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Code Issues Packages Projects Releases Wiki Activity

genesets route for local server (#2079)

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* first cut at GET /genesets route

* update existing tests to match code changes

* more GET /genesets and initial tests

* add missing test fixture

* geneset validation accepts OTA format

* genesets route: better error handling, more tests

* lint
This commit is contained in:
Bruce Martin
2021-02-26 17:53:07 -08:00
committed by GitHub
parent 09466a5c32
commit f3a3820ffa
18 changed files with 813 additions and 82 deletions
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local_server/test/unit/common/test_writable_annotation.py
+6 -6
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@@ -45,8 +45,8 @@ class WritableAnnotationTest(unittest.TestCase):
)
res = self.annotation_put_fbs(fbs)
self.assertEqual(res, json.dumps({"status": "OK"}))
self.assertTrue(path.exists(self.annotations.output_file))
df = pd.read_csv(self.annotations.output_file, index_col=0, header=0, comment="#")
self.assertTrue(path.exists(self.annotations.label_output_file))
df = pd.read_csv(self.annotations.label_output_file, index_col=0, header=0, comment="#")
self.assertEqual(df.shape, (n_rows, 2))
self.assertEqual(set(df.columns), {"cat_A", "cat_B"})
self.assertTrue(self.data.original_obs_index.equals(df.index))
@@ -62,14 +62,14 @@ class WritableAnnotationTest(unittest.TestCase):
)
res = self.annotation_put_fbs(fbs)
self.assertEqual(res, json.dumps({"status": "OK"}))
self.assertTrue(path.exists(self.annotations.output_file))
df = pd.read_csv(self.annotations.output_file, index_col=0, header=0, comment="#")
self.assertTrue(path.exists(self.annotations.label_output_file))
df = pd.read_csv(self.annotations.label_output_file, index_col=0, header=0, comment="#")
self.assertEqual(set(df.columns), {"cat_A", "cat_C"})
self.assertTrue(np.all(df["cat_A"] == ["label_A1"] * n_rows))
self.assertTrue(np.all(df["cat_C"] == ["label_C"] * n_rows))
# rotation
name, ext = path.splitext(self.annotations.output_file)
name, ext = path.splitext(self.annotations.label_output_file)
backup_dir = f"{name}-backups"
self.assertTrue(path.isdir(backup_dir))
found_files = listdir(backup_dir)
@@ -88,7 +88,7 @@ class WritableAnnotationTest(unittest.TestCase):
res = self.annotation_put_fbs(fbs)
self.assertEqual(res, json.dumps({"status": "OK"}))
name, ext = path.splitext(self.annotations.output_file)
name, ext = path.splitext(self.annotations.label_output_file)
backup_dir = f"{name}-backups"
self.assertTrue(path.isdir(backup_dir))
found_files = listdir(backup_dir)