diff --git a/.github/labeler.yml b/.github/labeler.yml deleted file mode 100644 index 23b83ad..0000000 --- a/.github/labeler.yml +++ /dev/null @@ -1,2 +0,0 @@ -'@requires-manifestservice': - - '**/*' diff --git a/.github/workflows/integration_tests.yaml b/.github/workflows/integration_tests.yaml new file mode 100644 index 0000000..4914e98 --- /dev/null +++ b/.github/workflows/integration_tests.yaml @@ -0,0 +1,25 @@ +name: Integration Tests + +on: pull_request + +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +jobs: + integration_tests: + name: Integration tests + uses: uc-cdis/.github/.github/workflows/integration_tests.yaml@master + with: + SERVICE_TO_TEST: manifestservice + secrets: + CI_AWS_ACCESS_KEY_ID: ${{ secrets.CI_AWS_ACCESS_KEY_ID }} + CI_AWS_SECRET_ACCESS_KEY: ${{ secrets.CI_AWS_SECRET_ACCESS_KEY }} + JENKINS_API_TOKEN: ${{ secrets.JENKINS_API_TOKEN }} + QA_DASHBOARD_S3_PATH: ${{ secrets.QA_DASHBOARD_S3_PATH }} + CI_TEST_ORCID_USERID: ${{ secrets.CI_TEST_ORCID_USERID }} + CI_TEST_ORCID_PASSWORD: ${{ secrets.CI_TEST_ORCID_PASSWORD }} + CI_TEST_RAS_USERID: ${{ secrets.CI_TEST_RAS_USERID }} + CI_TEST_RAS_PASSWORD: ${{ secrets.CI_TEST_RAS_PASSWORD }} + CI_SLACK_BOT_TOKEN: ${{ secrets.CI_SLACK_BOT_TOKEN }} + CI_SLACK_CHANNEL_ID: ${{ secrets.CI_SLACK_CHANNEL_ID }} diff --git a/.github/workflows/labeler.yml b/.github/workflows/labeler.yml deleted file mode 100644 index 6d259b8..0000000 --- a/.github/workflows/labeler.yml +++ /dev/null @@ -1,12 +0,0 @@ -name: "Pull Request Labeler" -on: - pull_request_target: - types: [opened] - -jobs: - triage: - runs-on: ubuntu-latest - steps: - - uses: actions/labeler@v3 - with: - repo-token: "${{ secrets.GITHUB_TOKEN }}" diff --git a/Dockerfile b/Dockerfile index 3f92d8a..0aa391c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,52 +1,67 @@ -# To run: docker run -v /path/to/wsgi.py:/var/www/manifestservice/wsgi.py --name=manifestservice -p 81:80 manifestservice -# To check running container: docker exec -it manifestservice /bin/bash +ARG AZLINUX_BASE_VERSION=master -FROM quay.io/cdis/python:python3.9-buster-2.0.0 +# Base stage with python-build-base +FROM quay.io/cdis/python-build-base:${AZLINUX_BASE_VERSION} as base + +# Comment this in, and comment out the line above, if quay is down +# FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/python-build-base:${AZLINUX_BASE_VERSION} as base ENV appname=manifestservice +ENV POETRY_NO_INTERACTION=1 \ + POETRY_VIRTUALENVS_IN_PROJECT=1 \ + POETRY_VIRTUALENVS_CREATE=1 + +WORKDIR /${appname} + +# create gen3 user +# Create a group 'gen3' with GID 1000 and a user 'gen3' with UID 1000 +RUN groupadd -g 1000 gen3 && \ + useradd -m -s /bin/bash -u 1000 -g gen3 gen3 && \ + chown -R gen3:gen3 /$appname && \ + chown -R gen3:gen3 /venv + + +# Builder stage +FROM base as builder + +USER gen3 + + +RUN python -m venv /venv + +COPY poetry.lock pyproject.toml /${appname}/ -RUN pip install --upgrade pip +RUN pip install poetry && \ + poetry install -vv --only main --no-interaction -# install poetry -RUN pip install --upgrade poetry +COPY --chown=gen3:gen3 . /$appname +COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /$appname/wsgi.py -RUN apt-get update \ - && apt-get install -y --no-install-recommends\ - libmcrypt4 libmhash2 mcrypt \ - curl bash git vim \ - && apt-get clean +# Run poetry again so this app itself gets installed too +RUN poetry install --without dev --no-interaction -RUN mkdir -p /var/www/$appname \ - && mkdir -p /var/www/.cache/Python-Eggs/ \ - && mkdir /run/nginx/ \ - && ln -sf /dev/stdout /var/log/nginx/access.log \ - && ln -sf /dev/stderr /var/log/nginx/error.log \ - && chown nginx -R /var/www/.cache/Python-Eggs/ \ - && chown nginx /var/www/$appname +RUN git config --global --add safe.directory /${appname} && COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" > /$appname/version_data.py \ + && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >> /$appname/version_data.py -EXPOSE 80 +# Final stage +FROM base -WORKDIR /$appname +COPY --from=builder /venv /venv +COPY --from=builder /$appname /$appname -# copy ONLY poetry artifact and install -# this will make sure than the dependencies is cached -COPY poetry.lock pyproject.toml /$appname/ -RUN poetry config virtualenvs.create false \ - && poetry install -vv --no-root --no-dev --no-interaction \ - && poetry show -v -COPY . /$appname -COPY ./deployment/uwsgi/uwsgi.ini /etc/uwsgi/uwsgi.ini -COPY ./deployment/uwsgi/wsgi.py /$appname/wsgi.py +# Switch to non-root user 'gen3' for the serving process +USER gen3 -# install Indexd and dependencies via poetry -RUN poetry config virtualenvs.create false \ - && poetry install -vv --no-dev --no-interaction \ - && poetry show -v +RUN source /venv/bin/activate -RUN COMMIT=`git rev-parse HEAD` && echo "COMMIT=\"${COMMIT}\"" >$appname/version_data.py \ - && VERSION=`git describe --always --tags` && echo "VERSION=\"${VERSION}\"" >>$appname/version_data.py +ENV PYTHONUNBUFFERED=1 \ + PYTHONIOENCODING=UTF-8 -WORKDIR /var/www/$appname +CMD ["gunicorn", "-c", "deployment/wsgi/gunicorn.conf.py"] -CMD /dockerrun.sh +# RUN apt-get update \ +# && apt-get install -y --no-install-recommends\ +# libmcrypt4 libmhash2 mcrypt \ +# curl bash git vim \ +# && apt-get clean diff --git a/Jenkinsfile b/Jenkinsfile deleted file mode 100644 index 2449f81..0000000 --- a/Jenkinsfile +++ /dev/null @@ -1,6 +0,0 @@ -#!groovy - -@Library('cdis-jenkins-lib@master') _ - -testPipeline { -} diff --git a/README.md b/README.md index f1da6db..e0dae47 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ # Manifest Service + ### Overview This service handles reading from and writing to a user's s3 folder containing their manifests. A manifest is a JSON file that lists records a researcher may be interested in analyzing. This service stores a manifest to a user folder in an s3 bucket and delivers it for later use, such as when the researcher wants to mount the manifest in their workspace. If the "prefix" config variable is set, user folders will be stored in a directory of that name within the s3 bucket. @@ -48,10 +49,29 @@ Create a cohort GUID in the user's folder: Post body: { "guid": "5183a350-9d56-4084-8a03-6471cafeb7fe" } Returns: { "filename" : "5183a350-9d56-4084-8a03-6471cafeb7fe" } +Lists a user's exported metadata objects: + + GET /metadata + Returns: { "metadata" : [ { "filename" : "metadata-2024-06-13T17-14-46.026593.json", "last_modified" : "2024-06-13 17:14:47" }, ... ] } + +Create an exported metadata object in the user's folder: + + POST /metadata + Post body: { "some_metadata_key": "some_metadata_value" } + Returns: { "filename" : "metadata-2024-06-13T17-14-46.026593.json" } + +Read the contents of an exported metadata object file in the user's folder: + + GET /metadata/ + Returns: { "body" : "the-body-of-the-exported-metadata-object-file-as-a-string" } + On failure, the above endpoints all return JSON in the form { "error" : "error-message" } +### OpenAPI spec + +The [OpenAPI](https://github.com/OAI/OpenAPI-Specification)/[Swagger 2.0](https://swagger.io/) specification of a service is stored in its `swagger.yaml` and can be visualized [here](http://petstore.swagger.io/?url=https://raw.githubusercontent.com/uc-cdis/manifestservice/master/openapi/swagger.yaml). ### Running the service locally If you want to run this service locally, fill out the config.json file with the correct values and then run: diff --git a/deployment/uwsgi/uwsgi.ini b/deployment/uwsgi/uwsgi.ini deleted file mode 100644 index 3c189e5..0000000 --- a/deployment/uwsgi/uwsgi.ini +++ /dev/null @@ -1,23 +0,0 @@ -[uwsgi] -protocol = uwsgi -socket = /var/run/gen3/uwsgi.sock -buffer-size = 32768 -uid = nginx -gid = nginx -chown-socket = nginx:nginx -chmod-socket = 666 -master = true -harakiri-verbose = 20 -disable-logging = true -wsgi-file=/manifestservice/wsgi.py -plugins = python3 -vacuum = true -chdir = /manifestservice/ -#virtualenv = $(VENV) -pythonpath = /usr/local/lib/python3.6/site-packages/ - - -# Use this to initialize application in worker processes, not master. This -# prevents the workers from all trying to open the same database -# connections at startup: -# lazy-apps = true diff --git a/deployment/wsgi/gunicorn.conf.py b/deployment/wsgi/gunicorn.conf.py new file mode 100644 index 0000000..039176f --- /dev/null +++ b/deployment/wsgi/gunicorn.conf.py @@ -0,0 +1,6 @@ +wsgi_app = "deployment.wsgi.wsgi:application" +bind = "0.0.0.0:8000" +workers = 1 +user = "gen3" +group = "gen3" +timeout = 300 diff --git a/deployment/uwsgi/wsgi.py b/deployment/wsgi/wsgi.py similarity index 100% rename from deployment/uwsgi/wsgi.py rename to deployment/wsgi/wsgi.py diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index f2d3d2f..59ba14f 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -1,13 +1,12 @@ +import json import flask import html import boto3 from flask import current_app as app import re -import requests import ntpath -from datetime import date, datetime +from datetime import datetime from authutils.token.validate import current_token, validate_request, set_current_token -from authutils import user as authutils_user from cdislogging import get_logger logger = get_logger("manifestservice_logger", log_level="info") @@ -191,7 +190,7 @@ def put_pfb_guid(): if not is_valid: return ( - flask.jsonify({"error": "The provided GUID: {} is invalid.".format(GUID)}), + flask.jsonify({"error": f"The provided GUID: {GUID} is invalid."}), 400, ) result, ok = _add_GUID_to_bucket(current_token, GUID) @@ -205,6 +204,136 @@ def put_pfb_guid(): return flask.jsonify(ret), 200 +@blueprint.route("/metadata", methods=["GET"]) +def get_metadata(): + """ + List all exported metadata objects associated with user + --- + responses: + 200: + description: Success + 403: + description: Unauthorized + """ + err, code = _authenticate_user() + if err is not None: + return err, code + + folder_name = _get_folder_name_from_token(current_token) + result, ok = _list_files_in_bucket( + flask.current_app.config.get("MANIFEST_BUCKET_NAME"), folder_name + ) + if not ok: + json_to_return = {"error": "Currently unable to connect to s3."} + return flask.jsonify(json_to_return), 500 + + json_to_return = {"external_file_metadata": result["metadata"]} + + return flask.jsonify(json_to_return), 200 + + +@blueprint.route("/metadata/", methods=["GET"]) +def get_metadata_file(file_name): + """ + List all exported metadata objects associated with user + --- + responses: + 200: + description: Success + 403: + description: Unauthorized + 400: + description: Bad request format + """ + + err, code = _authenticate_user() + if err is not None: + return err, code + + file_name = html.escape(file_name) + if not file_name.endswith("json"): + json_to_return = { + "error": "Incorrect usage. You can only use this pathway to request files of type JSON." + } + return flask.jsonify(json_to_return), 400 + + folder_name = _get_folder_name_from_token(current_token) + "/exported-metadata" + + return _get_file_contents( + flask.current_app.config.get("MANIFEST_BUCKET_NAME"), folder_name, file_name + ) + + +@blueprint.route("/metadata", methods=["PUT", "POST"]) +def put_metadata(): + """ + Create an exported metadata object + --- + responses: + 200: + description: Success + example: '({ "filename": "metadata-2024-06-13T17-14-46.026593.json" }, 200)' + 403: + description: Unauthorized + example: '({ "error": "" }, 403)' + 400: + description: Bad GUID format + example: '({ "error": "" }, 400)' + """ + + err, code = _authenticate_user() + if err is not None: + return err, code + if not flask.request.json: + return flask.jsonify({"error": "Please provide valid JSON."}), 400 + + metadata_body = flask.request.json + + result, ok = _add_metadata_to_bucket(current_token, metadata_body) + + if not ok: + json_to_return = {"error": "Currently unable to connect to s3."} + return flask.jsonify(json_to_return), 500 + + ret = {"filename": result} + + return flask.jsonify(ret), 200 + + +def _add_metadata_to_bucket(current_token, metadata_body): + """ + Creates a new file in the user's folder at user-/metadata/exported-data/ + with a filename corresponding to the GUID provided by the user. + """ + session = boto3.Session( + region_name="us-east-1", + ) + s3 = session.resource("s3") + + folder_name = _get_folder_name_from_token(current_token) + + result, ok = _list_files_in_bucket( + flask.current_app.config.get("MANIFEST_BUCKET_NAME"), folder_name + ) + + if not ok: + return None, False + filename = _generate_unique_filename( + result["metadata"], file_type="metadata" + ) + + filepath_in_bucket = folder_name + "/exported-metadata/" + filename + try: + obj = s3.Object( + flask.current_app.config.get("MANIFEST_BUCKET_NAME"), filepath_in_bucket + ) + obj.put(Body=bytes(json.dumps(metadata_body).encode('UTF-8'))) + except Exception as e: + return str(e), False + + return filename, True + + def _add_manifest_to_bucket(current_token, manifest_json): """ Puts the manifest_json string into a file and uploads it to s3. @@ -223,21 +352,18 @@ def _add_manifest_to_bucket(current_token, manifest_json): if not ok: return result, False - filename = _generate_unique_manifest_filename( - folder_name, - flask.current_app.config.get("MANIFEST_BUCKET_NAME"), + filename = _generate_unique_filename( result["manifests"], ) - manifest_as_bytes = str.encode(str(flask.request.json)) filepath_in_bucket = folder_name + "/" + filename try: obj = s3.Object( flask.current_app.config.get("MANIFEST_BUCKET_NAME"), filepath_in_bucket ) - response = obj.put(Body=manifest_as_bytes) + obj.put(Body=bytes(json.dumps(manifest_json).encode('UTF-8'))) except Exception as e: - logger.error("Failed to add manifest to bucket: {}".format(e)) + logger.error(f"Failed to add manifest to bucket: {e}") return str(e), False return filename, True @@ -269,7 +395,7 @@ def _add_GUID_to_bucket(current_token, GUID): obj = s3.Object( flask.current_app.config.get("MANIFEST_BUCKET_NAME"), filepath_in_bucket ) - response = obj.put(Body=str.encode("")) + obj.put(Body=str.encode("")) except Exception as e: return str(e), False @@ -305,30 +431,35 @@ def is_valid_manifest(manifest_json, required_keys): return True -def _generate_unique_manifest_filename( - folder_name, manifest_bucket_name, users_existing_manifest_files +def _generate_unique_filename( + users_existing_manifest_or_metadata_files, file_type="manifest" ): """ Returns a filename of the form manifest--.json that is unique among the files in the user's manifest folder. """ timestamp = datetime.now().isoformat() - existing_filenames = map(lambda x: x["filename"], users_existing_manifest_files) + existing_filenames = map( + lambda x: x["filename"], users_existing_manifest_or_metadata_files + ) filename = _generate_unique_filename_with_timestamp_and_increment( - timestamp, existing_filenames + timestamp, existing_filenames, file_type ) return filename def _generate_unique_filename_with_timestamp_and_increment( - timestamp, users_existing_manifest_files + timestamp, users_existing_manifest_files, file_type="manifest" ): """ A helper function for _generate_unique_manifest_filename(), which facilitates unit testing. Adds an increment to the filename if there happens to be another timestamped file with the same name (unlikely, but good to check). """ - filename_without_extension = "manifest-" + timestamp.replace(":", "-") + filename_prefix="manifest-" + if file_type=="metadata": + filename_prefix="metadata-" + filename_without_extension = filename_prefix + timestamp.replace(":", "-") extension = ".json" filename = filename_without_extension + extension @@ -354,7 +485,11 @@ def _list_files_in_bucket(bucket_name, folder): "cohorts": [ # For files in the cohorts/ folder { "filename": , "last_modified": }, ... - ] + ], + "metadata": [ + # For files in the exported-metadata/ folder + { "filename": , "last_modified": }, ... + ], } """ session = boto3.Session( @@ -364,6 +499,7 @@ def _list_files_in_bucket(bucket_name, folder): manifests = [] guids = [] + metadata = [] bucket = s3.Bucket(bucket_name) try: @@ -377,24 +513,30 @@ def _list_files_in_bucket(bucket_name, folder): object_summary.last_modified ), } - if not "cohorts/" in object_summary.key: - file_marker["filename"] = ntpath.basename(object_summary.key) - manifests.append(file_marker) - else: + if "cohorts/" in object_summary.key: file_marker["filename"] = object_summary.key.split("cohorts/")[1] guids.append(file_marker) + elif "metadata/" in object_summary.key: + file_marker["filename"] = object_summary.key.split("metadata/")[1] + metadata.append(file_marker) + else: + file_marker["filename"] = ntpath.basename(object_summary.key) + manifests.append(file_marker) except Exception as e: logger.error( - 'Failed to list files in bucket "{}" folder "{}": {}'.format( - bucket_name, folder, e - ) + f'Failed to list files in bucket "{bucket_name}" folder "{folder}": {e}' ) return str(e), False manifests_sorted = sorted(manifests, key=lambda i: i["last_modified_timestamp"]) guids_sorted = sorted(guids, key=lambda i: i["last_modified_timestamp"]) + metadata_sorted = sorted(metadata, key=lambda i: i["last_modified_timestamp"]) - rv = {"manifests": manifests_sorted, "cohorts": guids_sorted} + rv = { + "manifests": manifests_sorted, + "cohorts": guids_sorted, + "metadata": metadata_sorted, + } return rv, True @@ -428,6 +570,9 @@ def _authenticate_user(): def is_valid_GUID(GUID): + """ + Check if input value is a valid GUID + """ regex = re.compile( "^.*[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}$", re.I, diff --git a/openapi/README.md b/openapi/README.md index 31db66e..f2a5617 100644 --- a/openapi/README.md +++ b/openapi/README.md @@ -1,6 +1,6 @@ # OpenAPI spec -The [OpenAPI](https://github.com/OAI/OpenAPI-Specification)/[Swagger 2.0](https://swagger.io/) specification of a service is stored in its `swagger.yaml` file. It can be visualized using the Swagger UI at `http://petstore.swagger.io/?url=`. For example, the documentation found in this folder can be visualized [here](http://petstore.swagger.io/?url=https://raw.githubusercontent.com/uc-cdis/service-template/master/openapi/swagger.yaml). +The [OpenAPI](https://github.com/OAI/OpenAPI-Specification)/[Swagger 2.0](https://swagger.io/) specification of a service is stored in its `swagger.yaml` file. It can be visualized using the Swagger UI at `http://petstore.swagger.io/?url=`. For example, the documentation found in this folder can be visualized [here](http://petstore.swagger.io/?url=https://raw.githubusercontent.com/uc-cdis/manifestservice/master/openapi/swagger.yaml). # To generate the documentation diff --git a/openapi/swagger.yaml b/openapi/swagger.yaml index 5418cbb..d0d7670 100644 --- a/openapi/swagger.yaml +++ b/openapi/swagger.yaml @@ -83,4 +83,46 @@ paths: '403': description: Unauthorized summary: Returns the requested manifest file from the user's folder. + /metadata: + get: + responses: + '200': + description: Success + '403': + description: Unauthorized + summary: List all exported metadata objects associated with user + post: + responses: + '200': + description: Success + example: '({ "filename": "metadata-2024-06-13T17-14-46.026593.json" }, 200)' + '400': + description: Bad GUID format + example: '({ "error": "" }, 400)' + '403': + description: Unauthorized + example: '({ "error": "" }, 403)' + summary: Create an exported metadata object + put: + responses: + '200': + description: Success + example: '({ "filename": "metadata-2024-06-13T17-14-46.026593.json" }, 200)' + '400': + description: Bad GUID format + example: '({ "error": "" }, 400)' + '403': + description: Unauthorized + example: '({ "error": "" }, 403)' + summary: Create an exported metadata object + /metadata/{file_name}: + get: + responses: + '200': + description: Success + '400': + description: Bad request format + '403': + description: Unauthorized + summary: List all exported metadata objects associated with user swagger: '2.0' diff --git a/poetry.lock b/poetry.lock index c559b92..f4ea494 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,25 +1,26 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. [[package]] name = "anyio" -version = "4.0.0" +version = "4.4.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.0.0-py3-none-any.whl", hash = "sha256:cfdb2b588b9fc25ede96d8db56ed50848b0b649dca3dd1df0b11f683bb9e0b5f"}, - {file = "anyio-4.0.0.tar.gz", hash = "sha256:f7ed51751b2c2add651e5747c891b47e26d2a21be5d32d9311dfe9692f3e5d7a"}, + {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"}, + {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"}, ] [package.dependencies] exceptiongroup = {version = ">=1.0.2", markers = "python_version < \"3.11\""} idna = ">=2.8" sniffio = ">=1.1" +typing-extensions = {version = ">=4.1", markers = "python_version < \"3.11\""} [package.extras] -doc = ["Sphinx (>=7)", "packaging", "sphinx-autodoc-typehints 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zstd = ["zstandard (>=0.18.0)"] @@ -1253,18 +1306,22 @@ files = [ [[package]] name = "zipp" -version = "3.17.0" +version = "3.20.1" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false python-versions = ">=3.8" files = [ - {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"}, - {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"}, + {file = "zipp-3.20.1-py3-none-any.whl", hash = "sha256:9960cd8967c8f85a56f920d5d507274e74f9ff813a0ab8889a5b5be2daf44064"}, + {file = "zipp-3.20.1.tar.gz", hash = "sha256:c22b14cc4763c5a5b04134207736c107db42e9d3ef2d9779d465f5f1bcba572b"}, ] [package.extras] -docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"] -testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"] +check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"] +cover = ["pytest-cov"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [metadata] lock-version = "2.0" diff --git a/pyproject.toml b/pyproject.toml index 160c0f4..4d4e568 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "manifestservice" -version = "0.1.0" +version = "0.5.2" description = "Handles reading from and writing to a user's s3 folder containing their manifests" authors = ["CTDS UChicago "] license = "Apache-2.0" @@ -14,8 +14,9 @@ python = ">=3.9, <4.0" Flask = "^2.3.2" authutils = "<7" boto3 = "^1.17.48" -cryptography = ">=41.0.3" -requests = "^2.25.1" +cryptography = ">=42.0.5" +requests = "^2.32.0" +gunicorn = "^21.2.0" importlib-metadata = "^4.8.1" [tool.poetry.dev-dependencies] diff --git a/tests/conftest.py b/tests/conftest.py index ce9be61..37a3826 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -59,6 +59,7 @@ def mocks(mocker): {"filename": "manifest-a-b-c.json"}, ], "cohorts": [{"filename": "18e32c12-a053-4ac5-90a5-f01f70b5c2be"}], + "metadata": [{"filename": "metadata-2024-04-26T18-59-21.226440.json"}], }, True, ), @@ -78,6 +79,11 @@ def mocks(mocker): return_value=("a-guid-value", True), ) + all_mocks["_add_metadata_to_bucket"] = mocker.patch( + "manifestservice.manifests._add_metadata_to_bucket", + return_value=("manifest-xxx.json", True), + ) + return all_mocks diff --git a/tests/metadata_test.py b/tests/metadata_test.py new file mode 100644 index 0000000..afd062e --- /dev/null +++ b/tests/metadata_test.py @@ -0,0 +1,99 @@ +import json as json_utils +from manifestservice import manifests + +def test_generate_unique_metadata_filename_basic_date_generation(): + """ + Tests that the _generate_unique_filename_with_timestamp_and_increment() function + generates a unique filename for metadata file. + """ + timestamp = "a-b-c" + users_existing_metadata_files = [] + filename = manifests._generate_unique_filename_with_timestamp_and_increment( + timestamp, users_existing_metadata_files, file_type="metadata" + ) + assert filename == "metadata-a-b-c.json" + +def test_POST_successful_metadata_add(client, mocks): + """ + Test the Export metadata to Workspace pathway: a metadata file is added to the bucket. + Note that because s3 is being mocked, only an integration test can properly + verify file creation. + """ + test_metadata_contents = [ + { + "external_oidc_idp": "qdr-keycloak", + "file_retriever": "QDR", + "file_id": "45138", + } + ] + post_body = test_metadata_contents + + headers = {"Content-Type": "application/json", "Accept": "application/json"} + r = client.post("/metadata", data=json_utils.dumps(post_body), headers=headers) + + assert r.status_code == 200 + assert mocks["_authenticate_user"].call_count == 1 + assert mocks["_get_file_contents"].call_count == 0 + assert mocks["_add_metadata_to_bucket"].call_count == 1 + assert mocks["_add_GUID_to_bucket"].call_count == 0 + + json = r.json + returned_filename = json["filename"] + + assert returned_filename is not None + assert type(returned_filename) is str + + r = client.get("/metadata", headers=headers) + assert r.status_code == 200 + assert mocks["_authenticate_user"].call_count == 2 + assert mocks["_add_metadata_to_bucket"].call_count == 1 + assert mocks["_list_files_in_bucket"].call_count == 1 + assert mocks["_get_file_contents"].call_count == 0 + + json = r.json + metadata_files = json["external_file_metadata"] + assert type(metadata_files) is list + + r = client.get("/metadata/" + returned_filename, headers=headers) + assert r.status_code == 200 + assert mocks["_authenticate_user"].call_count == 3 + assert mocks["_add_metadata_to_bucket"].call_count == 1 + assert mocks["_list_files_in_bucket"].call_count == 1 + assert mocks["_get_file_contents"].call_count == 1 + + +def test_GET_metadata(client, mocks): + """ + Test GET /metadata + """ + headers = {"Content-Type": "application/json", "Accept": "application/json"} + r = client.get("/metadata", headers=headers) + + assert r.status_code == 200 + assert mocks["_authenticate_user"].call_count == 1 + assert mocks["_get_file_contents"].call_count == 0 + assert mocks["_add_metadata_to_bucket"].call_count == 0 + assert mocks["_list_files_in_bucket"].call_count == 1 + + json = r.json + metadata_returned = json["external_file_metadata"] + assert len(metadata_returned) == 1 + # From the s3 mock + assert ( + metadata_returned[0]["filename"] == "metadata-2024-04-26T18-59-21.226440.json" + ) + + +def test_GET_metadata_broken_s3(client, broken_s3_mocks): + """ + Test GET /metadata if s3 creds are broken + """ + headers = {"Content-Type": "application/json", "Accept": "application/json"} + r = client.get("/metadata", headers=headers) + + assert r.status_code == 500 + assert broken_s3_mocks["_authenticate_user"].call_count == 1 + + response = r.json + assert len(response.keys()) == 1 + assert response["error"] == "Currently unable to connect to s3."