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update getting GO tree #112

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Merged
mwittep merged 1 commit into from
Feb 10, 2026
Merged

update getting GO tree #112

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20 changes: 15 additions & 5 deletions server/backend_compute_statistics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,8 @@
from server.backend_tree_enrichment import FindClades
from server.serialize_sets import serialize_sets

import urllib.request

# class NoDaemonProcess(multiprocessing.Process):
# @property
# def daemon(self):
Expand Down Expand Up @@ -179,7 +181,13 @@ def load_go_basic():
:return: go: parsed obo-file
"""

go_obo_url = 'http://purl.obolibrary.org/obo/go/go-basic.obo'
url = "https://current.geneontology.org/ontology/go-basic.obo"
req = urllib.request.Request(
url,
headers={"User-Agent": "Mozilla/5.0"}
)

# go_obo_url = 'https://current.geneontology.org/ontology/go-basic.obo'
data_folder = os.getcwd() + '/data'
# Check if we have the ./data directory already
if (not os.path.isdir(data_folder)):
Expand All @@ -188,16 +196,18 @@ def load_go_basic():
except OSError as e:
if (e.errno != 17):
raise e
go_obo = data_folder + '/go-basic.obo'
# Check if we have the .obo file already
if (not os.path.isfile(data_folder + '/go-basic.obo')):
go_obo = wget.download(go_obo_url, data_folder + '/go-basic.obo')
with urllib.request.urlopen(req) as response, open(data_folder + '/go-basic.obo', "wb") as out:
out.write(response.read())
else:
time_since_last_modified = time.time() - os.path.getmtime(data_folder+'/go-basic.obo')
if time_since_last_modified > 604800:
os.remove(data_folder + '/go-basic.obo')
go_obo = wget.download(go_obo_url, data_folder + '/go-basic.obo')
else:
go_obo = data_folder + '/go-basic.obo'
with urllib.request.urlopen(req) as response, open(data_folder + '/go-basic.obo', "wb") as out:
out.write(response.read())

# parse hierarchy
go = obo_parser.GODag(go_obo)
return go
Expand Down
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