Merge pull request #4181 from broadinstitute/dev

Dev

.github/workflows/dev-hail-search-release.yaml

@@ -47,11 +47,11 @@ jobs:
           persist-credentials: false
           fetch-depth: 0
 
-      - name: update image tag in the broad seqr chart
+      - name: update image tag in the dev broad seqr chart
         uses: mikefarah/[email protected]
         with:
           cmd: >
-            yq -i '.hail-search.image.tag = "${{ github.event.workflow_run.head_sha }}"' charts/broad-seqr/values-dev.yaml
+            yq -i '.hail-search.image.tag = "${{ github.event.workflow_run.head_sha }}"' charts/dev-broad-seqr/values.yaml
 
       - name: Commit and Push changes
         uses: Andro999b/[email protected]

.github/workflows/dev-release.yaml

@@ -47,11 +47,11 @@ jobs:
           persist-credentials: false
           fetch-depth: 0
 
-      - name: update image tag in the broad seqr chart
+      - name: update image tag in the dev broad seqr chart
         uses: mikefarah/[email protected]
         with:
           cmd: >
-            yq -i '.seqr.image.tag = "${{ github.event.workflow_run.head_sha }}"' charts/broad-seqr/values-dev.yaml
+            yq -i '.seqr.image.tag = "${{ github.event.workflow_run.head_sha }}"' charts/dev-broad-seqr/values.yaml
 
       - name: Commit and Push changes
         uses: Andro999b/[email protected]

requirements.txt

@@ -20,7 +20,7 @@ cffi==1.15.1
     # via cryptography
 charset-normalizer==3.0.1
     # via requests
-cryptography==42.0.6
+cryptography==42.0.8
     # via social-auth-core
 defusedxml==0.7.1
     # via
@@ -131,7 +131,7 @@ pytz==2022.7.1
     #   django-notifications-hq
 redis==4.5.4
     # via -r requirements.in
-requests==2.32.0
+requests==2.32.2
     # via
     #   -r requirements.in
     #   django-anymail

seqr/views/apis/report_api.py

@@ -442,7 +442,13 @@ def _add_row(row, family_id, row_type):
         (FINDINGS_TABLE, genetic_findings_rows),
     ]
 
-    files, warnings = _populate_gregor_files(file_data)
+    files, warnings, errors = _populate_gregor_files(file_data)
+
+    if errors and not request_json.get('overrideValidation'):
+        raise ErrorsWarningsException(errors, warnings)
+    else:
+        warnings = errors + warnings
+
     write_multiple_files_to_gs(files, file_path, request.user, file_format='tsv')
 
     return create_json_response({
@@ -700,10 +706,7 @@ def _populate_gregor_files(file_data):
         for column, config in table_config.items():
             _validate_column_data(column, file_name, data, column_validator=config, warnings=warnings, errors=errors)
 
-    if errors:
-        raise ErrorsWarningsException(errors, warnings)
-
-    return files, warnings
+    return files, warnings, errors
 
 
 def _load_data_model_validators():

seqr/views/apis/users_api.py

@@ -49,9 +49,12 @@ def get_all_user_group_options(request):
 @login_and_policies_required
 def get_project_collaborator_options(request, project_guid):
     project = get_project_and_check_permissions(project_guid, request.user)
+    user_fields = {'display_name', 'username', 'email'}
     users = get_project_collaborators_by_username(
-        request.user, project, fields={'display_name', 'username', 'email'}, expand_user_groups=True,
+        request.user, project, fields=user_fields, expand_user_groups=True,
     )
+    if not users:
+        users = {request.user.username: get_json_for_user(request.user, user_fields)}
     return create_json_response(users)
 
 

seqr/views/apis/users_api_tests.py

@@ -60,6 +60,7 @@ def test_get_project_collaborator_options(self):
         users.update(self.COLLABORATOR_JSON)
         users.pop('[email protected]', None)
         self.assertDictEqual(response_json, users)
+        return url
 
     def test_get_all_collaborator_options(self):
         url = reverse(get_all_collaborator_options)
@@ -425,7 +426,7 @@ def _assert_403_response(self, response, **kwargs):
     _test_delete_collaborator_group_response = _assert_403_response
 
     def test_get_project_collaborator_options(self, *args, **kwargs):
-        super(AnvilUsersAPITest, self).test_get_project_collaborator_options(*args, **kwargs)
+        url = super(AnvilUsersAPITest, self).test_get_project_collaborator_options(*args, **kwargs)
         self.mock_list_workspaces.assert_not_called()
         self.assertEqual(self.mock_get_ws_acl.call_count, 1)
         self.mock_get_ws_acl.assert_called_with(
@@ -436,6 +437,10 @@ def test_get_project_collaborator_options(self, *args, **kwargs):
         self.mock_get_groups.assert_not_called()
         self.mock_get_group_members.assert_called_with(self.collaborator_user, 'Analysts', use_sa_credentials=True)
 
+        self.mock_get_ws_acl.side_effect = lambda *args: {}
+        response = self.client.get(url)
+        self.assertEqual(response.status_code, 200)
+        self.assertDictEqual(response.json(), {'test_user_collaborator': MAIN_COLLABORATOR_JSON['test_user_collaborator']})
 
     def test_set_password(self):
         super(AnvilUsersAPITest, self).test_set_password()

seqr/views/utils/anvil_metadata_utils.py

@@ -361,7 +361,7 @@ def _get_parsed_saved_discovery_variants_by_family(
             variant_fields += ['svType', 'svName', 'end']
 
         parsed_variant = {
-            'chrom': chrom,
+            'chrom': 'MT' if chrom == 'M' else chrom,
             'pos': pos,
             'variant_reference_assembly': GENOME_VERSION_LOOKUP[variant_json['genomeVersion']],
             'gene_id': gene_id,
@@ -624,7 +624,7 @@ def _get_mondo_condition_data(mondo_id):
             inheritance = HumanPhenotypeOntology.objects.get(hpo_id=inheritance['id']).name.replace(' inheritance', '')
         return {
             'known_condition_name': data['name'],
-            'condition_inheritance': inheritance,
+            'condition_inheritance': inheritance or 'Unknown',
         }
     except Exception:
         return {}

ui/pages/Report/components/Gregor.jsx

@@ -2,13 +2,20 @@ import React from 'react'
 import { Header } from 'semantic-ui-react'
 
 import { validators } from 'shared/components/form/FormHelpers'
-import { ButtonRadioGroup } from 'shared/components/form/Inputs'
+import { ButtonRadioGroup, InlineToggle } from 'shared/components/form/Inputs'
 import UploadFormPage from 'shared/components/page/UploadFormPage'
 import { CONSENT_CODES } from 'shared/utils/constants'
 import { HttpRequestHelper } from 'shared/utils/httpRequestHelper'
 
 const FIELDS = [
-
+  {
+    name: 'overrideValidation',
+    label: 'Upload with Validation Errors',
+    component: InlineToggle,
+    asFormInput: true,
+    fullHeight: true,
+    inline: false,
+  },
   {
     name: 'deliveryPath',
     label: 'AnVIL Delivery Bucket Path',

ui/shared/components/form/Inputs.jsx

@@ -486,7 +486,7 @@ BooleanCheckbox.propTypes = {
 
 export const AlignedBooleanCheckbox = AlignedCheckboxGroup.withComponent(BooleanCheckbox)
 
-const BaseInlineToggle = styled(({ divided, fullHeight, asFormInput, padded, ...props }) => <BooleanCheckbox {...props} toggle inline />)`
+const BaseInlineToggle = styled(({ divided, fullHeight, asFormInput, padded, inline = true, ...props }) => <BooleanCheckbox {...props} toggle inline={inline} />)`
   ${props => (props.asFormInput ?
     `label {
       font-weight: 700;