renamed uniprot_ac to uniprot

docker-django.env.dev

@@ -15,4 +15,4 @@ CELERY_BROKER_URL=redis://redis:6379/0
 FLOWER_PORT=8888
 FLOWER_BASIC_AUTH=drugstone:test
 GT_THREADS=2
-DB_UPDATE_ON_START=1
\ No newline at end of file
+DB_UPDATE_ON_START=0
\ No newline at end of file

drugstone/management/includes/DataLoader.py

@@ -226,7 +226,7 @@ class DataLoader:
 
     # @staticmethod
     # def load_pdis_disgenet() -> pd.DataFrame:
-    #     """Loads the DisGeNET PDis associations with UniprotAC Numbers and Mondo IDs
+    #     """Loads the DisGeNET PDis associations with Uniprot Numbers and Mondo IDs
     #
     #     Returns:
     #         pd.DataFrame: columns "protein_name", "disorder_name" and "score"

drugstone/management/includes/DatasetLoader.py

@@ -301,6 +301,8 @@ def is_licenced_drdi_source(source):
 
 
 def remove_old_pdi_data(new_datasets, licenced):
+    if new_datasets is None:
+        return
     for dataset in new_datasets:
         print("Deleting all except "+str(dataset))
         try:
@@ -316,6 +318,8 @@ def remove_old_pdi_data(new_datasets, licenced):
 
 
 def remove_old_ppi_data(new_datasets, licenced):
+    if new_datasets is None:
+        return
     for dataset in new_datasets:
         print("Deleting all except " + str(dataset))
         try:
@@ -331,6 +335,8 @@ def remove_old_ppi_data(new_datasets, licenced):
 
 
 def remove_old_pdis_data(new_datasets, licenced):
+    if new_datasets is None:
+        return
     for dataset in new_datasets:
         print("Deleting all except " + str(dataset))
         try:
@@ -346,6 +352,8 @@ def remove_old_pdis_data(new_datasets, licenced):
 
 
 def remove_old_drdi_data(new_datasets, licenced):
+    if new_datasets is None:
+        return
     for dataset in new_datasets:
         print("Deleting all except " + str(dataset))
         try:

drugstone/serializers.py

@@ -30,7 +30,7 @@ class DrDisDatasetSerializer(serializers.ModelSerializer):
 
 class ProteinNodeSerializer(serializers.ModelSerializer):
     drugstone_id = serializers.SerializerMethodField()
-    uniprot_ac = serializers.SerializerMethodField()
+    uniprot = serializers.SerializerMethodField()
     symbol = serializers.SerializerMethodField()
     ensg = serializers.SerializerMethodField()
     entrez = serializers.SerializerMethodField()
@@ -38,7 +38,7 @@ class ProteinNodeSerializer(serializers.ModelSerializer):
     def get_drugstone_id(self, obj):
         return [f'p{obj.id}']
 
-    def get_uniprot_ac(self, obj):
+    def get_uniprot(self, obj):
         return [obj.uniprot_code]
 
     def get_symbol(self, obj):
@@ -61,19 +61,19 @@ class ProteinNodeSerializer(serializers.ModelSerializer):
 
     class Meta:
         model = Protein
-        fields = ['drugstone_id', 'uniprot_ac', 'symbol', 'protein_name', 'entrez', 'ensg']
+        fields = ['drugstone_id', 'uniprot', 'symbol', 'protein_name', 'entrez', 'ensg']
 
 
 class ProteinSerializer(serializers.ModelSerializer):
     drugstone_id = serializers.SerializerMethodField()
-    uniprot_ac = serializers.SerializerMethodField()
+    uniprot = serializers.SerializerMethodField()
     symbol = serializers.SerializerMethodField()
     ensg = serializers.SerializerMethodField()
 
     def get_drugstone_id(self, obj):
         return f'p{obj.id}'
 
-    def get_uniprot_ac(self, obj):
+    def get_uniprot(self, obj):
         return obj.uniprot_code
 
     def get_symbol(self, obj):
@@ -93,7 +93,7 @@ class ProteinSerializer(serializers.ModelSerializer):
 
     class Meta:
         model = Protein
-        fields = ['drugstone_id', 'uniprot_ac', 'symbol', 'protein_name', 'entrez', 'ensg']
+        fields = ['drugstone_id', 'uniprot', 'symbol', 'protein_name', 'entrez', 'ensg']
 
 
 class DrugSerializer(serializers.ModelSerializer):

drugstone/util/query_db.py

@@ -30,7 +30,7 @@ def query_proteins_by_identifier(node_ids: Set[str], identifier: str) -> Tuple[L
         protein_attribute = 'symbol'
         q_list = map(lambda n: Q(gene__iexact=n), node_ids)
     elif identifier == 'uniprot':
-        protein_attribute = 'uniprot_ac'
+        protein_attribute = 'uniprot'
         q_list = map(lambda n: Q(uniprot_code__iexact=n), node_ids)
     elif identifier == 'ensg' or identifier == 'ensembl':
         protein_attribute = 'ensg'
@@ -66,7 +66,7 @@ def query_proteins_by_identifier(node_ids: Set[str], identifier: str) -> Tuple[L
 
 def get_protein_ids(id_space, proteins):
     if (id_space == 'uniprot'):
-        return [p['uniprot_ac'] for p in proteins]
+        return [p['uniprot'] for p in proteins]
     if (id_space == 'ensg' or id_space == 'ensembl'):
         return [p['ensg'] for p in proteins]
     if (id_space == 'symbol'):

drugstone/views.py

@@ -368,7 +368,7 @@ def result_view(request) -> Response:
         if 'drugstoneType' in detail and detail['drugstoneType'] == 'protein':
             detail['symbol'] = list(set(detail['symbol']))
             detail['entrez'] = list(set(detail['entrez']))
-            detail['uniprot_ac'] = list(set(detail['uniprot_ac']))
+            detail['uniprot'] = list(set(detail['uniprot']))
             if 'ensg' in detail:
                 detail['ensg'] = list(set(detail['ensg']))
 
@@ -420,7 +420,7 @@ def result_view(request) -> Response:
                 for i in proteins:
                     new_i = {
                         'id': i['id'],
-                        'uniprot_ac': i['uniprot_ac'] if 'uniprot_ac' in i else [],
+                        'uniprot': i['uniprot'] if 'uniprot' in i else [],
                         'gene': i['symbol'] if 'symbol' in i else [],
                         'name': i['protein_name'] if 'protein_name' in i else [],
                         'ensembl': i['ensg'] if 'ensg' in i else [],