def samples_search_by_name(args):
sample = Samples()
try:
result = sample.search(args.studyId, name=args.name)
print(result)
except ServerResponseException as e:
print(str(e), file=sys.stderr)
def individuals_create(args):
# 1st create individual
# TODO: Change this method to load the individuals from phenotips format or ped
"""
Call: python pyCGA [--host hostname] sid individuals create --studyId studyId --name paticipantId --gender --fatherId --motherId --family --wellIds
:param args:
"""
individual = Individuals()
sample = Samples()
try:
individualId = individual.create(args.studyId, args.name, args.family, args.fatherId,
args.motherId, args.gender)[0]["id"]
well_ids = args.wellIds.split(",")
for well in well_ids:
try:
sampleId = sample.search(args.studyId, name=well)[0]["id"]
print(sampleId)
try:
sample.update(str(sampleId), individualId=str(individualId))
except ServerResponseException as e:
print(str(e), file=sys.stderr)
except ServerResponseException as e:
print(str(e), file=sys.stderr)
except ServerResponseException as e:
print(str(e), file=sys.stderr)
def get_all_samples_names(studyId):
"""
:param study:
"""
sample = Samples()
result = sample.search(studyId=studyId, include="projects.studies.samples.name")
return [r["name"] for r in result]
def create_samples(args):
try:
sample = Samples()
result = sample.create(args.studyId, args.name, "Manually_added", "")[0]
print(result)
except ServerResponseException as e:
print(str(e), file=sys.stderr)
def samples_search_by_annotation(args):
sample = Samples()
try:
result = sample.search_by_annotation(args.studyId, args.variableSetName, *args.queries)
for r in result:
# print(int(AnnotationSet(*[annotation for annotation in r["annotationSets"] if args.variableSetName in annotation["attributes"]["annotateSetName"]][0]["annotations"]).get_json()["id"]))
print(AnnotationSet(*[annotation for annotation in r["annotationSets"] if args.variableSetName in annotation["attributes"]["annotateSetName"]][0]["annotations"]).get_json()["name"])
except ServerResponseException as e:
print(str(e), file=sys.stderr)
def samples_annotate(args):
try:
sample = Samples()
sample_id = sample.search(args.studyId, name=args.sampleName)[0]["id"]
result = sample.annotate(sample_id, args.variableSetName, args.annotationSetName, args.studyId,
args.jsonFile)
print(result)
except ServerResponseException as e:
print(str(e), file=sys.stderr)
def samples_share(args):
sample = Samples()
files = Files()
ids_sample = [s.rstrip("\n").split("\t")[0] for s in open(args.samples).readlines()]
for id in ids_sample:
# This line return the root folder
root = str(files.search(studyId=args.studyId, sampleIds=id, description="INTAKE")[0]["id"])
files.share(args.user, root)
try:
sample.share(args.user, id, include="projects.studies.samples.name")
except ServerResponseException as e:
print(str(e), file=sys.stderr)
def check_samples_acl(studyId, userId, group=None):
"""
Method to check permisions for one user
:param studyId:
:param userId:
"""
if group is not None:
userId += "," + group
sample = Samples()
options = {"acl.userId": userId}
result = sample.search(studyId=studyId, **options)
if not result:
return 'Your user don\'t have permissions in any of the Sample currently available in this Study, please check it with the administrator'
else:
return [sample["name"] for sample in result if sample["acl"]]
def get_annotation_sample(study_id, sample_id, variable_set_name):
"""
:param study_id:
:param sample_id:
:param variable_set_name:
:return:
"""
variable = Variables()
sample = Samples()
samples_info = sample.search(studyId=study_id, id=sample_id)
sample_annotations = []
variableSetId = variable.search(studyId=study_id, name=variable_set_name)[0]["id"]
for sample_info in samples_info:
sample_annotations.append(extract_annotation(sample_info, variableSetId))
return sample_annotations
def files_search_by_sample(args):
file_instance = Files()
sample = Samples()
for sampleName in args.sampleName:
try:
sampleId = sample.search(args.studyId, name=sampleName)[0]["id"]
results = file_instance.search(sampleIds=str(sampleId), studyId=args.studyId,
bioformat=args.fileType,
include="projects.studies.files.path,projects.studies.files.sampleIds",
path=args.path
)
for r in results:
print(sampleName +"\t"+ r["path"])
except ServerResponseException as e:
print(str(e), file=sys.stderr)
def setUp(self):
unregistered_session = {"host": host, "sid": ""}
self.user = Users(unregistered_session, instance=catalog_instance)
sid = self.user.login_method("pfurio", pwd)[0]["sessionId"]
self.token = {"user": "******", "host": host, "sid": str(sid), "instance": catalog_instance, "debug": True}
self.file_connector = Files(token=self.token)
self.sample_connector = Samples(token=self.token)
self.individual_connector = Individuals(token=self.token)
self.job_connector = Jobs(token=self.token)
self.variable_connector = Variables(token=self.token)
def individuals_search(args):
"""
Call: python pyCGA [--host hostname] sid individuals search --studyId studyId --name particiantId
:param args:
"""
individual = Individuals()
sample = Samples()
individual_results = individual.search(studyId=args.studyId, name=args.name)
for individual_result in individual_results:
gender = individual_result["gender"]
individualId = individual_result["id"]
print("ParticipantId in Catalog: "+ str(individualId))
try:
sample_result = sample.search(studyId=args.studyId, individualId=str(individualId))
for sample in sample_result:
print("Sample Name: " + sample["name"])
except ServerResponseException as e:
print(str(e), file=sys.stderr)
def share_samples(studyId, list_of_samples_file, user_id):
file_instance = Files()
sample_instance = Samples()
summary = {}
fd = open(list_of_samples_file)
for line in fd:
aline = line.rstrip("\n").split("\t")
if aline:
sample_name = aline[0]
root_folder = aline[1]
print(sample_name)
sample_objs = sample_instance.search(studyId=studyId, name=sample_name)
for sample_obj in sample_objs:
sample_id = str(sample_obj["id"])
folders_to_share = file_instance.search(studyId=studyId, path=root_folder,
sampleIds=sample_id
)
for folder_to_share in folders_to_share:
file_id = str(folder_to_share["id"])
file_instance.share(userId=user_id, fileId=file_id)
sample_instance.share(userId=user_id, sampleId=sample_id)
summary[sample_name] = [folders_to_share]
def id_converter(studyID, inputIDType, outputIDType, IdBatch=None, Id=None):
if IdBatch is None and Id is None:
raise Exception("Error, it was not found any id to convert")
if Id:
ids = Id
else:
ids = [line.split("\t")[0].replace("\n","") for line in open(IdBatch).readlines()]
for id in ids:
if inputIDType == "CatalogIndividualId":
if outputIDType == "IndividualName":
individual = Individuals()
individual_info = individual.info(id)[0]
yield [id, str(individual_info["name"])]
elif outputIDType == "SampleName":
sample = Samples()
sample_info = sample.search(studyID, individualId=id)
for info in sample_info:
yield [id, info["name"]]
elif outputIDType == "CatalogSampleId":
sample = Samples()
sample_info = sample.search(studyID, individualId=id)
for info in sample_info:
yield [id, str(info["id"])]
if inputIDType == "IndividualName":
if outputIDType == "CatalogIndividualId":
individual = Individuals()
individual_info = individual.search(studyID, name=id)[0]
yield [id, str(individual_info["id"])]
if outputIDType == "SampleName":
sample = Samples()
individual = Individuals()
individual_info = individual.search(studyID, name=id)[0]
sample_info = sample.search(studyID, individualId=str(individual_info["id"]))
for info in sample_info:
yield [id, info["name"]]
if outputIDType == "CatalogSampleId":
sample = Samples()
individual = Individuals()
individual_info = individual.search(studyID, name=id)[0]
sample_info = sample.search(studyID, individualId=str(individual_info["id"]))
for info in sample_info:
yield [id, str(info["id"])]
if inputIDType == "CatalogSampleId":
if outputIDType == "CatalogIndividualId":
sample = Samples()
sample_info = sample.info(id)[0]
yield [id, str(sample_info["individualId"])]
if outputIDType == "SampleName":
sample = Samples()
sample_info = sample.info(id)[0]
yield [id, str(sample_info["name"])]
if outputIDType == "IndividualName":
sample = Samples()
sample_info = sample.info(id)[0]
individual = Individuals()
individual_info = individual.info(str(sample_info["individualId"]))[0]
yield [id, str(individual_info["name"])]
if inputIDType == "SampleName":
if outputIDType == "CatalogIndividualId":
sample = Samples()
sample_info = sample.search(studyID, name=id)[0]
yield [id, str(sample_info["individualId"])]
if outputIDType == "CatalogSampleId":
sample = Samples()
sample_info = sample.search(studyID, name=id)[0]
yield [id, str(sample_info["id"])]
if outputIDType == "IndividualName":
sample = Samples()
sample_info = sample.search(studyID, name=id)[0]
individual = Individuals()
individual_info = individual.info(str(sample_info["individualId"]))[0]
yield [id, str(individual_info["name"])]