Merge pull request #247 from hms-dbmi/development

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hms-dbmi · Jul 26, 2024 · e389ba9 · e389ba9
2 parents 3a0c976 + 8b4d1ad
commit e389ba9
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diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,61 @@
+name: Release Build
+
+on:
+  push:
+    branches: [ master, development ]
+  pull_request:
+    branches: [ master, development ]
+  workflow_dispatch:
+    inputs:
+      force:
+        type: boolean
+        default: false
+
+jobs:
+  test-image:
+    uses: hms-dbmi/actions/.github/workflows/test-image-build.yml@main
+    secrets:
+      DOCKER_HUB_USERNAME: ${{ secrets.BLHMSDBMI_DOCKERHUB_USERNAME }}
+      DOCKER_HUB_PASSWORD: ${{ secrets.BLHMSDBMI_DOCKERHUB_PASSWORD }}
+    with:
+      repository: ${{ github.repository }}
+      commit: ${{ github.sha }}
+
+  scan-image:
+    uses: hms-dbmi/actions/.github/workflows/scan.yml@main
+    secrets:
+      DOCKER_HUB_USERNAME: ${{ secrets.BLHMSDBMI_DOCKERHUB_USERNAME }}
+      DOCKER_HUB_PASSWORD: ${{ secrets.BLHMSDBMI_DOCKERHUB_PASSWORD }}
+    with:
+      repository: ${{ github.repository }}
+      commit: ${{ github.sha }}
+
+  metadata:
+    runs-on: "ubuntu-latest"
+    outputs:
+      branch: ${{ steps.set_branch.outputs.branch }}
+      force: ${{ steps.force.outputs.force }}
+    steps:
+      - name: Set the current branch name
+        shell: bash
+        run: echo "branch=${GITHUB_HEAD_REF:-${GITHUB_REF#refs/heads/}}" >> $GITHUB_OUTPUT
+        id: set_branch
+      - name: Manage force input
+        id: force
+        env:
+          FORCE_INPUT: ${{ inputs.force }}
+        run: echo "force=${FORCE_INPUT:=false}" >> $GITHUB_OUTPUT
+
+  deploy:
+    uses: hms-dbmi/actions/.github/workflows/dbmisvc-app-deploy.yml@main
+    needs:
+      - "test-image"
+      - "metadata"
+    secrets:
+      GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    with:
+      filename: "${{ github.event.repository.name }}-${{ needs.metadata.outputs.branch }}.zip"
+      app: ${{ github.event.repository.name }}
+      role: ${{ vars[ format('BLHMSDBMI_PPM_DEPLOYMENT_{0}_ROLE_ARN', needs.metadata.outputs.branch) ] }}
+      bucket: ${{ vars[ format('BLHMSDBMI_PPM_DEPLOYMENT_{0}_BUCKET', needs.metadata.outputs.branch) ] }}
+      force: ${{ fromJson(needs.metadata.outputs.force) }}
diff --git a/.github/workflows/scan.yml b/.github/workflows/scan.yml
@@ -1,10 +1,6 @@
 name: Scan
 
 on:
-  push:
-    branches: [ master, development ]
-  pull_request:
-    branches: [ master, development ]
   schedule:
     - cron: '0 12 * * 1' # runs at 12:00 UTC on Mondays
   workflow_dispatch:

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,10 +1,6 @@
 name: Test Image Build
 
 on:
-  push:
-    branches: [ master, development ]
-  pull_request:
-    branches: [ master, development ]
   workflow_dispatch:
 
 jobs:

diff --git a/.gitignore b/.gitignore
@@ -340,5 +340,7 @@ $RECYCLE.BIN/
 # Windows shortcuts
 *.lnk
 
+# Node modules
+node_modules
 
 # End of https://www.gitignore.io/api/osx,linux,django,python,windows,pycharm,pycharm+iml,pycharm+all
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 minimum_pre_commit_version: "2.13.0"
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks.git
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     - id: trailing-whitespace
     - id: mixed-line-ending
@@ -11,6 +11,10 @@ repos:
   - repo: https://github.com/jazzband/pip-tools
     rev: 7.4.1
     hooks:
+      - id: pip-compile
+        name: pip-compile test-requirements.in
+        args: [test-requirements.in, --upgrade, --generate-hashes, --allow-unsafe, --output-file, test-requirements.txt]
+        files: ^test-requirements\.(in|txt)$
       - id: pip-compile
         name: pip-compile dev-requirements.in
         args: [dev-requirements.in, --upgrade, --generate-hashes, --allow-unsafe, --output-file, dev-requirements.txt]

diff --git a/.releaserc b/.releaserc
@@ -0,0 +1,29 @@
+{
+    "branches": [
+        "master",
+        "main",
+        "+([0-9])?(.{+([0-9]),x}).x",
+        {"name": "development", "channel": "pre/rc", "prerelease": "rc"},
+        {"name": "beta", "prerelease": true},
+        {"name": "alpha", "prerelease": true}
+    ],
+    "plugins": [
+        "@semantic-release/commit-analyzer",
+        "@semantic-release/release-notes-generator",
+        ["@semantic-release/changelog", {
+            "changelogFile": "CHANGELOG.md"
+        }],
+        ["@semantic-release/exec", {
+          "prepareCmd": "sed -ie \"s/^version.*/version = \\x22${nextRelease.version}\\x22/g\" pyproject.toml"
+        }],
+        ["@semantic-release/git", {
+            "assets": ["pyproject.toml", "CHANGELOG.md"]
+        }],
+        ["@semantic-release/github", {
+            "successComment": false,
+            "failComment": false,
+            "failTitle": false
+        }]
+    ],
+    "preset": "angular"
+}
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,19 @@
+# 1.0.0-rc.1 (2024-07-25)
+
+
+### Bug Fixes
+
+* **ci:** Refactored deployment; added versioning; passes app version to Sentry initialization ([76f3c2e](https://github.com/hms-dbmi/fhirquestionnaire/commit/76f3c2ed11d28f02abf10547710c7165bb5aebc3))
+* **dockerfile:** Fixed incorrect phantomjs library being used ([ea4414a](https://github.com/hms-dbmi/fhirquestionnaire/commit/ea4414a613f4265209029853c1b21d44edf9092b))
+* **requirements:** Updated Python requirements ([f3b1ab4](https://github.com/hms-dbmi/fhirquestionnaire/commit/f3b1ab48bdfccd5885ea60d43a3a1b83c66bba52))
+* **requirements:** Updated Python requirements ([a02bbd5](https://github.com/hms-dbmi/fhirquestionnaire/commit/a02bbd53a4423fd7de71f9d992cf545740f5928c))
+* **requirements:** Updated Python requirements ([11cca88](https://github.com/hms-dbmi/fhirquestionnaire/commit/11cca88467a621a7e85dd8f2ff1455cfef461e5b))
+* **requirements:** Updated Python requirements ([ef1a121](https://github.com/hms-dbmi/fhirquestionnaire/commit/ef1a121db605d937b8139826d88f972cefeaf087))
+* **requirements:** Updated Python requirements ([3713378](https://github.com/hms-dbmi/fhirquestionnaire/commit/37133781b68e6688cb20e74d8ef6e4437bed7467))
+* **requirements:** Updated Python requirements ([638cc84](https://github.com/hms-dbmi/fhirquestionnaire/commit/638cc84be3b3ce04e1ad6beaefaa344fff3e6746))
+* **requirements:** Updated Python requirements ([3154ba8](https://github.com/hms-dbmi/fhirquestionnaire/commit/3154ba8c7932d5787578d1c7d10090ea3ecc6552))
+* **requirements:** Updated Python requirements ([6a7e453](https://github.com/hms-dbmi/fhirquestionnaire/commit/6a7e45327346c36359d9787c30b5911e478b783f))
+* **requirements:** Updated Python requirements ([9351a10](https://github.com/hms-dbmi/fhirquestionnaire/commit/9351a10cac12580dd1d6c55593e4e5ed6cdec2b3))
+* **requirements:** Updated Python requirements ([b391c77](https://github.com/hms-dbmi/fhirquestionnaire/commit/b391c77ea9cadd67a99f0e6cd29a0eceab8d86ec))
+* **requirements:** Updated Python requirements ([68281b6](https://github.com/hms-dbmi/fhirquestionnaire/commit/68281b689de4d2b70141e924905f3b07c9bf6008))
+* **requirements:** Updated Python requirements ([7d4e6d9](https://github.com/hms-dbmi/fhirquestionnaire/commit/7d4e6d9fd1f7355c627b7364a98c4de17c476792))
diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM hmsdbmitc/dbmisvc:debian12-slim-python3.11-0.6.1 AS builder
+FROM hmsdbmitc/dbmisvc:debian12-slim-python3.11-0.6.2 AS builder
 
 # Install requirements
 RUN apt-get update \
@@ -22,7 +22,23 @@ RUN pip install -U wheel \
     && pip wheel -r /requirements.txt \
         --wheel-dir=/root/wheels
 
-FROM hmsdbmitc/dbmisvc:debian12-slim-python3.11-0.6.1
+FROM hmsdbmitc/dbmisvc:debian12-slim-python3.11-0.6.2
+
+ARG APP_NAME="ppm-questionnaire"
+ARG APP_CODENAME="fhirquestionnaire"
+ARG VERSION
+ARG COMMIT
+ARG DATE
+
+LABEL org.label-schema.schema-version=1.0 \
+    org.label-schema.vendor="HMS-DBMI" \
+    org.label-schema.version=${VERSION} \
+    org.label-schema.name=${APP_NAME} \
+    org.label-schema.build-date=${DATE} \
+    org.label-schema.description="PPM questionnaire service" \
+    org.label-schema.url="https://github.com/hms-dbmi/fhirquestionnaire" \
+    org.label-schema.vcs-url="https://github.com/hms-dbmi/fhirquestionnaire" \
+    org.label-schema.vcf-ref=${COMMIT}
 
 # Copy PhantomJS binary
 COPY --from=builder /tmp/phantomjs-2.1.1-linux-x86_64/bin/phantomjs /usr/local/bin/phantomjs
@@ -62,6 +78,10 @@ ENV DBMI_PARAMETER_STORE_PREFIX=ppm.questionnaire.${DBMI_ENV}
 ENV DBMI_PARAMETER_STORE_PRIORITY=true
 ENV DBMI_AWS_REGION=us-east-1
 
+ENV DBMI_APP_NAME=${APP_NAME}
+ENV DBMI_APP_CODENAME=${APP_CODENAME}
+ENV DBMI_APP_VERSION=${VERSION}
+ENV DBMI_APP_COMMIT=${COMMIT}
 ENV DBMI_APP_WSGI=fhirquestionnaire
 ENV DBMI_APP_ROOT=/app
 ENV DBMI_APP_DOMAIN=p2m2.dbmi.hms.harvard.edu

diff --git a/app/api/urls.py b/app/api/urls.py
@@ -9,7 +9,7 @@
 # Wire up our API using automatic URL routing.
 # Additionally, we include login URLs for the browsable API.
 urlpatterns = [
-    re_path(r'^consent/(?P<study>[\w\d-]+)/(?P<ppm_id>[\d]+)/?$', views.ConsentView.as_view(), name='consent'),
+    re_path(r'^consent/(?P<study>[\w\d-]+)/(?P<ppm_id>[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}|[\d]+)/?$', views.ConsentView.as_view(), name='consent'),
     re_path(r'^consent/(?P<study>[\w\d-]+)/?$', views.ConsentsView.as_view(), name='consents'),
     re_path(r'^questionnaire/?$', views.QuestionnaireView.as_view(), name='questionnaire'),
     re_path(r'^questionnaire/(?P<questionnaire_id>[\w\d-]+)/?$', views.QuestionnaireView.as_view(), name='questionnaire'),

diff --git a/app/api/views.py b/app/api/views.py
@@ -49,7 +49,7 @@ def get(self, request, study, ppm_id, format=None):
 
         try:
             # Check patient
-            if not FHIR.query_patient(patient=ppm_id):
+            if not FHIR.get_patient(patient=ppm_id):
                 return Response(f'Participant {ppm_id} does not exist', status=status.HTTP_404_NOT_FOUND)
 
             # Check FHIR
@@ -82,7 +82,7 @@ def post(self, request, study, ppm_id=None, format=None):
 
         try:
             # Check patient
-            if not FHIR.query_patient(patient=ppm_id):
+            if not FHIR.get_patient(patient=ppm_id):
                 return Response(f'Participant {ppm_id} does not exist', status=status.HTTP_404_NOT_FOUND)
 
             # Check if we should overwrite
@@ -140,18 +140,8 @@ def delete_consent_document_reference(request, study, ppm_id, document_reference
             # Get their consent composition
             composition = FHIR.get_consent_composition(patient=ppm_id, study=study)
             if not composition:
-                compositions = FHIR.query_consent_compositions(patient=ppm_id)
-                if not compositions:
-                    logger.error(f'PPM/{study}/{ppm_id}: No consent compositions')
-                    return False
-
-                elif len(compositions) > 1:
-                    logger.error(f'PPM/{study}/{ppm_id}: Too many generic consent '
-                                 f'compositions: {[r["resource"]["id"] for r in compositions]}')
-                    return False
-
-                else:
-                    composition = compositions[0]
+                logger.error(f'PPM/{study}/{ppm_id}: No consent compositions')
+                return False
 
             # Update it
             if FHIR.update_consent_composition(patient=ppm_id, study=study, composition=composition):
@@ -189,7 +179,7 @@ def create_consent_document_reference(request, study, ppm_id=None):
             ppm_id = FHIR.query_patient_id(get_jwt_email(request=request, verify=False))
 
         # Pull their record
-        bundle = FHIR.query_participant(patient=ppm_id, flatten_return=True)
+        participant = FHIR.get_participant(patient=ppm_id, flatten_return=True)
 
         # Get study title
         study_title = PPM.Study.title(study)
@@ -204,7 +194,7 @@ def create_consent_document_reference(request, study, ppm_id=None):
         # Submit consent PDF
         logger.debug(f"PPM/{study}: Rendering consent with template: {template_name}")
         response = render_pdf(f'People-Powered Medicine {study_title} Consent', request, template_name,
-                              context=bundle.get('composition'), options={})
+                              context=participant.get('composition'), options={})
 
         # Hash the content
         hash = hashlib.md5(response.content).hexdigest()
@@ -409,9 +399,9 @@ def get(self, request, questionnaire_id=None, format=None):
         if questionnaire_id:
 
             # Try to fetch it
-            questionnaire = FHIR.get_questionnaire(
-                questionnaire_id=questionnaire_id,
-                flatten_return=False
+            questionnaire = FHIR.fhir_read(
+                resource_type="Questionnaire",
+                resource_id=questionnaire_id,
             )
 
             # Return it or 404

diff --git a/app/consent/fhir/example-signature.json b/app/consent/fhir/example-signature.json
@@ -6,6 +6,33 @@
   "subjectType": [
     "patient"
   ],
+  "useContext": [
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "program",
+        "display": "Program"
+      },
+       "valueReference": {"reference": "ResearchStudy/ppm-example"}
+    },
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "task",
+        "display": "Workflow Task"
+      },
+       "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://peoplepoweredmedicine.org/fhir/questionnaire/context",
+            "code": "ppm-example",
+            "display": "ppm-example"
+          }
+        ],
+        "text": "ppm-example"
+      }
+    }
+  ],
   "item": [
     {
       "linkId": "display-1",

diff --git a/app/consent/fhir/guardian-signature-part-1.json b/app/consent/fhir/guardian-signature-part-1.json
@@ -14,6 +14,33 @@
   "subjectType": [
     "patient"
   ],
+  "useContext": [
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "program",
+        "display": "Program"
+      },
+       "valueReference": {"reference": "ResearchStudy/ppm-asd"}
+    },
+    {
+      "code": {
+        "system": "http://terminology.hl7.org/CodeSystem/usage-context-type",
+        "code": "task",
+        "display": "Workflow Task"
+      },
+       "valueCodeableConcept": {
+        "coding": [
+          {
+            "system": "https://peoplepoweredmedicine.org/fhir/questionnaire/context",
+            "code": "ppm-asd",
+            "display": "ppm-asd"
+          }
+        ],
+        "text": "ppm-asd"
+      }
+    }
+  ],
   "item": [
     {
       "linkId": "display-1",