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Repo variable and config updates #198

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Merged
merged 2 commits into from
Oct 6, 2023
Merged

Repo variable and config updates #198

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908249d
updated env variables
Oct 5, 2023
d2ed977
update ci workflow inputs
Oct 6, 2023
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3 changes: 1 addition & 2 deletions .envtemplate
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Expand Up @@ -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"
Expand All @@ -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 = []
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Should've noted this before, I would do AUTOBIDS_DICOM_PI_BLACKLIST="" (I don't think it will work properly otherwise)

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@kaitj kaitj Oct 5, 2023 •
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Hmm, I will leave this as is for now but make a mental note until we get a chance to try it out.


AUTOBIDS_HEURISTIC_GIT_URL="git@github.com:example/heuristics.git"
AUTOBIDS_HEURISTIC_REPO_PATH=""
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8 changes: 0 additions & 8 deletions .github/workflows/ci.yml
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Expand Up @@ -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]
Expand All @@ -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
Expand All @@ -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
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9 changes: 0 additions & 9 deletions .pylintrc
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6 changes: 2 additions & 4 deletions Dockerfile
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Expand Up @@ -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"]
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I think you can still use the entrypoint script if you want as long as CMD is the directive

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I'll give this a shot before merging in - if it works I'll add it back in

3 changes: 0 additions & 3 deletions MANIFEST.in
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5 changes: 0 additions & 5 deletions compose.yaml
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Expand Up @@ -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
Expand All @@ -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"
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36 changes: 0 additions & 36 deletions entrypoint.sh
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