mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-16 05:07:55 +08:00
d48647a655
* add sample ontologies file * add ontologies reducer * Move select category to own component * Dialog and Input factored out * refactoring categorical, partway * validationn * anno * suggest populates input * frontend for ontology working * initial implementation of back-end support for ontologies * edit is now dialog again * autosuggest working on edit * part way through create arbitrary label * handle choice in function * pass duplicate cat prop * editing works * update test to match new CLI params * fix occupancy alignment * edit category as dialogue * secondary button * remove stubbed out ontologies * add label setting upon new label creation * Update legal characters for labels (#1119) * Allow any term in the ontology (bypass legal name check) * Add hyphens and parens to legal characters in names * improve performance for large ontologies * correctly handle case where ontologies are disabled * fix logic error in CLI Co-authored-by: Bruce Martin <bruce@chanzuckerberg.com> * PR cleanup 1 * lint * validate user generated labels * finish hooking up connected suggest component * protect against undefined callbacks * Fix illegal characters error message * break out npm run commands * fix error detection on label edit Co-authored-by: Bruce Martin <bruce@chanzuckerberg.com> Co-authored-by: Sidney Bell <sidneymbell@users.noreply.github.com>
99 lines
3.3 KiB
Python
99 lines
3.3 KiB
Python
import unittest
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import json
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from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
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from server.app.util.errors import DriverError
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from server.app.util.data_locator import DataLocator
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class DataLoadEngineTest(unittest.TestCase):
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"""
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Test file loading, including deferred loading/update.
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"""
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def setUp(self):
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self.data_file = DataLocator("../example-dataset/pbmc3k.h5ad")
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self.data = ScanpyEngine()
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def test_init(self):
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self.assertIsNone(self.data.data)
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def test_delayed_load_args(self):
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args = {
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"layout": ["tsne"],
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"max_category_items": 1000,
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"obs_names": "foo",
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"var_names": "bar",
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"diffexp_lfc_cutoff": 0.1,
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"annotations": False,
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"annotations_file": None,
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"annotations_output_dir": None,
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"backed": False,
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"diffexp_may_be_slow": False,
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"disable_diffexp": False,
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"annotations_cell_ontology_enabled": False,
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"annotations_cell_ontology_obopath": None,
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"annotations_cell_ontology_terms": None,
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}
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self.data.update(args=args)
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self.assertEqual(args, self.data.config)
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def test_requires_data(self):
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with self.assertRaises(DriverError):
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self.data._create_schema()
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def test_delayed_load_data(self):
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self.data.update(data_locator=self.data_file)
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self.data._create_schema()
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self.assertEqual(self.data.cell_count, 2638)
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self.assertEqual(self.data.gene_count, 1838)
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epsilon = 0.000_005
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self.assertTrue(self.data.data.X[0, 0] - -0.171_469_51 < epsilon)
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def test_diffexp_topN(self):
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self.data.update(data_locator=self.data_file)
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f1 = {"filter": {"obs": {"index": [[0, 500]]}}}
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f2 = {"filter": {"obs": {"index": [[500, 1000]]}}}
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result = json.loads(self.data.diffexp_topN(f1["filter"], f2["filter"]))
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self.assertEqual(len(result), 10)
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result = json.loads(self.data.diffexp_topN(f1["filter"], f2["filter"], 20))
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self.assertEqual(len(result), 20)
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class DataLocatorEngineTest(unittest.TestCase):
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"""
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Test various types of data locators we expect to consume
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"""
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def setUp(self):
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self.args = {
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"layout": ["umap"],
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"max_category_items": 100,
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"obs_names": None,
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"var_names": None,
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"diffexp_lfc_cutoff": 0.01,
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}
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def stdAsserts(self, data):
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""" run these each time we load the data """
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self.assertIsNotNone(data)
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self.assertEqual(data.cell_count, 2638)
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self.assertEqual(data.gene_count, 1838)
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def test_posix_file(self):
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locator = DataLocator("../example-dataset/pbmc3k.h5ad")
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data = ScanpyEngine(locator, self.args)
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self.stdAsserts(data)
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def test_url_https(self):
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url = "https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad"
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locator = DataLocator(url)
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data = ScanpyEngine(locator, self.args)
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self.stdAsserts(data)
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def test_url_http(self):
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url = "http://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad"
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locator = DataLocator(url)
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data = ScanpyEngine(locator, self.args)
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self.stdAsserts(data)
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