Merge pull request #198 from kaitj/maint/config-update

Repo variable and config updates

.envtemplate

@@ -15,7 +15,6 @@ AUTOBIDS_DICOM_SERVER_STUDYINSTANCEUID_WILDCARD="" # Falsy
 AUTOBIDS_CFMM2TAR_PATH="/images/cfmm2tar.sif"
 AUTOBIDS_CFMM2TAR_BINDS="/home:/home,/tmp:/tmp"
 AUTOBIDS_CFMM2TAR_DOWNLOAD_DIR=""
-AUTOBIDS_CFMM2TAR_STORAGE_DIR=""
 AUTOBIDS_CFMM2TAR_TIMEOUT=100000
 AUTOBIDS_TAR2BIDS_PATH="/images/tar2bids.sif"
 AUTOBIDS_TAR2BIDS_BINDS="/home:/home,/tmp:/tmp"
@@ -35,7 +34,7 @@ AUTOBIDS_ARCHIVE_SSH_PORT=2222
 AUTOBIDS_ARCHIVE_SSH_KEY="~/.ssh/id_rsa.pub"
 AUTOBIDS_ARCHIVE_TIMEOUT=100000
 
-AUTOBIDS_DICOM_PI_BLACKLIST = []
+AUTOBIDS_DICOM_PI_BLACKLIST = [] 
 
 AUTOBIDS_HEURISTIC_GIT_URL="git@github.com:example/heuristics.git"
 AUTOBIDS_HEURISTIC_REPO_PATH=""

.github/workflows/ci.yml

@@ -16,9 +16,6 @@ jobs:
     name: Lint code
     if: github.event.pull_request.merged == false
     runs-on: ubuntu-latest
-    permissions:
-      actions: write
-      contents: read
     strategy:
       matrix:
         python-version: [3.8]
@@ -28,7 +25,6 @@ jobs:
         uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.2.1
         with:
           python-version: ${{ matrix.python-version }}
-          token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Run ruff
         run: poetry run ruff autobidsportal
@@ -55,16 +51,12 @@ jobs:
       matrix:
         python-version: [3.8]
         redis-version: [6]
-    permissions:
-      actions: write
-      contents: read
 
     steps:
       - name: Setup environment
         uses: khanlab/actions/.github/actions/action-setup_task-installPyProject@v0.2.1
         with:
           python-version: ${{ matrix.python-version }}
-          token: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Start Redis
         uses: supercharge/redis-github-action@1.1.0

Dockerfile

@@ -67,19 +67,17 @@ COPY --from=apptainer-builds /opt/apptainer-images /opt/apptainer-images/
 
 ENV OTHER_OPTIONS='--tls-aes'
 WORKDIR /opt/autobidsportal
-COPY ./entrypoint.sh /opt/autobidsportal/entrypoint.sh
 COPY ./autobidsportal.ini.example autobidsportal.ini
 COPY ./bids_form.py .
 
 RUN git config --system user.name "Autobids Portal" \
     && git config --system user.email "autobids@dummy.com" \
     && WHEEL=$(ls /opt/wheels | grep whl) \
     && pip install --no-cache-dir "/opt/wheels/${WHEEL}[deploy]" \
-    && rm -r /opt/wheels \
-    && chmod +x /opt/autobidsportal/entrypoint.sh
+    && rm -r /opt/wheels 
 
 ENV DCM4CHE_VERSION=5.24.1
 ENV PATH=/apps/dcm4che/dcm4che-${DCM4CHE_VERSION}/bin:/apps/DicomRaw:/apps/cfmm2tar:/opt/apptainer/bin:$PATH
 ENV _JAVA_OPTIONS="-Xmx2048m"
 
-ENTRYPOINT ["/opt/autobidsportal/entrypoint.sh"]
+CMD ["uwsgi", "--ini=autobidsportal.ini"]

compose.yaml

@@ -11,7 +11,6 @@ services:
       AUTOBIDS_LOG_LEVEL: INFO
       AUTOBIDS_ROOT_URL: autobidsportal
       AUTOBIDS_CFMM2TAR_DOWNLOAD_DIR: /cfmm2tar-download
-      AUTOBIDS_CFMM2TAR_STORAGE_DIR: /tar-files
       AUTOBIDS_TAR2BIDS_DOWNLOAD_DIR: /datasets
       AUTOBIDS_TAR2BIDS_TEMP_DIR: /tmp
       AUTOBIDS_HEURISTIC_REPO_PATH: /home
@@ -37,10 +36,6 @@ services:
       AUTOBIDS_DICOM_SERVER_PASSWORD: "password"
       AUTOBIDS_DICOM_SERVER_TLS: "true"
       AUTOBIDS_DICOM_SERVER_STUDYINSTANCEUID_WILDCARD: "false"
-      AUTOBIDS_GITLAB_ACTIVE: "true"
-      AUTOBIDS_GITLAB_URL: "http://127.0.0.1:8080"
-      AUTOBIDS_GITLAB_TOKEN: "BFavxxb7gAodznnorhv7"
-      AUTOBIDS_GITHUB_ACTIVE: "false"
       GIT_AUTHOR_NAME: "Autobids Portal"
       GIT_AUTHOR_EMAIL: "autobids@example.com"
       GIT_COMMITER_NAME: "Autobids Portal"