restrucred code, class

namespaceTranslator.py

@@ -15,154 +15,180 @@ import MySQLdb, reflectclient, os,urllib
 from reflectclient.config import EntityType
 import rdflib
 from SPARQLWrapper import SPARQLWrapper, JSON, XML, N3, RDF
-
+class namespaceTranslator:
 #LOAD NAMESPACE DICTIONARY
-
-def queryMeSHSPARQL():
-    #sparql = rdflib.URIRef("http://id.nlm.nih.gov/mesh/sparql")
-    sparql=SPARQLWrapper("http://id.nlm.nih.gov/mesh/sparql")
-    sparql.setQuery("""
-    PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-    PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
-    PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
-    PREFIX owl: <http://www.w3.org/2002/07/owl#>
-    PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#>
-    PREFIX mesh: <http://id.nlm.nih.gov/mesh/>
-    PREFIX mesh2015: <http://id.nlm.nih.gov/mesh/2015/>
-    PREFIX mesh2016: <http://id.nlm.nih.gov/mesh/2016/>
-    PREFIX mesh2017: <http://id.nlm.nih.gov/mesh/2017/>
-
-     SELECT ?d
-
-     FROM <http://id.nlm.nih.gov/mesh>
-
-       WHERE {
-        ?d a meshv:Descriptor .
-        ?d meshv:concept ?c .
-        ?c meshv:term ?term .
-        ?term rdfs:label ?label .
-
-        FILTER (REGEX(?label,"^insomnia$","i"))
-
-       }
-    """)
-    sparql.setReturnFormat(JSON)
-    result= sparql.query().convert()
-    print result
-
-def getDict(filename):
-    dict={}
-    for line in open(filename,'r'):
-        nspace=line.split()
-        dict[nspace[0]]=nspace[1]
-    return dict
-
-
-#LOAD reaction DICTIONARY
-def getReactionDict():
-    reactionDict={}
-    for line in open("inputs/reactionDictFile.txt",'r'):
-        nspace=line.split()
-        reactionDict[nspace[0]]=nspace[1]
-    return reactionDict
-
-def termToIdentifier(belnamespace,term):
-    if "GO" in belnamespace:
-        term=getGoIDfromTerm(term)
-    elif "CHEM" in belnamespace:
-        term=getChemicalIDfromTerm(term)
-    # else:
-    #     idAndElement=getIDandNamespacefromAbundance("UNKNOWN",term)
-    #     term=idAndElement[0]
-    return term
-
-#Get GOID from reflect
-def getGoIDfromTerm(term):
-    goID= term
-    #print term
-    reflect_client = reflectclient.ReflectClient()
-    GOresult=reflect_client.get_entities(term, [EntityType.biological_process,EntityType.cellular_component,EntityType.molecular_function])
-
-    if len(GOresult) >0:
-        goID=GOresult[0]['entities'][0]['identifier']
-    return goID
-
-def getIDandNamespacefromAbundance(term,elementName):
-    termId=term
-    #elementName="UNKNOWN"
-    idAndelement=[]
-    #check GO
-    reflect_client = reflectclient.ReflectClient()
-    # check for GO cellular component ->Complex
-    GOresult = reflect_client.get_entities(term, [EntityType.cellular_component,EntityType.biological_process, EntityType.molecular_function])
-    if len(GOresult) > 0 :
-        termId = GOresult[0]['entities'][0]['identifier']
-        entityType=GOresult[0]['entities'][0]['type']
-        if entityType == "-21" or entityType == "-23":
-             elementName = "PHENOTYPE"
-        elif entityType == "-22":
-            elementName = "COMPLEX"
-
-    #not found in GO, so check in mesh
-    if termId is term:
-        print termId +" : here"
-        meshID=getMeshIDfromTerm(term)
-        if meshID is not term:
-            termId=meshID
-            elementName="PHENOTYPE"
-    idAndelement=[termId,elementName]
-    #print idAndelement
-    return idAndelement
-
-
-#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
-    lowerTerm=term.lower()
-    mDict = getMeSHDict()
-    mesh_id = mDict[lowerTerm] if mDict.has_key(lowerTerm) is True else term
-    return mesh_id
-
-
-
-def getMeSHDict():
-    dict={}
-    filename="inputs/2017MeshTree.txt"
-    try:
-        # input file fetch from :https://www.nlm.nih.gov/mesh/2017/download/2017MeshTree.txt
-        if not os.path.exists(filename):
-            urllib.urlretrieve("https://www.nlm.nih.gov/mesh/2017/download/2017MeshTree.txt", filename)
-
-        else:
-            for line in open(filename,'r'):
-                line=line.replace('\x00','')
-                line=line.strip()
-                nspace=line.split("\t")
-                if len(nspace)==3:
-                    meshID=nspace[1]
-                    term=nspace[2].lower()
-                    dict[term]=meshID
-
-    except IndexError as dicterror:
-        print str("MeSH Dictionary error")
-    return dict
-#getMeshIDfromTerm("Drug-Induced Liver Injury")
-
-# getGoIDfromTerm("leukotriene production involved in inflammatory response")
-#getGoIDfromTerm("Stress, Physiological")
-# getChemicalIDfromTerm("lipopigment")
-#getIDandNamespacefromAbundance("synaptic transmission","UNKNOWN")
-#print getIDandNamespacefromAbundance("gamma Secretase Complex","UNKNOWN")
-#print getIDandNamespacefromAbundance("Insomnia","PHENOTYPE")
-# getIDandNamespacefromAbundance("Drug-Induced Liver Injury","UNKNOWN")
-# getIDandNamespacefromAbundance("Polymorphism, Single Nucleotide","UNKNOWN")
-queryMeSHSPARQL()
\ No newline at end of file
+    def __init__(self):
+        ''' Constructor for this class. '''
+        # Create some member animals
+        dict={}
+        filename="inputs/2017MeshTree.txt"
+        try:
+            # input file fetch from :https://www.nlm.nih.gov/mesh/2017/download/2017MeshTree.txt
+            if not os.path.exists(filename):
+                urllib.urlretrieve("https://www.nlm.nih.gov/mesh/2017/download/2017MeshTree.txt", filename)
+
+            else:
+                for line in open(filename,'r'):
+                    line=line.replace('\x00','')
+                    line=line.strip()
+                    nspace=line.split("\t")
+                    if len(nspace)==3:
+                        meshID=nspace[1]
+                        term=nspace[2].lower()
+                        dict[term]=meshID
+
+        except IndexError as dicterror:
+            print str("MeSH Dictionary error")
+        self.meshDict = dict
+
+    def queryMeSHSPARQL(self):
+        #sparql = rdflib.URIRef("http://id.nlm.nih.gov/mesh/sparql")
+        sparql=SPARQLWrapper("http://id.nlm.nih.gov/mesh/sparql")
+        sparql.setQuery("""
+        PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+        PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+        PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+        PREFIX owl: <http://www.w3.org/2002/07/owl#>
+        PREFIX meshv: <http://id.nlm.nih.gov/mesh/vocab#>
+        PREFIX mesh: <http://id.nlm.nih.gov/mesh/>
+        PREFIX mesh2015: <http://id.nlm.nih.gov/mesh/2015/>
+        PREFIX mesh2016: <http://id.nlm.nih.gov/mesh/2016/>
+        PREFIX mesh2017: <http://id.nlm.nih.gov/mesh/2017/>
+
+         SELECT ?d
+
+         FROM <http://id.nlm.nih.gov/mesh>
+
+           WHERE {
+            ?d a meshv:Descriptor .
+            ?d meshv:concept ?c .
+            ?c meshv:term ?term .
+            ?term rdfs:label ?label .
+
+            FILTER (REGEX(?label,"^insomnia$","i"))
+
+           }
+        """)
+        sparql.setReturnFormat(JSON)
+        result= sparql.query().convert()
+        print result
+
+    def getDict(self,filename):
+        dict={}
+        for line in open(filename,'r'):
+            nspace=line.split()
+            dict[nspace[0]]=nspace[1]
+        return dict
+
+
+    #LOAD reaction DICTIONARY
+    def getReactionDict(self):
+        reactionDict={}
+        for line in open("inputs/reactionDictFile.txt",'r'):
+            nspace=line.split()
+            reactionDict[nspace[0]]=nspace[1]
+        return reactionDict
+
+    def termToIdentifier(self,belnamespace,term):
+        if "GO" in belnamespace:
+            term=namespaceTranslator.getGoIDfromTerm(term)
+        elif "CHEM" in belnamespace:
+            term=namespaceTranslator.getChemicalIDfromTerm(term)
+        # else:
+        #     idAndElement=getIDandNamespacefromAbundance("UNKNOWN",term)
+        #     term=idAndElement[0]
+        return term
+
+    #Get GOID from reflect
+    def getGoIDfromTerm(self,term):
+        goID= term
+        #print term
+        reflect_client = reflectclient.ReflectClient()
+        GOresult=reflect_client.get_entities(term, [EntityType.biological_process,EntityType.cellular_component,EntityType.molecular_function])
+
+        if len(GOresult) >0:
+            goID=GOresult[0]['entities'][0]['identifier']
+        return goID
+
+    def getIDandNamespacefromAbundance(self,term,elementName):
+        termId=term
+        #elementName="UNKNOWN"
+        idAndelement=[]
+        #check GO
+        reflect_client = reflectclient.ReflectClient()
+        # check for GO cellular component ->Complex
+        GOresult = reflect_client.get_entities(term, [EntityType.cellular_component,EntityType.biological_process, EntityType.molecular_function])
+        if len(GOresult) > 0 :
+            termId = GOresult[0]['entities'][0]['identifier']
+            entityType=GOresult[0]['entities'][0]['type']
+            if entityType == "-21" or entityType == "-23":
+                 elementName = "PHENOTYPE"
+            elif entityType == "-22":
+                elementName = "COMPLEX"
+
+        #not found in GO, so check in mesh
+        if termId is term:
+            print termId +" : here"
+            meshID=self.getMeshIDfromTerm(term)
+            if meshID is not term:
+                termId=meshID
+                elementName="PHENOTYPE"
+        idAndelement=[termId,elementName]
+        #print idAndelement
+        return idAndelement
+
+
+    #Get pubchemID from reflect
+    def getChemicalIDfromTerm(self,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(self,term):
+        mesh_id=term
+        lowerTerm=term.lower()
+        mDict = self.meshDict #namespaceTranslator.getMeSHDict()
+        mesh_id = mDict[lowerTerm] if mDict.has_key(lowerTerm) is True else term
+        return mesh_id
+
+
+
+    def getMeSHDict(self):
+        dict={}
+        filename="inputs/2017MeshTree.txt"
+        try:
+            # input file fetch from :https://www.nlm.nih.gov/mesh/2017/download/2017MeshTree.txt
+            if not os.path.exists(filename):
+                urllib.urlretrieve("https://www.nlm.nih.gov/mesh/2017/download/2017MeshTree.txt", filename)
+
+            else:
+                for line in open(filename,'r'):
+                    line=line.replace('\x00','')
+                    line=line.strip()
+                    nspace=line.split("\t")
+                    if len(nspace)==3:
+                        meshID=nspace[1]
+                        term=nspace[2].lower()
+                        dict[term]=meshID
+
+        except IndexError as dicterror:
+            print str("MeSH Dictionary error")
+        return dict
+    #getMeshIDfromTerm("Drug-Induced Liver Injury")
+
+    # getGoIDfromTerm("leukotriene production involved in inflammatory response")
+    #getGoIDfromTerm("Stress, Physiological")
+    # getChemicalIDfromTerm("lipopigment")
+    #getIDandNamespacefromAbundance("synaptic transmission","UNKNOWN")
+    #print getIDandNamespacefromAbundance("gamma Secretase Complex","UNKNOWN")
+    #print getIDandNamespacefromAbundance("Insomnia","PHENOTYPE")
+    # getIDandNamespacefromAbundance("Drug-Induced Liver Injury","UNKNOWN")
+    # getIDandNamespacefromAbundance("Polymorphism, Single Nucleotide","UNKNOWN")
+
+
+NT= namespaceTranslator()
+print NT.getMeshIDfromTerm("Oligodendroglia")
\ No newline at end of file