Merged
Conversation
alimanfoo
reviewed
Sep 2, 2021
tests/test_ag3.py
Outdated
| # test a single sample set | ||
| sample_sets = "AG1000G-UG" | ||
| df_UG = ag3.sample_cohorts(sample_sets=sample_sets) | ||
| assert df_UG.sample_id[0] == "AC0007-C" |
Member
There was a problem hiding this comment.
Suggest:
df_UG_meta = ag3.sample_metadata(sample_sets=sample_set)
assert len(df_UG) == len(df_UG_meta)
assert df_UG['sample_id'].tolist() == df_UG_meta['sample_id'].tolist()
Member
There was a problem hiding this comment.
If compare with sample metadata, could make most of this generic, and use pytest.parameterize.
Collaborator
Author
|
@alimanfoo, I've allowed crosses in the code and switched the test to pytest.parameterize. It should be good to go now. |
Collaborator
Author
|
resolved by #61 |
kathrynmurie
pushed a commit
to kathrynmurie/malariagen-data-python
that referenced
this pull request
Oct 5, 2021
alimanfoo
added
the
BMGF-001927
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
resolves #51
Adds a method
Ag3.sample_cohorts(sample_sets, analysis)to access the Ag3 defined cohorts metadata. Tests have also been written for the method, but currently these point at the staging bucket. Once the metadata is copied to the release bucket, the tests should be updated.