Merge pull request #10 from FlyBase/fix_db_status

update db status vocab term
FlyBase · Aug 15, 2023 · 08442dd · 08442dd
2 parents cf654b0 + 3951394
commit 08442dd
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Showing 2 changed files with 7 additions and 6 deletions.
diff --git a/src/AGR_data_retrieval_curation_allele.py b/src/AGR_data_retrieval_curation_allele.py
@@ -139,7 +139,7 @@ def __init__(self, feature):
         self.in_collection_name = None                         # Will be library.name.
         self.is_extinct = None                                 # Make True if extinction reported; make False is stock exists; leave as None otherwise.
         self.reference_curies = []                             # Will be a list of reference curies (directly or indirectly related).
-        self.allele_database_status_dto = None                 # Will be "public" or "private" slot annotation.
+        self.allele_database_status_dto = None                 # Use term from "allele database status" CV.
         self.allele_inheritance_mode_dtos = []                 # Will be list of slot annotations. TEMPORARY: Suppress phenotype_curie_term.
         self.allele_mutation_type_dtos = []                    # Will be list of slot annotations.
         # Future ToDo:
@@ -1076,7 +1076,7 @@ def synthesize_inheritance_mode(self, allele):
                 inheritance_data[pheno_key] = [pub_curie]
         # Convert data into Alliance slot annotations.
         INHERITANCE_MODE_NAME = 0
-        PHENOTYPE_CURIE_NAME = 1    # TEMPORARY: Suppress until AGR has FBcv
+        # PHENOTYPE_CURIE_NAME = 1    # TEMPORARY: Suppress until AGR has FBcv
         PHENOTYPE_STATEMENT = 2
         for pheno_key, pub_curie_list in inheritance_data.items():
             for pub_curie in pub_curie_list:
@@ -1254,18 +1254,19 @@ def add_data_provider_info(self, allele):
 
     def flag_internal_alleles(self, allele):
         """Flag alleles as internal."""
+        allele.allele_database_status_dto = self.generic_audited_object.copy()
+        allele.allele_database_status_dto['database_status_name'] = 'approved'
+        # Allele database status may change depending on checks below.
         if allele.obsolete is True:
             allele.internal = True
             allele.internal_reasons.append('Obsolete')
+            allele.allele_database_status_dto['database_status_name'] = 'deleted'
         if allele.organism_abbr != 'Dmel':
             allele.internal = True
             allele.internal_reasons.append('Non-Dmel')
         if allele.allele_of_internal_gene is True:
             allele.internal = True
             allele.internal_reasons.append('Allele of internal Dmel gene type.')
-        allele_status = {False: 'public', True: 'private'}
-        allele.allele_database_status_dto = self.generic_audited_object.copy()
-        allele.allele_database_status_dto['database_status_name'] = allele_status[allele.internal]
         return
 
     def flag_unexportable_alleles(self, allele):

diff --git a/src/AGR_data_retrieval_curation_disease.py b/src/AGR_data_retrieval_curation_disease.py
@@ -168,7 +168,7 @@ def __init__(self):
     }
     generic_data_provider_dto = generic_audited_object.copy()
     generic_data_provider_dto['source_organization_abbreviation'] = 'FB'
-    generic_cross_reference_dto = {'prefix': 'FB', 'page_area': 'disease/fb', 'internal': False}
+    generic_cross_reference_dto = {'prefix': 'DOID', 'page_area': 'disease/fb', 'internal': False}
     relevant_qualifiers = [
         'model of',
         'DOES NOT model'