batch saving genomes #212
batch saving genomes #212
Conversation
Xiangs18
requested review from
jsfillman,
jkbaumohl and
Tianhao-Gu
as code owners
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## master #212 +/- ##
==========================================
+ Coverage 80.88% 81.07% +0.18%
==========================================
Files 11 11
Lines 2998 3017 +19
==========================================
+ Hits 2425 2446 +21
+ Misses 573 571 -2 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
…me_mass loop; 3. make the note much more explicit
| if "AnnotatedMetagenomeAssembly" in ws_datatype: | ||
| if params.get('upgrade') or 'feature_counts' not in data: | ||
| data = self._update_metagenome(data) |
There was a problem hiding this comment.
I really wish we had documented why this was ok to delete because I don't remember any more:
There was a problem hiding this comment.
More discussion here: #212 (comment)
There was a problem hiding this comment.
Codedov says there is a test where the type is AMA: https://app.codecov.io/gh/kbaseapps/GenomeFileUtil/blob/master/lib%2FGenomeFileUtil%2Fcore%2FGenomeInterface.py#L142
There was a problem hiding this comment.
Sijie - do you remember anything about why we thought this was safe to delete?
There was a problem hiding this comment.
Especially since it seems to be exercised by tests per Codecov
There was a problem hiding this comment.
Whoops, looks like there were some tests for this that were deleted also, those should be undeleted as well: #212 (comment)
There was a problem hiding this comment.
Restored test and updated logic to check all object types: Assembly, Genome, and Metagenome.
There was a problem hiding this comment.
Metagenome coverage issue is now fixed
There was a problem hiding this comment.
In this case although now the _update_metagenome function call is covered, there's no actual effect from the function call - it's a no op, and so if call were deleted no tests would fail. There needs to be a test that would fail if the function call were removed. A unit test here would be fine - I think there just needs to be a tests that calls save_genomes_mass and save_one_genome with no "molecule_type" field in the genome object
If there's already a test that saves a genome I'd think it'd be pretty easy to add a case for this
…est_genomes_with_upgrade
test/utility/genome_size_tests.py
Outdated
| cls.wsClient.create_workspace({'workspace': cls.wsName}) | ||
| cls.wsID = cls.dfuClient.ws_name_to_id(cls.wsName) |
There was a problem hiding this comment.
| cls.wsClient.create_workspace({'workspace': cls.wsName}) | |
| cls.wsID = cls.dfuClient.ws_name_to_id(cls.wsName) | |
| cls.wsID = cls.wsClient.create_workspace({'workspace': cls.wsName})[0] |
pretty sure that's the right syntax, but you might need to fix it if not. create-workspace def returns the wsid
No description provided.