merge from master

.github/workflows/ci.yml

@@ -41,7 +41,7 @@ jobs:
         DB_PASSWORD: metadata_pass
         PGPASSWORD: metadata_pass
       run: |
-        poetry run pytest --cov=src --cov=migrations/versions --cov-fail-under=94 --cov-report xml
+        poetry run pytest --cov=src --cov=migrations/versions --cov-fail-under=93 --cov-report xml
     - name: Submit coverage report
       if: github.ref == 'refs/heads/master'
       env:

.github/workflows/integration_tests.yaml

@@ -22,5 +22,7 @@ jobs:
       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_TEST_RAS_2_USERID: ${{ secrets.CI_TEST_RAS_2_USERID }}
+      CI_TEST_RAS_2_PASSWORD: ${{ secrets.CI_TEST_RAS_2_PASSWORD }}
       CI_SLACK_BOT_TOKEN: ${{ secrets.CI_SLACK_BOT_TOKEN }}
       CI_SLACK_CHANNEL_ID: ${{ secrets.CI_SLACK_CHANNEL_ID }}

Dockerfile

@@ -1,18 +1,38 @@
-FROM quay.io/cdis/python:python3.9-buster-2.0.0 as base
+ARG AZLINUX_BASE_VERSION=master
 
-FROM base as builder
-RUN pip install --upgrade pip poetry
-RUN apt-get update \
-    && apt-get install -y --no-install-recommends \
-    build-essential gcc make musl-dev libffi-dev libssl-dev git curl bash
+# Base stage with python-build-base
+FROM quay.io/cdis/python-nginx-al:${AZLINUX_BASE_VERSION} AS base
 
-COPY . /src/
-WORKDIR /src
-RUN python -m venv /env && . /env/bin/activate && poetry install --no-interaction --no-dev
+ENV appname=mds
 
+COPY --chown=gen3:gen3 /src/${appname} /${appname}
+
+WORKDIR /${appname}
+
+# Builder stage
+FROM base AS builder
+
+USER gen3
+
+COPY poetry.lock pyproject.toml /${appname}/
+
+# RUN python3 -m venv /env && . /env/bin/activate &&
+RUN poetry install -vv --no-interaction --without dev
+
+COPY --chown=gen3:gen3 . /${appname}
+COPY --chown=gen3:gen3 ./deployment/wsgi/wsgi.py /${appname}/wsgi.py
+
+RUN poetry install -vv --no-interaction --without dev
+
+ENV  PATH="$(poetry env info --path)/bin:$PATH"
+
+# Final stage
 FROM base
-COPY --from=builder /env /env
-COPY --from=builder /src /src
-ENV PATH="/env/bin/:${PATH}"
-WORKDIR /src
-CMD ["/env/bin/gunicorn", "mds.asgi:app", "-b", "0.0.0.0:80", "-k", "uvicorn.workers.UvicornWorker", "-c", "gunicorn.conf.py"]
+
+COPY --from=builder /${appname} /${appname}
+
+# Switch to non-root user 'gen3' for the serving process
+
+USER gen3
+
+CMD ["/bin/bash", "-c", "/${appname}/dockerrun.bash"]

gunicorn.conf.py → deployment/wsgi/gunicorn.conf.py

@@ -35,3 +35,10 @@ def __init__(self, cfg):
 
 
 logger_class = CDISLogger
+wsgi_app = "deployment.wsgi.wsgi:app"
+bind = "0.0.0.0:8000"
+workers = 1
+user = "gen3"
+group = "gen3"
+timeout = 300
+worker_class = "uvicorn.workers.UvicornWorker"

deployment/wsgi/wsgi.py

@@ -0,0 +1,3 @@
+from mds.main import get_app
+
+app = get_app()

dockerrun.bash

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+nginx
+poetry run gunicorn -c "/mds/deployment/wsgi/gunicorn.conf.py" mds.asgi:app

docs/dev.md

@@ -172,3 +172,12 @@ helm upgrade --install gen3/metadata
 You can also store your images in a local registry. Kind and Minikube are popular for their local registries:
 - https://kind.sigs.k8s.io/docs/user/local-registry/
 - https://minikube.sigs.k8s.io/docs/handbook/registry/#enabling-insecure-registries
+
+
+## Additional Notes
+
+When using the Metadata Service as a backend to retrieve results for the Discovery Page, query response times can increase if the database contains a large number of records. To improve performance in such cases, one recommended approach is to manually add an index on the `data->>_guid_type` field in the PostgreSQL database.
+
+```SQL
+create index metadata_guid_type on public.metadata((data->>'_guid_type'));
+```

docs/openapi.yaml

@@ -5,7 +5,8 @@ components:
         \ using in place of whatever GUID\n    specified"
       properties:
         aliases:
-          items: {}
+          items:
+            type: string
           title: Aliases
           type: array
       title: AliasObjInput
@@ -68,7 +69,9 @@ components:
       properties:
         loc:
           items:
-            type: string
+            anyOf:
+            - type: string
+            - type: integer
           title: Location
           type: array
         msg:
@@ -92,8 +95,8 @@ components:
       type: http
 info:
   title: Framework Services Object Management Service
-  version: 4.0.1
-openapi: 3.0.2
+  version: 4.0.2
+openapi: 3.1.0
 paths:
   /_status:
     get:
@@ -283,10 +286,12 @@ paths:
         \      }\n        },\n        ...\n    ]"
       operationId: get_aggregate_metadata_for_commons_aggregate_metadata__name__get
       parameters:
-      - in: path
+      - description: Return the results without grouping items by commons.
+        in: path
         name: name
         required: true
         schema:
+          description: Return the results without grouping items by commons.
           title: Name
           type: string
       responses:
@@ -434,7 +439,8 @@ paths:
         content:
           application/json:
             schema:
-              items: {}
+              items:
+                type: object
               title: Data List
               type: array
         required: true