def test_by_kfids_simple(dataservice_setup):
n = 2
populate_data(n)
desc = find_descendants_by_kfids(
DATASERVICE_URL,
"participants", ["PT_11111111"],
ignore_gfs_with_hidden_external_contribs=False,
kfids_only=False)
assert len(desc["participants"]) == 1
assert len(desc["biospecimens"]) == n
# parent level should be populated
assert isinstance(desc["participants"]["PT_11111111"], dict)
desc = find_descendants_by_kfids(
DATASERVICE_URL,
"participants", ["PT_10111111", "PT_11111111"],
ignore_gfs_with_hidden_external_contribs=False,
kfids_only=False)
assert len(desc["participants"]) == n
assert len(desc["biospecimens"]) == n * n
desc = find_descendants_by_kfids(
DATASERVICE_URL,
"studies", ["SD_11111111"],
ignore_gfs_with_hidden_external_contribs=False,
kfids_only=False)
assert len(desc["participants"]) == n
assert len(desc["biospecimens"]) == n * n
def test_yield_entities_from_filter(dataservice_setup):
n = 2
populate_data(n)
si = 1
filter = {"study_id": f"SD_{si}1111111"}
# Get all participants from one study
endpoint = "participants"
for ps in [
list(yield_entities_from_filter(DATASERVICE_URL, endpoint,
filter)),
list(yield_entities(DATASERVICE_URL, endpoint, filter)),
]:
assert len(ps) == n
for p in ps:
assert p["kf_id"].startswith(f"PT_{si}")
# Get all biospecimens from one study
endpoint = "biospecimens"
for bs in [
list(yield_entities_from_filter(DATASERVICE_URL, endpoint,
filter)),
list(yield_entities(DATASERVICE_URL, endpoint, filter)),
]:
assert len(bs) == (n * n)
for b in bs:
assert b["kf_id"].startswith(f"BS_{si}")
def test_yield_entities_from_kfids(dataservice_setup):
n = 2
populate_data(n)
kfid_set = {"SD_11111111", "PT_11111111", "BS_11111111"}
for es in [
list(yield_entities_from_kfids(DATASERVICE_URL, kfid_set)),
list(yield_entities(DATASERVICE_URL, None, kfid_set)),
]:
assert len(es) == len(kfid_set)
found_kfids = {e["kf_id"] for e in es}
assert kfid_set == found_kfids
def test_hide_unhide_entities(dataservice_setup):
n = 2
kfids = populate_data(n)
to_hide = {"PT_00111111", "BS_11111111"}
hide_kfids(DATASERVICE_URL, to_hide)
entities = list(yield_entities_from_kfids(DATASERVICE_URL, kfids))
hidden = [e for e in entities if e["kf_id"] in to_hide]
assert not hide_entities(DATASERVICE_URL, hidden)
entities = list(yield_entities_from_kfids(DATASERVICE_URL, kfids))
hidden = [e for e in entities if e["kf_id"] in to_hide]
for e in entities:
assert e["visible"] ^ (e["kf_id"] in to_hide)
assert unhide_entities(DATASERVICE_URL, hidden)
entities = list(yield_entities_from_kfids(DATASERVICE_URL, kfids))
hidden = [e for e in entities if e["kf_id"] in to_hide]
for e in entities:
assert e["visible"]
assert not unhide_entities(DATASERVICE_URL, hidden)
entities = list(yield_entities_from_kfids(DATASERVICE_URL, kfids))
hidden = [e for e in entities if e["kf_id"] in to_hide]
for e in entities:
assert e["visible"]
def test_hide_unhide_kfids(dataservice_setup):
n = 2
kfids = populate_data(n)
to_hide = {"PT_00111111", "BS_11111111"}
hide_kfids(DATASERVICE_URL, to_hide)
for e in yield_entities_from_kfids(DATASERVICE_URL, kfids):
assert e["visible"] ^ (e["kf_id"] in to_hide)
unhide_kfids(DATASERVICE_URL, to_hide)
for e in yield_entities_from_kfids(DATASERVICE_URL, kfids):
assert e["visible"]
def test_already_done(dataservice_setup):
n = 2
all_kfids = populate_data(n)
sdids = ["SD_11111111"]
changed = unhide_descendants_by_kfids(DATASERVICE_URL, "studies", sdids)
assert not changed
changed = hide_descendants_by_kfids(DATASERVICE_URL, "studies", sdids)
assert len(changed) == 1 + n + n * n
changed = unhide_descendants_by_kfids(DATASERVICE_URL, "studies", sdids)
assert len(changed) == 1 + n + n * n
def test_delete_many(dataservice_setup):
# iterating the wrong way clogs an executor
# see https://github.com/kids-first/kf-utils-python/pull/36#pullrequestreview-685334120
populate_data(1, 500, 0)
delete_entities(DATASERVICE_URL)