def search_read_group_sets(request):
"""
Mock function
"""
read_group_set_list = []
for i in xrange(10):
read_group_set = protocol.ReadGroupSet()
read_group_set.id = str(i)
read_group_set.name = "Hi there"
read_group_set_list.append(read_group_set)
return (read_group_set_list, "somepagetoken")
def search_read_group_sets(request):
ncbi_bioproject_id = request.dataset_id
page_size = 100 # Default page size
if request.page_size != 0:
page_size = request.page_size
esearch_params = {
'db': 'sra',
'dbfrom': 'bioproject',
'id': ncbi_bioproject_id,
'term': 'all[filter]'
}
esearch_response = requests.get(
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi",
esearch_params)
# parse xml response: get SRA IDs
ids = []
root = ET.fromstring(esearch_response.text)
for id in root.findall("./LinkSet/LinkSetDb"):
if (id.find("LinkName").text == "bioproject_sra_all"):
for sra in id.findall("./Link/Id"):
ids.append(sra.text)
# === get all data for these SRAs ===
readgroupsets = []
while (len(ids)):
readgroupset = protocol.ReadGroupSet()
# e.g., https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=sra&id=3543186,3543185,3543183
sra_ids = ids[:page_size]
ids = ids[page_size:]
esearch_params = {'db': 'sra', 'id': ','.join(sra_ids)}
esearch_response = requests.get(
"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi",
esearch_params)
# parse xml response: get relevant data for these SRAs
for child in ET.fromstring(esearch_response.text):
readgroup = readgroupset.read_groups.add()
for pid in child.findall("./SUBMISSION/IDENTIFIERS/PRIMARY_ID"):
readgroup.dataset_id = pid.text
for pid in child.findall("./RUN_SET/RUN/IDENTIFIERS/PRIMARY_ID"):
readgroup.id = pid.text
for eid in child.findall(
"./RUN_SET/RUN/Pool/Member/IDENTIFIERS/EXTERNAL_ID"):
readgroup.biosample_id = eid.text
for node in child.findall("./RUN_SET/RUN"):
if (node.attrib.has_key('assembly')):
readgroup.reference_set_id = node.attrib['assembly']
readgroupsets.append(readgroup)
return readgroupsets
def toProtocolElement(self):
"""
Returns the GA4GH protocol representation of this ReadGroupSet.
"""
readGroupSet = protocol.ReadGroupSet()
readGroupSet.id = self.getId()
readGroupSet.read_groups.extend([
readGroup.toProtocolElement()
for readGroup in self.getReadGroups()
])
readGroupSet.name = self.getLocalId()
readGroupSet.dataset_id = self.getParentContainer().getId()
readGroupSet.stats.CopyFrom(self.getStats())
self.serializeAttributes(readGroupSet)
return readGroupSet