Merge pull request #551 from UW-GAC/main

Deploy to stage

.env.dist

@@ -23,3 +23,8 @@ DJANGO_EMAIL_PORT=
 DJANGO_EMAIL_HOST_USER=
 DJANGO_EMAIL_HOST_PASSWORD=
 DJANGO_EMAIL_USE_TLS=
+
+# drupal api
+DRUPAL_API_CLIENT_ID=
+DRUPAL_API_CLIENT_SECRET=
+DRUPAL_API_REL_PATH=

.github/workflows/ci.yml

@@ -19,27 +19,6 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  linter:
-    runs-on: ubuntu-latest
-    steps:
-
-      - name: Checkout Code Repository
-        uses: actions/checkout@v4
-
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.9
-          cache: pip
-          cache-dependency-path: |
-            requirements/requirements.txt
-            requirements/test-requirements.txt
-
-      # Run all pre-commit hooks on all the files.
-      # Getting only staged files can be tricky in case a new PR is opened
-      # since the action is run on a branch in detached head state
-      - name: Install and Run Pre-commit
-        uses: pre-commit/[email protected]
 
   pytest-mariadb:
     runs-on: ubuntu-latest
@@ -50,7 +29,7 @@ jobs:
         # ahead of planned upgrades we can add versions as
         # needed
         python-version: [3.8]
-        mariadb-version: ["10.4"]
+        mariadb-version: ["10.4", "10.5"]
 
     services:
       mysql:

.pre-commit-config.yaml

@@ -10,22 +10,15 @@ repos:
       - id: end-of-file-fixer
       - id: check-yaml
 
-  - repo: https://github.com/psf/black
-    rev: 22.3.0
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.4.2
     hooks:
-      - id: black
-
-  - repo: https://github.com/timothycrosley/isort
-    rev: 5.12.0
-    hooks:
-      - id: isort
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 3.9.2
-    hooks:
-      - id: flake8
-        args: ['--config=setup.cfg']
-        additional_dependencies: [flake8-isort]
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format
 
   - repo: https://github.com/gitleaks/gitleaks
     rev: v8.16.1

.ruff.toml

@@ -0,0 +1,20 @@
+line-length = 120
+exclude = [
+    "**/migrations/**",
+    "*/static/CACHE/*",
+    "venv",
+    "docs",
+]
+
+[lint]
+extend-select = [
+    "E",
+    "F",
+    "W", # pycodestyle warnings
+    "I", # isort
+    "DJ", # flake8-django
+    "E501", # line-too-long
+]
+
+[lint.isort]
+known-first-party = ["primed", "config", ]

README.md

@@ -3,6 +3,8 @@
 
 [![Black code style](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 
+[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/UW-GAC/gregor-django/main.svg)](https://results.pre-commit.ci/latest/github/UW-GAC/gregor-django/main)
+
 [![image](https://img.shields.io/badge/License-MIT-blue.svg)](https://lbesson.mit-license.org/)
 
 [![Built with Cookiecutter Django](https://img.shields.io/badge/built%20with-Cookiecutter%20Django-ff69b4.svg?logo=cookiecutter)](https://github.com/pydanny/cookiecutter-django/)

add_cdsa_example_data.py

@@ -29,12 +29,8 @@
 major_version = factories.AgreementMajorVersionFactory.create(version=1)
 
 # Create some agreement versions
-v10 = factories.AgreementVersionFactory.create(
-    major_version=major_version, minor_version=0
-)
-v11 = factories.AgreementVersionFactory.create(
-    major_version=major_version, minor_version=1
-)
+v10 = factories.AgreementVersionFactory.create(major_version=major_version, minor_version=0)
+v11 = factories.AgreementVersionFactory.create(major_version=major_version, minor_version=1)
 
 # Create a couple signed CDSAs.
 dup = DataUsePermission.objects.get(abbreviation="GRU")
@@ -57,9 +53,7 @@
     signed_agreement__version=v10,
     study_site=StudySite.objects.get(short_name="CC"),
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1001.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1001.signed_agreement.anvil_access_group)
 
 cdsa_1002 = factories.MemberAgreementFactory.create(
     signed_agreement__cc_id=1002,
@@ -70,9 +64,7 @@
     signed_agreement__version=v10,
     study_site=StudySite.objects.get(short_name="CARDINAL"),
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1002.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1002.signed_agreement.anvil_access_group)
 
 cdsa_1003 = factories.MemberAgreementFactory.create(
     signed_agreement__cc_id=1003,
@@ -83,9 +75,7 @@
     signed_agreement__version=v10,
     study_site=StudySite.objects.get(short_name="CARDINAL"),
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1003.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1003.signed_agreement.anvil_access_group)
 
 cdsa_1004 = factories.MemberAgreementFactory.create(
     signed_agreement__cc_id=1004,
@@ -96,9 +86,7 @@
     signed_agreement__version=v11,
     study_site=StudySite.objects.get(short_name="CARDINAL"),
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1004.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1004.signed_agreement.anvil_access_group)
 
 cdsa_1005 = factories.DataAffiliateAgreementFactory.create(
     signed_agreement__cc_id=1005,
@@ -108,9 +96,7 @@
     study=Study.objects.get(short_name="Amish"),
     signed_agreement__version=v10,
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1005.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1005.signed_agreement.anvil_access_group)
 
 cdsa_1006 = factories.DataAffiliateAgreementFactory.create(
     signed_agreement__cc_id=1006,
@@ -122,9 +108,7 @@
     additional_limitations="This data can only be used for testing the app.",
     requires_study_review=True,
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1006.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1006.signed_agreement.anvil_access_group)
 
 cdsa_1007 = factories.DataAffiliateAgreementFactory.create(
     signed_agreement__cc_id=1007,
@@ -135,9 +119,7 @@
     study=Study.objects.get(short_name="MESA"),
     signed_agreement__version=v10,
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1007.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1007.signed_agreement.anvil_access_group)
 
 cdsa_1008 = factories.DataAffiliateAgreementFactory.create(
     signed_agreement__cc_id=1008,
@@ -148,9 +130,7 @@
     study=Study.objects.get(short_name="MESA"),
     signed_agreement__version=v10,
 )
-GroupGroupMembershipFactory.create(
-    parent_group=cdsa_group, child_group=cdsa_1008.signed_agreement.anvil_access_group
-)
+GroupGroupMembershipFactory.create(parent_group=cdsa_group, child_group=cdsa_1008.signed_agreement.anvil_access_group)
 
 cdsa_1009 = factories.NonDataAffiliateAgreementFactory.create(
     signed_agreement__cc_id=1009,
@@ -236,8 +216,6 @@
 cdsa_workspace_3 = factories.CDSAWorkspaceFactory.create(
     workspace__billing_project__name="demo-primed-cdsa",
     workspace__name="DEMO_PRIMED_CDSA_ARIC_1",
-    study=Study.objects.create(
-        short_name="ARIC", full_name="Atherosclerosis Risk in Communities"
-    ),
+    study=Study.objects.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities"),
     data_use_permission=dup,
 )

add_collaborative_analysis_example_data.py

@@ -55,27 +55,15 @@
 
 
 # Add accounts to the auth domains.
-account_1 = AccountFactory.create(
-    user__name="Adrienne", verified=True, email="[email protected]"
-)
-account_2 = AccountFactory.create(
-    user__name="Ben", verified=True, email="[email protected]"
-)
-account_3 = AccountFactory.create(
-    user__name="Matt", verified=True, email="[email protected]"
-)
-account_4 = AccountFactory.create(
-    user__name="Stephanie", verified=True, email="[email protected]"
-)
+account_1 = AccountFactory.create(user__name="Adrienne", verified=True, email="[email protected]")
+account_2 = AccountFactory.create(user__name="Ben", verified=True, email="[email protected]")
+account_3 = AccountFactory.create(user__name="Matt", verified=True, email="[email protected]")
+account_4 = AccountFactory.create(user__name="Stephanie", verified=True, email="[email protected]")
 
 # Set up collab analysis workspace one
 # analyst group
-GroupAccountMembershipFactory.create(
-    account=account_1, group=collaborative_analysis_workspace_1.analyst_group
-)
-GroupAccountMembershipFactory.create(
-    account=account_2, group=collaborative_analysis_workspace_1.analyst_group
-)
+GroupAccountMembershipFactory.create(account=account_1, group=collaborative_analysis_workspace_1.analyst_group)
+GroupAccountMembershipFactory.create(account=account_2, group=collaborative_analysis_workspace_1.analyst_group)
 # auth domains
 GroupAccountMembershipFactory.create(
     account=account_1,
@@ -84,12 +72,8 @@
 
 # Set up collab analysis workspace two
 # analyst group
-GroupAccountMembershipFactory.create(
-    account=account_3, group=collaborative_analysis_workspace_2.analyst_group
-)
-GroupAccountMembershipFactory.create(
-    account=account_4, group=collaborative_analysis_workspace_2.analyst_group
-)
+GroupAccountMembershipFactory.create(account=account_3, group=collaborative_analysis_workspace_2.analyst_group)
+GroupAccountMembershipFactory.create(account=account_4, group=collaborative_analysis_workspace_2.analyst_group)
 # auth domains
 GroupAccountMembershipFactory.create(
     account=account_3,

add_dbgap_example_data.py

@@ -10,23 +10,13 @@
 
 # Studies
 fhs = StudyFactory.create(short_name="FHS", full_name="Framingham Heart Study")
-mesa = StudyFactory.create(
-    short_name="MESA", full_name="Multi-Ethnic Study of Atherosclerosis"
-)
-aric = StudyFactory.create(
-    short_name="ARIC", full_name="Atherosclerosis Risk in Communities"
-)
+mesa = StudyFactory.create(short_name="MESA", full_name="Multi-Ethnic Study of Atherosclerosis")
+aric = StudyFactory.create(short_name="ARIC", full_name="Atherosclerosis Risk in Communities")
 
 # dbGaP study accessions
-dbgap_study_accession_fhs = factories.dbGaPStudyAccessionFactory.create(
-    dbgap_phs=7, studies=[fhs]
-)
-dbgap_study_accession_mesa = factories.dbGaPStudyAccessionFactory.create(
-    dbgap_phs=209, studies=[mesa]
-)
-dbgap_study_accession_aric = factories.dbGaPStudyAccessionFactory.create(
-    dbgap_phs=280, studies=[aric]
-)
+dbgap_study_accession_fhs = factories.dbGaPStudyAccessionFactory.create(dbgap_phs=7, studies=[fhs])
+dbgap_study_accession_mesa = factories.dbGaPStudyAccessionFactory.create(dbgap_phs=209, studies=[mesa])
+dbgap_study_accession_aric = factories.dbGaPStudyAccessionFactory.create(dbgap_phs=280, studies=[aric])
 
 
 # Create some dbGaP workspaces.
@@ -78,9 +68,7 @@
     dbgap_project_id=33119,
 )
 # Add a snapshot
-dar_snapshot_1 = factories.dbGaPDataAccessSnapshotFactory.create(
-    dbgap_application=dbgap_application_1
-)
+dar_snapshot_1 = factories.dbGaPDataAccessSnapshotFactory.create(dbgap_application=dbgap_application_1)
 # Add some data access requests.
 dar_1_1 = factories.dbGaPDataAccessRequestForWorkspaceFactory.create(
     dbgap_workspace=workspace_fhs_1,
@@ -112,9 +100,7 @@
     dbgap_project_id=33371,
 )
 # Add a snapshot
-dar_snapshot_2 = factories.dbGaPDataAccessSnapshotFactory.create(
-    dbgap_application=dbgap_application_2
-)
+dar_snapshot_2 = factories.dbGaPDataAccessSnapshotFactory.create(dbgap_application=dbgap_application_2)
 # Add some data access requests, only for FHS.
 dar_1_1 = factories.dbGaPDataAccessRequestForWorkspaceFactory.create(
     dbgap_workspace=workspace_fhs_1,

add_phenotype_inventory_input_example_data.py

@@ -0,0 +1,44 @@
+# Temporary script to create some test data.
+# Run with: python manage.py shell < add_phenotype_inventory_input_example_data.py
+
+from anvil_consortium_manager.tests.factories import (
+    ManagedGroupFactory,
+    WorkspaceGroupSharingFactory,
+)
+
+from primed.cdsa.tests.factories import CDSAWorkspaceFactory
+from primed.dbgap.tests.factories import dbGaPWorkspaceFactory
+from primed.miscellaneous_workspaces.tests.factories import OpenAccessWorkspaceFactory
+from primed.primed_anvil.tests.factories import StudyFactory
+
+# Create a dbGaP workspace.
+fhs = StudyFactory.create(short_name="FHS", full_name="Framingham Heart Study")
+workspace_dbgap = dbGaPWorkspaceFactory.create(
+    dbgap_study_accession__dbgap_phs=7,
+    dbgap_study_accession__studies=[fhs],
+    dbgap_version=33,
+    dbgap_participant_set=12,
+    dbgap_consent_code=1,
+    dbgap_consent_abbreviation="HMB",
+    workspace__name="DBGAP_FHS_v33_p12_HMB",
+)
+
+
+# Create a CDSA workspace.
+workspace_cdsa = CDSAWorkspaceFactory.create(
+    study__short_name="MESA",
+    workspace__name="CDSA_MESA_HMB",
+)
+
+# Create an open access workspace
+workspace_open_access = OpenAccessWorkspaceFactory.create(
+    workspace__name="OPEN_ACCESS_FHS",
+)
+workspace_open_access.studies.add(fhs)
+
+
+# Share workspaces with PRIMED_ALL
+primed_all = ManagedGroupFactory.create(name="PRIMED_ALL")
+WorkspaceGroupSharingFactory.create(workspace=workspace_dbgap.workspace, group=primed_all)
+WorkspaceGroupSharingFactory.create(workspace=workspace_cdsa.workspace, group=primed_all)
+WorkspaceGroupSharingFactory.create(workspace=workspace_open_access.workspace, group=primed_all)