Merge pull request #4208 from broadinstitute/vlm-contact-option

VLM configure contact

CHANGELOG.md

@@ -1,6 +1,7 @@
 # _seqr_ Changes
 
 ## dev
+* Add VLM contact for Projects (REQUIRES DB MIGRATION)
 
 ## 6/11/24
 * Add "Partial Phenotype Contribution" functional tag (REQUIRES DB MIGRATION)

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/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',
         ]
 
 

seqr/views/apis/anvil_workspace_api.py

@@ -184,6 +184,7 @@ def create_project_from_workspace(request, namespace, name):
         'workspace_name': name,
         'mme_primary_data_owner': request.user.get_full_name(),
         'mme_contact_url': 'mailto:{}'.format(request.user.email),
+        'vlm_contact_email': request.user.email,
     }
 
     project = create_model_from_json(Project, project_args, user=request.user)

seqr/views/apis/anvil_workspace_api_tests.py

@@ -559,14 +559,27 @@ def test_create_project_from_workspace(self):
         self.assertEqual(response.status_code, 200)
         project = Project.objects.get(workspace_namespace=TEST_WORKSPACE_NAMESPACE, workspace_name=TEST_NO_PROJECT_WORKSPACE_NAME)
         response_json = response.json()
-        self.assertEqual(project.guid, response_json['projectGuid'])
-        self.assertListEqual(
-            [project.genome_version, project.description, project.workspace_namespace, project.workspace_name],
-            ['38', 'A test project', TEST_WORKSPACE_NAMESPACE, TEST_NO_PROJECT_WORKSPACE_NAME])
-
-        self.assertListEqual(
-            [project.mme_contact_institution, project.mme_primary_data_owner, project.mme_contact_url],
-            ['Broad Center for Mendelian Genomics', 'Test Manager User', 'mailto:test_user_manager@test.com'])
+        self.assertDictEqual({k: getattr(project, k) for k in project._meta.json_fields}, {
+            'guid': response_json['projectGuid'],
+            'name': TEST_NO_PROJECT_WORKSPACE_NAME,
+            'description': 'A test project',
+            'workspace_namespace': TEST_WORKSPACE_NAMESPACE,
+            'workspace_name': TEST_NO_PROJECT_WORKSPACE_NAME,
+            'has_case_review': False,
+            'enable_hgmd': False,
+            'is_demo': False,
+            'all_user_demo': False,
+            'consent_code': None,
+            'created_date': mock.ANY,
+            'last_modified_date': mock.ANY,
+            'last_accessed_date': mock.ANY,
+            'genome_version': '38',
+            'is_mme_enabled': True,
+            'mme_contact_institution': 'Broad Center for Mendelian Genomics',
+            'mme_primary_data_owner': 'Test Manager User',
+            'mme_contact_url': 'mailto:test_user_manager@test.com',
+            'vlm_contact_email': 'test_user_manager@test.com',
+        })
 
         self._assert_valid_operation(project, test_add_data=False)
 

seqr/views/apis/project_api_tests.py

@@ -73,15 +73,30 @@ def test_create_and_delete_project(self, mock_airtable_logger):
 
         # check that project was created
         new_project = Project.objects.get(name='new_project')
-        self.assertEqual(new_project.description, 'new project description')
-        self.assertEqual(new_project.genome_version, '38')
-        self.assertEqual(new_project.consent_code, 'H')
-        self.assertTrue(new_project.is_demo)
-        self.assertFalse(new_project.is_mme_enabled)
         self.assertEqual(new_project.created_by, self.pm_user)
         self.assertEqual(new_project.projectcategory_set.count(), 0)
         expected_workspace_name = self.CREATE_PROJECT_JSON.get('workspaceName')
-        self.assertEqual(new_project.workspace_name, expected_workspace_name)
+        self.assertDictEqual({k: getattr(new_project, k) for k in new_project._meta.json_fields}, {
+            'guid': mock.ANY,
+            'name': 'new_project',
+            'description': 'new project description',
+            'workspace_namespace': self.CREATE_PROJECT_JSON.get('workspaceNamespace'),
+            'workspace_name': expected_workspace_name,
+            'has_case_review': False,
+            'enable_hgmd': False,
+            'is_demo': True,
+            'all_user_demo': False,
+            'consent_code': 'H',
+            'created_date': mock.ANY,
+            'last_modified_date': mock.ANY,
+            'last_accessed_date': mock.ANY,
+            'genome_version': '38',
+            'is_mme_enabled': False,
+            'mme_contact_institution': 'Broad Center for Mendelian Genomics',
+            'mme_primary_data_owner': 'Samantha Baxter',
+            'mme_contact_url': 'mailto:matchmaker@broadinstitute.org',
+            'vlm_contact_email': 'vlm@broadinstitute.org',
+        })
         self._check_created_project_groups(new_project)
 
         project_guid = new_project.guid

seqr/views/utils/test_utils.py

@@ -738,7 +738,7 @@ def _get_list_param(call, param):
     'projectGuid', 'projectCategoryGuids', 'canEdit', 'name', 'description', 'createdDate', 'lastModifiedDate',
     'lastAccessedDate',  'mmeContactUrl', 'genomeVersion', 'mmePrimaryDataOwner', 'mmeContactInstitution',
     'isMmeEnabled', 'workspaceName', 'workspaceNamespace', 'hasCaseReview', 'enableHgmd', 'isDemo', 'allUserDemo',
-    'userIsCreator', 'consentCode', 'isAnalystProject',
+    'userIsCreator', 'consentCode', 'isAnalystProject', 'vlmContactEmail',
 }
 
 ANALYSIS_GROUP_FIELDS = {'analysisGroupGuid', 'description', 'name', 'projectGuid', 'familyGuids'}

settings.py

@@ -352,6 +352,8 @@
 MME_DEFAULT_CONTACT_EMAIL = 'matchmaker@broadinstitute.org'
 MME_DEFAULT_CONTACT_HREF = 'mailto:{}'.format(MME_DEFAULT_CONTACT_EMAIL)
 
+VLM_DEFAULT_CONTACT_EMAIL = 'vlm@broadinstitute.org'
+
 MME_CONFIG_DIR = os.environ.get('MME_CONFIG_DIR', '')
 MME_NODES = {}
 if MME_CONFIG_DIR:

ui/shared/components/buttons/EditProjectButton.jsx

@@ -3,6 +3,8 @@ import { connect } from 'react-redux'
 import PropTypes from 'prop-types'
 
 import { updateProject } from 'redux/rootReducer'
+import { BaseSemanticInput } from '../form/Inputs'
+import { validators } from '../form/FormHelpers'
 import UpdateButton from './UpdateButton'
 import {
   EDITABLE_PROJECT_FIELDS,
@@ -11,10 +13,49 @@ import {
   MATCHMAKER_CONTACT_URL_FIELD,
 } from '../../utils/constants'
 
-const MATCHMAKER_PROJECT_FIELDS = [
+const setBoolVal = onChange => data => onChange(data.checked ? null : 'vlm@broadinstitute.org')
+
+const VlmContactInput = ({ value, onChange, ...props }) => ([
+  <BaseSemanticInput
+    {...props}
+    key="email"
+    inputType="Input"
+    label="Variant Matching Contact Email"
+    value={value}
+    onChange={onChange}
+    disabled={!value}
+    inline
+    width={9}
+  />,
+  <BaseSemanticInput
+    {...props}
+    key="disable"
+    label="Disable Contact for Variant Matches"
+    inputType="Checkbox"
+    checked={!value}
+    onChange={setBoolVal(onChange)}
+    inline
+    width={7}
+  />,
+])
+
+VlmContactInput.propTypes = {
+  value: PropTypes.string,
+  onChange: PropTypes.func,
+}
+
+const VLM_CONTACT_FIELD = {
+  name: 'vlmContactEmail',
+  parse: val => val || null,
+  format: val => val || '',
+  validate: value => (!value ? undefined : validators.requiredEmail(value)),
+  component: VlmContactInput,
+}
+
+const MATCHMAKER_PROJECT_FIELDS = [VLM_CONTACT_FIELD, ...[
   { ...MATCHMAKER_CONTACT_NAME_FIELD, name: 'mmePrimaryDataOwner' },
   { ...MATCHMAKER_CONTACT_URL_FIELD, name: 'mmeContactUrl' },
-].map(({ label, ...field }) => ({ ...field, label: `Matchmaker ${label}` }))
+].map(({ label, ...field }) => ({ ...field, label: `Matchmaker ${label}` }))]
 
 // Field mapping based on whether project has matchmaker and user is a PM. Usage: FIELD_LOOKUP[isMmeEnabled][isPm]
 const FIELD_LOOKUP = {