cleaning up biosample and participant by satra · Pull Request #312 · dandi/dandi-cli

satra · 2020-12-10T19:46:40Z

this is a draft PR to try and clean up the asset model. i haven't updated tests yet. putting the model changes here up for discussion.

satra · 2020-12-10T19:47:24Z

        nskey="dandi",
    )
+
+    wasDerivedFrom: Optional[List["BioSample"]] = Field(None, nskey="prov")


this recursive formulation should allow us to have cell ids, slice ids, and tissue ids.

satra · 2020-12-10T19:47:49Z

+
+
+class Participant(DandiBaseModel):
+    """Description about the sample that was studied"""


separating out participant details

satra · 2020-12-10T19:48:26Z

+    wasAttributedTo: List[Participant] = Field(
+        None, description="Participant(s) to which this file belongs to", nskey="prov"
+    )


a given asset may have multiple participants potentially. how we deal with this in the name is something we will have to figure out.

codecov · 2020-12-11T01:48:44Z

Codecov Report

Merging #312 (eb5a7cd) into master (d21b154) will increase coverage by 0.09%.
The diff coverage is 93.54%.

@@            Coverage Diff             @@
##           master     #312      +/-   ##
==========================================
+ Coverage   70.33%   70.42%   +0.09%     
==========================================
  Files          55       55              
  Lines        5077     5096      +19     
==========================================
+ Hits         3571     3589      +18     
- Misses       1506     1507       +1

Flag	Coverage Δ
unittests	`70.42% <93.54%> (+0.09%)`	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
dandi/tests/test_metadata.py	`100.00% <ø> (ø)`
dandi/tests/test_validate.py	`100.00% <ø> (ø)`
dandi/metadata.py	`74.76% <87.50%> (+0.58%)`	⬆️
dandi/models.py	`82.35% <100.00%> (+0.53%)`	⬆️

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* upstream/master: Close a file in a test case

yarikoptic · 2020-12-15T00:13:14Z

now master should be 3.9 testing friendly , so the only issues are of the lint

lint errors

Run tox -e lint
lint create: /home/runner/work/dandi-cli/dandi-cli/.tox/lint
lint installdeps: flake8
lint installed: flake8==3.8.4,importlib-metadata==3.3.0,mccabe==0.6.1,pycodestyle==2.6.0,pyflakes==2.2.0,typing-extensions==3.7.4.3,zipp==3.4.0
lint run-test-pre: PYTHONHASHSEED='1970909900'
lint run-test: commands[0] | flake8 --config=setup.cfg dandi setup.py
dandi/tests/test_metadata.py:592:101: E501 line too long (132 > 100 characters)
dandi/tests/test_metadata.py:638:101: E501 line too long (109 > 100 characters)
dandi/tests/test_metadata.py:673:101: E501 line too long (221 > 100 characters)
dandi/tests/test_metadata.py:741:101: E501 line too long (109 > 100 characters)
dandi/tests/test_metadata.py:766:101: E501 line too long (109 > 100 characters)
dandi/tests/test_metadata.py:787:101: E501 line too long (106 > 100 characters)
dandi/tests/test_metadata.py:808:101: E501 line too long (106 > 100 characters)
dandi/tests/test_metadata.py:834:101: E501 line too long (131 > 100 characters)
dandi/tests/test_metadata.py:870:101: E501 line too long (221 > 100 characters)
dandi/tests/test_metadata.py:880:101: E501 line too long (133 > 100 characters)
dandi/tests/test_metadata.py:901:101: E501 line too long (119 > 100 characters)
dandi/tests/test_metadata.py:942:101: E501 line too long (119 > 100 characters)
dandi/tests/test_metadata.py:963:101: E501 line too long (109 > 100 characters)
dandi/tests/test_metadata.py:1002:101: E501 line too long (109 > 100 characters)
dandi/tests/test_metadata.py:1012:101: E501 line too long (106 > 100 characters)
dandi/tests/test_metadata.py:1022:101: E501 line too long (133 > 100 characters)
dandi/tests/test_metadata.py:1032:101: E501 line too long (127 > 100 characters)
dandi/tests/test_metadata.py:1042:101: E501 line too long (155 > 100 characters)
dandi/tests/test_metadata.py:1097:101: E501 line too long (102 > 100 characters)
dandi/tests/test_metadata.py:1127:101: E501 line too long (1147 > 100 characters)
dandi/tests/test_metadata.py:1149:101: E501 line too long (124 > 100 characters)
ERROR: InvocationError for command /home/runner/work/dandi-cli/dandi-cli/.tox/lint/bin/flake8 --config=setup.cfg dandi setup.py (exited with code 1)
___________________________________ summary ____________________________________
ERROR:   lint: commands failed
Error: Process completed with exit code 1.

aren't you using pre-commit?!

* upstream/master: Add comment explaining why Python 3.9 on Windows testing is disabled Downgrade hdf5 on macOS to 1.8 Install hdf5 for Python 3.9 tests

satra · 2020-12-15T00:28:34Z

pre-commit isn't catching these linting things. do remember pre-commit uses black which is opinionated.

yarikoptic · 2020-12-15T01:54:08Z

hm, I just remember it splitting long lines for me and staying largely inline with what we have setup for linters... odd

yarikoptic · 2020-12-16T17:37:43Z

Dear @jwodder , could you please finalize this PR (if I got it right -- only linting is remaining) so we could merge it (@satra I believe is already holidaying officially so we should not pester him to not ruin that important nowadays activity).

jwodder · 2020-12-16T17:52:47Z

@yarikoptic Delinted.

* upstream/master: Split up download methods Simplify code Download method for new API Update pagination Fix more API calls Include dandiset ID and version ID in `file_name` Correct the calls to the validation endpoints Wait for Django API Docker container to be ready Test of new upload method upload() method for new API Set API URL for Docker Compose to point to API container Basic updates for new API Fix tests Ensure log path is always printed, even on error Record sys.argv and os.getcwd() as logfile-specific log messages Tee all logs to user log directory

* upstream/enh/subject: Break long lines

satra · 2020-12-18T14:53:33Z

@yarikoptic - the tests that fail here are the same tests that fail on master and unrelated to this PR.

yarikoptic · 2020-12-18T19:58:56Z

hm, something changed in API server I guess -- #283 which had dealt with new code for API was all green when merged 2 days ago. so indeed let's just proceed with merge and #322 is now dedicated to test failure

cleaning up biosample and participant

f6978f7

satra commented Dec 10, 2020

View reviewed changes

satra added 3 commits December 10, 2020 20:28

fix: tests

fa92dde

remove redundant import

6115f7e

fix: validation test

71e21a0

satra changed the title ~~[WIP] cleaning up biosample and participant~~ cleaning up biosample and participant Dec 11, 2020

satra mentioned this pull request Dec 11, 2020

h5py started to error on install with python 3.9 #313

Closed

satra added 2 commits December 11, 2020 16:34

fix: dandiset metadata

9befe54

Merge remote-tracking branch 'upstream/master' into enh/subject

46e03ba

* upstream/master: Close a file in a test case

Merge remote-tracking branch 'upstream/master' into enh/subject

2d0837f

* upstream/master: Add comment explaining why Python 3.9 on Windows testing is disabled Downgrade hdf5 on macOS to 1.8 Install hdf5 for Python 3.9 tests

yarikoptic assigned jwodder Dec 16, 2020

Break long lines

5e15370

satra added 2 commits December 18, 2020 09:37

Merge remote-tracking branch 'upstream/enh/subject' into enh/subject

eb5a7cd

* upstream/enh/subject: Break long lines

yarikoptic merged commit e7af24a into master Dec 18, 2020

yarikoptic deleted the enh/subject branch December 18, 2020 19:59

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cleaning up biosample and participant#312

cleaning up biosample and participant#312
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		class Participant(DandiBaseModel):
		"""Description about the sample that was studied"""

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