lonly7star / abagen Goto Github PK

Issue description

There is Order-Dependent flakiness in this testing code. The test will fail on the exact 36th run on a continual run.

Steps to reproduce the issue

1. run pytest with flake-finder with command pytest -k test_gene.py --flake-finder
2. or directly use the list to reproduce the failure.

    list_36 =  [6437, 19829, 17943, 4635, 16444, 4341, 8346, 1622, 19656, 15336]
    samples = GENES.loc[list_36]

What's the expected result?

• The test pass

What's the actual result?

• The test will fail on line 19 with the output:
  > assert sorted(names['name']) == sorted(samples['name'])
AssertionError: assert ['RIKEN cDNA ...delta 2', ...] == ['RIKEN cDNA ...ining 9', ...]
E At index 1 diff: 'RIKEN cDNA 9130019P16 gene' != 'RIKEN cDNA A230044A09 gene (non-RefSeq)'
E Left contains one more item: 'vaccinia related kinase 1'
E Use -v to get the full diff

Additional details / screenshot

The reason for this failure is the names will have 11 lines of Dataframe instead of 10.
The Dataframe of "samples"

and the retrieved result Dataframe of "name"

Noticed the "RIKEN cDNA" has a duplicated line which caused the asserted error.

The duplicated key is generated on the code from abagen\abagen\utis.py, line 64
response = urlopen(url)
where it passed a Querying request to the server https://api.brain-map.org/api/v2/data/.. and the server returns with 11 lines of data include the extra line instead of 10 lines.

I suspect the flakiness is caused by the server-side that returns the duplicate key/value part.

As to the client part, a suggested fix is to add a check duplication for the return JSON.