def toProtocolElement(self):
dataset = protocol.Dataset()
dataset.id = self.getId()
dataset.name = pb.string(self.getLocalId())
dataset.description = pb.string(self.getDescription())
self.serializeAttributes(dataset)
return dataset
def search_datasets(request):
"""
Mock Function
"""
dataset_list = []
for i in xrange(10):
dataset = protocol.Dataset()
dataset.id = str(i)
dataset.name = "Hi there"
dataset_list.append(dataset)
return (dataset_list, "0:0")
def testRoundTripDatasetProtobufString(self):
id_ = "id"
name = "name"
description = "description"
dataset = protocol.Dataset()
dataset.id = id_
dataset.name = name
dataset.description = description
pbStr = protocol.toProtobufString(dataset)
newDataset = protocol.fromProtobufString(pbStr, Dataset)
self.assertEquals(newDataset.id, id_)
self.assertEquals(newDataset.name, name)
self.assertEquals(newDataset.description, description)
def testRoundTripDataset(self):
id_ = "id"
name = "name"
description = "description"
dataset = protocol.Dataset()
dataset.id = id_
dataset.name = name
dataset.description = description
jsonStr = protocol.toJson(dataset)
newDataset = protocol.fromJson(jsonStr, Dataset)
self.assertEquals(dataset.id, id_)
self.assertEquals(dataset.name, name)
self.assertEquals(dataset.description, description)
datasetDict = protocol.toJsonDict(newDataset)
self.assertEquals(datasetDict['id'], id_)
self.assertEquals(datasetDict['name'], name)
self.assertEquals(datasetDict['description'], description)
def search_datasets(request):
# TODO safely cast page token
page_size = 100 # Default page size
if request.page_size != 0:
page_size = request.page_size
page_token = 0
if request.page_token != '':
page_token = int(request.page_token)
offset = page_token * request.page_size
esearch_params = {
'db': 'bioproject',
'term': 'all[filter]',
'retmax': page_size,
'retstart': offset
}
esearch_response = requests.get(
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi",
esearch_params)
# get IDs
ids = []
root = ET.fromstring(esearch_response.text)
for id_ in root.findall("./IdList/Id"):
ids.append(id_.text)
# get summaries
esummary_params = {'db': 'bioproject', 'id': ','.join(ids)}
esummary_response = requests.get(
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi",
params=esummary_params)
root = ET.fromstring(esummary_response.text.encode('utf-8'))
dataset_list = []
for ds in root.findall("./DocumentSummarySet/DocumentSummary"):
dataset = protocol.Dataset()
# uid = ds.find('Project_Id').text
dataset.id = ds.find('Project_Acc').text # id
dataset.name = ds.find('Project_Title').text # name
dataset.description = ds.find('Project_Description').text
dataset_list.append(dataset)
return dataset_list