Added reflect-client for Go terms

namespaceTranslator.py

@@ -11,8 +11,8 @@
 ##############################################################################################
 
 # Import the modules needed to run the script.
-import MySQLdb
-
+import MySQLdb, reflectclient
+from reflectclient.config import EntityType
 #LOAD NAMESPACE DICTIONARY
 def getDict(filename):
     dict={}
@@ -30,20 +30,45 @@ def getReactionDict():
         reactionDict[nspace[0]]=nspace[1]
     return reactionDict
 
-#Get GOID from GOOSE
+def termToIdentifier(belnamespace,term):
+    if "GO" in belnamespace or belnamespace is "":
+        term=getGoIDfromTerm(term)
+    if "CHEM" in belnamespace:
+        term=getChemicalIDfromTerm(term)
+    return term
+
+#Get GOID from reflect
 def getGoIDfromTerm(term):
-    print "get conn"
-    cnx = MySQLdb.connect(user='go_select', passwd='amigo', host='spitz.lbl.gov', db='go_latest', port=4085)
-    cursor=cnx.cursor()
-    print"connected and querying"
-    query="SELECT acc FROM term WHERE name='cell migration'"
-    cursor.execute(query)
-    print "query done"
-    row=cursor.fetchone()
-    cnx.close()
-    print row
-    return row
-
-print "try"
-getGoIDfromTerm("cell migration")
-print "done"
\ No newline at end of file
+    goID= term
+    print term
+    reflect_client = reflectclient.ReflectClient()
+    GOresult=reflect_client.get_entities(term, [EntityType.biological_process,EntityType.cellular_component,EntityType.molecular_function])
+    print GOresult
+    print len(GOresult)
+    if len(GOresult) >0:
+        goID=GOresult[0]['entities'][0]['identifier']
+    print goID
+    return goID
+
+#Get pubchemID from reflect
+def getChemicalIDfromTerm(term):
+    chemID= term
+    reflect_client = reflectclient.ReflectClient()
+    chemResult=reflect_client.get_entities(term, [EntityType.chemicals])
+    if len(chemResult) >0:
+        chemID=chemResult[0]['entities'][0]['identifier']
+    return chemID
+
+#Get meshID from reflect
+def getMeshIDfromTerm(term):
+    mesh_id= term
+    reflect_client = reflectclient.ReflectClient()
+    meshResult=reflect_client.get_entities(term, [EntityType.diseases])
+    print meshResult
+    if len(meshResult) >0:
+        mesh_id=meshResult[0]['entities'][0]['identifier']
+    return mesh_id
+#getMeshIDfromTerm("Parkinson's Disease")
+
+getGoIDfromTerm("leukotriene production involved in inflammatory response")
+getGoIDfromTerm("inflammatory response")