#!/usr/bin/python

# save the contents of this file to your computer and save with the .py extension

# This script  uses the phospho.ELM database webservice (wsdl at: http://phospho.elm.eu.org/webservice/phosphoELMdb.wsdl) to demonstrate
# by example the full functionality of the phospho.ELM db webservice.

# (Note: As an initial starting point it is recommended that first time users of the web-service should load the WSDL file above to SoapUI and investigate the Web Service
# operations in that environment. SoapUI is a desktop application for inspecting, invoking, developing and functional/load/compliance testing of Web Services over HTTP.
# It can be downloaded free of charge from http://www.soapui.org/.)

# script written by: Kate Gould (gould@embl.de)

# Installation of ZSI-2.0 from http://pywebsvcs.sourceforge.net/ is a prerequisite for
# this script to work

# following im[orted modules generated via ZSI command:
# wsdl2py --url=http://phospho.elm.eu.org/webservice/phosphoELMdb.wsdl

from phosphoELMdb_services import phosphoELMdbLocator, phosphoELMdbBindingSOAP, getKinaseListRequestMsg, getBindingDomainListRequestMsg, getInstancesByProteinSequenceAccessionSearchWithAllThroughputDataRequestMsg, getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnlyRequestMsg,  getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputDataRequestMsg, getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnlyRequestMsg, getInstancesByKinaseTextSearchRequestMsg, getInstancesByBindingDomainTextSearchRequestMsg, getSubstrateByIdentifierRequestMsg, getInstanceByIdentifierRequestMsg, getInstancesWithPdbEntryAssignedRequestMsg, getInstancesByPubMedIdRequestMsg, getSubstratesByNameSearchRequestMsg, getSubstratesByGeneNameSearchRequestMsg

import time

def writeInstancesInfo(result, outputFile):

    """ writes the instance object(s) to the specified output file. """
    
    # determine if we are dealing with an Instance object or a list of Instance objects
    if (isinstance(result._Instance, list) == True):
        initialLoop = True
        for instance in result._Instance:

            if initialLoop == True:
                outputFile.write("\n")
                initialLoop = False
            else:
                # instance list separator
                outputFile.write("\n****************************************************************************\n")
                
            writeIndividualInstanceInfo(instance, outputFile)
            
    # else it is an individual instance object    
    else:
        writeIndividualInstanceInfo(result._Instance, outputFile)
                                                                                                    
def writeIndividualInstanceInfo(instance, outputFile):

    """ writes an instance object to the specified output file. """
    
    for sequence in instance._SequenceReference:
        outputFile.write("sequence identifier database: " + sequence._Database + "\n")
        outputFile.write("sequence identifier: " + sequence._Accession + "\n")
        
    outputFile.write("UniPROT is primary acc: " + str(instance._UniPROTIsPrimaryAcc) + "\n")
    otherAccessions = ''
    firstLoop = True
    for otherAccession in instance._OtherAccession:
        if firstLoop == True:
            otherAccessions = otherAccession._Database + " : " + otherAccession._Accession
            firstLoop = False
        else:
            otherAccessions = otherAccessions + ',' + otherAccession._Database + " : " + otherAccession._Accession

    outputFile.write("other accession(s): " + otherAccessions + "\n\n")
                                                            
    outputFile.write("instance identifier: " + instance._attrs['Accession'] + "\n")
    outputFile.write("entry date: " + time.strftime("%d %b %Y", instance._attrs['EntryDate']) + "\n") # str(instance._attrs['EntryDate']) + "\n")
    outputFile.write("substrate identifier: " + instance._Substrate + "\n\n")
    
    outputFile.write("phospho position: " + str(instance._Position) + "\n")
    outputFile.write("phospho residue: " + instance._Residue + "\n")
    outputFile.write("sequence: " + instance._Sequence + "\n")
    outputFile.write("species: " + instance._Species + "\n")

    domainRefDatabase = ''
    domainRefDomain = ''

    if instance._DomainReference != None:
        domainRefDatabase = instance._DomainReference._Database
        domainRefDomain = instance._DomainReference._Domain
    
    outputFile.write("\ndomain reference database: " + domainRefDatabase + " \n")
    outputFile.write("domain reference domain: " + domainRefDomain + "\n\n")

    note = ''
    if instance._Note != None:
        note = instance._Note
    outputFile.write("Note: " + note + "\n")

    reliabilityId = ''
    if instance._ReliabilityId != None:
        reliabilityId = str(instance._ReliabilityId)
    outputFile.write("Reliability Id: " + reliabilityId + "\n")
                     
    bindingDomains = ''
    firstLoop = True
    for bindingDomain in instance._BindingDomain:
        if firstLoop == True:
            bindingDomains = bindingDomain
            firstLoop = False
        else:
            bindingDomains = bindingDomains + ',' + bindingDomain

    outputFile.write("binding domain(s): " + bindingDomains + "\n")

    elmAccessions = ''
    firstLoop = True
    for elmAccession in instance._ELMAccession:
        if firstLoop == True:
            elmAccessions = elmAccession
            firstLoop = False
        else:
            elmAccessions = elmAccessions + ',' + elmAccession

    outputFile.write("elm(s): " + elmAccessions + "\n")
                                                                                                                                                
    kinases = ''
    firstLoop = True
    for kinase in instance._Kinase:
        if firstLoop == True:
            kinases = kinase
            firstLoop = False
        else:
            kinases = kinases + ',' + kinase
                
    outputFile.write("kinase(s): " + kinases + "\n")

    pdbIds = ''
    firstLoop = True
    for pdbId in instance._PdbId:
        if firstLoop == True:
            pdbIds = pdbId
            firstLoop = False
        else:
            pdbIds = pdbIds + ',' + pdbId                                                    
    outputFile.write("\npdb ids(s): " + pdbIds + "\n")

    evidenceReferences = ''
    outputFile.write("\nLiterature reference(s): \n")
    for evidenceRef in instance._EvidenceReference:
        evidenceReferences = evidenceRef._LiteratureReference._Database + " : " + evidenceRef._LiteratureReference._Accession + "\n"
        evidenceReferences = evidenceReferences + "Method: " + evidenceRef._Method + "\nSource: " + evidenceRef._Source + "\n"
        outputFile.write("\n" + evidenceReferences)
                                                                 
    outputFile.write("\n")

def writeSubstratesInfo(result, outputFile):

    """ writes the substrate object(s) to the specified output file. """
    
    # determine if we are dealing with a Substrate object or a list of Substrate objects
    if (isinstance(result._Substrate, list) == True):
        initialLoop = True
        for substrate in result._Substrate:
        
            if initialLoop == True:
                outputFile.write("\n")
                initialLoop = False
            else:
                # substrate list separator
                outputFile.write("\n****************************************************************************\n")

            writeIndividualSubstrateInfo(substrate, outputFile)
            
    else:
        writeIndividualSubstrateInfo(result._Substrate, outputFile)

def writeIndividualSubstrateInfo(substrate, outputFile):

    """ writes an instance object to the specified output file. """
    
    outputFile.write("name: " + substrate._Name + "\n")    
    outputFile.write("substrate identifier: " + substrate._attrs['Accession'] + "\n")
    outputFile.write("description: " + substrate._Description + "\n")

    synonyms = ''
    firstLoop = True
    for synonym in substrate._Synonym:
        if firstLoop == True:
            synonyms = synonym
            firstLoop = False
        else:
            synonyms = synonyms + ', ' + synonym
    outputFile.write("synonym(s): " + synonyms + "\n")
                                                            
    expressionList = ''
    initialLoop = True
    for expression in substrate._Expression:
        if initialLoop == True:
            expressionList = expression
            initialLoop = False
        else:
            expressionList = expressionList + ", " + expression
    outputFile.write("expression: " + expressionList + "\n")
    
    instances = ''
    firstLoop = True
    for instance in substrate._Instance:
        if firstLoop == True:
            instances = instance
            firstLoop = False
        else:
            instances = instances + ', ' + instance
    outputFile.write("Instance identifier(s): " + instances + "\n")

    databaseURL = ''
    
    if substrate._DatabaseURL != '':
        databaseURL = "http://www.biocarta.com/pathfiles/" + substrate._DatabaseURL

    outputFile.write("Database URL to Biocarta: " + databaseURL + "\n")

    if len(substrate._Interaction) > 0:
        outputFile.write("\nSubstrate Interaction Partner(s):\n\n")
        for interaction in substrate._Interaction:
            outputFile.write("Interaction Database : " + interaction._MintID._Database + "\n")
            outputFile.write("Interaction ID: " + interaction._MintID._Accession + "\n")
            outputFile.write("Interactor Database: " + interaction._InteractorReference._Database + "\n")
            outputFile.write("Interactor ID: " + interaction._InteractorReference._Accession + "\n")
            outputFile.write("Interactor Identifier: " + interaction._InteractorIdentifier + "\n\n")

    if len(substrate._GOterm) > 0:
        outputFile.write("\nSubstrate GO term(s):\n\n")
        for goterm in substrate._GOterm:
            outputFile.write("Ontology : " + goterm._Ontology + "\n")
            outputFile.write("GO Accession: " + goterm._GOAccession + "\n")
            outputFile.write("GO Term: " + goterm._Term + "\n")
            
                                                                                                                                               
def main():
                                            
    pelmdbws = phosphoELMdbLocator().getphosphoELMdb()

    # example entries for the various methods
    
    proteinSequenceAccessionNumber = 'P12931'
    kinaseQueryText = 'ALK'
    bindingDomainQueryText = 'Lyn SH2'
    substrateIdentifier = 's000212'
    instanceIdentifier = 'I004550'
    substrateName = 'creb'
    pubmedId = '92065884'
    queryGeneName = 'PRKG1'
    
    # 1.getKinaseList method
    req = getKinaseListRequestMsg()
    result = pelmdbws.getKinaseList(req);

    kinaseListFile = open("getKinaseListResults", "w")
    kinaseListFile.write('List of kinases in phospho.ELM database: \n\n')
    
    for name in result._Kinase:
        kinaseListFile.write(name + "\n")

    kinaseListFile.close()

    
    # 2. getBindingDomainList method
    req = getBindingDomainListRequestMsg()
    result = pelmdbws.getBindingDomainList(req);

    bindingDomainListFile = open("getBindingDomainListResults", "w")
    bindingDomainListFile.write('List of binding domains in phospho.ELM database: \n\n')
    
    for name in result._BindingDomain:
        bindingDomainListFile.write(name + "\n")

    bindingDomainListFile.close()
    

    # 3. getInstancesByProteinSequenceAccessionSearchWithAllThroughputData method

    req = getInstancesByProteinSequenceAccessionSearchWithAllThroughputDataRequestMsg()
    req._ProteinSequenceAccession = proteinSequenceAccessionNumber
    result = pelmdbws.getInstancesByProteinSequenceAccessionSearchWithAllThroughputData(req)

    instancesByProteinSequenceAccessionSearchWithAllThroughputDataFile = open("getInstancesByProteinSequenceAccessionSearchWithAllThroughputDataResults", "w")
    instancesByProteinSequenceAccessionSearchWithAllThroughputDataFile.write("results for getInstancesByProteinSequenceAccessionSearchWithAllThroughputData method\n\n")

    writeInstancesInfo(result, instancesByProteinSequenceAccessionSearchWithAllThroughputDataFile)
    
    instancesByProteinSequenceAccessionSearchWithAllThroughputDataFile.close()
                                                                                                                                                                
    # 4. getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnly method
    
    req = getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnlyRequestMsg()
    req._ProteinSequenceAccession = proteinSequenceAccessionNumber
    result = pelmdbws.getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnly(req)

    instancesByProteinSequenceAccessionSearchWithLowThroughputDataOnlyFile = open("getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnlyResults", "w")
    instancesByProteinSequenceAccessionSearchWithLowThroughputDataOnlyFile.write("results for getInstancesByProteinSequenceAccessionSearchWithLowThroughputDataOnly method\n\n")

    writeInstancesInfo(result, instancesByProteinSequenceAccessionSearchWithLowThroughputDataOnlyFile)

    instancesByProteinSequenceAccessionSearchWithLowThroughputDataOnlyFile.close()
                
    # 5. getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputData method

    req = getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputDataRequestMsg()
    req._ProteinSequenceAccession = proteinSequenceAccessionNumber
    result = pelmdbws.getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputData(req)

    instancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputDataFile = open("getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputDataResults", "w")
    instancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputDataFile.write("results for getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputData method\n\n")

    writeInstancesInfo(result, instancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputDataFile)

    instancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithAllThroughputDataFile.close()

    # 6. getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnly method

    req = getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnlyRequestMsg()
    req._ProteinSequenceAccession = proteinSequenceAccessionNumber
    result = pelmdbws.getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnly(req)

    instancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnlyFile = open("getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnlyResults", "w")
    instancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnlyFile.write("results for getInstancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnly method\n\n")

    writeInstancesInfo(result, instancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnlyFile)

    instancesByProteinSequenceAccessionSearchForAllRelatedSpeciesWithLowThroughputDataOnlyFile.close()
                                                                
    # 7. getInstancesByKinaseTextSearch method
    
    req = getInstancesByKinaseTextSearchRequestMsg()
    req._QueryText = kinaseQueryText
    result = pelmdbws.getInstancesByKinaseTextSearch(req)
    
    instancesByKinaseTextSearchFile = open("getInstancesByKinaseTextSearchResults", "w")
    instancesByKinaseTextSearchFile.write("results for getInstancesByKinaseTextSearch method:\n\n")

    writeInstancesInfo(result, instancesByKinaseTextSearchFile)

    instancesByKinaseTextSearchFile.close()
    
    # 8. getInstancesByBindingDomainTextSearch method
    
    req = getInstancesByBindingDomainTextSearchRequestMsg()
    req._QueryText = bindingDomainQueryText
    result = pelmdbws.getInstancesByBindingDomainTextSearch(req)
    
    instancesByBindingDomainTextSearchFile = open("getInstancesByBindingDomainTextSearchResults", "w")
    instancesByBindingDomainTextSearchFile.write("results for getInstancesByBindingDomainTextSearch method:\n\n")

    writeInstancesInfo(result, instancesByBindingDomainTextSearchFile)

    instancesByBindingDomainTextSearchFile.close()
                            
    
    # 9. getSubstrateByIdentifier method
    
    req = getSubstrateByIdentifierRequestMsg()
    req._SubstrateIdentifier = substrateIdentifier
    result = pelmdbws.getSubstrateByIdentifier(req)


    substrateByIdentifierFile = open("getSubstrateByIdentifierResults", "w")
    substrateByIdentifierFile.write("results for substrateByIdentifier method: \n\n")
    
    writeSubstratesInfo(result, substrateByIdentifierFile)
    
    substrateByIdentifierFile.close()

    # 10. getInstanceByIdentifierRequest method

    req = getInstanceByIdentifierRequestMsg()
    req._InstanceIdentifier = instanceIdentifier
    result = pelmdbws.getInstanceByIdentifier(req)

    instanceByIdentifierFile = open("getInstanceByIdentifierResults", "w")
    instanceByIdentifierFile.write("results for instanceByIdentifier method: \n\n")

    
    writeInstancesInfo(result, instanceByIdentifierFile)

    instanceByIdentifierFile.close()

    # 11. getInstancesWithPdbEntryAssigned method
    
    req = getInstancesWithPdbEntryAssignedRequestMsg()
    result = pelmdbws.getInstancesWithPdbEntryAssigned(req)
    
    instancesWithPdbEntryAssignedFile = open("getInstancesWithPdbEntryAssignedResults" , "w")
    instancesWithPdbEntryAssignedFile.write("results for getInstancesWithPdbEntryAssigned method: \n\n")

    writeInstancesInfo(result, instancesWithPdbEntryAssignedFile)

    instancesWithPdbEntryAssignedFile.close()
    
    # 12. getInstancesByPubMedId method
    req = getInstancesByPubMedIdRequestMsg()
    req._pubmedId = pubmedId
    result = pelmdbws.getInstancesByPubMedId(req)

    instancesByPubMedIdFile = open("getInstancesByPubMedIdResults" , "w")
    instancesByPubMedIdFile.write("results for getInstancesByPubMedId method: \n\n")

    writeInstancesInfo(result, instancesByPubMedIdFile)

    instancesByPubMedIdFile.close()
        
    # 13. getSubstratesByNameSearch method
    
    req = getSubstratesByNameSearchRequestMsg()
    req._SubstrateName = substrateName
    result = pelmdbws.getSubstratesByNameSearch(req);

    substratesByNameSearchFile = open("getSubstratesByNameSearchResults", "w")
    substratesByNameSearchFile.write("results for getSubstratesByNameSearch method: \n\n")

    writeSubstratesInfo(result, substratesByNameSearchFile)

    substratesByNameSearchFile.close()

    # 14. getSubstratesByGeneNameSearchRequestMsg method

    req  = getSubstratesByGeneNameSearchRequestMsg()
    req._GeneName = queryGeneName
    result = pelmdbws.getSubstratesByGeneNameSearch(req)

    substratesByGeneNameSearchFile = open("getSubstratesByGeneNameSearchResults", "w")
    substratesByGeneNameSearchFile.write("results for getSubstratesByGeneNameSearch method: \n\n")

    writeSubstratesInfo(result, substratesByGeneNameSearchFile)

    substratesByGeneNameSearchFile.close()
                
if __name__ == '__main__':
    main()