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Failure of metadata #222

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andrewdavidsmith opened this issue Oct 25, 2024 · 0 comments
Open

Failure of metadata #222

andrewdavidsmith opened this issue Oct 25, 2024 · 0 comments
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@andrewdavidsmith
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Describe the bug
Failure of metadata on some SRA accessions when VALUE is not a key for value_x.

To Reproduce

$ pysradb metadata --detailed ERP009821
Traceback (most recent call last):
  File "/code/external/pysradb/.venv/bin/pysradb", line 8, in <module>
    sys.exit(parse_args())
             ^^^^^^^^^^^^
  File "/code/external/pysradb/pysradb/cli.py", line 1173, in parse_args
    metadata(
  File "/code/external/pysradb/pysradb/cli.py", line 69, in metadata
    df = sradb.sra_metadata(
         ^^^^^^^^^^^^^^^^^^^
  File "/code/external/pysradb/pysradb/sraweb.py", line 596, in sra_metadata
    value = value_x["VALUE"]
            ~~~~~~~^^^^^^^^^
KeyError: 'VALUE'

Desktop (please complete the following information):

  • OS: Ubuntu 20.04
  • Python version 3.12

Additional context
pysradb version: clone at 35dbf24
@andrewdavidsmith andrewdavidsmith added the bug Something isn't working label Oct 25, 2024
andrewdavidsmith added a commit to andrewdavidsmith/pysradb that referenced this issue Oct 25, 2024
@andrewdavidsmith
pysradb/sraweb.py: adding a default None value when VALUE is not a ke…
85f1e8e 
…y in the value_x dict; this works for the test case in issue saketkc#222
@andrewdavidsmith andrewdavidsmith mentioned this issue Oct 25, 2024
Merged
saketkc added a commit that referenced this issue Oct 25, 2024
@andrewdavidsmith @saketkc
Handle missing VALUE in value_x dict (#223)
85abf88 
* pysradb/sraweb.py: adding a default None value when VALUE is not a key in the value_x dict; this works for the test case in issue #222

* Drop Python 3.7, 3.8

* Update release notes

* Update release notes

* Suppress ena search test

---------

Co-authored-by: Saket Choudhary <[email protected]>
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@andrewdavidsmith