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Code Issues Packages Projects Releases Wiki Activity

annotations CLI and file UX rework (#1049)

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* rename config param label-file

* annotations rework - CLI params, file naming and backups

* lint

* improve cli option error checks

* enable session cookies

* enable session cookies

* add session id

* name annotations file in multi-dataset and multi-user safe manner

* pass data user hash to front-end

* add annotation collection name support to front-end

* add constant for annotation data collection name

* parameterize annotation collection name; make it sticky in the session

* clarify comments

* hard wire a temporary data collection name for testing

* prettier

* test comment

* package command

* set annotations  filename dialog

* name  and hash are visible

* wire up data collection capture
This commit is contained in:
Bruce Martin
2019-11-25 15:28:28 -08:00
committed by GitHub
parent 575f71aaee
commit a593e95ab3
18 changed files with 551 additions and 130 deletions
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server/test/test_writable_annotation.py
+18 -12
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@@ -16,14 +16,16 @@ from server.app.util.data_locator import DataLocator
class WritableAnnotationTest(unittest.TestCase):
def setUp(self):
self.tmpDir = tempfile.mkdtemp()
self.label_file = path.join(self.tmpDir, "labels.csv")
self.annotations_file = path.join(self.tmpDir, "test_annotations.csv")
args = {
"layout": ["umap"],
"max_category_items": 100,
"obs_names": None,
"var_names": None,
"diffexp_lfc_cutoff": 0.01,
"label_file": self.label_file
"annotations": True,
"annotations_file": self.annotations_file,
"annotations_output_dir": None
}
self.data = ScanpyEngine(DataLocator("example-dataset/pbmc3k.h5ad"), args)
@@ -59,8 +61,8 @@ class WritableAnnotationTest(unittest.TestCase):
})
res = self.data.annotation_put_fbs("obs", fbs)
self.assertEqual(res, json.dumps({"status": "OK"}))
self.assertTrue(path.exists(self.label_file))
df = pd.read_csv(self.label_file, index_col=0, header=0, comment='#')
self.assertTrue(path.exists(self.annotations_file))
df = pd.read_csv(self.annotations_file, index_col=0, header=0, comment='#')
self.assertEqual(df.shape, (n_rows, 2))
self.assertEqual(set(df.columns), set(['cat_A', 'cat_B']))
self.assertTrue(self.data.original_obs_index.equals(df.index))
@@ -74,15 +76,18 @@ class WritableAnnotationTest(unittest.TestCase):
})
res = self.data.annotation_put_fbs("obs", fbs)
self.assertEqual(res, json.dumps({"status": "OK"}))
self.assertTrue(path.exists(self.label_file))
df = pd.read_csv(self.label_file, index_col=0, header=0, comment='#')
self.assertTrue(path.exists(self.annotations_file))
df = pd.read_csv(self.annotations_file, index_col=0, header=0, comment='#')
self.assertEqual(set(df.columns), set(['cat_A', 'cat_C']))
self.assertTrue(np.all(df['cat_A'] == ['label_A1' for l in range(0, n_rows)]))
self.assertTrue(np.all(df['cat_C'] == ['label_C' for l in range(0, n_rows)]))
# rotation
name, ext = path.splitext(self.label_file)
self.assertTrue(path.exists(f"{name}-1{ext}"))
name, ext = path.splitext(self.annotations_file)
backup_dir = f"{name}-backups"
self.assertTrue(path.isdir(backup_dir))
found_files = listdir(backup_dir)
self.assertEqual(len(found_files), 1)
def test_file_rotation_to_max_9(self):
# verify we stop rotation at 9
@@ -95,10 +100,11 @@ class WritableAnnotationTest(unittest.TestCase):
res = self.data.annotation_put_fbs("obs", fbs)
self.assertEqual(res, json.dumps({"status": "OK"}))
name, ext = path.splitext(self.label_file)
expected_files = [self.label_file] + [f"{name}-{i}{ext}" for i in range(1, 10)]
found_files = [path.join(self.tmpDir, p) for p in listdir(self.tmpDir)]
self.assertEqual(set(expected_files), set(found_files))
name, ext = path.splitext(self.annotations_file)
backup_dir = f"{name}-backups"
self.assertTrue(path.isdir(backup_dir))
found_files = listdir(backup_dir)
self.assertTrue(len(found_files) <= 9)
def test_put_get_roundtrip(self):
# verify that OBS PUTs (annotation_put_fbs) are accessible via