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Change Biomart behaviour #38

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Merged
ladislav-hovan merged 1 commit into from
Jun 1, 2026
Merged

Change Biomart behaviour #38

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7 changes: 4 additions & 3 deletions src/sponge/modules/utils/data_retrieval.py
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Original file line number Diff line number Diff line change
Expand Up @@ -182,16 +182,17 @@ def retrieve_ensembl_data(
xml_query = create_xml_query(dataset_name, requested_fields, filters)
REQUEST_STRING = '/martservice?query='
link = ensembl_url + REQUEST_STRING + xml_query
MAX_ITERATIONS = 30
MAX_ITERATIONS = 50
FAILURE = ['Query ERROR', 'Service unavailable']
for _ in range(MAX_ITERATIONS):
r = requests.get(link, stream=True)
r.raise_for_status()
bytes = download_with_progress(r)
if not 'Query ERROR' in bytes.getvalue().decode():
if not True in [x in bytes.getvalue().decode() for x in FAILURE]:
break
# Try every half a second
time.sleep(0.5)
if 'Query ERROR' in bytes.getvalue().decode():
if True in [x in bytes.getvalue().decode() for x in FAILURE]:
raise ConnectionError('No results have been retrieved from Ensembl in '
'the given time')

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