Code cleanup

hubmapconsortium · Nov 21, 2023 · 393d40f · 393d40f
1 parent 2659c68
commit 393d40f
Show file tree

Hide file tree

Showing 6 changed files with 0 additions and 146 deletions.
diff --git a/entity-api-spec.yaml b/entity-api-spec.yaml
@@ -406,59 +406,6 @@ components:
             - section
             - suspension
           description: "A code representing the type of specimen. Must be an organ, block, section, or suspension"
-        specimen_type:
-          type: string
-          enum:
-            - atacseq
-            - biopsy
-            - blood
-            - cell_lysate
-            - clarity_hydrogel
-            - codex
-            - cryosections_curls_from_fresh_frozen_oct
-            - cryosections_curls_rnalater
-            - ffpe_block
-            - ffpe_slide
-            - fixed_frozen_section_slide
-            - fixed_tissue_piece
-            - flash_frozen_liquid_nitrogen
-            - formalin_fixed_oct_block
-            - fresh_frozen_oct_block
-            - fresh_frozen_section_slide
-            - fresh_frozen_tissue
-            - fresh_frozen_tissue_section
-            - fresh_tissue
-            - frozen_cell_pellet_buffy_coat
-            - gdna
-            - module
-            - nuclei
-            - nuclei_rnalater
-            - organ
-            - organ_piece
-            - other
-            - pbmc
-            - pfa_fixed_frozen_oct_block
-            - plasma
-            - protein
-            - ran_poly_a_enriched
-            - rna_total
-            - rnalater_treated_and_stored
-            - rnaseq
-            - scatacseq
-            - scrnaseq
-            - segment
-            - seqfish
-            - sequence_library
-            - serum
-            - single_cell_cryopreserved
-            - snatacseq
-            - snrnaseq
-            - tissue_lysate
-            - wgs
-          description: "DEPRECATED:  No longer a required field. A code representing the type of specimen.  Must be one of the codes specified in: [tissue sample types](https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/tissue_sample_types.yaml)"
-        specimen_type_other:
-          type: string
-          description: "The user provided sample type if the 'other' sample_type is chosen."
         protocol_url:
           type: string
           description: "The protocols.io doi url pointing the protocol under wich the sample was obtained and/or prepared."

diff --git a/src/app.py b/src/app.py
@@ -436,7 +436,6 @@ def get_ancestor_organs(id):
         bad_request_error(f"Unable to get the ancestor organs for this: {normalized_entity_type},"
                           " supported entity types: Sample, Dataset, Publication")
 
-    # specimen_type -> sample_category 12/15/2022
     if normalized_entity_type == 'Sample' and entity_dict['sample_category'].lower() == 'organ':
         bad_request_error("Unable to get the ancestor organ of an organ.")
 
@@ -939,7 +938,6 @@ def create_entity(entity_type):
         # Check existence of the direct ancestor (either another Sample or Donor)
         direct_ancestor_dict = query_target_entity(direct_ancestor_uuid, user_token)
 
-        # specimen_type -> sample_category 12/15/2022
         # `sample_category` is required on create
         sample_category = json_data_dict['sample_category'].lower()
 
@@ -1112,7 +1110,6 @@ def create_multiple_samples(count):
     # sample's direct ancestor is a Donor.
     # Must be one of the codes from: https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/organ_types.yaml
     if direct_ancestor_dict['entity_type'] == 'Donor':
-        # specimen_type -> sample_category 12/15/2022
         # `sample_category` is required on create
         if json_data_dict['sample_category'].lower() != 'organ':
             bad_request_error("The sample_category must be organ since the direct ancestor is a Donor")
@@ -2828,8 +2825,6 @@ def get_prov_info():
                 first_sample_hubmap_id_list.append(item['hubmap_id'])
                 first_sample_submission_id_list.append(item['submission_id'])
                 first_sample_uuid_list.append(item['uuid'])
-
-                # specimen_type -> sample_category 12/15/2022
                 first_sample_type_list.append(item['sample_category'])
 
                 first_sample_portal_url_list.append(app.config['DOI_REDIRECT_URL'].replace('<entity_type>', 'sample').replace('<identifier>', item['uuid']))
@@ -3148,8 +3143,6 @@ def get_prov_info_for_dataset(id):
             first_sample_hubmap_id_list.append(item['hubmap_id'])
             first_sample_submission_id_list.append(item['submission_id'])
             first_sample_uuid_list.append(item['uuid'])
-
-            # specimen_type -> sample_category 12/15/2022
             first_sample_type_list.append(item['sample_category'])
 
             first_sample_portal_url_list.append(
@@ -3267,7 +3260,6 @@ def get_prov_info_for_dataset(id):
         else:
             requested_samples = {}
             for uuid in dataset_samples.keys():
-                # specimen_type -> sample_category 12/15/2022
                 if dataset_samples[uuid]['sample_category'] in include_samples:
                     requested_samples[uuid] = dataset_samples[uuid]
             internal_dict[HEADER_DATASET_SAMPLES] = requested_samples
@@ -3479,7 +3471,6 @@ def get_sample_prov_info():
             organ_hubmap_id = sample['organ_hubmap_id']
             organ_submission_id = sample['organ_submission_id']
         else:
-            # sample_specimen_type -> sample_category 12/15/2022
             if sample['sample_category'] == "organ":
                 organ_uuid = sample['sample_uuid']
                 organ_type = organ_types_dict[sample['sample_organ']]['description'].lower()
@@ -3507,10 +3498,7 @@ def get_sample_prov_info():
         internal_dict[HEADER_SAMPLE_HAS_METADATA] = sample_has_metadata
         internal_dict[HEADER_SAMPLE_HAS_RUI_INFO] = sample_has_rui_info
         internal_dict[HEADER_SAMPLE_DIRECT_ANCESTOR_ID] = sample['sample_ancestor_id']
-
-        # sample_specimen_type -> sample_category 12/15/2022
         internal_dict[HEADER_SAMPLE_TYPE] = sample['sample_category']
-
         internal_dict[HEADER_SAMPLE_HUBMAP_ID] = sample['sample_hubmap_id']
         internal_dict[HEADER_SAMPLE_SUBMISSION_ID] = sample['sample_submission_id']
         internal_dict[HEADER_SAMPLE_DIRECT_ANCESTOR_ENTITY_TYPE] = sample['sample_ancestor_entity']

diff --git a/src/schema/schema_manager.py b/src/schema/schema_manager.py
@@ -1356,7 +1356,6 @@ def create_hubmap_ids(normalized_class, json_data_dict, user_token, user_info_di
             parent_id = json_data_dict['direct_ancestor_uuid']
             json_to_post['parent_ids'] = [parent_id]
 
-            # specimen_type -> sample_category 12/15/2022
             # 'Sample.sample_category' is marked as `required_on_create` in the schema yaml
             if json_data_dict['sample_category'].lower() == 'organ':
                 # The 'organ' field containing the 2 digit organ code is required in this case

diff --git a/src/schema/schema_neo4j_queries.py b/src/schema/schema_neo4j_queries.py
@@ -442,24 +442,8 @@ def get_dataset_organ_and_donor_info(neo4j_driver, uuid):
     donor_metadata = None
 
     with neo4j_driver.session() as session:
-        # Old time-consuming single query, it takes a significant amounts of DB hits
-        # query = (f"MATCH (e:Dataset)<-[:ACTIVITY_INPUT|ACTIVITY_OUTPUT*]-(s:Sample)<-[:ACTIVITY_INPUT|ACTIVITY_OUTPUT*]-(d:Donor) "
-        #          f"WHERE e.uuid='{uuid}' AND s.specimen_type='organ' AND EXISTS(s.organ) "
-        #          f"RETURN s.organ AS organ_name, d.metadata AS donor_metadata")
-
-        # logger.info("======get_dataset_organ_and_donor_info() query======")
-        # logger.info(query)
-
-        # with neo4j_driver.session() as session:
-        #     record = session.read_transaction(execute_readonly_tx, query)
-
-        #     if record:
-        #         organ_name = record['organ_name']
-        #         donor_metadata = record['donor_metadata']
-
         # To improve the query performance, we implement the two-step queries to drastically reduce the DB hits
         sample_query = (f"MATCH (e:Dataset)<-[:ACTIVITY_INPUT|ACTIVITY_OUTPUT*]-(s:Sample) "
-                        # specimen_type -> sample_category 12/15/2022
                         f"WHERE e.uuid='{uuid}' AND s.sample_category='organ' AND EXISTS(s.organ) "
                         f"RETURN DISTINCT s.organ AS organ_name, s.uuid AS sample_uuid")
 
@@ -473,7 +457,6 @@ def get_dataset_organ_and_donor_info(neo4j_driver, uuid):
             sample_uuid = sample_record['sample_uuid']
 
             donor_query = (f"MATCH (s:Sample)<-[:ACTIVITY_OUTPUT]-(a:Activity)<-[:ACTIVITY_INPUT]-(d:Donor) "
-                           # specimen_type -> sample_category 12/15/2022
                            f"WHERE s.uuid='{sample_uuid}' AND s.sample_category='organ' AND EXISTS(s.organ) "
                            f"RETURN DISTINCT d.metadata AS donor_metadata")
 

diff --git a/src/schema_templating/example-yaml-templates/api-template-test/entity-Template.yaml b/src/schema_templating/example-yaml-templates/api-template-test/entity-Template.yaml
@@ -398,60 +398,6 @@ x-ref-components:
             - consortium
             - public
           description: "One of the values: public, consortium."
-        specimen_type:
-          type: string
-          enum:
-            - atacseq
-            - biopsy
-            - blood
-            - cell_lysate
-            - clarity_hydrogel
-            - codex
-            - cryosections_curls_from_fresh_frozen_oct
-            - cryosections_curls_rnalater
-            - ffpe_block
-            - ffpe_slide
-            - fixed_frozen_section_slide
-            - fixed_tissue_piece
-            - flash_frozen_liquid_nitrogen
-            - formalin_fixed_oct_block
-            - fresh_frozen_oct_block
-            - fresh_frozen_section_slide
-            - fresh_frozen_tissue
-            - fresh_frozen_tissue_section
-            - fresh_tissue
-            - frozen_cell_pellet_buffy_coat
-            - gdna
-            - module
-            - nuclei
-            - nuclei_rnalater
-            - organ
-            - organ_piece
-            - other
-            - pbmc
-            - pfa_fixed_frozen_oct_block
-            - plasma
-            - protein
-            - ran_poly_a_enriched
-            - rna_total
-            - rnalater_treated_and_stored
-            - rnaseq
-            - scatacseq
-            - scrnaseq
-            - segment
-            - seqfish
-            - sequence_library
-            - serum
-            - sequence_library
-            - single_cell_cryopreserved
-            - snatacseq
-            - snrnaseq
-            - tissue_lysate
-            - wgs
-          description: "A code representing the type of specimen.  Must be one of the codes specified in: [tissue sample types](https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/tissue_sample_types.yaml)"
-        specimen_type_other:
-          type: string
-          description: "The user provided sample type if the 'other' sample_type is chosen."
         protocol_url:
           type: string
           description: "The protocols.io doi url pointing the protocol under wich the sample was obtained and/or prepared."

diff --git a/src/schema_templating/example-yaml-templates/sample-schema.yaml b/src/schema_templating/example-yaml-templates/sample-schema.yaml
@@ -72,15 +72,6 @@ Sample:
         - consortium
         - public
       description: "One of the values: public, consortium."
-    specimen_type:
-      type: string
-      enum:
-        X-replace-enum-list:
-          enum-file-ref: https://raw.githubusercontent.com/hubmapconsortium/search-api/main/src/search-schema/data/definitions/enums/tissue_sample_types.yaml
-      description: "A code representing the type of specimen.  Must be one of the codes specified in: [tissue sample types](https://github.com/hubmapconsortium/search-api/blob/main/src/search-schema/data/definitions/enums/tissue_sample_types.yaml)"
-    specimen_type_other:
-      type: string
-      description: "The user provided sample type if the 'other' sample_type is chosen."
     protocol_url:
       type: string
       description: "The protocols.io doi url pointing the protocol under wich the sample was obtained and/or prepared."