Merge branch 'production_ready' into 'master'

Production ready

See merge request pdbe-kb/services/pdbe-graph-api!390

app/compound.py

@@ -13,6 +13,7 @@ import random
 import collections
 import more_itertools as mit
 import config
+import ast
 
 from plugins import request_handler
 import util_common
@@ -20,6 +21,7 @@ import neo4j_model
 from residue import get_mappings_for_residue_binding_site
 
 from itertools import groupby
+from util_common import parse_number
 
 print('[COMPOUND] Starting')
 

app/uniprot.py

@@ -3207,18 +3207,20 @@ def get_uniprot_variation_api(uniprot_accession):
         api_result[uniprot_accession]["features"].append(items)
 
     # PDBE-3712: Get Missense3D variation details
+    # PDBE-3956: Get FoldX variation details
     query = """
-    MATCH (unp:UniProt {ACCESSION: $uniprot_accession})-[:HAS_UNP_RESIDUE]->(unpRes:UNPResidue)<-[:MAP_TO_UNIPROT_RESIDUE]-(pdbRes:PDBResidue)<-[resRel:FUNPDBE_ANNOTATION_FOR]-(funGroup:FunPDBeResidueGroup)-[:FUNPDBE_RESIDUE_GROUP_OF]->(funEntry:FunPDBeEntry {DATA_RESOURCE:'Missense3D'})
-    WITH toInteger(unpRes.ID) AS unpRes, pdbRes.CHEM_COMP_ID AS pdbResCode, resRel.AA_VARIANT AS variant, resRel.AA_VARIANT_CAUSES AS causes, SPLIT(funEntry.SQL_ID, '_')[0] AS pdbId, funEntry.RESOURCE_ENTRY_URL AS entryUrl, funGroup.LABEL AS label ORDER BY unpRes
-    RETURN unpRes, pdbResCode, variant, causes, pdbId, entryUrl, label
+    MATCH (unp:UniProt {ACCESSION: $uniprot_accession})-[:HAS_UNP_RESIDUE]->(unpRes:UNPResidue)<-[:MAP_TO_UNIPROT_RESIDUE]-(pdbRes:PDBResidue)<-[resRel:FUNPDBE_ANNOTATION_FOR]-(funGroup:FunPDBeResidueGroup)-[:FUNPDBE_RESIDUE_GROUP_OF]->(funEntry:FunPDBeEntry)
+        WHERE funEntry.DATA_RESOURCE IN ['Missense3D', 'FoldX']
+    WITH toInteger(unpRes.ID) AS unpRes, pdbRes.CHEM_COMP_ID AS pdbResCode, resRel.AA_VARIANT AS variant, resRel.AA_VARIANT_CAUSES AS causes, SPLIT(funEntry.SQL_ID, '_')[0] AS pdbId, funEntry.RESOURCE_ENTRY_URL AS entryUrl, funGroup.LABEL AS label, funEntry.DATA_RESOURCE AS resource ORDER BY unpRes
+    RETURN unpRes, pdbResCode, variant, causes, pdbId, entryUrl, label, resource
     """
 
-    missense_details = list(graph.run(query, parameters = {
+    details = list(graph.run(query, parameters = {
         "uniprot_accession": uniprot_accession
     }))
 
-    for row in missense_details:
-        (unp_res_id, pdb_res_code, variant, variant_causes, pdb_id, entry_url, label) = row
+    for row in details:
+        (unp_res_id, pdb_res_code, variant, variant_causes, pdb_id, entry_url, label, resource) = row
 
         result_data = {
             "type": "VARIANT",
@@ -3229,10 +3231,10 @@ def get_uniprot_variation_api(uniprot_accession):
             "wildType": get_amino_three_to_one(pdb_res_code),
             "polyphenPrediction": "",
             "polyphenScore": None,
-            "clinicalSignificances": "missense",
+            "clinicalSignificances": "missense" if resource == "Missense3D" else "foldx",
             "siftScore": None,
             "consequenceType": variant_causes,
-            "genomicLocation": f"""Missense3D_{pdb_id}_{get_amino_three_to_one(pdb_res_code)}>{get_amino_three_to_one(variant)}""",
+            "genomicLocation": f"""{resource}_{pdb_id}_{get_amino_three_to_one(pdb_res_code)}>{get_amino_three_to_one(variant)}""",
             "sourceType": "prediction",
             "category": label,
             "resourceUrl": entry_url