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refactor config to support different config options for datasets in different dataroots. (#1596)

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This will give us the ability to specify different config options for
different dataroots.

the key of the dataroot dictionary is no longer the same as the dataroot_url.
Previously key==dataroot_url, and now those are separated.

Added an "is_multi_dataset" function to simplify logic where it branched on single vs multi.

Simplified the rest.py interface by no longer passing in the user annotations object, since
that can be retrieved from the dataset.
This commit is contained in:
bmccandless
2020-07-10 16:21:40 -07:00
committed by GitHub
parent 13246cb6d1
commit f69d141336
21 changed files with 1021 additions and 710 deletions
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server/test/test_app_config.py
+50 -20
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@@ -11,60 +11,90 @@ import requests
class AppConfigTest(unittest.TestCase):
def test_update(self):
c = AppConfig()
c.update(server__verbose=True, multi_dataset__dataroot="datadir")
v = c.changes_from_default()
self.assertCountEqual(v, [("server__verbose", True, False), ("multi_dataset__dataroot", "datadir", None)])
c.update_server_config(app__verbose=True, multi_dataset__dataroot="datadir")
v = c.server_config.changes_from_default()
self.assertCountEqual(v, [("app__verbose", True, False), ("multi_dataset__dataroot", "datadir", None)])
c = AppConfig()
c.update(server__scripts=(), server__inline_scripts=())
v = c.changes_from_default()
c.update_default_dataset_config(app__scripts=(), app__inline_scripts=())
v = c.server_config.changes_from_default()
self.assertCountEqual(v, [])
c = AppConfig()
c.update(server__scripts=[], server__inline_scripts=[])
v = c.changes_from_default()
c.update_default_dataset_config(app__scripts=[], app__inline_scripts=[])
v = c.default_dataset_config.changes_from_default()
self.assertCountEqual(v, [])
c = AppConfig()
c.update(server__scripts=("a", "b"), server__inline_scripts=["c", "d"])
v = c.changes_from_default()
self.assertCountEqual(v, [("server__scripts", ["a", "b"], []), ("server__inline_scripts", ["c", "d"], [])])
c.update_default_dataset_config(app__scripts=("a", "b"), app__inline_scripts=["c", "d"])
v = c.default_dataset_config.changes_from_default()
self.assertCountEqual(v, [("app__scripts", ["a", "b"], []), ("app__inline_scripts", ["c", "d"], [])])
def test_multi_dataset(self):
c = AppConfig()
# test for illegal url_dataroots
for illegal in ("a/b", "../b", "!$*", "\\n", "", "(bad)"):
c.update(multi_dataset__dataroot={illegal: f"{PROJECT_ROOT}/example-dataset"})
for illegal in ("../b", "!$*", "\\n", "", "(bad)"):
c.update_server_config(
multi_dataset__dataroot={"tag": {"base_url": illegal, "dataroot": "{PROJECT_ROOT}/example-dataset"}}
)
with self.assertRaises(ConfigurationError):
c.complete_config()
# test for legal url_dataroots
for legal in (
"d",
"this.is-okay_",
):
c.update(multi_dataset__dataroot={legal: f"{PROJECT_ROOT}/example-dataset"})
for legal in ("d", "this.is-okay_", "a/b"):
c.update_server_config(
multi_dataset__dataroot={"tag": {"base_url": legal, "dataroot": "{PROJECT_ROOT}/example-dataset"}}
)
c.complete_config()
# test that multi dataroots work end to end
c.update(
c.update_server_config(
multi_dataset__dataroot=dict(
set1=f"{PROJECT_ROOT}/example-dataset", set2=f"{PROJECT_ROOT}/server/test/test_datasets"
s1=dict(dataroot=f"{PROJECT_ROOT}/example-dataset", base_url="set1/1/2"),
s2=dict(dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", base_url="set2"),
s3=dict(dataroot=f"{PROJECT_ROOT}/server/test/test_datasets", base_url="set3"),
)
)
# Change this default to test if the dataroot overrides below work.
c.update_default_dataset_config(app__about_legal_tos="tos_default.html")
# specialize the configs for set1
c.add_dataroot_config(
"s1", user_annotations__enable=False, diffexp__enable=True, app__about_legal_tos="tos_set1.html"
)
# specialize the configs for set2
c.add_dataroot_config(
"s2", user_annotations__enable=True, diffexp__enable=False, app__about_legal_tos="tos_set2.html"
)
# no specializations for set3 (they get the default dataset config)
c.complete_config()
with test_server(app_config=c) as server:
session = requests.Session()
r = session.get(f"{server}/set1/pbmc3k.h5ad/api/v0.2/config")
r = session.get(f"{server}/set1/1/2/pbmc3k.h5ad/api/v0.2/config")
data_config = r.json()
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
assert data_config["config"]["parameters"]["annotations"] is False
assert data_config["config"]["parameters"]["disable-diffexp"] is False
assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set1.html"
r = session.get(f"{server}/set2/pbmc3k.cxg/api/v0.2/config")
data_config = r.json()
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
assert data_config["config"]["parameters"]["annotations"] is True
assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_set2.html"
r = session.get(f"{server}/set3/pbmc3k.cxg/api/v0.2/config")
data_config = r.json()
assert data_config["config"]["displayNames"]["dataset"] == "pbmc3k"
assert data_config["config"]["parameters"]["annotations"] is True
assert data_config["config"]["parameters"]["disable-diffexp"] is False
assert data_config["config"]["parameters"]["about_legal_tos"] == "tos_default.html"
r = session.get(f"{server}/health")
assert r.json()["status"] == "pass"