From ab69822884edd10aa7bb71c881ae283e7447ff88 Mon Sep 17 00:00:00 2001 From: EliseCastle23 Date: Wed, 22 Nov 2023 11:22:17 -0700 Subject: [PATCH 01/47] Updating Docker image to use new AL2 image, Gunicorn, and multi-stage build. --- Dockerfile | 89 +++-- deployment/uwsgi/uwsgi.ini | 23 -- deployment/wsgi/gunicorn.conf.py | 6 + deployment/{uwsgi => wsgi}/wsgi.py | 0 poetry.lock | 551 +++++++++++++++-------------- pyproject.toml | 1 + 6 files changed, 345 insertions(+), 325 deletions(-) delete mode 100644 deployment/uwsgi/uwsgi.ini create mode 100644 deployment/wsgi/gunicorn.conf.py rename deployment/{uwsgi => wsgi}/wsgi.py (100%) 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/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. 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"0.3.1" +version = "0.4.1" description = "Handles reading from and writing to a user's s3 folder containing their manifests" authors = ["CTDS UChicago "] license = "Apache-2.0" @@ -14,7 +14,7 @@ python = ">=3.9, <4.0" Flask = "^2.3.2" authutils = "<7" boto3 = "^1.17.48" -cryptography = ">=41.0.6" +cryptography = ">=42.0.5" requests = "^2.25.1" importlib-metadata = "^4.8.1" From 424b81defeef40eee3f940a6a8d5dc431bf790ca Mon Sep 17 00:00:00 2001 From: Hara Prasad Juvvala Date: Fri, 29 Mar 2024 10:37:51 -0700 Subject: [PATCH 04/47] Add GH action workflow for integration tests --- .github/workflows/integration_tests.yaml | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 .github/workflows/integration_tests.yaml diff --git a/.github/workflows/integration_tests.yaml b/.github/workflows/integration_tests.yaml new file mode 100644 index 0000000..638cc0c --- /dev/null +++ b/.github/workflows/integration_tests.yaml @@ -0,0 +1,19 @@ +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 }} From dad86f899d2bc4b8f17cef9539974bfc3eba8aef Mon Sep 17 00:00:00 2001 From: Hara Prasad Juvvala Date: Fri, 29 Mar 2024 11:33:41 -0700 Subject: [PATCH 05/47] remove jenkins pipeline (using GH Actions for integration tests) --- Jenkinsfile | 6 ------ 1 file changed, 6 deletions(-) delete mode 100644 Jenkinsfile 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 { -} From 6552215ccb15b982fb9fe6a80b7fe3d1a5b1ff98 Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Thu, 11 Apr 2024 15:49:29 -0500 Subject: [PATCH 06/47] adding 3 new routes for manifest retrieval/upload, and some helper functions + formatting with python black --- manifestservice/manifests/__init__.py | 172 ++++++++++++++++++++++++-- 1 file changed, 163 insertions(+), 9 deletions(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index f2d3d2f..b4fa164 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -205,6 +205,140 @@ 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 = {"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) + + 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": "5183a350-9d56-4084-8a03-6471cafeb7fe" }, 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 + + # TODO: Figure out how to create the + metadata_body = flask.request.json + + # TODO: Implement _add_metadata_to_bucket and figure out what to pass on for second parameter + 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-/cohorts/ + 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) + + # TODO: implement everything after line 315: after 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_metadata_filename( + result["metadata"], + ) + + metadata_as_bytes = str.encode(str(metadata_body)) + filepath_in_bucket = folder_name + "/exported-metadata/" + filename + try: + obj = s3.Object( + flask.current_app.config.get("MANIFEST_BUCKET_NAME"), filepath_in_bucket + ) + response = obj.put(Body=metadata_as_bytes) + 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. @@ -305,9 +439,7 @@ 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_manifest_filename(users_existing_manifest_files): """ Returns a filename of the form manifest--.json that is unique among the files in the user's manifest folder. @@ -320,6 +452,15 @@ def _generate_unique_manifest_filename( return filename +def _generate_unique_metadata_filename(users_existing_metadata_files): + timestamp = datetime.now().isoformat() + existing_filenames = map(lambda x: x["filename"], users_existing_metadata_files) + filename = _generate_unique_filename_with_timestamp_and_increment( + timestamp, existing_filenames + ) + return filename + + def _generate_unique_filename_with_timestamp_and_increment( timestamp, users_existing_manifest_files ): @@ -342,6 +483,7 @@ def _generate_unique_filename_with_timestamp_and_increment( return filename +# TODO: Add metadata object to returned values. Call this from new metadata endpoint, but remember to filter out the manifests and cohorts def _list_files_in_bucket(bucket_name, folder): """ Lists the files in an s3 bucket. Returns a dictionary. @@ -354,7 +496,10 @@ def _list_files_in_bucket(bucket_name, folder): "cohorts": [ # For files in the cohorts/ folder { "filename": , "last_modified": }, ... - ] + ], + "metadata": [ + { "filename": , "last_modified": }, ... + ], } """ session = boto3.Session( @@ -364,6 +509,7 @@ def _list_files_in_bucket(bucket_name, folder): manifests = [] guids = [] + metadata = [] bucket = s3.Bucket(bucket_name) try: @@ -377,12 +523,15 @@ 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( @@ -393,8 +542,13 @@ def _list_files_in_bucket(bucket_name, folder): 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 From 6184caa1bb0ca206220d90ef1ed4d3e9f8664079 Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Tue, 30 Apr 2024 15:34:28 -0500 Subject: [PATCH 07/47] decorator path wrong for get_metadata_file function --- manifestservice/manifests/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index b4fa164..ca98b84 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -233,7 +233,7 @@ def get_metadata(): return flask.jsonify(json_to_return), 200 -@blueprint.route("/metadata/", methods=["GET"]) +@blueprint.route("/metadata/exported-metadata/", methods=["GET"]) def get_metadata_file(file_name): """ List all exported metadata objects associated with user From 676fb401cb7a572ee46868b3af818edca2041edf Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Tue, 30 Apr 2024 15:45:08 -0500 Subject: [PATCH 08/47] changing back decorator but adding subpath to folder_name variable --- manifestservice/manifests/__init__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index ca98b84..89fa913 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -233,7 +233,7 @@ def get_metadata(): return flask.jsonify(json_to_return), 200 -@blueprint.route("/metadata/exported-metadata/", methods=["GET"]) +@blueprint.route("/metadata/", methods=["GET"]) def get_metadata_file(file_name): """ List all exported metadata objects associated with user @@ -258,7 +258,7 @@ def get_metadata_file(file_name): } return flask.jsonify(json_to_return), 400 - folder_name = _get_folder_name_from_token(current_token) + 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 From e95febefd261e72ddf71bb57b06f6f49ce438dec Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Tue, 30 Apr 2024 15:56:14 -0500 Subject: [PATCH 09/47] added one too many forward slashes / --- manifestservice/manifests/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index 89fa913..a79ec31 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -258,7 +258,7 @@ def get_metadata_file(file_name): } return flask.jsonify(json_to_return), 400 - folder_name = _get_folder_name_from_token(current_token) + "/exported-metadata/" + 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 From 7f6a02cd61ca25529a5053e5eb1d8d5072bde905 Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Tue, 30 Apr 2024 16:02:22 -0500 Subject: [PATCH 10/47] test --- manifestservice/manifests/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index a79ec31..89fa913 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -258,7 +258,7 @@ def get_metadata_file(file_name): } return flask.jsonify(json_to_return), 400 - folder_name = _get_folder_name_from_token(current_token) + "exported-metadata/" + 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 From 22d118dc85537be83c98ce6ea47d39757e1ad146 Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Tue, 30 Apr 2024 16:07:19 -0500 Subject: [PATCH 11/47] test 2 --- manifestservice/manifests/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index 89fa913..10358dd 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -258,7 +258,7 @@ def get_metadata_file(file_name): } return flask.jsonify(json_to_return), 400 - folder_name = _get_folder_name_from_token(current_token) + "/exported-metadata/" + 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 From 018b6cb6ed8cf6a85e55a483ce9d9637b297c72e Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Thu, 2 May 2024 12:43:42 -0500 Subject: [PATCH 12/47] Fixing docstring description of get metadata --- manifestservice/manifests/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index 10358dd..eae4a35 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -305,7 +305,7 @@ def put_metadata(): def _add_metadata_to_bucket(current_token, metadata_body): """ - Creates a new file in the user's folder at user-/cohorts/ + 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( From 588d394de1d3ee6c07398b7f7029e21523d2eddb Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Thu, 2 May 2024 15:15:52 -0500 Subject: [PATCH 13/47] black formmating --- manifestservice/manifests/__init__.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index eae4a35..d0e7dc6 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -323,7 +323,7 @@ def _add_metadata_to_bucket(current_token, metadata_body): if not ok: return None, False filename = _generate_unique_metadata_filename( - result["metadata"], + result["external_file_metadata"], ) metadata_as_bytes = str.encode(str(metadata_body)) @@ -497,8 +497,8 @@ def _list_files_in_bucket(bucket_name, folder): # For files in the cohorts/ folder { "filename": , "last_modified": }, ... ], - "metadata": [ - { "filename": , "last_modified": }, ... + "external_file_metadata": [ + { "external_oidc_idp": "qdr-keycloak", "file_retriever": "QDR", "study_id": "doi:10.5064/F6N2GOC9" }, ... ], } """ @@ -526,8 +526,10 @@ def _list_files_in_bucket(bucket_name, folder): 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] + elif "external_file_metadata/" in object_summary.key: + file_marker["filename"] = object_summary.key.split( + "external_file_metadata/" + )[1] metadata.append(file_marker) else: file_marker["filename"] = ntpath.basename(object_summary.key) @@ -547,7 +549,7 @@ def _list_files_in_bucket(bucket_name, folder): rv = { "manifests": manifests_sorted, "cohorts": guids_sorted, - "metadata": metadata_sorted, + "external_file_metadata": metadata_sorted, } return rv, True From 14298f4c940372e2f9ea63918ce048b92fe0fa2c Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Thu, 2 May 2024 15:39:17 -0500 Subject: [PATCH 14/47] black formatting, again --- manifestservice/manifests/__init__.py | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index d0e7dc6..420fe7b 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -228,7 +228,7 @@ def get_metadata(): json_to_return = {"error": "Currently unable to connect to s3."} return flask.jsonify(json_to_return), 500 - json_to_return = {"metadata": result["metadata"]} + json_to_return = {"external_file_metadata": result["metadata"]} return flask.jsonify(json_to_return), 200 @@ -497,7 +497,7 @@ def _list_files_in_bucket(bucket_name, folder): # For files in the cohorts/ folder { "filename": , "last_modified": }, ... ], - "external_file_metadata": [ + "metadata": [ { "external_oidc_idp": "qdr-keycloak", "file_retriever": "QDR", "study_id": "doi:10.5064/F6N2GOC9" }, ... ], } @@ -526,10 +526,8 @@ def _list_files_in_bucket(bucket_name, folder): if "cohorts/" in object_summary.key: file_marker["filename"] = object_summary.key.split("cohorts/")[1] guids.append(file_marker) - elif "external_file_metadata/" in object_summary.key: - file_marker["filename"] = object_summary.key.split( - "external_file_metadata/" - )[1] + 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) @@ -549,7 +547,7 @@ def _list_files_in_bucket(bucket_name, folder): rv = { "manifests": manifests_sorted, "cohorts": guids_sorted, - "external_file_metadata": metadata_sorted, + "metadata": metadata_sorted, } return rv, True From 35dae1315f1579481ce22946297bb072cb34dece Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Thu, 2 May 2024 15:44:09 -0500 Subject: [PATCH 15/47] bug fix --- manifestservice/manifests/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index 420fe7b..a379881 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -323,7 +323,7 @@ def _add_metadata_to_bucket(current_token, metadata_body): if not ok: return None, False filename = _generate_unique_metadata_filename( - result["external_file_metadata"], + result["metadata"], ) metadata_as_bytes = str.encode(str(metadata_body)) From 02e09a6dacb4977f65d07ffe9c35b0482f7c48a2 Mon Sep 17 00:00:00 2001 From: Krishna Agarwal <159047652+krishnaa05@users.noreply.github.com> Date: Fri, 3 May 2024 08:50:07 -0500 Subject: [PATCH 16/47] Changes for integration yaml (#45) --- .github/labeler.yml | 2 -- .github/workflows/integration_tests.yaml | 6 ++++++ .github/workflows/labeler.yml | 12 ------------ 3 files changed, 6 insertions(+), 14 deletions(-) delete mode 100644 .github/labeler.yml delete mode 100644 .github/workflows/labeler.yml 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 index 638cc0c..4914e98 100644 --- a/.github/workflows/integration_tests.yaml +++ b/.github/workflows/integration_tests.yaml @@ -17,3 +17,9 @@ jobs: 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 }}" From c75317263b2c0f9986a21dae821e75ce93a3e406 Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Fri, 3 May 2024 15:26:30 -0500 Subject: [PATCH 17/47] removed TODO comments --- manifestservice/manifests/__init__.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index a379881..feb55a0 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -288,10 +288,8 @@ def put_metadata(): if not flask.request.json: return flask.jsonify({"error": "Please provide valid JSON."}), 400 - # TODO: Figure out how to create the metadata_body = flask.request.json - # TODO: Implement _add_metadata_to_bucket and figure out what to pass on for second parameter result, ok = _add_metadata_to_bucket(current_token, metadata_body) if not ok: @@ -315,7 +313,6 @@ def _add_metadata_to_bucket(current_token, metadata_body): folder_name = _get_folder_name_from_token(current_token) - # TODO: implement everything after line 315: after 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 ) @@ -483,7 +480,6 @@ def _generate_unique_filename_with_timestamp_and_increment( return filename -# TODO: Add metadata object to returned values. Call this from new metadata endpoint, but remember to filter out the manifests and cohorts def _list_files_in_bucket(bucket_name, folder): """ Lists the files in an s3 bucket. Returns a dictionary. From 3f46bc514f56ae287e0134d48ccd07fc2b609d49 Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Mon, 6 May 2024 16:42:16 -0500 Subject: [PATCH 18/47] Black formatting --- manifestservice/manifests/__init__.py | 24 +++++++++--------------- 1 file changed, 9 insertions(+), 15 deletions(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index feb55a0..0173767 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -319,7 +319,7 @@ def _add_metadata_to_bucket(current_token, metadata_body): if not ok: return None, False - filename = _generate_unique_metadata_filename( + filename = _generate_unique_manifest_or_metadata_filename( result["metadata"], ) @@ -354,9 +354,7 @@ 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_manifest_or_metadata_filename( result["manifests"], ) manifest_as_bytes = str.encode(str(flask.request.json)) @@ -436,22 +434,17 @@ def is_valid_manifest(manifest_json, required_keys): return True -def _generate_unique_manifest_filename(users_existing_manifest_files): +def _generate_unique_manifest_or_metadata_filename( + users_existing_manifest_or_metadata_files, +): """ 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) - filename = _generate_unique_filename_with_timestamp_and_increment( - timestamp, existing_filenames + existing_filenames = map( + lambda x: x["filename"], users_existing_manifest_or_metadata_files ) - return filename - - -def _generate_unique_metadata_filename(users_existing_metadata_files): - timestamp = datetime.now().isoformat() - existing_filenames = map(lambda x: x["filename"], users_existing_metadata_files) filename = _generate_unique_filename_with_timestamp_and_increment( timestamp, existing_filenames ) @@ -494,7 +487,8 @@ def _list_files_in_bucket(bucket_name, folder): { "filename": , "last_modified": }, ... ], "metadata": [ - { "external_oidc_idp": "qdr-keycloak", "file_retriever": "QDR", "study_id": "doi:10.5064/F6N2GOC9" }, ... + # For files in the exported-metadata/ folder + { "filename": , "last_modified": }, ... ], } """ From 5edf92bf5706fa51f81425377f40e47927eabc41 Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Tue, 7 May 2024 10:44:41 -0500 Subject: [PATCH 19/47] Refactoring function name --- manifestservice/manifests/__init__.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index 0173767..60dc598 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -319,7 +319,7 @@ def _add_metadata_to_bucket(current_token, metadata_body): if not ok: return None, False - filename = _generate_unique_manifest_or_metadata_filename( + filename = _generate_unique_filename( result["metadata"], ) @@ -354,7 +354,7 @@ def _add_manifest_to_bucket(current_token, manifest_json): if not ok: return result, False - filename = _generate_unique_manifest_or_metadata_filename( + filename = _generate_unique_filename( result["manifests"], ) manifest_as_bytes = str.encode(str(flask.request.json)) @@ -434,7 +434,7 @@ def is_valid_manifest(manifest_json, required_keys): return True -def _generate_unique_manifest_or_metadata_filename( +def _generate_unique_filename( users_existing_manifest_or_metadata_files, ): """ From 8c8c08729b0d776edef2548939c124de1fde2daf Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Thu, 9 May 2024 13:17:57 -0500 Subject: [PATCH 20/47] Python Black formatting --- pyproject.toml | 2 +- tests/conftest.py | 3 ++ tests/metadata_test.py | 88 ++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 92 insertions(+), 1 deletion(-) create mode 100644 tests/metadata_test.py diff --git a/pyproject.toml b/pyproject.toml index 033c783..bae72cd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "manifestservice" -version = "0.4.1" +version = "0.5.0" description = "Handles reading from and writing to a user's s3 folder containing their manifests" authors = ["CTDS UChicago "] license = "Apache-2.0" diff --git a/tests/conftest.py b/tests/conftest.py index ce9be61..abef776 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -59,6 +59,9 @@ def mocks(mocker): {"filename": "manifest-a-b-c.json"}, ], "cohorts": [{"filename": "18e32c12-a053-4ac5-90a5-f01f70b5c2be"}], + "external_file_metadata": [ + {"filename": "manifest-2024-04-26T18-59-21.226440.json"} + ], }, True, ), diff --git a/tests/metadata_test.py b/tests/metadata_test.py new file mode 100644 index 0000000..9878c33 --- /dev/null +++ b/tests/metadata_test.py @@ -0,0 +1,88 @@ +import json as json_utils + + +def test_POST_successful_metadata_add(client, mocks): + """ + Test the Export PFB to Workspace pathway: a cohort 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("/file/" + 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["_add_GUID_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"] == "manifest-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." From 3b5cf73d3c59c122f2efbfc9da3f50306ffb0e9a Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Thu, 9 May 2024 13:59:30 -0500 Subject: [PATCH 21/47] fixing breaking tests --- tests/metadata_test.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/metadata_test.py b/tests/metadata_test.py index 9878c33..fde057f 100644 --- a/tests/metadata_test.py +++ b/tests/metadata_test.py @@ -14,7 +14,7 @@ def test_POST_successful_metadata_add(client, mocks): "file_id": "45138", } ] - post_body = {test_metadata_contents} + 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) @@ -42,7 +42,7 @@ def test_POST_successful_metadata_add(client, mocks): metadata_files = json["external_file_metadata"] assert type(metadata_files) is list - r = client.get("/file/" + returned_filename, headers=headers) + 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 From 49d9981d65b6bd905735743b69c3940e4392ac4d Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Thu, 9 May 2024 14:27:44 -0500 Subject: [PATCH 22/47] black formatting --- tests/conftest.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index abef776..d9b7a97 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -59,9 +59,7 @@ def mocks(mocker): {"filename": "manifest-a-b-c.json"}, ], "cohorts": [{"filename": "18e32c12-a053-4ac5-90a5-f01f70b5c2be"}], - "external_file_metadata": [ - {"filename": "manifest-2024-04-26T18-59-21.226440.json"} - ], + "metadata": [{"filename": "manifest-2024-04-26T18-59-21.226440.json"}], }, True, ), From d3e2ff29fc82fab5a7083eb4c7cb4813765cc584 Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Thu, 9 May 2024 14:34:21 -0500 Subject: [PATCH 23/47] fixing key error --- tests/conftest.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/tests/conftest.py b/tests/conftest.py index d9b7a97..3e14205 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -59,7 +59,9 @@ def mocks(mocker): {"filename": "manifest-a-b-c.json"}, ], "cohorts": [{"filename": "18e32c12-a053-4ac5-90a5-f01f70b5c2be"}], - "metadata": [{"filename": "manifest-2024-04-26T18-59-21.226440.json"}], + "external_file_metadata": [ + {"filename": "manifest-2024-04-26T18-59-21.226440.json"} + ], }, True, ), @@ -79,6 +81,11 @@ def mocks(mocker): return_value=("a-guid-value", True), ) + all_mocks["_add_metadata_to_bucket"] = mocker.patch( + "manifestservice.manifests._add_manifest_to_bucket", + return_value=("manifest-xxx.json", True), + ) + return all_mocks From 77b7868a3da42fbe4744483c788e15c32ef95eed Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Thu, 9 May 2024 14:44:27 -0500 Subject: [PATCH 24/47] fixing config again --- tests/conftest.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/conftest.py b/tests/conftest.py index 3e14205..db70441 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -82,7 +82,7 @@ def mocks(mocker): ) all_mocks["_add_metadata_to_bucket"] = mocker.patch( - "manifestservice.manifests._add_manifest_to_bucket", + "manifestservice.manifests._add_metadata_to_bucket", return_value=("manifest-xxx.json", True), ) From e702f6594d3928c72471cd4317d6aac631003a4d Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Thu, 9 May 2024 14:50:21 -0500 Subject: [PATCH 25/47] black --- tests/conftest.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index db70441..937c47b 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -59,9 +59,7 @@ def mocks(mocker): {"filename": "manifest-a-b-c.json"}, ], "cohorts": [{"filename": "18e32c12-a053-4ac5-90a5-f01f70b5c2be"}], - "external_file_metadata": [ - {"filename": "manifest-2024-04-26T18-59-21.226440.json"} - ], + "metadata": [{"filename": "manifest-2024-04-26T18-59-21.226440.json"}], }, True, ), From 57dc3fdc5688755836b061912906387a3a169ca9 Mon Sep 17 00:00:00 2001 From: Piotr Senkow Date: Fri, 10 May 2024 15:04:43 -0500 Subject: [PATCH 26/47] small verbiage change --- tests/metadata_test.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/tests/metadata_test.py b/tests/metadata_test.py index fde057f..3409858 100644 --- a/tests/metadata_test.py +++ b/tests/metadata_test.py @@ -3,7 +3,7 @@ def test_POST_successful_metadata_add(client, mocks): """ - Test the Export PFB to Workspace pathway: a cohort is added to the bucket. + 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. """ @@ -61,7 +61,6 @@ def test_GET_metadata(client, mocks): 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["_add_GUID_to_bucket"].call_count == 0 assert mocks["_list_files_in_bucket"].call_count == 1 json = r.json From 5a00bfe35093977e367fec67a7c3228effe20dc3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 13 May 2024 14:55:14 +0000 Subject: [PATCH 27/47] Bump werkzeug from 3.0.1 to 3.0.3 Bumps [werkzeug](https://github.com/pallets/werkzeug) from 3.0.1 to 3.0.3. - [Release notes](https://github.com/pallets/werkzeug/releases) - [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/werkzeug/compare/3.0.1...3.0.3) --- updated-dependencies: - dependency-name: werkzeug dependency-type: indirect ... 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Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.3 to 3.1.4. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/jinja/compare/3.1.3...3.1.4) --- updated-dependencies: - dependency-name: jinja2 dependency-type: indirect ... 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"dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 15 May 2024 02:49:30 +0000 Subject: [PATCH 30/47] Bump idna from 3.6 to 3.7 Bumps [idna](https://github.com/kjd/idna) from 3.6 to 3.7. - [Release notes](https://github.com/kjd/idna/releases) - [Changelog](https://github.com/kjd/idna/blob/master/HISTORY.rst) - [Commits](https://github.com/kjd/idna/compare/v3.6...v3.7) --- updated-dependencies: - dependency-name: idna dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 8c88b3d..f1abc0f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -573,13 +573,13 @@ socks = ["socksio (==1.*)"] [[package]] name = "idna" -version = "3.6" +version = "3.7" description = "Internationalized Domain Names in Applications (IDNA)" optional = false python-versions = ">=3.5" files = [ - {file = "idna-3.6-py3-none-any.whl", hash = "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f"}, - {file = "idna-3.6.tar.gz", hash = "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca"}, + {file = "idna-3.7-py3-none-any.whl", hash = "sha256:82fee1fc78add43492d3a1898bfa6d8a904cc97d8427f683ed8e798d07761aa0"}, + {file = "idna-3.7.tar.gz", hash = "sha256:028ff3aadf0609c1fd278d8ea3089299412a7a8b9bd005dd08b9f8285bcb5cfc"}, ] [[package]] From 8d907cc6ee66badf8dde88169350b6b8e025b20b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 21 May 2024 06:39:55 +0000 Subject: [PATCH 31/47] --- updated-dependencies: - dependency-name: requests dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- poetry.lock | 10 +++++----- pyproject.toml | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/poetry.lock b/poetry.lock index 97667ec..6005f86 100644 --- a/poetry.lock +++ b/poetry.lock @@ -996,13 +996,13 @@ rpds-py = ">=0.7.0" [[package]] name = "requests" -version = "2.31.0" +version = "2.32.0" description = "Python HTTP for Humans." optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"}, - {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"}, + {file = "requests-2.32.0-py3-none-any.whl", hash = "sha256:f2c3881dddb70d056c5bd7600a4fae312b2a300e39be6a118d30b90bd27262b5"}, + {file = "requests-2.32.0.tar.gz", hash = "sha256:fa5490319474c82ef1d2c9bc459d3652e3ae4ef4c4ebdd18a21145a47ca4b6b8"}, ] [package.dependencies] @@ -1293,4 +1293,4 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p [metadata] lock-version = "2.0" python-versions = ">=3.9, <4.0" -content-hash = "134d77c11f81e772bba1e8ab4bf627f969cf489056f6bede419db28c054b3bc5" +content-hash = "c91cfdc09960b9facfd43273d8212d0d4cea5c48195e5ad7491e6b6ab52d8e5c" diff --git a/pyproject.toml b/pyproject.toml index bae72cd..53ff2f3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,7 +15,7 @@ Flask = "^2.3.2" authutils = "<7" boto3 = "^1.17.48" cryptography = ">=42.0.5" -requests = "^2.25.1" +requests = "^2.32.0" importlib-metadata = "^4.8.1" [tool.poetry.dev-dependencies] From e4d67d3aa3acb8a37fa6dc1e89318a50f47f650b Mon Sep 17 00:00:00 2001 From: Mingfei Shao Date: Wed, 22 May 2024 10:26:16 -0500 Subject: [PATCH 32/47] trigger action From 5c9e5555a06fcceca084e3971a2bbc12d181de97 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 10 Jun 2024 16:08:22 +0000 Subject: [PATCH 33/47] Bump authlib from 1.3.0 to 1.3.1 Bumps [authlib](https://github.com/lepture/authlib) from 1.3.0 to 1.3.1. - [Release notes](https://github.com/lepture/authlib/releases) - [Changelog](https://github.com/lepture/authlib/blob/master/docs/changelog.rst) - [Commits](https://github.com/lepture/authlib/compare/v1.3.0...v1.3.1) --- updated-dependencies: - dependency-name: authlib dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 6005f86..1075a29 100644 --- a/poetry.lock +++ b/poetry.lock @@ -64,13 +64,13 @@ tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "p [[package]] name = "authlib" -version = "1.3.0" +version = "1.3.1" description = "The ultimate Python library in building OAuth and OpenID Connect servers and clients." optional = false python-versions = ">=3.8" files = [ - {file = "Authlib-1.3.0-py2.py3-none-any.whl", hash = "sha256:9637e4de1fb498310a56900b3e2043a206b03cb11c05422014b0302cbc814be3"}, - {file = "Authlib-1.3.0.tar.gz", hash = "sha256:959ea62a5b7b5123c5059758296122b57cd2585ae2ed1c0622c21b371ffdae06"}, + {file = "Authlib-1.3.1-py2.py3-none-any.whl", hash = "sha256:d35800b973099bbadc49b42b256ecb80041ad56b7fe1216a362c7943c088f377"}, + {file = "authlib-1.3.1.tar.gz", hash = "sha256:7ae843f03c06c5c0debd63c9db91f9fda64fa62a42a77419fa15fbb7e7a58917"}, ] [package.dependencies] From 8efa601ca7e588ddecd774dcdc36a51bf6f8f9de Mon Sep 17 00:00:00 2001 From: Mingfei Shao Date: Mon, 10 Jun 2024 11:28:30 -0500 Subject: [PATCH 34/47] trigger action From bfc66236e61d6706d3a0af2ba839b8b4b6e5e99d Mon Sep 17 00:00:00 2001 From: Mingfei Shao Date: Thu, 13 Jun 2024 13:22:58 -0500 Subject: [PATCH 35/47] update open api docs --- openapi/swagger.yaml | 42 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/openapi/swagger.yaml b/openapi/swagger.yaml index 5418cbb..6665474 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": "5183a350-9d56-4084-8a03-6471cafeb7fe" }, 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": "5183a350-9d56-4084-8a03-6471cafeb7fe" }, 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' From 6231c9ac19fe0f8cf3568df618cf006d731cabc1 Mon Sep 17 00:00:00 2001 From: Mingfei Shao Date: Thu, 13 Jun 2024 14:12:20 -0500 Subject: [PATCH 36/47] update readme --- README.md | 20 ++++++++++++++++++++ openapi/README.md | 2 +- 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index f1da6db..7300531 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" : "manifest-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" : "manifest-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/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 From a7dba7bb39f65bd7d031a39c3d9cc480b726904b Mon Sep 17 00:00:00 2001 From: Mingfei Shao Date: Thu, 13 Jun 2024 14:22:10 -0500 Subject: [PATCH 37/47] update for filename --- README.md | 4 ++-- manifestservice/manifests/__init__.py | 30 +++++++++++++++------------ tests/metadata_test.py | 2 +- 3 files changed, 20 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 7300531..e0dae47 100644 --- a/README.md +++ b/README.md @@ -52,13 +52,13 @@ Create a cohort GUID in the user's folder: Lists a user's exported metadata objects: GET /metadata - Returns: { "metadata" : [ { "filename" : "manifest-2024-06-13T17-14-46.026593.json", "last_modified" : "2024-06-13 17:14:47" }, ... ] } + 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" : "manifest-2024-06-13T17-14-46.026593.json" } + Returns: { "filename" : "metadata-2024-06-13T17-14-46.026593.json" } Read the contents of an exported metadata object file in the user's folder: diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index 60dc598..caa7068 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -191,7 +191,7 @@ 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) @@ -320,7 +320,7 @@ def _add_metadata_to_bucket(current_token, metadata_body): if not ok: return None, False filename = _generate_unique_filename( - result["metadata"], + result["metadata"], file_type="metadata" ) metadata_as_bytes = str.encode(str(metadata_body)) @@ -329,7 +329,7 @@ def _add_metadata_to_bucket(current_token, metadata_body): obj = s3.Object( flask.current_app.config.get("MANIFEST_BUCKET_NAME"), filepath_in_bucket ) - response = obj.put(Body=metadata_as_bytes) + obj.put(Body=metadata_as_bytes) except Exception as e: return str(e), False @@ -364,9 +364,9 @@ def _add_manifest_to_bucket(current_token, manifest_json): obj = s3.Object( flask.current_app.config.get("MANIFEST_BUCKET_NAME"), filepath_in_bucket ) - response = obj.put(Body=manifest_as_bytes) + obj.put(Body=manifest_as_bytes) 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 @@ -398,7 +398,7 @@ 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 @@ -435,7 +435,7 @@ def is_valid_manifest(manifest_json, required_keys): def _generate_unique_filename( - users_existing_manifest_or_metadata_files, + users_existing_manifest_or_metadata_files, file_type="manifest" ): """ Returns a filename of the form manifest--.json that is @@ -446,20 +446,23 @@ def _generate_unique_filename( 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 ): """ 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 @@ -524,9 +527,7 @@ def _list_files_in_bucket(bucket_name, folder): 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 @@ -572,6 +573,9 @@ 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/tests/metadata_test.py b/tests/metadata_test.py index 3409858..9043b59 100644 --- a/tests/metadata_test.py +++ b/tests/metadata_test.py @@ -68,7 +68,7 @@ def test_GET_metadata(client, mocks): assert len(metadata_returned) == 1 # From the s3 mock assert ( - metadata_returned[0]["filename"] == "manifest-2024-04-26T18-59-21.226440.json" + metadata_returned[0]["filename"] == "metadata-2024-04-26T18-59-21.226440.json" ) From 81574643b5ccddeef9b9cd3097db4bbe7ccbecf3 Mon Sep 17 00:00:00 2001 From: Mingfei Shao Date: Thu, 13 Jun 2024 14:24:37 -0500 Subject: [PATCH 38/47] update docs --- manifestservice/manifests/__init__.py | 2 +- openapi/swagger.yaml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index caa7068..e86ee98 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -273,7 +273,7 @@ def put_metadata(): responses: 200: description: Success - example: '({ "filename": "5183a350-9d56-4084-8a03-6471cafeb7fe" }, 200)' + example: '({ "filename": "metadata-2024-06-13T17-14-46.026593.json" }, 200)' 403: description: Unauthorized example: '({ "error": "" }, 403)' diff --git a/openapi/swagger.yaml b/openapi/swagger.yaml index 6665474..d0d7670 100644 --- a/openapi/swagger.yaml +++ b/openapi/swagger.yaml @@ -95,7 +95,7 @@ paths: responses: '200': description: Success - example: '({ "filename": "5183a350-9d56-4084-8a03-6471cafeb7fe" }, 200)' + example: '({ "filename": "metadata-2024-06-13T17-14-46.026593.json" }, 200)' '400': description: Bad GUID format example: '({ "error": "" }, 400)' @@ -107,7 +107,7 @@ paths: responses: '200': description: Success - example: '({ "filename": "5183a350-9d56-4084-8a03-6471cafeb7fe" }, 200)' + example: '({ "filename": "metadata-2024-06-13T17-14-46.026593.json" }, 200)' '400': description: Bad GUID format example: '({ "error": "" }, 400)' From 3d275f69076f90f4db7b263c1594c00f9624cca2 Mon Sep 17 00:00:00 2001 From: Mingfei Shao Date: Thu, 13 Jun 2024 14:32:07 -0500 Subject: [PATCH 39/47] fix tests --- manifestservice/manifests/__init__.py | 2 +- tests/conftest.py | 2 +- tests/metadata_test.py | 12 ++++++++++++ 3 files changed, 14 insertions(+), 2 deletions(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index e86ee98..d95ea91 100644 --- a/manifestservice/manifests/__init__.py +++ b/manifestservice/manifests/__init__.py @@ -452,7 +452,7 @@ def _generate_unique_filename( def _generate_unique_filename_with_timestamp_and_increment( - timestamp, users_existing_manifest_files, file_type + timestamp, users_existing_manifest_files, file_type="manifest" ): """ A helper function for _generate_unique_manifest_filename(), which facilitates unit testing. diff --git a/tests/conftest.py b/tests/conftest.py index 937c47b..37a3826 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -59,7 +59,7 @@ def mocks(mocker): {"filename": "manifest-a-b-c.json"}, ], "cohorts": [{"filename": "18e32c12-a053-4ac5-90a5-f01f70b5c2be"}], - "metadata": [{"filename": "manifest-2024-04-26T18-59-21.226440.json"}], + "metadata": [{"filename": "metadata-2024-04-26T18-59-21.226440.json"}], }, True, ), diff --git a/tests/metadata_test.py b/tests/metadata_test.py index 9043b59..afd062e 100644 --- a/tests/metadata_test.py +++ b/tests/metadata_test.py @@ -1,5 +1,17 @@ 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): """ From abfeb5505a54c6f42df1ad384da62df578c90504 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 17 Jun 2024 22:19:09 +0000 Subject: [PATCH 40/47] Bump urllib3 from 1.26.18 to 1.26.19 Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.18 to 1.26.19. - [Release notes](https://github.com/urllib3/urllib3/releases) - [Changelog](https://github.com/urllib3/urllib3/blob/1.26.19/CHANGES.rst) - [Commits](https://github.com/urllib3/urllib3/compare/1.26.18...1.26.19) --- updated-dependencies: - dependency-name: urllib3 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 25 ++++--------------------- 1 file changed, 4 insertions(+), 21 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1075a29..0980b03 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1216,13 +1216,13 @@ traceback2 = "*" [[package]] name = "urllib3" -version = "1.26.18" +version = "1.26.19" description = "HTTP library with thread-safe connection pooling, file post, and more." optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7" files = [ - {file = "urllib3-1.26.18-py2.py3-none-any.whl", hash = "sha256:34b97092d7e0a3a8cf7cd10e386f401b3737364026c45e622aa02903dffe0f07"}, - {file = "urllib3-1.26.18.tar.gz", hash = "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"}, + {file = "urllib3-1.26.19-py2.py3-none-any.whl", hash = "sha256:37a0344459b199fce0e80b0d3569837ec6b6937435c5244e7fd73fa6006830f3"}, + {file = "urllib3-1.26.19.tar.gz", hash = "sha256:3e3d753a8618b86d7de333b4223005f68720bcd6a7d2bcb9fbd2229ec7c1e429"}, ] [package.extras] @@ -1230,23 +1230,6 @@ brotli = ["brotli (==1.0.9)", "brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotl secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] -[[package]] -name = "urllib3" -version = "2.0.7" -description = "HTTP library with thread-safe connection pooling, file post, and more." -optional = false -python-versions = ">=3.7" -files = [ - {file = "urllib3-2.0.7-py3-none-any.whl", hash = "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e"}, - {file = "urllib3-2.0.7.tar.gz", hash = "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84"}, -] - -[package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] -secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"] -socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] -zstd = ["zstandard (>=0.18.0)"] - [[package]] name = "werkzeug" version = "3.0.3" From a837aa03825f218d9ba7dadfa1688e2856165557 Mon Sep 17 00:00:00 2001 From: Mingfei Shao Date: Mon, 17 Jun 2024 21:40:19 -0500 Subject: [PATCH 41/47] trigger gh action From 4fe18a0cd7f288b29b25473336d6732b016fbbdc Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Sat, 6 Jul 2024 01:42:43 +0000 Subject: [PATCH 42/47] Bump certifi from 2024.2.2 to 2024.7.4 Bumps [certifi](https://github.com/certifi/python-certifi) from 2024.2.2 to 2024.7.4. - [Commits](https://github.com/certifi/python-certifi/compare/2024.02.02...2024.07.04) --- updated-dependencies: - dependency-name: certifi dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/poetry.lock b/poetry.lock index 0980b03..6323096 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "anyio" @@ -191,13 +191,13 @@ files = [ [[package]] name = "certifi" -version = "2024.2.2" +version = "2024.7.4" description = "Python package for providing Mozilla's CA Bundle." optional = false python-versions = ">=3.6" files = [ - {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"}, - {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"}, + {file = "certifi-2024.7.4-py3-none-any.whl", hash = "sha256:c198e21b1289c2ab85ee4e67bb4b4ef3ead0892059901a8d5b622f24a1101e90"}, + {file = "certifi-2024.7.4.tar.gz", hash = "sha256:5a1e7645bc0ec61a09e26c36f6106dd4cf40c6db3a1fb6352b0244e7fb057c7b"}, ] [[package]] From e12b148942ae1601f9bc5902af6d1ebd23257754 Mon Sep 17 00:00:00 2001 From: Mingfei Shao Date: Tue, 9 Jul 2024 13:39:57 -0500 Subject: [PATCH 43/47] trigger gh action From 12076d5a697711641eada34c8320b2c5060eb2de Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 9 Jul 2024 19:00:36 +0000 Subject: [PATCH 44/47] Bump zipp from 3.17.0 to 3.19.1 Bumps [zipp](https://github.com/jaraco/zipp) from 3.17.0 to 3.19.1. - [Release notes](https://github.com/jaraco/zipp/releases) - [Changelog](https://github.com/jaraco/zipp/blob/main/NEWS.rst) - [Commits](https://github.com/jaraco/zipp/compare/v3.17.0...v3.19.1) --- updated-dependencies: - dependency-name: zipp dependency-type: indirect ... Signed-off-by: dependabot[bot] --- poetry.lock | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/poetry.lock b/poetry.lock index 0980b03..f0cde4a 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. [[package]] name = "anyio" @@ -1260,18 +1260,18 @@ files = [ [[package]] name = "zipp" -version = "3.17.0" +version = "3.19.1" 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-3.19.1-py3-none-any.whl", hash = "sha256:2828e64edb5386ea6a52e7ba7cdb17bb30a73a858f5eb6eb93d8d36f5ea26091"}, + {file = "zipp-3.19.1.tar.gz", hash = "sha256:35427f6d5594f4acf82d25541438348c26736fa9b3afa2754bcd63cdb99d8e8f"}, ] [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"] +doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] +test = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] [metadata] lock-version = "2.0" From f5b8bbf9746a75b1913c296acf970513fd037dd9 Mon Sep 17 00:00:00 2001 From: Mingfei Shao Date: Tue, 13 Aug 2024 15:47:14 -0500 Subject: [PATCH 45/47] json type --- manifestservice/manifests/__init__.py | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/manifestservice/manifests/__init__.py b/manifestservice/manifests/__init__.py index d95ea91..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") @@ -323,13 +322,12 @@ def _add_metadata_to_bucket(current_token, metadata_body): result["metadata"], file_type="metadata" ) - metadata_as_bytes = str.encode(str(metadata_body)) 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=metadata_as_bytes) + obj.put(Body=bytes(json.dumps(metadata_body).encode('UTF-8'))) except Exception as e: return str(e), False @@ -357,14 +355,13 @@ def _add_manifest_to_bucket(current_token, manifest_json): 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 ) - obj.put(Body=manifest_as_bytes) + obj.put(Body=bytes(json.dumps(manifest_json).encode('UTF-8'))) except Exception as e: logger.error(f"Failed to add manifest to bucket: {e}") return str(e), False From d28654577ac0c67d3a564b7d096ace634795409f Mon Sep 17 00:00:00 2001 From: Mingfei Shao Date: Tue, 13 Aug 2024 21:38:47 -0500 Subject: [PATCH 46/47] update version --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 53ff2f3..7e90f07 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "manifestservice" -version = "0.5.0" +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" From 959623aa61ff5f694d6e7ecb5e7d5a0a088b9f0e Mon Sep 17 00:00:00 2001 From: Jawad Qureshi Date: Wed, 4 Sep 2024 14:39:33 -0500 Subject: [PATCH 47/47] Rebase off master --- Dockerfile | 89 ++-- deployment/uwsgi/uwsgi.ini | 23 - deployment/wsgi/gunicorn.conf.py | 6 + deployment/{uwsgi => wsgi}/wsgi.py | 0 poetry.lock | 747 ++++++++++++++++------------- pyproject.toml | 1 + 6 files changed, 462 insertions(+), 404 deletions(-) delete mode 100644 deployment/uwsgi/uwsgi.ini create mode 100644 deployment/wsgi/gunicorn.conf.py rename deployment/{uwsgi => wsgi}/wsgi.py (100%) 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/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/poetry.lock b/poetry.lock index 42e129e..1f9a5dd 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,14 @@ -# This file is automatically @generated by Poetry 1.8.3 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 = "4.3.0" +version = "4.4.0" description = "High level compatibility layer for multiple asynchronous event loop implementations" optional = false python-versions = ">=3.8" files = [ - {file = "anyio-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"}, - {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"}, + {file = "anyio-4.4.0-py3-none-any.whl", hash = "sha256:c1b2d8f46a8a812513012e1107cb0e68c17159a7a594208005a57dc776e1bdc7"}, + {file = "anyio-4.4.0.tar.gz", hash = "sha256:5aadc6a1bbb7cdb0bede386cac5e2940f5e2ff3aa20277e991cf028e0585ce94"}, ] [package.dependencies] @@ -45,32 +45,32 @@ files = [ [[package]] name = "attrs" -version = "23.2.0" +version = "24.2.0" description = "Classes Without Boilerplate" optional = false python-versions = ">=3.7" files = [ - {file = "attrs-23.2.0-py3-none-any.whl", hash = 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