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Add user-defined category-label colors (#1402)

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* Add user-defined category-label colors

Fixes https://github.com/chanzuckerberg/cellxgene/issues/1152

As described in https://github.com/chanzuckerberg/cellxgene/issues/1307

* Respond to feedback from @bkmartinjr in nodejs

* Respond to feedback from @bkmartinjr in python

* Add tests to the server module

* Autoformat python, run linter

* Make colors_get error handling specific

* Respond to feedback from @bkmartinjr

* Respond to feedback from @bkmartinjr

* Fix whitespace

* Fix python lint errrors

* Update documentation

* Add --disable-user-colors option to launch and cxgtool.py

* Fix python formatting

* Rename '--disable-user-colors' to '--disable-custom-colors'
This commit is contained in:
Matt Weiden
2020-04-26 22:52:57 -07:00
committed by GitHub
parent 3c191c3f93
commit 546e272a60
91 changed files with 801 additions and 271 deletions
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server/test/test_nan_anndata_adaptor.py
+5 -22
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@@ -8,39 +8,22 @@ import server.test.decode_fbs as decode_fbs
from server.data_anndata.anndata_adaptor import AnndataAdaptor
from server.common.errors import FilterError
from server.common.data_locator import DataLocator
from server.common.app_config import AppConfig
from server.test import PROJECT_ROOT, app_config
class NaNTest(unittest.TestCase):
def setUp(self):
self.args = {
"embeddings__names": ["umap"],
"presentation__max_categories": 100,
"single_dataset__obs_names": None,
"single_dataset__var_names": None,
"diffexp__lfc_cutoff": 0.01,
"limits__diffexp_cellcount_max": None,
"limits__column_request_max": None,
}
config = AppConfig()
config.update(**self.args)
locator = DataLocator("test/test_datasets/nan.h5ad")
config.update(single_dataset__datapath=locator.path)
config.complete_config()
self.data_locator = DataLocator(f"{PROJECT_ROOT}/server/test/test_datasets/nan.h5ad")
self.config = app_config(self.data_locator.path)
with warnings.catch_warnings():
warnings.simplefilter("ignore", category=UserWarning)
self.data = AnndataAdaptor(locator, config)
self.data = AnndataAdaptor(self.data_locator, self.config)
self.data._create_schema()
def test_load(self):
with self.assertWarns(UserWarning):
config = AppConfig()
config.update(**self.args)
locator = DataLocator("test/test_datasets/nan.h5ad")
config.update(single_dataset__datapath=locator.path)
config.complete_config()
self.data = AnndataAdaptor(locator, config)
self.data = AnndataAdaptor(self.data_locator, self.config)
def test_init(self):
self.assertEqual(self.data.cell_count, 100)