Merge pull request #4216 from broadinstitute/dev

Dev

.github/workflows/docker-lint.yaml

@@ -11,6 +11,7 @@ on:
       - deploy/docker/seqr/Dockerfile
       - hail_search/deploy/Dockerfile
       - .hadolint.yaml
+      - .docker-compose.yaml
       - .github/workflows/docker-lint.yaml
   pull_request:
     types: [opened, synchronize, reopened]
@@ -21,13 +22,16 @@ on:
       - deploy/docker/seqr/Dockerfile
       - hail_search/deploy/Dockerfile
       - .hadolint.yaml
+      - .docker-compose.yaml
       - .github/workflows/docker-lint.yaml
 
 jobs:
   hadolint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2 
+      - uses: actions/checkout@v2
+      - name: Validate docker compose
+        run: docker-compose -f docker-compose.yml config
       - uses: hadolint/hadolint-action@v1.5.0
         with:
           dockerfile: deploy/docker/seqr/Dockerfile

CHANGELOG.md

@@ -2,6 +2,9 @@
 
 ## dev
 
+## 7/8/24
+* Add VLM contact for Projects (REQUIRES DB MIGRATION)
+
 ## 6/11/24
 * Add "Partial Phenotype Contribution" functional tag (REQUIRES DB MIGRATION)
 

requirements-dev.in

@@ -1,7 +1,7 @@
 -c requirements.txt # use the generated reqs as a constraint
 coverage<5.2
 django-compressor
-django-debug-toolbar<3.3  # https://github.com/jazzband/django-debug-toolbar
+django-debug-toolbar      # https://github.com/jazzband/django-debug-toolbar
 mock                      # mock objects for unit tests
 pip-tools                 # tool for managing our python dependency tree
 responses                 # mock HTTP responses for unit tests

requirements-dev.txt

@@ -22,7 +22,7 @@ click==8.1.3
     # via pip-tools
 coverage==5.1
     # via -r requirements-dev.in
-django==3.2.25
+django==4.2.13
     # via
     #   -c requirements.txt
     #   django-appconf
@@ -47,10 +47,6 @@ pip-tools==6.12.2
     # via -r requirements-dev.in
 pyproject-hooks==1.0.0
     # via build
-pytz==2022.7.1
-    # via
-    #   -c requirements.txt
-    #   django
 rcssmin==1.1.1
     # via django-compressor
 requests==2.32.2
@@ -69,9 +65,7 @@ sqlparse==0.5.0
 toml==0.10.2
     # via responses
 tomli==2.0.1
-    # via
-    #   build
-    #   pyproject-hooks
+    # via build
 types-toml==0.10.8.5
     # via responses
 urllib3==1.26.19

requirements.in

@@ -1,20 +1,20 @@
-Django<3.3                        # core server-side framework
+Django>=4.2,<4.3                  # core server-side framework
 django-anymail                    # for sending emails using cloud-based mail service providers
 django-csp                        # for setting CSP headers
 django-guardian                   # object-level permissions for database records. Behind a major version due to missing Python 2 support
 django-hijack                     # allows admins to login as other user
 django-notifications-hq           # notification app
 django-cors-headers               # allows CORS requests for client-side development
-django-storages[google]==1.11.1   # alternative GCS storage backend for the django media_root
-social-auth-app-django            # the package for Django to authenticate users with social medieas
+django-storages[google]           # alternative GCS storage backend for the django media_root
+social-auth-app-django>5.0.0      # the package for Django to authenticate users with social medieas
 social-auth-core                  # the Python social authentication package. Required by social-auth-app-django
 elasticsearch==7.9.1              # elasticsearch client
 elasticsearch-dsl==7.2.1          # elasticsearch query utilities
 gunicorn                          # web server
 jmespath
 openpyxl                          # library for reading/writing Excel files
 pillow                            # required dependency of Djagno ImageField-type database records
-psycopg2                          # postgres database access
+psycopg                           # postgres database access
 pyliftover                        # GRCh37/GRCh38 liftover
 requests                          # simpler way to make http requests
 redis<4.6                         # client lib for the redis in-memory database - used for caching server-side objects

requirements.txt

@@ -26,7 +26,7 @@ defusedxml==0.7.1
     # via
     #   python3-openid
     #   social-auth-core
-django==3.2.25
+django==4.2.13
     # via
     #   -r requirements.in
     #   django-anymail
@@ -38,6 +38,7 @@ django==3.2.25
     #   django-notifications-hq
     #   django-storages
     #   jsonfield
+    #   social-auth-app-django
 django-anymail==9.0
     # via -r requirements.in
 django-cors-headers==3.13.0
@@ -107,7 +108,7 @@ protobuf==3.20.2
     # via
     #   google-api-core
     #   googleapis-common-protos
-psycopg2==2.9.5
+psycopg==3.2.1
     # via -r requirements.in
 pyasn1==0.4.8
     # via
@@ -117,7 +118,7 @@ pyasn1-modules==0.2.8
     # via google-auth
 pycparser==2.21
     # via cffi
-pyjwt==2.6.0
+pyjwt==2.8.0
     # via social-auth-core
 pyliftover==0.4
     # via -r requirements.in
@@ -126,9 +127,7 @@ python-dateutil==2.8.2
 python3-openid==3.2.0
     # via social-auth-core
 pytz==2022.7.1
-    # via
-    #   django
-    #   django-notifications-hq
+    # via django-notifications-hq
 redis==4.5.4
     # via -r requirements.in
 requests==2.32.2
@@ -159,9 +158,9 @@ slacker==0.14.0
     # via -r requirements.in
 slugify==0.0.1
     # via -r requirements.in
-social-auth-app-django==5.0.0
+social-auth-app-django==5.4.1
     # via -r requirements.in
-social-auth-core==4.3.0
+social-auth-core==4.5.4
     # via
     #   -r requirements.in
     #   social-auth-app-django
@@ -175,6 +174,8 @@ tenacity==8.3.0
     # via -r requirements.in
 tqdm==4.66.3
     # via -r requirements.in
+typing-extensions==4.12.2
+    # via psycopg
 urllib3==1.26.19
     # via
     #   elasticsearch

seqr/fixtures/1kg_project.json

@@ -20,6 +20,7 @@
     "has_case_review": true,
 	"mme_primary_data_owner": "PI",
     "mme_contact_url": "mailto:test@broadinstitute.org,matchmaker@broadinstitute.org",
+    "vlm_contact_email": "test@broadinstitute.org,vlm@broadinstitute.org",
 	"last_accessed_date": "2017-09-15T18:15:50.827Z"
     }
 },
@@ -41,6 +42,7 @@
 	"can_view_group": 3,
 	"is_mme_enabled": false,
 	"mme_primary_data_owner": "",
+    "vlm_contact_email": "vlm@broadinstitute.org",
 	"last_accessed_date": "2017-09-15T18:15:50.827Z"
     }
 },
@@ -63,6 +65,7 @@
     "is_demo": true,
 	"mme_primary_data_owner": "",
     "mme_contact_url": "mailto:seqr-test@gmail.com,test@broadinstitute.org",
+    "vlm_contact_email": "seqr-test@gmail.com,test@broadinstitute.org",
 	"last_accessed_date": "2017-09-15T18:15:50.827Z"
     }
 },
@@ -81,6 +84,7 @@
 	    "last_accessed_date": "2017-09-15T18:15:50.827Z",
         "consent_code": "H",
         "genome_version": "38",
+        "vlm_contact_email": "vlm@broadinstitute.org",
     "workspace_name": "anvil-non-analyst-project 1000 Genomes Demo",
     "workspace_namespace": "ext-data"
     }

seqr/fixtures/social_auth.json

@@ -6,7 +6,12 @@
         "user": 10,
         "provider": "google-oauth2",
         "uid": "test_user@broadinstitute.org",
-        "extra_data": "{\"expires\": 3599, \"auth_time\": 1603287741, \"token_type\": \"Bearer\", \"access_token\": \"ya29.EXAMPLE\"}",
+        "extra_data": {
+            "expires": 3599,
+            "auth_time": 1603287741,
+            "token_type": "Bearer",
+            "access_token": "ya29.EXAMPLE"
+        },
         "created": "2020-03-12T23:09:54.180Z",
         "modified": "2020-03-12T23:09:54.180Z"
     }
@@ -17,7 +22,12 @@
         "user": 11,
         "provider": "google-oauth2",
         "uid": "test_user_manager@test.com",
-        "extra_data": "{\"expires\": 3599, \"auth_time\": 1603287741, \"token_type\": \"Bearer\", \"access_token\": \"ya29.EXAMPLE\"}",
+        "extra_data": {
+            "expires": 3599,
+            "auth_time": 1603287741,
+            "token_type": "Bearer",
+            "access_token": "ya29.EXAMPLE"
+        },
         "created": "2020-03-12T23:09:54.180Z",
         "modified": "2020-03-12T23:09:54.180Z"
     }
@@ -28,7 +38,12 @@
         "user": 12,
         "provider": "google-oauth2",
         "uid": "test_user_no_staff@test.com",
-        "extra_data": "{\"expires\": 3599, \"auth_time\": 1603287741, \"token_type\": \"Bearer\", \"access_token\": \"ya29.EXAMPLE\"}",
+        "extra_data": {
+            "expires": 6666,
+            "auth_time": 1603287741,
+            "token_type": "Bearer",
+            "access_token": "ya29.EXAMPLE"
+        },
         "created": "2020-03-12T23:09:54.180Z",
         "modified": "2020-03-12T23:09:54.180Z"
     }
@@ -39,7 +54,12 @@
         "user": 13,
         "provider": "google-oauth2",
         "uid": "test_user_no_access@test.com",
-        "extra_data": "{\"expires\": 3599, \"auth_time\": 1603287741, \"token_type\": \"Bearer\", \"access_token\": \"ya29.EXAMPLE\"}",
+        "extra_data": {
+            "expires": 3599,
+            "auth_time": 1603287741,
+            "token_type": "Bearer",
+            "access_token": "ya29.EXAMPLE"
+        },
         "created": "2020-03-12T23:09:54.180Z",
         "modified": "2020-03-12T23:09:54.180Z"
     }
@@ -50,7 +70,12 @@
         "user": 17,
         "provider": "google-oauth2",
         "uid": "test_pm_user@test.com",
-        "extra_data": "{\"expires\": 3599, \"auth_time\": 1603287741, \"token_type\": \"Bearer\", \"access_token\": \"ya29.EXAMPLE\"}",
+        "extra_data": {
+            "expires": 3599,
+            "auth_time": 1603287741,
+            "token_type": "Bearer",
+            "access_token": "ya29.EXAMPLE"
+        },
         "created": "2020-03-12T23:09:54.180Z",
         "modified": "2020-03-12T23:09:54.180Z"
     }
@@ -61,7 +86,12 @@
         "user": 15,
         "provider": "google-oauth2",
         "uid": "test_superuser@test.com",
-        "extra_data": "{\"expires\": 3599, \"auth_time\": 1603287741, \"token_type\": \"Bearer\", \"access_token\": \"ya29.EXAMPLE\"}",
+        "extra_data": {
+            "expires": 3599,
+            "auth_time": 1603287741,
+            "token_type": "Bearer",
+            "access_token": "ya29.EXAMPLE"
+        },
         "created": "2020-03-12T23:09:54.180Z",
         "modified": "2020-03-12T23:09:54.180Z"
     }

seqr/migrations/0024_varianttag_metadata.py

@@ -2,6 +2,7 @@
 from collections import defaultdict
 from django.contrib.postgres.aggregates import StringAgg
 from django.db import migrations, models
+from django.db.models import TextField
 from django.db.models.functions import Concat
 from django.utils import timezone
 from seqr.utils.logging_utils import log_model_update, log_model_bulk_update, SeqrLogger
@@ -120,7 +121,11 @@ def merge_duplicate_tags(apps, schema_editor):
     db_alias = schema_editor.connection.alias
 
     updated_tags = VariantTag.objects.using(db_alias).filter(variant_tag_type__name__in=SANGER_TAGS.values()).annotate(
-        group_id=Concat('variant_tag_type__guid', StringAgg('saved_variants__guid', ',', ordering='saved_variants__guid')))
+        group_id=Concat(
+            'variant_tag_type__guid',
+            StringAgg('saved_variants__guid', ',', ordering='saved_variants__guid'),
+            output_field=TextField()
+        ))
     if not updated_tags:
         logger.info('No updated tags found, skipping validation tag merging', user=None)
         return

seqr/migrations/0068_project_vlm_contact_email.py

@@ -0,0 +1,29 @@
+# Generated by Django 3.2.23 on 2024-06-28 15:44
+
+from django.db import migrations, models
+
+
+def update_vlm_contact_email(apps, schema_editor):
+    Project = apps.get_model('seqr', 'Project')
+    db_alias = schema_editor.connection.alias
+
+    projects = Project.objects.using(db_alias).all()
+    for project in projects:
+        project.vlm_contact_email = project.mme_contact_url.replace('mailto:', '').replace('matchmaker', 'vlm')
+    Project.objects.using(db_alias).bulk_update(projects, ['vlm_contact_email'])
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('seqr', '0067_alter_variantfunctionaldata_functional_data_tag'),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name='project',
+            name='vlm_contact_email',
+            field=models.TextField(blank=True, default='vlm@broadinstitute.org', null=True),
+        ),
+        migrations.RunPython(update_vlm_contact_email, reverse_code=migrations.RunPython.noop),
+    ]

seqr/models.py

@@ -17,7 +17,8 @@
 from seqr.utils.xpos_utils import get_chrom_pos
 from seqr.views.utils.terra_api_utils import anvil_enabled
 from reference_data.models import GENOME_VERSION_GRCh37, GENOME_VERSION_CHOICES
-from settings import MME_DEFAULT_CONTACT_NAME, MME_DEFAULT_CONTACT_HREF, MME_DEFAULT_CONTACT_INSTITUTION
+from settings import MME_DEFAULT_CONTACT_NAME, MME_DEFAULT_CONTACT_HREF, MME_DEFAULT_CONTACT_INSTITUTION, \
+    VLM_DEFAULT_CONTACT_EMAIL
 
 logger = SeqrLogger(__name__)
 
@@ -196,6 +197,8 @@ class Project(ModelWithGUID):
     mme_contact_url = models.TextField(null=True, blank=True, default=MME_DEFAULT_CONTACT_HREF)
     mme_contact_institution = models.TextField(null=True, blank=True, default=MME_DEFAULT_CONTACT_INSTITUTION)
 
+    vlm_contact_email = models.TextField(null=True, blank=True, default=VLM_DEFAULT_CONTACT_EMAIL)
+
     has_case_review = models.BooleanField(default=False)
     enable_hgmd = models.BooleanField(default=False)
     all_user_demo = models.BooleanField(default=False)
@@ -261,6 +264,7 @@ class Meta:
             'name', 'description', 'created_date', 'last_modified_date', 'genome_version', 'mme_contact_institution',
             'last_accessed_date', 'is_mme_enabled', 'mme_primary_data_owner', 'mme_contact_url', 'guid', 'consent_code',
             'workspace_namespace', 'workspace_name', 'has_case_review', 'enable_hgmd', 'is_demo', 'all_user_demo',
+            'vlm_contact_email',
         ]