mirror of
https://github.com/chanzuckerberg/cellxgene.git
synced 2026-09-17 05:47:58 +08:00
20317fd08f
* initial commit of URL support for launch * lint * modify tests to use new data locator * add locator unit tests * fix typo in faq * more lint * update faq per PR review
88 lines
2.9 KiB
Python
88 lines
2.9 KiB
Python
import unittest
|
|
import json
|
|
|
|
from server.app.scanpy_engine.scanpy_engine import ScanpyEngine
|
|
from server.app.util.errors import DriverError
|
|
from server.app.util.data_locator import DataLocator
|
|
|
|
|
|
class DataLoadEngineTest(unittest.TestCase):
|
|
"""
|
|
Test file loading, including deferred loading/update.
|
|
"""
|
|
def setUp(self):
|
|
self.data_file = DataLocator("example-dataset/pbmc3k.h5ad")
|
|
self.data = ScanpyEngine()
|
|
|
|
def test_init(self):
|
|
self.assertIsNone(self.data.data)
|
|
|
|
def test_delayed_load_args(self):
|
|
args = {
|
|
"layout": ["tsne"],
|
|
"max_category_items": 1000,
|
|
"obs_names": "foo",
|
|
"var_names": "bar",
|
|
"diffexp_lfc_cutoff": 0.1,
|
|
}
|
|
self.data.update(args=args)
|
|
self.assertEqual(args, self.data.config)
|
|
|
|
def test_requires_data(self):
|
|
with self.assertRaises(DriverError):
|
|
self.data._create_schema()
|
|
|
|
def test_delayed_load_data(self):
|
|
self.data.update(data=self.data_file)
|
|
self.data._create_schema()
|
|
self.assertEqual(self.data.cell_count, 2638)
|
|
self.assertEqual(self.data.gene_count, 1838)
|
|
epsilon = 0.000_005
|
|
self.assertTrue(self.data.data.X[0, 0] - -0.171_469_51 < epsilon)
|
|
|
|
def test_diffexp_topN(self):
|
|
self.data.update(data=self.data_file)
|
|
f1 = {"filter": {"obs": {"index": [[0, 500]]}}}
|
|
f2 = {"filter": {"obs": {"index": [[500, 1000]]}}}
|
|
result = json.loads(self.data.diffexp_topN(f1["filter"], f2["filter"]))
|
|
self.assertEqual(len(result), 10)
|
|
result = json.loads(self.data.diffexp_topN(f1["filter"], f2["filter"], 20))
|
|
self.assertEqual(len(result), 20)
|
|
|
|
|
|
class DataLocatorEngineTest(unittest.TestCase):
|
|
"""
|
|
Test various types of data locators we expect to consume
|
|
"""
|
|
def setUp(self):
|
|
self.args = {
|
|
"layout": ["umap"],
|
|
"max_category_items": 100,
|
|
"obs_names": None,
|
|
"var_names": None,
|
|
"diffexp_lfc_cutoff": 0.01,
|
|
}
|
|
|
|
def stdAsserts(self, data):
|
|
""" run these each time we load the data """
|
|
self.assertIsNotNone(data)
|
|
self.assertEqual(data.cell_count, 2638)
|
|
self.assertEqual(data.gene_count, 1838)
|
|
|
|
def test_posix_file(self):
|
|
locator = DataLocator("example-dataset/pbmc3k.h5ad")
|
|
data = ScanpyEngine(locator, self.args)
|
|
self.stdAsserts(data)
|
|
|
|
def test_url_https(self):
|
|
url = "https://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad"
|
|
locator = DataLocator(url)
|
|
data = ScanpyEngine(locator, self.args)
|
|
self.stdAsserts(data)
|
|
|
|
def test_url_http(self):
|
|
url = "http://raw.githubusercontent.com/chanzuckerberg/cellxgene/master/example-dataset/pbmc3k.h5ad"
|
|
locator = DataLocator(url)
|
|
data = ScanpyEngine(locator, self.args)
|
|
self.stdAsserts(data)
|