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Estelle/test meta analysis #365

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merged 4 commits into from
Dec 17, 2024
Merged

Estelle/test meta analysis #365

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1114b02
Add a meta-analysis test.
EstelleDa Nov 18, 2024
a5c4943
Add some meta-analysis tests.
EstelleDa Nov 21, 2024
c4dbfa2
Merge codes and solve conflicts.
EstelleDa Dec 4, 2024
039da08
Add some more checks in meta-analysis tests.
EstelleDa Dec 13, 2024
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113 changes: 113 additions & 0 deletions tests/routers/test_score_set.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1256,6 +1256,119 @@ def test_multiple_score_set_meta_analysis_multiple_experiment_sets_different_sco
assert meta_score_set_3["urn"] == "urn:mavedb:00000003-0-3"


def test_cannot_add_score_set_to_meta_analysis_experiment(session, data_provider, client, setup_router_db, data_files):
experiment = create_experiment(client)
score_set_1 = create_seq_score_set_with_variants(
client, session, data_provider, experiment["urn"], data_files / "scores.csv"
)

score_set_1 = (client.post(f"/api/v1/score-sets/{score_set_1['urn']}/publish")).json()
meta_score_set_1 = create_seq_score_set_with_variants(
client,
session,
data_provider,
None,
data_files / "scores.csv",
update={"title": "Test Meta Analysis", "metaAnalyzesScoreSetUrns": [score_set_1["urn"]]},
)

meta_score_set_1 = (client.post(f"/api/v1/score-sets/{meta_score_set_1['urn']}/publish")).json()
assert isinstance(MAVEDB_SCORE_SET_URN_RE.fullmatch(meta_score_set_1["urn"]), re.Match)
score_set_2 = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
score_set_2["experimentUrn"] = meta_score_set_1['experiment']['urn']
jsonschema.validate(instance=score_set_2, schema=ScoreSetCreate.schema())

response = client.post("/api/v1/score-sets/", json=score_set_2)
response_data = response.json()
assert response.status_code == 403
assert "Score sets may not be added to a meta-analysis experiment." in response_data["detail"]


def test_create_single_score_set_meta_analysis_to_others_score_set(session, data_provider, client, setup_router_db, data_files):
experiment = create_experiment(client)
score_set = create_seq_score_set_with_variants(
client, session, data_provider, experiment["urn"], data_files / "scores.csv"
)

score_set = (client.post(f"/api/v1/score-sets/{score_set['urn']}/publish")).json()
change_ownership(session, score_set["urn"], ScoreSetDbModel)
meta_score_set = create_seq_score_set_with_variants(
client,
session,
data_provider,
None,
data_files / "scores.csv",
update={"title": "Test Meta Analysis", "metaAnalyzesScoreSetUrns": [score_set["urn"]]},
)

score_set_refresh = (client.get(f"/api/v1/score-sets/{score_set['urn']}")).json()
assert meta_score_set["metaAnalyzesScoreSetUrns"] == [score_set["urn"]]
assert score_set_refresh["metaAnalyzedByScoreSetUrns"] == [meta_score_set["urn"]]
assert isinstance(MAVEDB_TMP_URN_RE.fullmatch(meta_score_set["urn"]), re.Match)


def test_multiple_score_set_meta_analysis_single_experiment_with_different_creator(
session, data_provider, client, setup_router_db, data_files
):
experiment = create_experiment(client)
score_set_1 = create_seq_score_set_with_variants(
client, session, data_provider, experiment["urn"], data_files / "scores.csv", update={"title": "Score Set 1"}
)
score_set_2 = create_seq_score_set_with_variants(
client, session, data_provider, experiment["urn"], data_files / "scores.csv", update={"title": "Score Set 2"}
)

score_set_1 = (client.post(f"/api/v1/score-sets/{score_set_1['urn']}/publish")).json()
score_set_2 = (client.post(f"/api/v1/score-sets/{score_set_2['urn']}/publish")).json()

change_ownership(session, score_set_2["urn"], ScoreSetDbModel)
meta_score_set = create_seq_score_set_with_variants(
client,
session,
data_provider,
None,
data_files / "scores.csv",
update={"title": "Test Meta Analysis", "metaAnalyzesScoreSetUrns": [score_set_1["urn"], score_set_2["urn"]]},
)
score_set_1_refresh = (client.get(f"/api/v1/score-sets/{score_set_1['urn']}")).json()
assert meta_score_set["metaAnalyzesScoreSetUrns"] == sorted([score_set_1["urn"], score_set_2["urn"]])
assert score_set_1_refresh["metaAnalyzedByScoreSetUrns"] == [meta_score_set["urn"]]

meta_score_set = (client.post(f"/api/v1/score-sets/{meta_score_set['urn']}/publish")).json()
assert meta_score_set["urn"] == "urn:mavedb:00000001-0-1"
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In so far as we check the URNs of test objects, I think we only need to check that the URN matches the URN RegEx.

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I added the RegEx checks to all meta-analysis tests, but I support keeping them cause the meta-analysis urn is more special. This way is more accurate. RegEx only confirms they match the basic rules, but can't make sure the middle one is number 0 or letters.



def test_multiple_score_set_meta_analysis_multiple_experiment_sets_with_different_creator(
session, data_provider, client, setup_router_db, data_files
):
experiment_1 = create_experiment(client, {"title": "Experiment 1"})
experiment_2 = create_experiment(client, {"title": "Experiment 2"})
score_set_1 = create_seq_score_set_with_variants(
client, session, data_provider, experiment_1["urn"], data_files / "scores.csv", update={"title": "Score Set 1"}
)
score_set_2 = create_seq_score_set_with_variants(
client, session, data_provider, experiment_2["urn"], data_files / "scores.csv", update={"title": "Score Set 2"}
)

score_set_1 = (client.post(f"/api/v1/score-sets/{score_set_1['urn']}/publish")).json()
score_set_2 = (client.post(f"/api/v1/score-sets/{score_set_2['urn']}/publish")).json()

change_ownership(session, score_set_2["urn"], ScoreSetDbModel)
meta_score_set = create_seq_score_set_with_variants(
client,
session,
data_provider,
None,
data_files / "scores.csv",
update={"title": "Test Meta Analysis", "metaAnalyzesScoreSetUrns": [score_set_1["urn"], score_set_2["urn"]]},
)
score_set_1_refresh = (client.get(f"/api/v1/score-sets/{score_set_1['urn']}")).json()
assert meta_score_set["metaAnalyzesScoreSetUrns"] == sorted([score_set_1["urn"], score_set_2["urn"]])
assert score_set_1_refresh["metaAnalyzedByScoreSetUrns"] == [meta_score_set["urn"]]

meta_score_set = (client.post(f"/api/v1/score-sets/{meta_score_set['urn']}/publish")).json()
assert meta_score_set["urn"] == "urn:mavedb:00000003-0-1"
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Same RegEx comment as above.


########################################################################################################################
# Score set search
########################################################################################################################
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