retrievecBioPortalAPI.py

# Import libraries
import json
from urllib.request import urlopen


# Extract Mutation data
def retrieveGenomicVariants(studyId, listInfoGenomicVariants):
	listGenomicVariants = []	# List to store all the information
	# API to find the Molecular Profile ID
	listMolecularProfiles = f"https://www.cbioportal.org/api/studies/{studyId}/molecular-profiles"
	response = urlopen(listMolecularProfiles)
	listMolecularProfiles = json.loads(response.read())
	# For now, we are only interested in the Mutation Data
	# Take the object with MUTATION_EXTENDED as Molecular Alteration Type
	for molecularProfiles in listMolecularProfiles:
		if molecularProfiles['molecularAlterationType'] != 'MUTATION_EXTENDED':
			continue
		molecularProfileId = molecularProfiles['molecularProfileId']
	# API to find the sample list related with mutation data
	listSampleID = f"https://www.cbioportal.org/api/studies/{studyId}/sample-lists"
	response = urlopen(listSampleID)
	listSampleID = json.loads(response.read())
	# Take the sampleList Id for the mutation data -> Category = all_cases_with_mutation_data
	for sampleID in listSampleID:
		if sampleID['category'] != 'all_cases_with_mutation_data':
			continue
		sampleID=sampleID["sampleListId"]
		# After having the Molecular Profile Id and sampleList Id we can query for genomics variants data
		listMolecularData = f"https://www.cbioportal.org/api/molecular-profiles/{molecularProfileId}/mutations?sampleListId={sampleID}"
		response = urlopen(listMolecularData)
		listMolecularData = json.loads(response.read())
		for molecularData in listMolecularData:		# For all the entries having a mutation
			dictGenomicVariant = {}					# Dict for storing data of each mutation object
			for infoGenomicVariant in listInfoGenomicVariants:	# For all variables that can map with Beacon
				if not infoGenomicVariant in molecularData:
					continue
				dictGenomicVariant[infoGenomicVariant] = molecularData[infoGenomicVariant] # Store the info in the dict
			listGenomicVariants.append(dictGenomicVariant)
	return listGenomicVariants

# Extract Clinical Data from Patients and Samples
def retrieveAPIData(configVariables, studyId, patientORsample):
	if patientORsample =='patients':
		patientORsampleId = 'patientId'
	else:
		patientORsampleId = 'sampleId'
	# List of Ids of the patients and samples
	samplePatientIdsJson = f"https://www.cbioportal.org/api/studies/{studyId}/{patientORsample}"
	response = urlopen(samplePatientIdsJson)
	samplePatientIdsJson = json.loads(response.read())
	
	# Extract Sample or Patient data
	listSamplePatients = [] # List of all patient or sample data
	for samplePatientIdvar in samplePatientIdsJson:					# For each sampleId or patientId
		samplePatientId = samplePatientIdvar[patientORsampleId]
		dictSamplePatientId = {'id': samplePatientId}	# Dict for storing data of each entry
		if patientORsampleId == 'sampleId':
			dictSamplePatientId['individualId'] = samplePatientIdvar['patientId']
		for configVariable in configVariables:						# For each variable in the config.ini file
			# API search
			urlData=f"https://www.cbioportal.org/api/studies/{studyId}/{patientORsample}/{samplePatientId}/clinical-data?attributeId={configVariables[configVariable]}"
			response = urlopen(urlData)
			dataJson = json.loads(response.read())
			if not dataJson:	# If variable do not have any values, remove it
				continue
			dictSamplePatientId[configVariable] = dataJson[0]["value"]	# Insert values in dictionary
		listSamplePatients.append(dictSamplePatientId)					# Append all the entries in a list
	return listSamplePatients