '$email'; SET @project := '$PROJ'; SET @minc_dir := '$MINC_TOOLKIT_DIR'; SOURCE install_database.sql"

install/install_database.sql

@@ -0,0 +1,25 @@
+-- This file contains a few statements to adapt a core LORIS database to LORIS-MRI.
+-- This file is ran by the installation or the database dockerfile, it usually
+-- should not be ran as a standalone.
+
+-- The script arguments must be set as SQL variables when calling the script.
+-- @email     -- User email address
+-- @project   -- Project name
+-- @minc_dir  -- MINC Toolkit directory
+
+UPDATE Config SET Value = @email
+  WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = 'mail_user');
+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/')
+  WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = 'dataDirBasepath');
+UPDATE Config SET Value = CONCAT('/data/', @project, '/data/')
+  WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = 'imagePath');
+UPDATE Config SET Value = CONCAT('/data/', @project, '/data/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');
+UPDATE Config SET Value = CONCAT('/opt/', @project, '/bin/mri/')
+  WHERE ConfigID = (SELECT ID FROM ConfigSettings WHERE Name = 'MRICodePath');

test/test_example.py → python/tests/integration/test_poc.py

@@ -1,7 +1,9 @@
-# tests/test_example.py
+# Proof-of-concept integration tests. TODO: Replace with real tests
+
+
 def test_addition():
     assert 1 + 1 == 2
 
+
 def test_subtraction():
     assert 2 - 1 == 1
-

test/db.Dockerfile

@@ -0,0 +1,41 @@
+FROM mariadb:latest
+
+ARG BASE_DIR
+
+COPY test/database/SQL/0000-00-00-schema.sql /0000-00-00-schema.sql
+COPY test/database/SQL/0000-00-01-Modules.sql /0000-00-01-Modules.sql
+COPY test/database/SQL/0000-00-02-Permission.sql /0000-00-02-Permission.sql
+COPY test/database/SQL/0000-00-03-ConfigTables.sql /0000-00-03-ConfigTables.sql
+COPY test/database/SQL/0000-00-04-Help.sql /0000-00-04-Help.sql
+COPY test/database/SQL/0000-00-05-ElectrophysiologyTables.sql /0000-00-05-ElectrophysiologyTables.sql
+COPY test/database/raisinbread/RB_files/*.sql /RB_files/
+COPY test/database/raisinbread/instruments/instrument_sql/aosi.sql  /aosi.sql
+COPY test/database/raisinbread/instruments/instrument_sql/bmi.sql  /bmi.sql
+COPY test/database/raisinbread/instruments/instrument_sql/medical_history.sql  /medical_history.sql
+COPY test/database/raisinbread/instruments/instrument_sql/mri_parameter_form.sql  /mri_parameter_form.sql
+COPY test/database/raisinbread/instruments/instrument_sql/radiology_review.sql  /radiology_review.sql
+COPY test/database/test/test_instrument/testtest.sql /test_instrument.sql
+
+RUN echo "Use LorisTest;" | cat - \
+    0000-00-00-schema.sql \
+    0000-00-01-Modules.sql \
+    0000-00-02-Permission.sql \
+    0000-00-03-ConfigTables.sql \
+    0000-00-04-Help.sql \
+    0000-00-05-ElectrophysiologyTables.sql \
+    aosi.sql \
+    bmi.sql \
+    medical_history.sql \
+    mri_parameter_form.sql \
+    radiology_review.sql \
+    test_instrument.sql \
+    RB_files/*.sql > /docker-entrypoint-initdb.d/0000-compiled.sql
+
+RUN echo "Use LorisTest;" >> /docker-entrypoint-initdb.d/0001-paths.sql
+RUN echo "UPDATE Config SET Value='${BASE_DIR}/' WHERE ConfigID=(SELECT ID FROM ConfigSettings WHERE Name='base');" >> /docker-entrypoint-initdb.d/0001-paths.sql
+RUN echo "GRANT UPDATE,INSERT,SELECT,DELETE,DROP,CREATE TEMPORARY TABLES ON LorisTest.* TO 'SQLTestUser'@'%' IDENTIFIED BY 'TestPassword' WITH GRANT OPTION;" >> /docker-entrypoint-initdb.d/0004-sql-user.sql
+
+# Run the LORIS-MRI database installation script
+COPY install/install_database.sql /tmp/install_database.sql
+RUN echo "SET @email := 'root@localhost'; SET @project := 'loris'; SET @minc_dir = '/opt/minc/1.9.18';" >> 0001-paths.sql
+RUN cat /tmp/install_database.sql >> /docker-entrypoint-initdb.d/0001-paths.sql