chore(ci): Merging 'development'

* development: (618 commits) chore(release): 1.0.0-rc.1 [skip ci] fix(reporting): Updated Sentry reporting; implemented automated versioning for CI routines HYP-HOTFIX-061224 - Examples fix(requirements): Updated Python requirements HYP-302 - Filter out child groups with no active projects HYP-302 - Added top-level navigation functionality develop(actions): Removed Snyk secret develop(requirements): Updated dev requirements fix(requirements): Updated Python requirements develop(actions): Configured Actions to use Organization secrets develop(dependencies): Reverted to Python 3.11 due to AWS CLIv2 incompatibility; updated Python dependencies develop(dependencies): Updated pre-commit develop(dependencies): Updated Python version, Docker image and Python dependencies HYP-301 - Hides 'Already Completed' button on signed agreement forms when a user starts filling out form PPM-HOTFIX-112823 - Updated language about N2C2 and LLM usage fix(requirements): Updated Python requirements fix(requirements): Updated Python requirements HYP-297 - Added fixture for DataProject model change HYP-297 - Added badge for commercial only projects HYP-HOTFIX-091323 - Set uploads to use S3v4 signatures ...
hms-dbmi · Aug 1, 2024 · 53f4b19 · 53f4b19
2 parents fa2f135 + a634ec1
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diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -0,0 +1,60 @@
+name: Release Build
+
+on:
+  push:
+    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_DBMISVC_DEPLOYMENT_{0}_ROLE_ARN', needs.metadata.outputs.branch) ] }}
+      bucket: ${{ vars[ format('BLHMSDBMI_DBMISVC_DEPLOYMENT_{0}_BUCKET', needs.metadata.outputs.branch) ] }}
+      force: ${{ fromJson(needs.metadata.outputs.force) }}
+      backmerge: development
diff --git a/.github/workflows/scan.yml b/.github/workflows/scan.yml
@@ -1,8 +1,6 @@
 name: Scan
 
 on:
-  push:
-    branches: [ master, development ]
   pull_request:
     branches: [ master, development ]
   schedule:

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -1,8 +1,6 @@
 name: Test Image Build
 
 on:
-  push:
-    branches: [ master, development ]
   pull_request:
     branches: [ master, development ]
   workflow_dispatch:

diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,4 @@ app/db.sqlite3
 app/hypatio/local_settings.py
 .vscode/settings.json
 backup
+node_modules
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,15 +1,20 @@
 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
     - id: check-byte-order-marker
     - id: check-merge-conflict
     - id: detect-aws-credentials
+      args: [--allow-missing-credentials]
   - 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 +1,34 @@
+# 1.0.0-rc.1 (2024-07-31)
+
+
+### Bug Fixes
+
+* **reporting:** Updated Sentry reporting; implemented automated versioning for CI routines ([3449c4d](https://github.com/hms-dbmi/hypatio-app/commit/3449c4d6f8f38520542c757070a45ba2781d80da))
+* **requirements:** Updated Python requirements ([b7c16fc](https://github.com/hms-dbmi/hypatio-app/commit/b7c16fc9241f46062f6a5ef20b884f73b2188a9c))
+* **requirements:** Updated Python requirements ([d5fac44](https://github.com/hms-dbmi/hypatio-app/commit/d5fac449348b4cb924001fae58e71b13a70fd91d))
+* **requirements:** Updated Python requirements ([8cd71f6](https://github.com/hms-dbmi/hypatio-app/commit/8cd71f6c090157b927ed3cd6d4b31ffa14958fbc))
+* **requirements:** Updated Python requirements ([479f562](https://github.com/hms-dbmi/hypatio-app/commit/479f562976aacbc36b1da18c7d008df9c2a4777f))
+* **requirements:** Updated Python requirements ([6186407](https://github.com/hms-dbmi/hypatio-app/commit/6186407200178a3d7699a57e31330707f379159f))
+* **requirements:** Updated Python requirements ([0876e7a](https://github.com/hms-dbmi/hypatio-app/commit/0876e7a2edde9cb84d7f3438f913f5a068a02a86))
+* **requirements:** Updated Python requirements ([ea0367a](https://github.com/hms-dbmi/hypatio-app/commit/ea0367a90f2ce284846c0debc76860b4b031449e))
+* **requirements:** Updated Python requirements ([4f76a09](https://github.com/hms-dbmi/hypatio-app/commit/4f76a097b923f04f9ba612f359f5189e4227e32e))
+* **requirements:** Updated Python requirements ([ad7054b](https://github.com/hms-dbmi/hypatio-app/commit/ad7054b8660cb5f6df44e253c88c3986b1bb9550))
+* **requirements:** Updated Python requirements ([acde20f](https://github.com/hms-dbmi/hypatio-app/commit/acde20ffd6bca00c1903ee97abcbbc6351b02f01))
+* **requirements:** Updated Python requirements ([b47cce0](https://github.com/hms-dbmi/hypatio-app/commit/b47cce003cabfd38f87d6a6d51b6549d3cbd7004))
+* **requirements:** Updated Python requirements ([14cfb90](https://github.com/hms-dbmi/hypatio-app/commit/14cfb90f5b94ff7c051a69de6611d837db693df4))
+* **requirements:** Updated Python requirements ([219f75b](https://github.com/hms-dbmi/hypatio-app/commit/219f75b57a21505b8a873f6e12163ba30ddf065f))
+* **requirements:** Updated Python requirements ([8186602](https://github.com/hms-dbmi/hypatio-app/commit/8186602cdbfab9ea7e6219396fa27beb69c8ab0d))
+* **requirements:** Updated Python requirements ([c6f0f5b](https://github.com/hms-dbmi/hypatio-app/commit/c6f0f5b66be7d0107945f969517b5c7077a80809))
+* **requirements:** Updated Python requirements ([4f578f6](https://github.com/hms-dbmi/hypatio-app/commit/4f578f6d8ab1f138e3c841bac1430119ee77b882))
+* **requirements:** Updated Python requirements ([398e025](https://github.com/hms-dbmi/hypatio-app/commit/398e02523fe629e5fc3f0548bdfe03f2b5564867))
+* **requirements:** Updated Python requirements ([9c4c16f](https://github.com/hms-dbmi/hypatio-app/commit/9c4c16f80fd0b2e74fe840762ab19bbaf9aab2d6))
+* **requirements:** Updated Python requirements ([9d40b7b](https://github.com/hms-dbmi/hypatio-app/commit/9d40b7b08aead1d7273da1a891e15dd3c7f51f6d))
+* **requirements:** Updated Python requirements ([385ae17](https://github.com/hms-dbmi/hypatio-app/commit/385ae177d171a5e8d2159f94623cceb2157aa089))
+* **requirements:** Updated Python requirements ([0403b2b](https://github.com/hms-dbmi/hypatio-app/commit/0403b2b2224c873a1d4c0a03dc49e91362401dd1))
+* **requirements:** Updated Python requirements ([8e5c26d](https://github.com/hms-dbmi/hypatio-app/commit/8e5c26d606765c565c012a94c7d47b8d1dd17404))
+* **requirements:** Updated Python requirements ([1917c7f](https://github.com/hms-dbmi/hypatio-app/commit/1917c7fea19bf16a38017214e8a22d94f718040f))
+* **requirements:** Updated Python requirements ([35139f3](https://github.com/hms-dbmi/hypatio-app/commit/35139f317a607f94baca9b3654af397566d884bd))
+* **requirements:** Updated Python requirements ([0646eaf](https://github.com/hms-dbmi/hypatio-app/commit/0646eafd196de443ca9933c59ec5f7ee1dc6b031))
+* **requirements:** Updated Python requirements ([13296d0](https://github.com/hms-dbmi/hypatio-app/commit/13296d0f4546536c343e69f5b387b265232b3845))
+* **requirements:** Updated Python requirements ([e5beb03](https://github.com/hms-dbmi/hypatio-app/commit/e5beb037968ce8e824723ef406116cfe6795f273))
+* **requirements:** Updated Python requirements ([7427625](https://github.com/hms-dbmi/hypatio-app/commit/7427625cd1d181781195735428b8388834c2488d))
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 \
@@ -20,7 +20,23 @@ 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="dbmi-data-portal"
+ARG APP_CODENAME="hypatio"
+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=${DATE} \
+    org.label-schema.description="DBMI Data Portal" \
+    org.label-schema.url="https://github.com/hms-dbmi/hypatio-app" \
+    org.label-schema.vcs-url="https://github.com/hms-dbmi/hypatio-app" \
+    org.label-schema.vcf-ref=${COMMIT}
 
 # Copy Python wheels from builder
 COPY --from=builder /root/wheels /root/wheels
@@ -59,6 +75,10 @@ ENV DBMI_PARAMETER_STORE_PRIORITY=true
 ENV DBMI_AWS_REGION=us-east-1
 
 # App config
+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=hypatio
 ENV DBMI_APP_ROOT=/app
 ENV DBMI_APP_DB=true

diff --git a/app/hypatio/settings.py b/app/hypatio/settings.py
@@ -16,6 +16,8 @@
 
 from os.path import normpath, join, dirname, abspath
 from dbmi_client import environment
+from dbmi_client import reporting
+from dbmi_client.logging import config
 
 # Build paths inside the project like this: os.path.join(BASE_DIR, ...)
 BASE_DIR = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
@@ -301,68 +303,49 @@
 
 #####################################################################################
 
-LOGGING = {
-    'version': 1,
-    'disable_existing_loggers': False,
-    'formatters': {
-        'console': {
-            'format': '[HYPATIO] - [%(asctime)s][%(levelname)s][%(name)s.%(funcName)s:%(lineno)d] - %(message)s',
-        },
+#####################################################################################
+# Logging settings
+#####################################################################################
+
+# Configure  Sentry
+reporting.sentry(
+    sentry_dsn=environment.get_str("SENTRY_DSN", required=True),
+    release=f'{environment.get_str("DBMI_APP_NAME")}@{environment.get_str("DBMI_APP_VERSION")}',
+    environment=environment.get_str("DBMI_ENV", "prod"),
+    sentry_trace_rate=environment.get_float("SENTRY_TRACES_RATE", default=0.0),
+    sentry_profile_rate=environment.get_float("SENTRY_PROFILES_RATE", default=0.0),
+)
+
+# Output the standard logging configuration
+LOGGING = config('HYPATIO', root_level=logging.DEBUG)
+
+# Disable warning level for 4xx request logging
+LOGGING['loggers'].update({
+    'django.request': {
+        'handlers': ['console'],
+        'level': 'ERROR',
+        'propagate': True,
     },
-    'handlers': {
-        'sentry': {
-            'level': 'ERROR',
-            'class': 'raven.contrib.django.raven_compat.handlers.SentryHandler',
-        },
-        'console': {
-            'level': 'DEBUG',
-            'class': 'logging.StreamHandler',
-            'formatter': 'console',
-            'stream': sys.stdout,
-        },
+    'boto3': {
+        'handlers': ['console'],
+        'level': 'INFO',
+        'propagate': True,
     },
-    'root': {
-        'handlers': ['console', ],
-        'level': 'DEBUG'
+    'botocore': {
+        'handlers': ['console'],
+        'level': 'INFO',
+        'propagate': True,
     },
-    'loggers': {
-        'django': {
-            'handlers': ['console', ],
-            'level': 'INFO',
-            'propagate': True,
-        },
-        'raven': {
-            'level': 'WARNING',
-            'handlers': ['console'],
-            'propagate': False,
-        },
-        'sentry.errors': {
-            'level': 'WARNING',
-            'handlers': ['console'],
-            'propagate': False,
-        },
-        'botocore': {
-            'level': 'WARNING',
-            'handlers': ['console'],
-            'propagate': True,
-        },
-        'boto3': {
-            'level': 'WARNING',
-            'handlers': ['console'],
-            'propagate': True,
-        },
-        's3transfer': {
-            'level': 'WARNING',
-            'handlers': ['console'],
-            'propagate': True,
-        },
+    's3transfer': {
+        'handlers': ['console'],
+        'level': 'INFO',
+        'propagate': True,
     },
-}
+    'urllib3': {
+        'handlers': ['console'],
+        'level': 'INFO',
+        'propagate': True,
+    },
+})
 
-RAVEN_CONFIG = {
-    'dsn': environment.get_str("RAVEN_URL", required=True),
-    # If you are using git, you can also automatically configure the
-    # release based on the git info.
-    'release': '1',
-    'site': 'HYPATIO'
-}
+#####################################################################################
diff --git a/app/hypatio/views.py b/app/hypatio/views.py
@@ -38,7 +38,15 @@ def group_context():
             # Check for group
             active_group = next((g for g in groups if project in g.dataproject_set.all()), None)
 
+        # Pull out top-level groups
+        parent_groups_keys = groups.filter(parent__isnull=False).values_list('parent', flat=True)
+        parent_groups = Group.objects.filter(id__in=parent_groups_keys)
+
+        # Remove groups that will be placed under a parent group
+        groups = groups.filter(parent__isnull=True)
+
         return {
+            "parent_groups": parent_groups,
             "groups": groups,
             "active_group": active_group,
         }

diff --git a/app/projects/migrations/0104_group_parent.py b/app/projects/migrations/0104_group_parent.py
@@ -0,0 +1,19 @@
+# Generated by Django 4.2.11 on 2024-04-25 13:33
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('projects', '0103_dataproject_commercial_only'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='group',
+            name='parent',
+            field=models.ForeignKey(blank=True, null=True, on_delete=django.db.models.deletion.PROTECT, to='projects.group'),
+        ),
+    ]
diff --git a/app/projects/models.py b/app/projects/models.py
@@ -694,6 +694,7 @@ class Group(models.Model):
     title = models.CharField(max_length=255, blank=False, null=False)
     description = models.TextField(blank=True)
     navigation_title = models.CharField(max_length=20, blank=True, null=True)
+    parent = models.ForeignKey("Group", on_delete=models.PROTECT, blank=True, null=True)
 
     # Meta
     created = models.DateTimeField(auto_now_add=True)
@@ -702,6 +703,8 @@ class Group(models.Model):
     def __str__(self):
         return self.title
 
+    def active_project_child_groups(self):
+        return self.group_set.filter(dataproject__isnull=False, dataproject__visible=True).distinct()
 
 ################################################################################
 # Deprecated models