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ebi-ait / dcp-ingest-central

Central point of access for the Ingestion Service of the HCA DCP
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Ambiguous geo-to-hca spreadsheet generator error for GSE119945 #878

Open rachadele opened 2 years ago

rachadele commented 2 years ago

Overview Ingest spreadsheet generator is throwing an ambiguous error I've never seen before when trying to register GSE119945 (screenshot included)

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Screen Shot 2022-10-10 at 9 02 41 AM
amnonkhen commented 2 years ago

Issue will be investigated later this week.

relevant logs:

[_internal.py:225 - _log() ] 2022-10-10 15:24:57,842 - werkzeug - INFO - 10.70.1.47 - - [10/Oct/2022 15:24:57] "POST /spreadsheet-from-accession?accession=GSE119945 HTTP/1.1" 500 -
Exception: Error creating spreadsheet for accession GSE119945. not well-formed (invalid token): line 1, column 0
raise Exception(f'Error creating spreadsheet for accession {accession}. {e}') from e
File "/usr/local/lib/python3.6/site-packages/geo_to_hca/geo_to_hca.py", line 227, in create_spreadsheet_using_accession
workbook = geo_to_hca.create_spreadsheet_using_accession(geo_or_srp_accession)
File "/app/broker/import_geo/routes.py", line 56, in _generate_geo_workbook
Traceback (most recent call last):
The above exception was the direct cause of the following exception:
xml.etree.ElementTree.ParseError: not well-formed (invalid token): line 1, column 0
File "<string>", line None
parser.feed(text)
File "/usr/local/lib/python3.6/xml/etree/ElementTree.py", line 1314, in XML
return xm.fromstring(sra_url.content)
File "/usr/local/lib/python3.6/site-packages/geo_to_hca/utils/sra_utils.py", line 142, in request_accession_info
xml = sra_utils.request_accession_info(parts_list[p], accession_type=accession_type)
File "/usr/local/lib/python3.6/site-packages/geo_to_hca/utils/utils.py", line 89, in get_experimental_metadata
xml_content_result, size = get_experimental_metadata(accessions_list, accession_type=accession_type)
File "/usr/local/lib/python3.6/site-packages/geo_to_hca/utils/utils.py", line 99, in fetch_experimental_metadata
attribute_lists = utils.fetch_experimental_metadata(biosample_accessions,accession_type='biosample')
File "/usr/local/lib/python3.6/site-packages/geo_to_hca/utils/get_tab.py", line 78, in get_specimen_from_organism_tab_xls
tab_name="Specimen from organism")
File "/usr/local/lib/python3.6/site-packages/geo_to_hca/geo_to_hca.py", line 169, in create_spreadsheet_using_accession
Traceback (most recent call last):
[routes.py:58 - _generate_geo_workbook() ] 2022-10-10 15:24:57,838 - broker.import_geo.routes - ERROR - Error creating spreadsheet for accession GSE119945. not well-formed (invalid token): line 1, column 0
[geo_to_hca.py:167 - create_spreadsheet_using_accession() ] 2022-10-10 15:24:57,048 - geo_to_hca.geo_to_hca - INFO - Getting Specimen from Organism tab
[_internal.py:225 - _log() ] 2022-10-10 15:24:50,122 - werkzeug - INFO - 10.70.1.47 - - [10/Oct/2022 15:24:50] "POST /spreadsheet-from-accession?accession=GSE119945 HTTP/1.1" 500 -
Exception: Error creating spreadsheet for accession GSE119945. not well-formed (invalid token): line 1, column 0
raise Exception(f'Error creating spreadsheet for accession {accession}. {e}') from e
File "/usr/local/lib/python3.6/site-packages/geo_to_hca/geo_to_hca.py", line 227, in create_spreadsheet_using_accession
workbook = geo_to_hca.create_spreadsheet_using_accession(geo_or_srp_accession)
File "/app/broker/import_geo/routes.py", line 56, in _generate_geo_workbook
Traceback (most recent call last):
The above exception was the direct cause of the following exception:
xml.etree.ElementTree.ParseError: not well-formed (invalid token): line 1, column 0
File "<string>", line None
parser.feed(text)
File "/usr/local/lib/python3.6/xml/etree/ElementTree.py", line 1314, in XML
return xm.fromstring(sra_url.content)
File "/usr/local/lib/python3.6/site-packages/geo_to_hca/utils/sra_utils.py", line 142, in request_accession_info
xml = sra_utils.request_accession_info(parts_list[p], accession_type=accession_type)
File "/usr/local/lib/python3.6/site-packages/geo_to_hca/utils/utils.py", line 89, in get_experimental_metadata
xml_content_result, size = get_experimental_metadata(accessions_list, accession_type=accession_type)
File "/usr/local/lib/python3.6/site-packages/geo_to_hca/utils/utils.py", line 99, in fetch_experimental_metadata
attribute_lists = utils.fetch_experimental_metadata(biosample_accessions,accession_type='biosample')
File "/usr/local/lib/python3.6/site-packages/geo_to_hca/utils/get_tab.py", line 78, in get_specimen_from_organism_tab_xls
tab_name="Specimen from organism")
File "/usr/local/lib/python3.6/site-packages/geo_to_hca/geo_to_hca.py", line 169, in create_spreadsheet_using_accession
Traceback (most recent call last):
[routes.py:58 - _generate_geo_workbook() ] 2022-10-10 15:24:50,119 - broker.import_geo.routes - ERROR - Error creating spreadsheet for accession GSE119945. not well-formed (invalid token): line 1, column 0
[geo_to_hca.py:167 - create_spreadsheet_using_accession() ] 2022-10-10 15:24:49,206 - geo_to_hca.geo_to_hca - INFO - Getting Specimen from Organism tab
[_internal.py:225 - _log() ] 2022-10-10 15:24:44,819 - werkzeug - INFO - 10.70.1.47 - - [10/Oct/2022 15:24:44] "POST /import-accession?accession=GSE119945 HTTP/1.1" 500 -
amnonkhen commented 1 year ago

same error message as #872.