updated env variables

Updated while meeting with Tristan, some additional notes:

Production
==========
can largely go from docker
need singularity installed
generate unit file so things run with systemd
crontab for relevant commands

DATALAD_SSH_IDENTITYFILE - needs access to graham
- generate new ssh key on machine and add to allowed_authorized users

sqlalchemy & redis set up on machine
cfmm2tar and tar2bids download -> set up large storage volume on cloud service, mount on machine, add to fstab

Need to be pointed at
=====================
git.sharcnet.ca
repository needs to be cloned on production machine

mailjet - free

Author: Jason Kai

.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=""

.pylintrc

@@ -67,7 +67,6 @@ 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 .
 
@@ -82,4 +81,4 @@ 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"]

Dockerfile

@@ -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"