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merge fast-api into dev

Merged Bryan BRANCOTTE requested to merge dev-fastapi into dev

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  • Bryan BRANCOTTE added 105 commits

    added 105 commits

    • 70ffa5e9 - Merge branch 'dev-fastapi' into 'dev-nuxt'
    • dc281cd9 - Fixed a few things that went bad in the merge
    • 8d6e5bd8 - A fantastic progress bar
    • 6088ff7a - re-organize commands to cache some layer
    • 77357c75 - backend does not need the client
    • cb719987 - re-organize commands to cache some layer, user non-root user (k8s compliance)
    • 7ab38b5e - build backend image (also used for celery) and client image
    • ce27e08b - add build stage
    • 0b04a136 - Flask dependencies are still needed
    • 31511da5 - get install_requires list from requirements.txt
    • 74c1ad4c - Copy data and download initTable.hdf5 on first startup. Celery wait after data to flagged as ready.
    • a760d11c - static client is not needed locally
    • 2363e44b - Merge branch 'dev-nuxt' into dev-fastapi-k8s
    • a33e1db4 - tests on centos and python3.X does not need docker image to be built
    • 142529fe - use nginx-unprivileged, adapte docker-compose
    • 2ab6cd76 - ignore .venv
    • 272decf8 - creating helm chart
    • 82374961 - add deploy ci job
    • 9114489b - keep data, only ignore initTable.hdf5, and project_* directories
    • 8e1c38c0 - add chart templates
    • 81ba73e4 - set back JASS_DATA_DIR to /code/data, remove data_persistent
    • 27a33e05 - add a pvc shared by all deployment in the namespace to store jass data
    • 16a42ab3 - add command to deploy app locally
    • 1d3d9ec9 - fetch password and cookie as asked by rabbitmq
    • 04d5840d - fetch data from API_URL, as backend is not always on localhost
    • 8c6764b7 - python 3.6 is deprecated. Add tests with 3.10
    • ba146935 - python 3.7 compatibility
    • 855ded5e - python 3.6 is deprecated, removing testing it into centos7
    • f8596427 - python 3.7 compatibility
    • 41522d57 - adapting tests to fastapi and pydantic
    • a925f773 - removing former mention of Flask
    • 8dfd3006 - needed by tests
    • a9b4fdf8 - run test in backend docker image
    • 06eef6bd - add service, and give 777 to egg dirs
    • 4e0a2d80 - wrap ids in PhenotypeIdList (a pydantic.BaseModel), provide nice error when...
    • 5e078a34 - updated test data
    • f9047e19 - update test data to pickel protocol 4, ability to generate test with pickel protocol 4
    • 50e777d9 - update serve to use uvicorn
    • 8f22e3fd - base64 -d for decode
    • 746e3a4d - constant name to be shared between all app in the namespace
    • 483ebf29 - Merge branch 'dev-fastapi-k8s-fixing-tests-2' into 'dev-fastapi-k8s'
    • 66a3d429 - delete rabbitmq pvc
    • c3a7275a - resilience to missing secret
    • 8b704cbc - manage the shared pvc manually
    • 1b2e775a - fix ingress prefix path
    • 7f73d438 - fix ingress prefix path
    • be098b97 - add notes.md
    • f3809815 - provide API_URL to client during build
    • 68b7a53e - move projects into a dedicated folder
    • 79292da8 - update api call after backend changes
    • 719127ed - change default endpoint
    • eeb0924b - parallel matrix for python versions
    • b662e2d5 - fixing typo in target
    • abfd94f9 - split rabbitmq credentials into multiple env variables
    • df7a3fd8 - provide rabbitMQ credentials
    • d067456a - Merge branch 'dev-fastapi-k8s-move-projects' into 'dev-fastapi-k8s'
    • 750aa0a4 - ignore projects/project_*
    • 75bc98b9 - test image right after building it
    • 96b9e860 - use less cpu
    • cac5e31d - render error message when failing
    • 73888cde - let nuxt handle 404, not nginx (and thus serve /projects/uid)
    • 13346097 - add .dockerignore
    • 6b0be27d - use node 16
    • e15e1fc8 - cleanup
    • 179d02af - prevent error when re-creating an already existing projects
    • 1457ec7c - keep a trace of last visit/load of a project, add a command to remove project...
    • 01ba95a4 - keep a trace of last visit/load of a project, add a command to remove project...
    • f9c40440 - keep __main__.py line ending as is
    • 38dbd44a - use default amount of days
    • ca313308 - start analysis only on creation of the project
    • 7213c9ff - testing presence of k8s secrets
    • 0fc8ab31 - set env
    • a352f037 - test when missing
    • b12bbbbb - fix conditional fetching of rabbitmq credentials
    • 6b82d022 - serve static files under /webui/, allows nuxt client to override base path with env var BASE_PATH
    • d67b3286 - no error when client not built
    • 449a0c58 - write permission is not needed
    • 463e561f - Fix parser help for clean-project-data
    • fcf2c306 - enable by default the static server
    • 098f6175 - re-use container created to build the static client to run `yarn dev`
    • 041f6f61 - prevent too long cronjob name
    • 9b7ff5f3 - less log for rabbitmq in the docker-compsoe
    • ac3c2353 - add mock gen cov data into test data
    • fdca2602 - remove ending - after truncating the name
    • b2bbfe85 - Merge branch 'add-gene-cov-into-test-data' into 'dev-fastapi-k8s'
    • cd085f23 - test docker deployment
    • 0d6647d0 - add bash
    • a6cb3aa9 - alpine install
    • 1ba6069c - docker-compose image
    • 3946c706 - always have the artifacts
    • 9224f8d7 - wait some time before testing the docker-compose, add comments
    • f2837649 - test the yarn dev client
    • 6d04c2aa - add curl
    • 106906d2 - remove test of client in development mode
    • 49fcc503 - test with static client, fixe path
    • b3b671a6 - clean every day
    • 33a1dba8 - add a sidekick pod
    • cff18bc3 - update python version compatibility
    • 79fa516b - update doc about docker-compose and kubernetes
    • 370009f2 - protect git history of doc/source/install.rst
    • c33036cb - typo
    • 917c219b - formatting
    • cd5051e4 - more storage
    • 0504a52a - Only keep for 3 days in dev
    • dddd0f04 - Merge branch 'dev-fastapi-k8s' into 'dev-fastapi'

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  • added 1 commit

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  • Bryan BRANCOTTE marked this merge request as ready

    marked this merge request as ready

  • Bryan BRANCOTTE added 3 commits

    added 3 commits

    • 693f6840 - 1 commit from branch dev
    • 645234bb - Merge branch 'dev' into dev-fastapi-merging-dev
    • 93416864 - Merge branch 'dev-fastapi-merging-dev' into 'dev-fastapi'

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  • Bryan BRANCOTTE mentioned in commit baf1f344

    mentioned in commit baf1f344

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