diff --git a/.github/workflows/test_backend.yaml b/.github/workflows/test_backend.yaml index 19c1383..e984598 100644 --- a/.github/workflows/test_backend.yaml +++ b/.github/workflows/test_backend.yaml @@ -19,6 +19,7 @@ jobs: - name: Checkout code uses: actions/checkout@v3 + - name: Start test docker services run: | make start-test-infra @@ -42,7 +43,6 @@ jobs: until nc -z river-localstack 4566; do sleep 1; done - name: Run tests - uses: prefix-dev/setup-pixi@v0.8.1 env: GH_USERNAME: ${{ secrets.GH_USERNAME }} GH_ACCESS_TOKEN: ${{ secrets.GH_ACCESS_TOKEN }} diff --git a/LICENSE b/LICENSE index bfef380..e72bfdd 100644 --- a/LICENSE +++ b/LICENSE @@ -1,437 +1,674 @@ -Attribution-NonCommercial-ShareAlike 4.0 International - -======================================================================= - -Creative Commons Corporation ("Creative Commons") is not a law firm and -does not provide legal services or legal advice. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + Copyright (C) + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. \ No newline at end of file diff --git a/Makefile b/Makefile index 33e1719..6c9a631 100644 --- a/Makefile +++ b/Makefile @@ -8,6 +8,7 @@ SLURM_IMAGE := nttg8100/river-slurm:$(SLURM_VERSION) LOCALSTACK_IMAGE := localstack/localstack:latest NODE_VERSION := 20.17.0 PYTHON_VERSION := 3.12.11 +PYPY_VERSION := 3.11-v7.3.20-linux64 # DEV ## Setup the dependencies @@ -15,6 +16,13 @@ PYTHON_VERSION := 3.12.11 ~/.pixi/bin/pixi: which pixi || curl -fsSL https://pixi.dev/install.sh | bash +# install pypy +.PHONY: install-backend-deps +backend/pypy${PYPY_VERSION}/bin/pypy3: + wget https://downloads.python.org/pypy/pypy${PYPY_VERSION}.tar.bz2 -O backend/pypy${PYPY_VERSION}.tar.bz2 + tar xf backend/pypy${PYPY_VERSION}.tar.bz2 -C backend + cd backend && ./pypy${PYPY_VERSION}/bin/pypy3 -m ensurepip && ./pypy${PYPY_VERSION}/bin/pypy3 -mpip install -r requirements.txt + dev-frontend: ~/.pixi/bin/pixi cd frontend && pixi run npm install -f @@ -37,17 +45,17 @@ start-localstack: start-dev-db: docker compose up dev-db -d -migrate-dev-db: - cd backend && APP_ENV="dev" pixi run aerich init-db || echo "DB already existed" - cd backend && APP_ENV="dev" pixi run aerich migrate || echo "Nothing to migrate" - cd backend && APP_ENV="dev" pixi run aerich upgrade +migrate-dev-db: backend/pypy${PYPY_VERSION}/bin/pypy3 + cd backend && APP_ENV="dev" ./pypy${PYPY_VERSION}/bin/pypy3 -m aerich init-db || echo "DB already existed" + cd backend && APP_ENV="dev" ./pypy${PYPY_VERSION}/bin/pypy3 -m aerich migrate || echo "Nothing to migrate" + cd backend && APP_ENV="dev" ./pypy${PYPY_VERSION}/bin/pypy3 -m aerich upgrade start-test-db: docker compose up test-db -d -migrate-test-db: ~/.pixi/bin/pixi - cd backend && pixi run aerich init-db || echo "DB already existed" - cd backend && pixi run aerich upgrade +migrate-test-db: backend/pypy${PYPY_VERSION}/bin/pypy3 + cd backend && ./pypy${PYPY_VERSION}/bin/pypy3 -m aerich init-db || echo "DB already existed" + cd backend && ./pypy${PYPY_VERSION}/bin/pypy3 -m aerich upgrade format-backend: black . --line-length 120 @@ -62,11 +70,11 @@ start-dev-infra: start-slurm start-redis start-dev-db @echo "Start infra setup" ## Start dev -start-backend: ~/.pixi/bin/pixi - cd backend && pixi run python dev.py +start-backend: backend/pypy${PYPY_VERSION}/bin/pypy3 + cd backend && APP_ENV=dev ./pypy${PYPY_VERSION}/bin/pypy -m socketify app.main:app --reload start-celery: ~/.pixi/bin/pixi - cd backend && APP_ENV=dev pixi run celery -A app.celery worker --loglevel=info + cd backend && APP_ENV=dev ./pypy${PYPY_VERSION}/bin/pypy -m celery -A app.celery worker --loglevel=info start-frontend: ~/.pixi/bin/pixi cd frontend && pixi run npm start @@ -80,30 +88,33 @@ start-traefik: ~/.pixi/bin/pixi .PHONY: start-test-infra test-auth test-health test-organization test-all start-test-infra: start-test-db start-redis start-localstack start-slurm @echo "Start test infra setup" - -test-auth: - cd backend && pixi run pytest --cov=app/service_auth app/service_auth --cov-report=term-missing -vvvvvv -test-health: - cd backend && pixi run pytest --cov=app/service_health app/service_health --cov-report=term-missing -vvvvvv +install-test-deps: backend/pypy${PYPY_VERSION}/bin/pypy3 + cd backend && ./pypy${PYPY_VERSION}/bin/pypy3 -mpip install pytest pytest-cov pytest-asyncio + +test-auth: install-test-deps + cd backend && ./pypy${PYPY_VERSION}/bin/pypy3 -m pytest --cov=app/service_auth app/service_auth --cov-report=term-missing -vvvvvv + +test-health: install-test-deps + cd backend && ./pypy${PYPY_VERSION}/bin/pypy3 -m pytest --cov=app/service_health app/service_health --cov-report=term-missing -vvvvvv -test-organization: - cd backend && pixi run pytest --cov=app/service_organization app/service_organization --cov-report=term-missing -vvvvvv +test-organization: install-test-deps + cd backend && ./pypy${PYPY_VERSION}/bin/pypy3 -m pytest --cov=app/service_organization app/service_organization --cov-report=term-missing -vvvvvv -test-credential: - cd backend && pixi run pytest --cov=app/service_credential app/service_credential --cov-report=term-missing -vvvvvv -k "github" +test-credential: install-test-deps + cd backend && ./pypy${PYPY_VERSION}/bin/pypy3 -m pytest --cov=app/service_credential app/service_credential --cov-report=term-missing -vvvvvv -k "github" -test-analysis: - cd backend && pixi run pytest --cov=app/service_analysis app/service_analysis --cov-report=term-missing -vvvvvv +test-analysis: install-test-deps + cd backend && ./pypy${PYPY_VERSION}/bin/pypy3 -m pytest --cov=app/service_analysis app/service_analysis --cov-report=term-missing -vvvvvv -test-project: - cd backend && pixi run pytest --cov=app/service_project app/service_project --cov-report=term-missing -vvvvvv +test-project: install-test-deps + cd backend && ./pypy${PYPY_VERSION}/bin/pypy3 -m pytest --cov=app/service_project app/service_project --cov-report=term-missing -vvvvvv -test-storage: - cd backend && pixi run pytest --cov=app/service_storage app/service_storage --cov-report=term-missing -vvvvvv +test-storage: install-test-deps + cd backend && ./pypy${PYPY_VERSION}/bin/pypy3 -m pytest --cov=app/service_storage app/service_storage --cov-report=term-missing -vvvvvv -test-job: - cd backend && pixi run pytest --cov=app/service_job app/service_job --cov-report=term-missing -vvvvvv +test-job: install-test-deps + cd backend && ./pypy${PYPY_VERSION}/bin/pypy3 -m pytest --cov=app/service_job app/service_job --cov-report=term-missing -vvvvvv test-all: test-health test-auth test-organization test-credential test-analysis test-project echo "Running all tests..." diff --git a/README.md b/README.md index 3155d4a..47ab4d1 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,8 @@ # Rapid Integration and Visualization for Enhanced Research Platform + +![RIVER Platform Overview](docs/images/graphical_abstract.png) + + Rapid Integration and Visualization for Enhanced Research (RIVER) is an integrated ecosystem for data and computing, designed with a monolithic architecture using a Python backend ("backsheep") and a JavaScript frontend ("vite"). While the current structure is monolithic, it is architected for potential refactoring into microservices. For scientific applications, River aims to be lightweight and serve as a system controller—connecting data, software, and users. For quick recorded video demo, follow here: https://www.youtube.com/watch?v=boabEFNIkNA @@ -179,13 +183,6 @@ Refer to the `Makefile` for additional targets and details. ## License -[![CC BY-NC-SA 4.0][cc-by-nc-sa-shield]][cc-by-nc-sa] - -This work is licensed under a -[Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License][cc-by-nc-sa]. - -[![CC BY-NC-SA 4.0][cc-by-nc-sa-image]][cc-by-nc-sa] +This project is licensed under the GNU General Public License v3.0 - see the [LICENSE](LICENSE) file for details. -[cc-by-nc-sa]: http://creativecommons.org/licenses/by-nc-sa/4.0/ -[cc-by-nc-sa-image]: https://licensebuttons.net/l/by-nc-sa/4.0/88x31.png -[cc-by-nc-sa-shield]: https://img.shields.io/badge/License-CC%20BY--NC--SA%204.0-lightgrey.svg +[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) diff --git a/backend/.dockerignore b/backend/.dockerignore index a19be95..a5d9ca8 100644 --- a/backend/.dockerignore +++ b/backend/.dockerignore @@ -6,4 +6,7 @@ env **/*.pyc **/*.md **/__pycache__ -*.sqlite3* \ No newline at end of file +*.sqlite3* +pypy* +.pixi +bombardier-linux-amd64 \ No newline at end of file diff --git a/backend/.gitignore b/backend/.gitignore index 18e076e..90eaee5 100644 --- a/backend/.gitignore +++ b/backend/.gitignore @@ -102,3 +102,6 @@ venv.bak/ .pytest # pixi environments .pixi/* !.pixi/config.toml +bombardier-linux-amd64 +*tar.bz2 +pypy3* \ No newline at end of file diff --git a/backend/Dockerfile b/backend/Dockerfile index 708e89f..71deeb3 100644 --- a/backend/Dockerfile +++ b/backend/Dockerfile @@ -1,19 +1,25 @@ -# Build the Server -FROM python:3.12.11-slim AS server_builder +FROM pypy:3.11-slim + ENV PYTHONUNBUFFERED=1 WORKDIR /app -COPY requirements.txt . -RUN pip install --upgrade pip && pip install -r requirements.txt -COPY . . +RUN apt-get update && apt-get install -y \ + build-essential pkg-config \ + libffi-dev libssl-dev libsodium-dev make libpq-dev \ + && rm -rf /var/lib/apt/lists/* + +COPY requirements.txt . +RUN pip install --upgrade pip && pip install --no-cache-dir -r requirements.txt -# Entrypoint script runs migrations then starts server +COPY app ./app +COPY domain ./domain +COPY migrations ./migrations +COPY pyproject.toml . +COPY settings.yaml . COPY run_server.sh ./ RUN chmod +x run_server.sh - +RUN apt-get update && apt-get install -y libuv1 EXPOSE 8000 -# Run as non-root in production RUN useradd -m appuser -USER appuser - +USER appuser \ No newline at end of file diff --git a/backend/app/conftest.py b/backend/app/conftest.py index 9f03e78..25983dd 100644 --- a/backend/app/conftest.py +++ b/backend/app/conftest.py @@ -270,7 +270,7 @@ async def user_aws(test_client, cookies_admin, user_aws_arn): } aws = await create_instance( test_client, - f"/api/users/creds/{cred["id"]}/", + f"/api/users/creds/{cred['id']}/", aws_data, cookies_admin, 201, @@ -311,7 +311,7 @@ async def org_aws(test_client, organization, cookies_org_manager): } aws = await create_instance( test_client, - f"/api/orgs/{organization}/creds/{cred["id"]}/", + f"/api/orgs/{organization}/creds/{cred['id']}/", aws_data, cookies_org_manager, 201, diff --git a/backend/app/db.py b/backend/app/db.py index 3491f93..6918c66 100644 --- a/backend/app/db.py +++ b/backend/app/db.py @@ -13,7 +13,7 @@ def get_db_url(): if ENV == "prod": logger.info("Using PostgreSQL database") return ( - f"postgres://{os.getenv('POSTGRES_USER', 'river')}:" + f"psycopg://{os.getenv('POSTGRES_USER', 'river')}:" f"{os.getenv('POSTGRES_PASSWORD', 'password')}@" f"{os.getenv('POSTGRES_HOST', 'localhost')}:" f"{os.getenv('POSTGRES_PORT', '5432')}/" @@ -21,9 +21,9 @@ def get_db_url(): ) elif ENV == "test": logger.info("Using PostgreSQL database for testing") - return "postgres://river:password@localhost:5434/river_test" + return "psycopg://river:password@localhost:5434/river_test" logger.info("Using PostgreSQL database for development") - return "postgres://river:password@localhost:5433/river_dev" + return "psycopg://river:password@localhost:5433/river_dev" MODELS = [ diff --git a/backend/app/main.py b/backend/app/main.py index f7bb5fa..d5ebdaf 100644 --- a/backend/app/main.py +++ b/backend/app/main.py @@ -86,8 +86,8 @@ async def configure_redis(app): JobController, ] ) - -# Database +print("Failed here") +# Database 2 3 register_tortoise( app, config=TORTOISE_ORM, diff --git a/backend/app/service_analysis/controller.py b/backend/app/service_analysis/controller.py index fd20c1b..f4858fa 100644 --- a/backend/app/service_analysis/controller.py +++ b/backend/app/service_analysis/controller.py @@ -95,7 +95,7 @@ async def get_analysis( return ok( { - "items": result, + "item": result, "page": page, "page_size": page_size, "total": total_count, diff --git a/backend/app/service_analysis/tests/test_analysis.py b/backend/app/service_analysis/tests/test_analysis.py index 764a33a..aa137ee 100644 --- a/backend/app/service_analysis/tests/test_analysis.py +++ b/backend/app/service_analysis/tests/test_analysis.py @@ -51,16 +51,16 @@ async def test_basic_analysis( # list instance as admin res_admin = await list_instance(test_client, f"{BASE_URL}/", cookies_admin, 200) - assert len(res_admin["items"]) == 1 - assert_instance_fields(res_admin["items"][0], EXPECTED_FIELDS) + assert len(res_admin["item"]) == 1 + assert_instance_fields(res_admin["item"][0], EXPECTED_FIELDS) # list instance as contributor res_contrib = await list_instance(test_client, f"{BASE_URL}/", cookies_contributor, 200) - assert len(res_contrib["items"]) == 1 - assert_instance_fields(res_contrib["items"][0], EXPECTED_FIELDS) + assert len(res_contrib["item"]) == 1 + assert_instance_fields(res_contrib["item"][0], EXPECTED_FIELDS) # delete as admin (should fail) - delete_url = f'{BASE_URL}/{res_admin["items"][0]["id"]}/' + delete_url = f"{BASE_URL}/{res_admin['item'][0]['id']}/" await delete_instance(test_client, delete_url, cookies_admin, 204) # delete as superuser (should pass) @@ -93,23 +93,23 @@ async def get_page(page, page_size): # page 1 data = await get_page(1, 10) assert data["page"] == 1 - assert len(data["items"]) == 10 + assert len(data["item"]) == 10 # page 2 data = await get_page(2, 10) assert data["page"] == 2 - assert len(data["items"]) == 10 + assert len(data["item"]) == 10 # last page data = await get_page(4, 10) assert data["page"] == 4 - assert len(data["items"]) == 0 + assert len(data["item"]) == 0 # too large page data = await get_page(99, 10) - assert data["items"] == [] + assert data["item"] == [] # search by url res = await test_client.get(f"{BASE_URL}/", query={"search": "repo-1"}, cookies=cookies_admin) data = await res.json() assert res.status == 200 - assert any("repo-1" in item["url"] for item in data["items"]) + assert any("repo-1" in item["url"] for item in data["item"]) diff --git a/backend/app/service_credential/tests/test_aws.py b/backend/app/service_credential/tests/test_aws.py index a96702a..b6ea664 100644 --- a/backend/app/service_credential/tests/test_aws.py +++ b/backend/app/service_credential/tests/test_aws.py @@ -98,7 +98,7 @@ async def test_credential_aws( # success aws_instance = await create_instance( test_client, - f"{BASE_URL}/users/creds/{cred_instance_user_aws["id"]}/", + f"{BASE_URL}/users/creds/{cred_instance_user_aws['id']}/", aws_data, cookies=cookies_admin, ) @@ -117,7 +117,7 @@ async def test_credential_aws( bad_data["aws"]["endpoint_url"] = "http://localhost:8081" instance = await create_instance( test_client, - f"{BASE_URL}/users/creds/{cred_instance_user_aws["id"]}/", + f"{BASE_URL}/users/creds/{cred_instance_user_aws['id']}/", bad_data, cookies_admin, 400, @@ -149,7 +149,7 @@ async def test_credential_aws( # success aws_instance = await create_instance( test_client, - f"{BASE_URL}/orgs/{organization}/creds/{cred_instance_org_aws["id"]}/", + f"{BASE_URL}/orgs/{organization}/creds/{cred_instance_org_aws['id']}/", aws_data, cookies=cookies_org_manager, ) @@ -168,7 +168,7 @@ async def test_credential_aws( bad_data["aws"]["endpoint_url"] = "http://localhost:8081" instance = await create_instance( test_client, - f"{BASE_URL}/orgs/{organization}/creds/{cred_instance_org_aws["id"]}/", + f"{BASE_URL}/orgs/{organization}/creds/{cred_instance_org_aws['id']}/", bad_data, cookies_org_manager, 400, @@ -254,7 +254,7 @@ async def test_credential_aws( aws_data["aws"]["endpoint_url"] = os.environ["ENDPOINT_URL"] aws_instance = await update_instance( test_client, - f"{BASE_URL}/users/creds/{cred_instance_user_aws["id"]}/", + f"{BASE_URL}/users/creds/{cred_instance_user_aws['id']}/", aws_data, cookies=cookies_admin, expected_status=201, @@ -286,7 +286,7 @@ async def test_credential_aws( aws_data["aws"]["endpoint_url"] = os.environ["ENDPOINT_URL"] aws_instance = await update_instance( test_client, - f"{BASE_URL}/orgs/{organization}/creds/{cred_instance_org_aws["id"]}/", + f"{BASE_URL}/orgs/{organization}/creds/{cred_instance_org_aws['id']}/", aws_data, cookies=cookies_org_manager, expected_status=201, @@ -303,11 +303,11 @@ async def test_credential_aws( # Delete await delete_instance( test_client, - f"{BASE_URL}/users/creds/{cred_instance_user_aws["id"]}/", + f"{BASE_URL}/users/creds/{cred_instance_user_aws['id']}/", cookies_admin, ) await delete_instance( test_client, - f"{BASE_URL}/orgs/{organization}/creds/{cred_instance_org_aws["id"]}/", + f"{BASE_URL}/orgs/{organization}/creds/{cred_instance_org_aws['id']}/", cookies_org_manager, ) diff --git a/backend/app/service_credential/tests/test_base.py b/backend/app/service_credential/tests/test_base.py index 391d8c5..7c7af97 100644 --- a/backend/app/service_credential/tests/test_base.py +++ b/backend/app/service_credential/tests/test_base.py @@ -46,7 +46,7 @@ async def test_credential_base( error = await update_instance( test_client, - f"{BASE_URL}/users/creds/{cred_instance_user_aws["id"]}/", + f"{BASE_URL}/users/creds/{cred_instance_user_aws['id']}/", bad_data, cookies_admin, 400, @@ -65,7 +65,7 @@ async def test_credential_base( } error = await update_instance( test_client, - f"{BASE_URL}/users/creds/{cred_instance_user_aws["id"]}/", + f"{BASE_URL}/users/creds/{cred_instance_user_aws['id']}/", bad_data, cookies_admin, 400, diff --git a/backend/app/service_job/controller.py b/backend/app/service_job/controller.py index 32e5d60..3947c13 100644 --- a/backend/app/service_job/controller.py +++ b/backend/app/service_job/controller.py @@ -149,7 +149,7 @@ async def list_web_job( return ok( { - "items": result, + "item": result, "page": page, "page_size": page_size, "total": total_count, diff --git a/backend/app/service_job/tests/test_api_web_job.py b/backend/app/service_job/tests/test_api_web_job.py index 1e078ff..94a5a8b 100644 --- a/backend/app/service_job/tests/test_api_web_job.py +++ b/backend/app/service_job/tests/test_api_web_job.py @@ -80,8 +80,8 @@ async def test_create_list_job( ) assert res.status == 200 result = await res.json() - assert "items" in result - assert len(result["items"]) == 5 + assert "item" in result + assert len(result["item"]) == 5 assert result["total"] >= 15 # List jobs with pagination (page=3, page_size=5) @@ -92,8 +92,8 @@ async def test_create_list_job( ) assert res.status == 200 result = await res.json() - assert "items" in result - assert len(result["items"]) == 5 + assert "item" in result + assert len(result["item"]) == 5 # Search for a specific job by name search_name = "customer-03" @@ -104,7 +104,7 @@ async def test_create_list_job( ) assert res.status == 200 result = await res.json() - assert any(job["name"] == search_name for job in result["items"]) + assert any(job["name"] == search_name for job in result["item"]) # get log of current running job # TODO: test job log diff --git a/backend/app/service_organization/controller.py b/backend/app/service_organization/controller.py index 3842d0b..67638d6 100644 --- a/backend/app/service_organization/controller.py +++ b/backend/app/service_organization/controller.py @@ -69,7 +69,7 @@ async def list_organization( return ok( { - "items": result, + "item": result, "page": page, "page_size": page_size, "total": total_count, diff --git a/backend/app/service_organization/tests/test_organization.py b/backend/app/service_organization/tests/test_organization.py index 1339057..96a59dd 100644 --- a/backend/app/service_organization/tests/test_organization.py +++ b/backend/app/service_organization/tests/test_organization.py @@ -45,8 +45,8 @@ async def check_page(page, expected_count): res_data = await res.json() assert res.status == 200 assert res_data["page"] == page - assert len(res_data["items"]) == expected_count - for item in res_data["items"]: + assert len(res_data["item"]) == expected_count + for item in res_data["item"]: assert_instance_fields(item, expected_fields) await check_page(1, 10) @@ -58,22 +58,22 @@ async def check_page(page, expected_count): res_data = await res.json() assert res.status == 200 assert res_data["total"] == 1 - assert "29" in res_data["items"][0]["name"] + assert "29" in res_data["item"][0]["name"] # search by description res = await test_client.get(f"{BASE_URL}", query={"search": "Description-1"}, cookies=cookies_org_manager) res_data = await res.json() assert res.status == 200 assert res_data["total"] == 11 - assert len(res_data["items"]) == 11 - for item in res_data["items"]: + assert len(res_data["item"]) == 11 + for item in res_data["item"]: assert_instance_fields(item, expected_fields) # Update - update_org = res_data["items"][0] + update_org = res_data["item"][0] updated_org = await update_instance( test_client, - f"{BASE_URL}/{update_org["id"]}/", + f"{BASE_URL}/{update_org['id']}/", data={ "name": "New name", "description": "New description", @@ -90,7 +90,7 @@ async def check_page(page, expected_count): # delete 1 remains 29 await delete_instance( test_client, - f"{BASE_URL}/{update_org["id"]}/", + f"{BASE_URL}/{update_org['id']}/", cookies=cookies_org_manager, ) res = await test_client.get( @@ -99,4 +99,4 @@ async def check_page(page, expected_count): cookies=cookies_org_manager, ) res_data = await res.json() - assert len(res_data["items"]) == 29 + assert len(res_data["item"]) == 29 diff --git a/backend/app/service_project/controller.py b/backend/app/service_project/controller.py index 4d300d8..e3aac61 100644 --- a/backend/app/service_project/controller.py +++ b/backend/app/service_project/controller.py @@ -148,7 +148,7 @@ async def list_projects( return ok( { - "items": result, + "item": result, "page": page, "page_size": page_size, "total": total_count, diff --git a/backend/app/service_project/tests/test_project.py b/backend/app/service_project/tests/test_project.py index 6117db2..6d0c08a 100644 --- a/backend/app/service_project/tests/test_project.py +++ b/backend/app/service_project/tests/test_project.py @@ -184,8 +184,8 @@ async def test_project_CRUD_and_search( res_data = await res.json() assert res.status == 200 assert res_data["page"] == 1 - assert len(res_data["items"]) == 5 - for item in res_data["items"]: + assert len(res_data["item"]) == 5 + for item in res_data["item"]: assert_instance_fields(item, expected_fields) # second page @@ -193,8 +193,8 @@ async def test_project_CRUD_and_search( res_data = await res.json() assert res.status == 200 assert res_data["page"] == 2 - assert len(res_data["items"]) == 3 - for item in res_data["items"]: + assert len(res_data["item"]) == 3 + for item in res_data["item"]: assert_instance_fields(item, expected_fields) # Search name @@ -203,7 +203,7 @@ async def test_project_CRUD_and_search( res_data = await res.json() assert res.status == 200 assert res_data["total"] == 2 - assert "public project 1" in res_data["items"][0]["name"] + assert "public project 1" in res_data["item"][0]["name"] # failed due to invalid format filters res = await test_client.get( @@ -233,7 +233,7 @@ async def test_project_CRUD_and_search( res_data = await res.json() assert res.status == 200 assert res_data["total"] == 2 - assert "public project 1" in res_data["items"][0]["name"] + assert "public project 1" in res_data["item"][0]["name"] # Search by role res = await test_client.get( @@ -265,8 +265,8 @@ async def test_project_CRUD_and_search( res_data = await res.json() assert res.status == 200 assert res_data["total"] == 8 - assert len(res_data["items"]) == 5 - for item in res_data["items"]: + assert len(res_data["item"]) == 5 + for item in res_data["item"]: assert_instance_fields(item, expected_fields) # Get by desc sorting (asc by default) @@ -283,13 +283,13 @@ async def test_project_CRUD_and_search( res_data = await res.json() assert res.status == 200 assert res_data["total"] == 8 - assert len(res_data["items"]) == 5 - for item in res_data["items"]: + assert len(res_data["item"]) == 5 + for item in res_data["item"]: assert_instance_fields(item, expected_fields) - assert res_data["items"][0]["name"] == "user public project 1" # this one if not sorting will be last + assert res_data["item"][0]["name"] == "user public project 1" # this one if not sorting will be last # Test RBAC for update/delete - project_id = res_data["items"][0]["id"] + project_id = res_data["item"][0]["id"] update_data = {"name": "Edited name", "description": "Edited description"} for cookies in [cookies_contributor, cookies_viewer]: diff --git a/backend/app/utils/executor/ssh.py b/backend/app/utils/executor/ssh.py index 0150e1a..918cfb5 100644 --- a/backend/app/utils/executor/ssh.py +++ b/backend/app/utils/executor/ssh.py @@ -213,6 +213,7 @@ def _create_traefik_config(job: WebJob): config_path = os.path.join(TRAEFIK_DYNAMIC_FOLDER, f"{job.id}.yaml") if not os.path.exists(config_path) and job.local_port: with open(config_path, "w") as f: + tls_block = "tls:\n certResolver: myresolver" if IS_SSL else "" if not job.analysis.has_base_url: f.write( f"""http: @@ -226,7 +227,7 @@ def _create_traefik_config(job: WebJob): - job-auth-{job.id} - strip-job-{job.id} - job-header-{job.id} - {"tls:\n certResolver: myresolver" if IS_SSL else ""} + {tls_block} middlewares: job-auth-{job.id}: @@ -265,7 +266,7 @@ def _create_traefik_config(job: WebJob): middlewares: - job-auth-{job.id} - job-header-{job.id} - {"tls:\n certResolver: myresolver" if IS_SSL else ""} + {tls_block} middlewares: job-auth-{job.id}: @@ -304,7 +305,7 @@ def _create_traefik_config(job: WebJob): out, error, exit_code = self._run_cmd( f"squeue --job {job.external_id} --format='%.18i %.9T %.10M %.20V %R' --noheader | head -n1" ) - logger.info(f"squeue output: {out.strip() if out else ""}, error: {error.strip()}, exit_code: {exit_code}") + logger.info(f"squeue output: {out.strip() if out else ''}, error: {error.strip()}, exit_code: {exit_code}") if exit_code == 0 and out.strip(): _get_update_info(update_info, out, job, method="squeue") @@ -518,6 +519,9 @@ def _generate_script(self, server: str, job: WebJob, params: dict) -> str: pixi global install $pkg fi done +pixi config append default-channels bioconda --global +pixi config append default-channels conda-forge --global +pixi global install nextflow jq git singularity python=3.14 # === Install Goofys if missing === if [ ! -f "$GOOFYS_PATH" ]; then diff --git a/backend/dev.py b/backend/dev.py deleted file mode 100644 index 9625755..0000000 --- a/backend/dev.py +++ /dev/null @@ -1,40 +0,0 @@ -""" -Runs the application for local development. This file should not be used to start the -application for production. - -Refer to https://www.uvicorn.org/deployment/ for production deployments. -""" - -import os - -import uvicorn -from blacksheep.server.env import get_global_route_prefix -from rich.console import Console - -try: - import uvloop -except ModuleNotFoundError: - pass -else: - uvloop.install() - -if __name__ == "__main__": - os.environ["APP_ENV"] = "dev" - os.environ["APP_SHOW_ERROR_DETAILS"] = "1" - port = int(os.environ.get("APP_PORT", 8000)) - - prefix = get_global_route_prefix() - if prefix: - prefix = prefix.strip("/") + "/" - console = Console() - console.rule("[bold yellow]Running for local development", align="left") - console.print(f"[bold yellow]Visit http://localhost:{port}/{prefix}docs/\n") - - uvicorn.run( - "app.main:app", - host="0.0.0.0", - port=port, - lifespan="on", - log_level="info", - reload=True, - ) diff --git a/backend/perf/.gitattributes b/backend/perf/.gitattributes new file mode 100644 index 0000000..887a2c1 --- /dev/null +++ b/backend/perf/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true diff --git a/backend/perf/.gitignore b/backend/perf/.gitignore new file mode 100644 index 0000000..78701b7 --- /dev/null +++ b/backend/perf/.gitignore @@ -0,0 +1,6 @@ +# pixi environments +.pixi/* +!.pixi/config.toml +bombardier-linux-amd64 +*tar.bz2 +pypy3* \ No newline at end of file diff --git a/backend/perf/app.py b/backend/perf/app.py new file mode 100644 index 0000000..262cd3f --- /dev/null +++ b/backend/perf/app.py @@ -0,0 +1,9 @@ +from blacksheep import Application, get, json, Response + + +app = Application() + + +@get("/") +async def main() -> Response: + return json({"word": "Hello, world."}) diff --git a/backend/perf/install.sh b/backend/perf/install.sh new file mode 100644 index 0000000..d1db931 --- /dev/null +++ b/backend/perf/install.sh @@ -0,0 +1,82 @@ +# app.py +# from blacksheep import Application, get, json, Response +# app = Application() +# @get("/") +# async def main() -> Response: +# return json({"word": "Hello, world."}) + + +wget https://downloads.python.org/pypy/pypy3.11-v7.3.20-linux64.tar.bz2 +tar xf pypy3.11-v7.3.20-linux64.tar.bz2 +./pypy3.11-v7.3.20-linux64/bin/pypy -m ensurepip +./pypy3.11-v7.3.20-linux64/bin/pypy -mpip install -U pip wheel +./pypy3.11-v7.3.20-linux64/bin/pypy -mpip install -r requirements.txt + + + +# pypy3.11 socketify +./pypy3.11-v7.3.20-linux64/bin/pypy -m socketify app:app --worker 2 --port 8000 +# Statistics Avg Stdev Max +# Reqs/sec 74211.09 12903.77 100972.59 +# Latency 26.98ms 51.94ms 2.11s +# Latency Distribution +# 50% 20.63ms +# 75% 25.27ms +# 90% 27.38ms +# 95% 28.58ms +# 99% 46.24ms +# HTTP codes: +# 1xx - 0, 2xx - 735564, 3xx - 0, 4xx - 0, 5xx - 0 +# others - 2122 +# Errors: +# dial tcp 127.0.0.1:8000: i/o timeout - 2122 +# Throughput: 15.13MB/s + +python3 -m socketify app:app --worker 2 --port 8000 +# Statistics Avg Stdev Max +# Reqs/sec 34403.79 3142.19 37926.64 +# Latency 57.90ms 52.75ms 1.57s +# Latency Distribution +# 50% 56.23ms +# 75% 58.88ms +# 90% 61.92ms +# 95% 64.79ms +# 99% 72.06ms +# HTTP codes: +# 1xx - 0, 2xx - 344418, 3xx - 0, 4xx - 0, 5xx - 0 +# others - 0 +# Throughput: 7.12MB/s + +# pypy3.11 uvicorn +./pypy3.11-v7.3.20-linux64/bin/pypy -m uvicorn app:app --worker 2 --port 8000 +# Statistics Avg Stdev Max +# Reqs/sec 13141.26 5064.85 25282.57 +# Latency 150.86ms 30.82ms 362.74ms +# Latency Distribution +# 50% 147.12ms +# 75% 177.15ms +# 90% 208.16ms +# 95% 219.70ms +# 99% 241.41ms +# HTTP codes: +# 1xx - 0, 2xx - 132371, 3xx - 0, 4xx - 0, 5xx - 0 +# others - 0 +# Throughput: 2.63MB/s + +# pypy3.11 granian +./pypy3.11-v7.3.20-linux64/bin/pypy -m granian --interface asgi app:app --workers 2 --port 8000 +# Statistics Avg Stdev Max +# Reqs/sec 32187.19 11796.75 64494.40 +# Latency 62.13ms 221.46ms 6.03s +# Latency Distribution +# 50% 25.63ms +# 75% 31.89ms +# 90% 41.30ms +# 95% 53.67ms +# 99% 2.00s +# HTTP codes: +# 1xx - 0, 2xx - 317537, 3xx - 0, 4xx - 0, 5xx - 0 +# others - 3854 +# Errors: +# dial tcp 127.0.0.1:8000: i/o timeout - 3854 +# Throughput: 6.29MB/s \ No newline at end of file diff --git a/backend/perf/pixi.lock b/backend/perf/pixi.lock new file mode 100644 index 0000000..f1f2ce5 --- /dev/null +++ b/backend/perf/pixi.lock @@ -0,0 +1,821 @@ +version: 6 +environments: + default: + channels: + - url: https://conda.anaconda.org/conda-forge/ + - url: https://conda.anaconda.org/bioconda/ + indexes: + - https://pypi.org/simple + packages: + linux-64: + - conda: https://conda.anaconda.org/conda-forge/linux-64/_go_select-2.3.0-cgo.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + - conda: https://conda.anaconda.org/conda-forge/linux-64/binutils_impl_linux-64-2.45-default_hfdba357_104.conda + - conda: https://conda.anaconda.org/conda-forge/linux-64/binutils_linux-64-2.45-default_h4852527_104.conda + - 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sha256: fcd5cf9e305d7b8338754470cf69cf81f420459dbae8a3b40cee57417f4614a7 - requires_python: '>=3.9' - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda sha256: a4166e3d8ff4e35932510aaff7aa90772f84b4d07e9f6f83c614cba7ceefe0eb md5: 6432cb5d4ac0046c3ac0a8a0f95842f9 diff --git a/backend/pixi.toml b/backend/pixi.toml index f1afd71..68a77ea 100644 --- a/backend/pixi.toml +++ b/backend/pixi.toml @@ -1,7 +1,7 @@ [workspace] channels = ["conda-forge", "bioconda"] name = "backend" -platforms = ["linux-64", "osx-arm64", "win-64"] +platforms = ["linux-64"] version = "0.1.0" [tasks] @@ -31,3 +31,8 @@ boto3 = "==1.35.99" psutil = "==7.0.0" sshtunnel = "==0.4.0" celery = "==5.5.3" +pytest = ">=9.0.2, <10" +pytest-asyncio = ">=1.3.0, <2" +pytest-cov = ">=7.0.0, <8" +psycopg = ">=3.3.2, <4" +psycopg-pool = ">=3.3.0, <4" diff --git a/backend/requirements.txt b/backend/requirements.txt index f0c2369..ed5fe02 100644 --- a/backend/requirements.txt +++ b/backend/requirements.txt @@ -1,6 +1,4 @@ blacksheep[full]==2.4.0 -uvicorn==0.34.3 -uvloop==0.21.0 essentials-configuration[full]==2.0.4 MarkupSafe==3.0.2 pydantic==2.11.7 @@ -11,11 +9,13 @@ dotenv==0.9.9 cryptography==45.0.6 aerich==0.9.1 redis==6.4.0 -httpx==0.28.1 -asyncpg==0.30.0 paramiko==3.5.1 pygithub==2.7.0 boto3==1.35.99 psutil==7.0.0 sshtunnel==0.4.0 -celery==5.5.3 \ No newline at end of file +celery==5.5.3 +socketify==0.0.31 +psycopg[binary]==3.3.2 +psycopg-pool==3.3.0 +anyio==4.12.0 \ No newline at end of file diff --git a/backend/run_server.sh b/backend/run_server.sh index d1c3e2e..28917fb 100644 --- a/backend/run_server.sh +++ b/backend/run_server.sh @@ -10,9 +10,7 @@ aerich migrate || echo "Nothing to migrate" aerich upgrade # Start the BlackSheep server (adjust app import if needed) echo "Starting BlackSheep app..." -uvicorn app.main:app \ +pypy -m socketify app.main:app \ --host 0.0.0.0 \ --port 8000 \ - --lifespan on \ - --log-level debug \ - --workers "${UVICORN_WORKERS:-2}" \ No newline at end of file + --workers "$(nproc --all)" \ No newline at end of file diff --git a/docs/Readme.developer.md b/docs/Readme.developer.md index 47d6cc6..31c7b4e 100644 --- a/docs/Readme.developer.md +++ b/docs/Readme.developer.md @@ -289,9 +289,8 @@ Create `river/main.sh` with the following content: ```bash cd $RIVER_HOME/jobs/$job_id/analysis ENV=$repo_name-$tag -micromamba create -n $ENV python=3.12 -y -micromamba run -n $ENV pip install -r requirements.txt -micromamba run -n $ENV streamlit run TFinder-v1.py --server.port $PORT --server.headless true +eval "$(pixi shell-hook --manifest-path analysis)" +streamlit run TFinder-v1.py --server.port $PORT --server.headless true ``` **Final directory structure:** @@ -397,4 +396,4 @@ There are 2 models: Human vs mouse Instead of creating the paramter to select which Shiny app is used, it can be simply tagged with different model On the RIVER UI, you can select the tag to deploy your specific model. -> **Configured TFFinder to support RIVER platform**: https://github.com/riverxdata/bioinfor-sw-CircNetVis \ No newline at end of file +> **Configured TFFinder to support RIVER platform**: https://github.com/riverxdata/bioinfor-sw-CircNetVis diff --git a/docs/images/graphical_abstract.png b/docs/images/graphical_abstract.png new file mode 100644 index 0000000..7924970 Binary files /dev/null and b/docs/images/graphical_abstract.png differ diff --git a/pixi.lock b/pixi.lock deleted file mode 100644 index 4fcbb37..0000000 --- a/pixi.lock +++ /dev/null @@ -1,35 +0,0 @@ -version: 6 -environments: - 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