move func again

Author: hanars

seqr/urls.py

@@ -39,7 +39,6 @@
     edit_individuals_handler, \
     delete_individuals_handler, \
     import_gregor_metadata, \
-    load_rna_seq_sample_data, \
     receive_individuals_table_handler, \
     save_individuals_table_handler, \
     receive_individuals_metadata_handler, \
@@ -147,7 +146,7 @@
 from seqr.views.apis.project_api import create_project_handler, update_project_handler, delete_project_handler, \
     project_page_data, project_families, project_overview, project_mme_submisssions, project_individuals, \
     project_analysis_groups, update_project_workspace, project_family_notes, project_collaborators, project_locus_lists, \
-    project_samples, project_notifications, mark_read_project_notifications, subscribe_project_notifications
+    project_samples, project_notifications, mark_read_project_notifications, subscribe_project_notifications, load_rna_seq_sample_data
 from seqr.views.apis.project_categories_api import update_project_categories_handler
 from seqr.views.apis.anvil_workspace_api import anvil_workspace_page, create_project_from_workspace, \
     grant_workspace_access, validate_anvil_vcf, add_workspace_data, get_anvil_vcf_list, get_anvil_igv_options

seqr/views/apis/individual_api.py

@@ -9,16 +9,14 @@
 from django.db.models import prefetch_related_objects
 
 from reference_data.models import HumanPhenotypeOntology
-from seqr.models import Individual, Family, RnaSample, CAN_VIEW
+from seqr.models import Individual, Family, CAN_VIEW
 from seqr.utils.file_utils import file_iter
 from seqr.utils.gene_utils import get_genes, get_gene_ids_for_gene_symbols
-from seqr.utils.logging_utils import SeqrLogger
 
 from seqr.views.utils.anvil_metadata_utils import PARTICIPANT_TABLE, PHENOTYPE_TABLE, EXPERIMENT_TABLE, \
     EXPERIMENT_LOOKUP_TABLE, FINDINGS_TABLE, FINDING_METADATA_COLUMNS, TRANSCRIPT_FIELDS, GENE_COLUMN, parse_population
-from seqr.views.utils.dataset_utils import post_process_rna_data, RNA_DATA_TYPE_CONFIGS
-from seqr.views.utils.file_utils import save_uploaded_file, load_uploaded_file, parse_file, get_temp_file_path
-from seqr.views.utils.json_to_orm_utils import update_individual_from_json, update_model_from_json
+from seqr.views.utils.file_utils import save_uploaded_file, load_uploaded_file, parse_file
+from seqr.views.utils.json_to_orm_utils import update_individual_from_json
 from seqr.views.utils.json_utils import create_json_response, _to_snake_case, _to_camel_case
 from seqr.views.utils.orm_to_json_utils import _get_json_for_model, _get_json_for_individuals, add_individual_hpo_details, \
     _get_json_for_families, get_json_for_rna_seq_outliers, get_project_collaborators_by_username, INDIVIDUAL_DISPLAY_NAME_EXPR, \
@@ -32,7 +30,6 @@
 from seqr.views.utils.individual_utils import delete_individuals, add_or_update_individuals_and_families
 from seqr.views.utils.variant_utils import bulk_create_tagged_variants
 
-logger = SeqrLogger(__name__)
 
 @login_and_policies_required
 def update_individual_handler(request, individual_guid):
@@ -948,30 +945,3 @@ def get_hpo_terms(request, hpo_parent_id):
             for hpo in HumanPhenotypeOntology.objects.filter(parent_id=hpo_parent_id)
         }
     })
-
-
-@pm_or_data_manager_required
-def load_rna_seq_sample_data(request, sample_guid):
-    sample = RnaSample.objects.get(guid=sample_guid)
-    logger.info(f'Loading outlier data for {sample.individual.individual_id}', request.user)
-
-    request_json = json.loads(request.body)
-    file_name = request_json['fileName']
-    data_type = request_json['dataType']
-    config = RNA_DATA_TYPE_CONFIGS[data_type]
-
-    file_path = get_temp_file_path(f'{file_name}/{sample_guid}.json.gz')
-    try:
-        data_rows = [json.loads(line) for line in file_iter(file_path, user=request.user)]
-        data_rows, error = post_process_rna_data(sample_guid, data_rows, **config.get('post_process_kwargs', {}))
-    except FileNotFoundError:
-        logger.error(f'No saved temp data found for {sample_guid} with file prefix {file_name}', request.user)
-        error = 'Data for this sample was not properly parsed. Please re-upload the data'
-    if error:
-        return create_json_response({'error': error}, status=400)
-
-    model_cls = config['model_class']
-    model_cls.bulk_create(request.user, [model_cls(sample=sample, **data) for data in data_rows], batch_size=1000)
-    update_model_from_json(sample, {'is_active': True}, user=request.user)
-
-    return create_json_response({'success': True})

seqr/views/apis/individual_api_tests.py

@@ -16,7 +16,7 @@
 from seqr.views.apis.individual_api import edit_individuals_handler, update_individual_handler, \
     delete_individuals_handler, receive_individuals_table_handler, save_individuals_table_handler, \
     receive_individuals_metadata_handler, save_individuals_metadata_table_handler, update_individual_hpo_terms, \
-    get_hpo_terms, get_individual_rna_seq_data, import_gregor_metadata, load_rna_seq_sample_data
+    get_hpo_terms, get_individual_rna_seq_data, import_gregor_metadata
 from seqr.views.apis.data_manager_api_tests import RNA_DATA_TYPE_PARAMS
 from seqr.views.apis.report_api_tests import PARTICIPANT_TABLE, PHENOTYPE_TABLE, EXPERIMENT_TABLE, EXPERIMENT_LOOKUP_TABLE, GENETIC_FINDINGS_TABLE
 from seqr.views.utils.test_utils import AuthenticationTestCase, AnvilAuthenticationTestCase, INDIVIDUAL_FIELDS, \

seqr/views/apis/project_api.py

@@ -13,7 +13,11 @@
 
 from matchmaker.models import MatchmakerSubmission
 from seqr.models import Project, Family, Individual, Sample, RnaSample, FamilyNote, PhenotypePrioritization, CAN_EDIT
+from seqr.utils.file_utils import file_iter
+from seqr.utils.logging_utils import SeqrLogger
 from seqr.views.utils.airtable_utils import AirtableSession, ANVIL_REQUEST_TRACKING_TABLE
+from seqr.views.utils.dataset_utils import post_process_rna_data, RNA_DATA_TYPE_CONFIGS
+from seqr.views.utils.file_utils import get_temp_file_path
 from seqr.views.utils.individual_utils import delete_individuals
 from seqr.views.utils.json_utils import create_json_response, _to_snake_case, _to_camel_case
 from seqr.views.utils.json_to_orm_utils import update_project_from_json, create_model_from_json, update_model_from_json
@@ -23,12 +27,14 @@
     FAMILY_ADDITIONAL_VALUES
 from seqr.views.utils.permissions_utils import get_project_and_check_permissions, check_project_permissions, \
     check_user_created_object_permissions, pm_required, user_is_pm, login_and_policies_required, \
-    has_workspace_perm, has_case_review_permissions, is_internal_anvil_project
+    has_workspace_perm, has_case_review_permissions, is_internal_anvil_project, pm_or_data_manager_required
 from seqr.views.utils.project_context_utils import families_discovery_tags, \
     add_project_tag_type_counts, get_project_analysis_groups, get_project_locus_lists
 from seqr.views.utils.terra_api_utils import is_anvil_authenticated, anvil_enabled
 from settings import BASE_URL
 
+logger = SeqrLogger(__name__)
+
 
 @pm_required
 def create_project_handler(request):
@@ -456,3 +462,30 @@ def _delete_project(project_guid, user):
             record_and_filters={'AnVIL Project URL': f'{BASE_URL}project/{project_guid}/project_page'},
             update={'Status': 'Project Deleted'},
         )
+
+
+@pm_or_data_manager_required
+def load_rna_seq_sample_data(request, sample_guid):
+    sample = RnaSample.objects.get(guid=sample_guid)
+    logger.info(f'Loading outlier data for {sample.individual.individual_id}', request.user)
+
+    request_json = json.loads(request.body)
+    file_name = request_json['fileName']
+    data_type = request_json['dataType']
+    config = RNA_DATA_TYPE_CONFIGS[data_type]
+
+    file_path = get_temp_file_path(f'{file_name}/{sample_guid}.json.gz')
+    try:
+        data_rows = [json.loads(line) for line in file_iter(file_path, user=request.user)]
+        data_rows, error = post_process_rna_data(sample_guid, data_rows, **config.get('post_process_kwargs', {}))
+    except FileNotFoundError:
+        logger.error(f'No saved temp data found for {sample_guid} with file prefix {file_name}', request.user)
+        error = 'Data for this sample was not properly parsed. Please re-upload the data'
+    if error:
+        return create_json_response({'error': error}, status=400)
+
+    model_cls = config['model_class']
+    model_cls.bulk_create(request.user, [model_cls(sample=sample, **data) for data in data_rows], batch_size=1000)
+    update_model_from_json(sample, {'is_active': True}, user=request.user)
+
+    return create_json_response({'success': True})