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When downloading biosample it appears to download an empty file. Need to add try to the check xml script.
2017-05-31 19:12:26,762 - INFO - Querying BioSample: with 25,487 ids
2017-05-31 19:12:26,762 - INFO - Saving to cache: /home/fearjm/tmp/.cache/sra2mongo/biosample
2017-05-31 19:12:42,466 - INFO - There are 25,487 records.
2017-05-31 19:12:42,476 - INFO - Downloading BioSample documents
2017-05-31 19:12:42,476 - INFO - Saving to cache: /home/fearjm/tmp/.cache/sra2mongo/biosample
killing process with pid: 8972
Traceback (most recent call last):
File "/home/fearjm/miniconda3/envs/test_sra2mongo/bin/sra2mongo", line 11, in <module>
load_entry_point('sramongo', 'console_scripts', 'sra2mongo')()
File "/home/fearjm/devel/sramongo/sramongo/sra2mongo.py", line 441, in main
raise err
File "/home/fearjm/devel/sramongo/sramongo/sra2mongo.py", line 403, in main
fetch_ncbi(query, cache, runinfo_retmode=None, db='biosample')
File "/home/fearjm/devel/sramongo/sramongo/sra2mongo.py", line 227, in fetch_ncbi
if (cache_xml is not None) & (catch_xml_error(StringIO(cache_xml)) is False):
File "/home/fearjm/devel/sramongo/sramongo/sra2mongo.py", line 205, in catch_xml_error
tree = ElementTree.parse(xml)
File "/home/fearjm/miniconda3/envs/test_sra2mongo/lib/python3.5/xml/etree/ElementTree.py", line 1195, in parse
tree.parse(source, parser)
File "/home/fearjm/miniconda3/envs/test_sra2mongo/lib/python3.5/xml/etree/ElementTree.py", line 596, in parse
self._root = parser._parse_whole(source)
xml.etree.ElementTree.ParseError: no element found: line 1, column 0
The text was updated successfully, but these errors were encountered:
When downloading biosample it appears to download an empty file. Need to add try to the check xml script.
The text was updated successfully, but these errors were encountered: