added p prefix to affinity parameter, discarding empty affinity or af…

…finity parameter

parsers/PHAROS/src/loadPHAROS.py

@@ -19,7 +19,7 @@ class PHAROSLoader(SourceDataLoader):
     source_data_url = "https://pharos.nih.gov/"
     license = "Data accessed from Pharos and TCRD is publicly available from the primary sources listed above. Please respect their individual licenses regarding proper use and redistribution."
     attribution = 'Sheils, T., Mathias, S. et al, "TCRD and Pharos 2021: mining the human proteome for disease biology", Nucl. Acids Res., 2021. DOI: 10.1093/nar/gkaa993'
-    parsing_version: str = '1.4'
+    parsing_version: str = '1.5'
 
     GENE_TO_DISEASE_QUERY: str = """select distinct x.value, d.did, d.name, p.sym, d.dtype, d.score
                                 from disease d 
@@ -100,16 +100,15 @@ def parse_data(self) -> dict:
 
         :return: parsed meta data results
         """
-
         if self.ping_pharos_db():
             self.logger.info('Pinging PHAROS database successful..')
         else:
             error_message = "PHAROS DB was not accessible. " \
                             "Manually stand up PHAROS DB and configure environment variables before trying again."
             raise SourceDataFailedError(error_message=error_message)
 
-        final_record_count: int = 0
-        final_skipped_count: int = 0
+        final_record_count = 0
+        final_skipped_count = 0
 
         # get the nodes and edges for each dataset
         self.logger.info('Querying for gene to disease..')
@@ -141,11 +140,8 @@ def parse_data(self) -> dict:
 
     def parse_gene_to_disease(self) -> (int, int):
         """
-        gets gene to disease records from the pharos DB and creates nodes
-        :param node_list: list, the node list to append this data to
-        :return: list, the node list and record counters
+        gets gene to disease records from the pharos DB and creates nodes and edges
         """
-        # init the record counters
         record_counter: int = 0
         skipped_record_counter: int = 0
 
@@ -210,11 +206,9 @@ def parse_gene_to_disease(self) -> (int, int):
 
     def parse_gene_to_drug_activity(self) -> (int, int):
         """
-        gets gene to drug activity records from the pharos DB and creates nodes
-        :param node_list: list, the node list to append this data to
+        gets gene to drug activity records from the pharos DB and creates nodes and edges
         :return: list, the node list and record counters
         """
-        # init the record counters
         record_counter: int = 0
         skipped_record_counter: int = 0
 
@@ -269,11 +263,9 @@ def parse_gene_to_drug_activity(self) -> (int, int):
 
     def parse_gene_to_cmpd_activity(self) -> (int, int):
         """
-        gets gene to compound activity records from the pharos DB and creates nodes
-        :param node_list: list, the node list to append this data to
+        gets gene to compound activity records from the pharos DB and creates nodes and edges
         :return: list, the node list and record counters
         """
-        # init the record counters
         record_counter: int = 0
         skipped_record_counter: int = 0
 
@@ -356,9 +348,13 @@ def get_edge_props(self, result) -> (str, list, dict, str):
 
         # if there was affinity data save it
         props: dict = {}
-        if result['affinity'] is not None:
-            props['affinity'] = float(result['affinity'])
-            props['affinity_parameter'] = result['affinity_parameter']
+        affinity = result['affinity']
+        if affinity is not None and affinity != '':
+            props['affinity'] = float(affinity)
+
+        affinity_paramater = result['affinity_parameter']
+        if affinity_paramater:
+            props['affinity_parameter'] = f'p{result["affinity_parameter"]}'
 
         # return to the caller
         return predicate, pmids, props, provenance