test_score_set.py

# ruff: noqa: E402

import csv
import json
import re
from copy import deepcopy
from datetime import date
from io import StringIO
from unittest.mock import patch

import jsonschema
import pytest
from humps import camelize
from sqlalchemy import select

arq = pytest.importorskip("arq")
cdot = pytest.importorskip("cdot")
fastapi = pytest.importorskip("fastapi")

from mavedb.lib.exceptions import NonexistentOrcidUserError
from mavedb.lib.validation.urn_re import MAVEDB_EXPERIMENT_URN_RE, MAVEDB_SCORE_SET_URN_RE, MAVEDB_TMP_URN_RE
from mavedb.models.enums.processing_state import ProcessingState
from mavedb.models.enums.target_category import TargetCategory
from mavedb.models.experiment import Experiment as ExperimentDbModel
from mavedb.models.score_set import ScoreSet as ScoreSetDbModel
from mavedb.models.variant import Variant as VariantDbModel
from mavedb.view_models.orcid import OrcidUser
from mavedb.view_models.score_set import ScoreSet, ScoreSetCreate
from tests.helpers.constants import (
    EXTRA_LICENSE,
    EXTRA_USER,
    SAVED_DOI_IDENTIFIER,
    SAVED_EXTRA_CONTRIBUTOR,
    SAVED_MINIMAL_DATASET_COLUMNS,
    SAVED_PUBMED_PUBLICATION,
    SAVED_SHORT_EXTRA_LICENSE,
    TEST_BIORXIV_IDENTIFIER,
    TEST_BRNICH_SCORE_CALIBRATION_CLASS_BASED,
    TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED,
    TEST_CROSSREF_IDENTIFIER,
    TEST_EXPERIMENT_WITH_KEYWORD,
    TEST_GNOMAD_DATA_VERSION,
    TEST_INACTIVE_LICENSE,
    TEST_MAPPED_VARIANT_WITH_HGVS_G_EXPRESSION,
    TEST_MAPPED_VARIANT_WITH_HGVS_P_EXPRESSION,
    TEST_MINIMAL_ACC_SCORESET,
    TEST_MINIMAL_ACC_SCORESET_RESPONSE,
    TEST_MINIMAL_SEQ_SCORESET,
    TEST_MINIMAL_SEQ_SCORESET_RESPONSE,
    TEST_ORCID_ID,
    TEST_PATHOGENICITY_SCORE_CALIBRATION,
    TEST_PUBMED_IDENTIFIER,
    TEST_SAVED_BRNICH_SCORE_CALIBRATION_RANGE_BASED,
    TEST_SAVED_CLINVAR_CONTROL,
    TEST_SAVED_GENERIC_CLINICAL_CONTROL,
    TEST_SAVED_GNOMAD_VARIANT,
    TEST_SAVED_TAXONOMY,
    TEST_USER,
    VALID_CLINGEN_CA_ID,
)
from tests.helpers.dependency_overrider import DependencyOverrider
from tests.helpers.util.common import (
    deepcamelize,
    parse_ndjson_response,
    update_expected_response_for_created_resources,
)
from tests.helpers.util.contributor import add_contributor
from tests.helpers.util.experiment import create_experiment
from tests.helpers.util.license import change_to_inactive_license
from tests.helpers.util.score_calibration import (
    create_publish_and_promote_score_calibration,
    create_test_score_calibration_in_score_set_via_client,
)
from tests.helpers.util.score_set import (
    create_seq_score_set,
    create_seq_score_set_with_mapped_variants,
    create_seq_score_set_with_variants,
    link_clinical_controls_to_mapped_variants,
    link_gnomad_variants_to_mapped_variants,
    publish_score_set,
)
from tests.helpers.util.user import change_ownership
from tests.helpers.util.variant import (
    clear_first_mapped_variant_post_mapped,
    create_mapped_variants_for_score_set,
    mock_worker_variant_insertion,
)

########################################################################################################################
# Score set schemas
########################################################################################################################


def test_TEST_MINIMAL_SEQ_SCORESET_is_valid():
    jsonschema.validate(instance=TEST_MINIMAL_SEQ_SCORESET, schema=ScoreSetCreate.model_json_schema())


def test_TEST_MINIMAL_ACC_SCORESET_is_valid():
    jsonschema.validate(instance=TEST_MINIMAL_ACC_SCORESET, schema=ScoreSetCreate.model_json_schema())


########################################################################################################################
# Score set creation
########################################################################################################################


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        (
            [
                {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
                {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
            ]
        )
    ],
    indirect=["mock_publication_fetch"],
)
def test_create_minimal_score_set(client, mock_publication_fetch, setup_router_db):
    experiment = create_experiment(client)
    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_post_payload["experimentUrn"] = experiment["urn"]

    response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
    assert response.status_code == 200
    response_data = response.json()

    jsonschema.validate(instance=response_data, schema=ScoreSet.model_json_schema())
    assert isinstance(MAVEDB_TMP_URN_RE.fullmatch(response_data["urn"]), re.Match)

    expected_response = update_expected_response_for_created_resources(
        deepcopy(TEST_MINIMAL_SEQ_SCORESET_RESPONSE), experiment, response_data
    )
    expected_response["experiment"].update({"numScoreSets": 1})

    assert sorted(expected_response.keys()) == sorted(response_data.keys())
    for key in expected_response:
        assert (key, expected_response[key]) == (key, response_data[key])

    response = client.get(f"/api/v1/score-sets/{response_data['urn']}")
    assert response.status_code == 200


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        (
            [
                {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
                {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
            ]
        )
    ],
    indirect=["mock_publication_fetch"],
)
def test_create_score_set_with_contributor(client, mock_publication_fetch, setup_router_db):
    experiment = create_experiment(client)
    score_set = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set["experimentUrn"] = experiment["urn"]
    score_set.update({"contributors": [{"orcid_id": TEST_ORCID_ID}]})

    with patch(
        "mavedb.lib.orcid.fetch_orcid_user",
        lambda orcid_id: OrcidUser(orcid_id=orcid_id, given_name="ORCID", family_name="User"),
    ):
        response = client.post("/api/v1/score-sets/", json=score_set)

    assert response.status_code == 200
    response_data = response.json()

    jsonschema.validate(instance=response_data, schema=ScoreSet.model_json_schema())
    assert isinstance(MAVEDB_TMP_URN_RE.fullmatch(response_data["urn"]), re.Match)

    expected_response = update_expected_response_for_created_resources(
        deepcopy(TEST_MINIMAL_SEQ_SCORESET_RESPONSE), experiment, response_data
    )
    expected_response["contributors"] = [
        {
            "recordType": "Contributor",
            "orcidId": TEST_ORCID_ID,
            "givenName": "ORCID",
            "familyName": "User",
        }
    ]
    expected_response["experiment"].update({"numScoreSets": 1})

    assert sorted(expected_response.keys()) == sorted(response_data.keys())
    for key in expected_response:
        assert (key, expected_response[key]) == (key, response_data[key])

    response = client.get(f"/api/v1/score-sets/{response_data['urn']}")
    assert response.status_code == 200


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        [
            {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
            {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
        ]
    ],
    indirect=["mock_publication_fetch"],
)
def test_create_score_set_with_score_calibration(client, mock_publication_fetch, setup_router_db):
    experiment = create_experiment(client)
    score_set = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set["experimentUrn"] = experiment["urn"]
    score_set.update(
        {
            "scoreCalibrations": [deepcamelize(TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED)],
        }
    )

    response = client.post("/api/v1/score-sets/", json=score_set)
    assert response.status_code == 200
    response_data = response.json()

    jsonschema.validate(instance=response_data, schema=ScoreSet.model_json_schema())
    assert isinstance(MAVEDB_TMP_URN_RE.fullmatch(response_data["urn"]), re.Match)

    expected_response = update_expected_response_for_created_resources(
        deepcopy(TEST_MINIMAL_SEQ_SCORESET_RESPONSE), experiment, response_data
    )
    expected_response["experiment"].update({"numScoreSets": 1})
    expected_calibration = deepcopy(TEST_SAVED_BRNICH_SCORE_CALIBRATION_RANGE_BASED)
    expected_calibration["urn"] = response_data["scoreCalibrations"][0]["urn"]
    expected_calibration["private"] = True
    expected_calibration["primary"] = False
    expected_calibration["investigatorProvided"] = True
    # Match functional classifications by a stable identifier (label).
    response_fcs_by_label = {
        fc["label"]: fc for fc in response_data["scoreCalibrations"][0]["functionalClassifications"]
    }
    for expected_fc in expected_calibration["functionalClassifications"]:
        label = expected_fc["label"]
        if label in response_fcs_by_label:
            expected_fc["id"] = response_fcs_by_label[label]["id"]

    expected_response["scoreCalibrations"] = [expected_calibration]

    assert sorted(expected_response.keys()) == sorted(response_data.keys())
    for key in expected_response:
        assert (key, expected_response[key]) == (key, response_data[key])

    response = client.get(f"/api/v1/score-sets/{response_data['urn']}")
    assert response.status_code == 200


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        (
            [
                {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
                {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
            ]
        )
    ],
    indirect=["mock_publication_fetch"],
)
def test_cannot_create_score_set_with_class_based_calibration(client, mock_publication_fetch, setup_router_db):
    experiment = create_experiment(client)
    score_set = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set["experimentUrn"] = experiment["urn"]
    score_set.update(
        {
            "scoreCalibrations": [deepcamelize(TEST_BRNICH_SCORE_CALIBRATION_CLASS_BASED)],
        }
    )

    response = client.post("/api/v1/score-sets/", json=score_set)
    assert response.status_code == 409
    response_data = response.json()
    assert "Class-based calibrations are not supported on score set creation" in response_data["detail"]


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        (
            [
                {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
                {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
            ]
        )
    ],
    indirect=["mock_publication_fetch"],
)
def test_cannot_create_score_set_with_nonexistent_contributor(client, mock_publication_fetch, setup_router_db):
    experiment = create_experiment(client)
    score_set = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set["experimentUrn"] = experiment["urn"]
    score_set.update({"contributors": [{"orcid_id": TEST_ORCID_ID}]})

    with patch(
        "mavedb.lib.orcid.fetch_orcid_user",
        side_effect=NonexistentOrcidUserError(f"No ORCID user was found for ORCID ID {TEST_ORCID_ID}."),
    ):
        response = client.post("/api/v1/score-sets/", json=score_set)

    assert response.status_code == 404
    response_data = response.json()
    assert "No ORCID user was found for ORCID ID 1111-1111-1111-1111." in response_data["detail"]


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        (
            [
                {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
                {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
            ]
        )
    ],
    indirect=["mock_publication_fetch"],
)
def test_cannot_create_score_set_without_email(client, mock_publication_fetch, setup_router_db):
    experiment = create_experiment(client)
    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_post_payload["experimentUrn"] = experiment["urn"]
    client.put("api/v1/users/me", json={"email": None})
    response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
    assert response.status_code == 403
    response_data = response.json()
    assert response_data["detail"] in "There must be an email address associated with your account to use this feature."


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        (
            [
                {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
                {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
            ]
        )
    ],
    indirect=["mock_publication_fetch"],
)
def test_cannot_create_score_set_with_invalid_target_gene_category(client, mock_publication_fetch, setup_router_db):
    experiment = create_experiment(client)
    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_post_payload["experimentUrn"] = experiment["urn"]
    score_set_post_payload["targetGenes"][0]["category"] = "some_invalid_target_category"
    response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
    assert response.status_code == 422
    response_data = response.json()
    assert "Input should be" in response_data["detail"][0]["msg"]
    assert all(field in response_data["detail"][0]["msg"] for field in TargetCategory._member_names_)


########################################################################################################################
# Score set updating
########################################################################################################################


@pytest.mark.parametrize(
    "attribute,updated_data,expected_response_data",
    [
        ("title", "Updated Title", "Updated Title"),
        ("method_text", "Updated Method Text", "Updated Method Text"),
        ("abstract_text", "Updated Abstract Text", "Updated Abstract Text"),
        ("short_description", "Updated Abstract Text", "Updated Abstract Text"),
        ("extra_metadata", {"updated": "metadata"}, {"updated": "metadata"}),
        ("data_usage_policy", "data_usage_policy", "data_usage_policy"),
        ("contributors", [{"orcid_id": EXTRA_USER["username"]}], [SAVED_EXTRA_CONTRIBUTOR]),
        ("primary_publication_identifiers", [{"identifier": TEST_PUBMED_IDENTIFIER}], [SAVED_PUBMED_PUBLICATION]),
        ("secondary_publication_identifiers", [{"identifier": TEST_PUBMED_IDENTIFIER}], [SAVED_PUBMED_PUBLICATION]),
        ("doi_identifiers", [{"identifier": TEST_CROSSREF_IDENTIFIER}], [SAVED_DOI_IDENTIFIER]),
        ("license_id", EXTRA_LICENSE["id"], SAVED_SHORT_EXTRA_LICENSE),
        ("target_genes", TEST_MINIMAL_ACC_SCORESET["targetGenes"], TEST_MINIMAL_ACC_SCORESET_RESPONSE["targetGenes"]),
    ],
)
@pytest.mark.parametrize(
    "mock_publication_fetch",
    [({"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"})],
    indirect=["mock_publication_fetch"],
)
def test_can_update_score_set_data_before_publication(
    client, setup_router_db, attribute, updated_data, expected_response_data, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    expected_response = update_expected_response_for_created_resources(
        deepcopy(TEST_MINIMAL_SEQ_SCORESET_RESPONSE), experiment, score_set
    )
    expected_response["experiment"].update({"numScoreSets": 1})

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}")
    assert response.status_code == 200
    response_data = response.json()

    assert sorted(expected_response.keys()) == sorted(response_data.keys())
    for key in expected_response:
        assert (key, expected_response[key]) == (key, response_data[key])

    score_set_update_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_update_payload.update({camelize(attribute): updated_data})

    response = client.put(f"/api/v1/score-sets/{score_set['urn']}", json=score_set_update_payload)
    assert response.status_code == 200

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}")
    assert response.status_code == 200
    response_data = response.json()

    # Although the client provides the license id, the response includes the full license.
    if attribute == "license_id":
        attribute = "license"

    assert expected_response_data == response_data[camelize(attribute)]


@pytest.mark.parametrize(
    "attribute,updated_data,expected_response_data",
    [
        ("title", "Updated Title", "Updated Title"),
        ("method_text", "Updated Method Text", "Updated Method Text"),
        ("abstract_text", "Updated Abstract Text", "Updated Abstract Text"),
        ("short_description", "Updated Abstract Text", "Updated Abstract Text"),
        ("extra_metadata", {"updated": "metadata"}, {"updated": "metadata"}),
        ("data_usage_policy", "data_usage_policy", "data_usage_policy"),
        ("contributors", [{"orcid_id": EXTRA_USER["username"]}], [SAVED_EXTRA_CONTRIBUTOR]),
        ("primary_publication_identifiers", [{"identifier": TEST_PUBMED_IDENTIFIER}], [SAVED_PUBMED_PUBLICATION]),
        ("secondary_publication_identifiers", [{"identifier": TEST_PUBMED_IDENTIFIER}], [SAVED_PUBMED_PUBLICATION]),
        ("doi_identifiers", [{"identifier": TEST_CROSSREF_IDENTIFIER}], [SAVED_DOI_IDENTIFIER]),
        ("license_id", EXTRA_LICENSE["id"], SAVED_SHORT_EXTRA_LICENSE),
        ("target_genes", TEST_MINIMAL_ACC_SCORESET["targetGenes"], TEST_MINIMAL_ACC_SCORESET_RESPONSE["targetGenes"]),
    ],
)
@pytest.mark.parametrize(
    "mock_publication_fetch",
    [({"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"})],
    indirect=["mock_publication_fetch"],
)
def test_can_patch_score_set_data_before_publication(
    client, setup_router_db, attribute, updated_data, expected_response_data, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    expected_response = update_expected_response_for_created_resources(
        deepcopy(TEST_MINIMAL_SEQ_SCORESET_RESPONSE), experiment, score_set
    )
    expected_response["experiment"].update({"numScoreSets": 1})

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}")
    assert response.status_code == 200
    response_data = response.json()

    assert sorted(expected_response.keys()) == sorted(response_data.keys())
    for key in expected_response:
        assert (key, expected_response[key]) == (key, response_data[key])

    data = {}
    if isinstance(updated_data, (dict, list)):
        form_value = json.dumps(updated_data)
    else:
        form_value = str(updated_data)
    data[attribute] = form_value

    response = client.patch(f"/api/v1/score-sets-with-variants/{score_set['urn']}", data=data)
    assert response.status_code == 200

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}")
    assert response.status_code == 200
    response_data = response.json()

    # Although the client provides the license id, the response includes the full license.
    if attribute == "license_id":
        attribute = "license"

    assert expected_response_data == response_data[camelize(attribute)]


@pytest.mark.parametrize(
    "form_field,filename,mime_type",
    [
        ("scores_file", "scores.csv", "text/csv"),
        ("counts_file", "counts.csv", "text/csv"),
        ("score_columns_metadata_file", "score_columns_metadata.json", "application/json"),
        ("count_columns_metadata_file", "count_columns_metadata.json", "application/json"),
    ],
)
@pytest.mark.parametrize(
    "mock_publication_fetch",
    [({"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"})],
    indirect=["mock_publication_fetch"],
)
def test_can_patch_score_set_data_with_files_before_publication(
    client, setup_router_db, form_field, filename, mime_type, data_files, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    expected_response = update_expected_response_for_created_resources(
        deepcopy(TEST_MINIMAL_SEQ_SCORESET_RESPONSE), experiment, score_set
    )
    expected_response["experiment"].update({"numScoreSets": 1})

    if form_field == "counts_file" or form_field == "scores_file":
        data_file_path = data_files / filename
        files = {form_field: (filename, open(data_file_path, "rb"), mime_type)}
        with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
            response = client.patch(f"/api/v1/score-sets-with-variants/{score_set['urn']}", files=files)
            worker_queue.assert_called_once()
            assert response.status_code == 200
    elif form_field == "score_columns_metadata_file" or form_field == "count_columns_metadata_file":
        data_file_path = data_files / filename
        with open(data_file_path, "rb") as f:
            data = json.load(f)
            response = client.patch(f"/api/v1/score-sets-with-variants/{score_set['urn']}", data=data)
            assert response.status_code == 200


@pytest.mark.parametrize(
    "attribute,updated_data,expected_response_data",
    [
        ("title", "Updated Title", "Updated Title"),
        ("method_text", "Updated Method Text", "Updated Method Text"),
        ("abstract_text", "Updated Abstract Text", "Updated Abstract Text"),
        ("short_description", "Updated Abstract Text", "Updated Abstract Text"),
        ("extra_metadata", {"updated": "metadata"}, {"updated": "metadata"}),
        ("data_usage_policy", "data_usage_policy", "data_usage_policy"),
        ("contributors", [{"orcid_id": EXTRA_USER["username"]}], [SAVED_EXTRA_CONTRIBUTOR]),
        ("primary_publication_identifiers", [{"identifier": TEST_PUBMED_IDENTIFIER}], [SAVED_PUBMED_PUBLICATION]),
        ("secondary_publication_identifiers", [{"identifier": TEST_PUBMED_IDENTIFIER}], [SAVED_PUBMED_PUBLICATION]),
        ("doi_identifiers", [{"identifier": TEST_CROSSREF_IDENTIFIER}], [SAVED_DOI_IDENTIFIER]),
        ("license_id", EXTRA_LICENSE["id"], SAVED_SHORT_EXTRA_LICENSE),
        ("dataset_columns", None, SAVED_MINIMAL_DATASET_COLUMNS),
    ],
)
@pytest.mark.parametrize(
    "mock_publication_fetch",
    [({"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"})],
    indirect=["mock_publication_fetch"],
)
def test_can_update_score_set_supporting_data_after_publication(
    session,
    data_provider,
    client,
    setup_router_db,
    attribute,
    updated_data,
    expected_response_data,
    mock_publication_fetch,
    data_files,
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    published_urn = published_score_set["urn"]
    response = client.get(f"/api/v1/score-sets/{published_urn}")
    assert response.status_code == 200
    response_data = response.json()

    expected_response = update_expected_response_for_created_resources(
        deepcopy(TEST_MINIMAL_SEQ_SCORESET_RESPONSE), response_data["experiment"], response_data
    )
    expected_response["experiment"].update({"publishedDate": date.today().isoformat()})
    expected_response.update(
        {
            "urn": published_urn,
            "publishedDate": date.today().isoformat(),
            "numVariants": 3,
            "private": False,
            "datasetColumns": SAVED_MINIMAL_DATASET_COLUMNS,
            "processingState": ProcessingState.success.name,
        }
    )
    expected_response["experiment"].update({"numScoreSets": 1})

    assert sorted(expected_response.keys()) == sorted(response_data.keys())
    for key in expected_response:
        assert (key, expected_response[key]) == (key, response_data[key])

    score_set_update_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_update_payload.update({camelize(attribute): updated_data})
    response = client.put(f"/api/v1/score-sets/{published_urn}", json=score_set_update_payload)
    assert response.status_code == 200

    response = client.get(f"/api/v1/score-sets/{published_urn}")
    assert response.status_code == 200
    response_data = response.json()

    # Although the client provides the license id, the response includes the full license.
    if attribute == "license_id":
        attribute = "license"

    assert expected_response_data == response_data[camelize(attribute)]


@pytest.mark.parametrize(
    "attribute,updated_data,expected_response_data",
    [
        ("target_genes", TEST_MINIMAL_ACC_SCORESET["targetGenes"], TEST_MINIMAL_SEQ_SCORESET_RESPONSE["targetGenes"]),
        ("dataset_columns", {"countColumns": [], "scoreColumns": ["score"]}, SAVED_MINIMAL_DATASET_COLUMNS),
    ],
)
@pytest.mark.parametrize(
    "mock_publication_fetch",
    [({"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"})],
    indirect=["mock_publication_fetch"],
)
def test_cannot_update_score_set_target_data_after_publication(
    client,
    setup_router_db,
    attribute,
    expected_response_data,
    updated_data,
    session,
    data_provider,
    data_files,
    mock_publication_fetch,
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    published_urn = published_score_set["urn"]
    response = client.get(f"/api/v1/score-sets/{published_urn}")
    assert response.status_code == 200
    response_data = response.json()

    expected_response = update_expected_response_for_created_resources(
        deepcopy(TEST_MINIMAL_SEQ_SCORESET_RESPONSE), response_data["experiment"], response_data
    )
    expected_response["experiment"].update({"publishedDate": date.today().isoformat()})
    expected_response.update(
        {
            "urn": published_urn,
            "publishedDate": date.today().isoformat(),
            "numVariants": 3,
            "private": False,
            "datasetColumns": SAVED_MINIMAL_DATASET_COLUMNS,
            "processingState": ProcessingState.success.name,
        }
    )
    expected_response["experiment"].update({"numScoreSets": 1})

    assert sorted(expected_response.keys()) == sorted(response_data.keys())
    for key in expected_response:
        assert (key, expected_response[key]) == (key, response_data[key])

    score_set_update_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_update_payload.update(
        {
            camelize(attribute): updated_data,
        }
    )
    response = client.put(f"/api/v1/score-sets/{published_urn}", json=score_set_update_payload)
    assert response.status_code == 200

    response = client.get(f"/api/v1/score-sets/{published_urn}")
    assert response.status_code == 200
    response_data = response.json()

    if expected_response_data:
        assert expected_response_data == response_data[camelize(attribute)]
    else:
        assert camelize(attribute) not in response_data.keys()


def test_cannot_update_score_set_with_nonexistent_contributor(
    client,
    setup_router_db,
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])

    score_set_update_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_update_payload.update({"contributors": [{"orcid_id": TEST_ORCID_ID}]})

    with patch(
        "mavedb.lib.orcid.fetch_orcid_user",
        side_effect=NonexistentOrcidUserError(f"No ORCID user was found for ORCID ID {TEST_ORCID_ID}."),
    ):
        response = client.put(f"/api/v1/score-sets/{score_set['urn']}", json=score_set_update_payload)

    assert response.status_code == 404
    response_data = response.json()
    assert "No ORCID user was found for ORCID ID 1111-1111-1111-1111." in response_data["detail"]


########################################################################################################################
# Score set fetching
########################################################################################################################


def test_get_own_private_score_set(client, setup_router_db):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    expected_response = update_expected_response_for_created_resources(
        deepcopy(TEST_MINIMAL_SEQ_SCORESET_RESPONSE), experiment, score_set
    )
    expected_response["experiment"].update({"numScoreSets": 1})

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}")
    assert response.status_code == 200
    response_data = response.json()

    assert sorted(expected_response.keys()) == sorted(response_data.keys())
    for key in expected_response:
        assert (key, expected_response[key]) == (key, response_data[key])


def test_cannot_get_other_user_private_score_set(session, client, setup_router_db):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    change_ownership(session, score_set["urn"], ScoreSetDbModel)
    response = client.get(f"/api/v1/score-sets/{score_set['urn']}")
    assert response.status_code == 404
    response_data = response.json()
    assert f"score set with URN '{score_set['urn']}' not found" in response_data["detail"]


def test_anonymous_user_cannot_get_user_private_score_set(session, client, setup_router_db, anonymous_app_overrides):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    change_ownership(session, score_set["urn"], ScoreSetDbModel)
    with DependencyOverrider(anonymous_app_overrides):
        response = client.get(f"/api/v1/score-sets/{score_set['urn']}")

    assert response.status_code == 404
    response_data = response.json()
    assert f"score set with URN '{score_set['urn']}' not found" in response_data["detail"]


def test_contributor_can_get_other_users_private_score_set(session, client, setup_router_db):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    change_ownership(session, score_set["urn"], ScoreSetDbModel)
    add_contributor(
        session,
        score_set["urn"],
        ScoreSetDbModel,
        TEST_USER["username"],
        TEST_USER["first_name"],
        TEST_USER["last_name"],
    )

    expected_response = update_expected_response_for_created_resources(
        deepcopy(TEST_MINIMAL_SEQ_SCORESET_RESPONSE), experiment, score_set
    )
    expected_response["contributors"] = [
        {
            "recordType": "Contributor",
            "orcidId": TEST_USER["username"],
            "givenName": TEST_USER["first_name"],
            "familyName": TEST_USER["last_name"],
        }
    ]
    expected_response["createdBy"] = {
        "recordType": "User",
        "orcidId": EXTRA_USER["username"],
        "firstName": EXTRA_USER["first_name"],
        "lastName": EXTRA_USER["last_name"],
    }
    expected_response["modifiedBy"] = {
        "recordType": "User",
        "orcidId": EXTRA_USER["username"],
        "firstName": EXTRA_USER["first_name"],
        "lastName": EXTRA_USER["last_name"],
    }
    expected_response["experiment"].update({"numScoreSets": 1})

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}")
    assert response.status_code == 200
    response_data = response.json()

    assert sorted(expected_response.keys()) == sorted(response_data.keys())
    for key in expected_response:
        assert (key, expected_response[key]) == (key, response_data[key])


def test_admin_can_get_other_user_private_score_set(session, client, admin_app_overrides, setup_router_db):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    expected_response = update_expected_response_for_created_resources(
        deepcopy(TEST_MINIMAL_SEQ_SCORESET_RESPONSE), experiment, score_set
    )
    expected_response["experiment"].update({"numScoreSets": 1})
    with DependencyOverrider(admin_app_overrides):
        response = client.get(f"/api/v1/score-sets/{score_set['urn']}")

    assert response.status_code == 200
    response_data = response.json()
    assert sorted(expected_response.keys()) == sorted(response_data.keys())
    for key in expected_response:
        assert (key, expected_response[key]) == (key, response_data[key])


########################################################################################################################
# Multiple score set fetching
########################################################################################################################


def test_get_score_sets_by_comma_separated_urns(client, setup_router_db):
    experiment = create_experiment(client)
    first_score_set = create_seq_score_set(client, experiment["urn"])
    second_score_set = create_seq_score_set(client, experiment["urn"])

    response = client.get(
        "/api/v1/score-sets/",
        params={"urns": f"{first_score_set['urn']}, {second_score_set['urn']}"},
    )
    assert response.status_code == 200

    response_data = response.json()
    assert [item["urn"] for item in response_data] == [first_score_set["urn"], second_score_set["urn"]]

    for item in response_data:
        jsonschema.validate(instance=item, schema=ScoreSet.model_json_schema())


def test_get_score_sets_requires_at_least_one_urn(client, setup_router_db):
    response = client.get("/api/v1/score-sets/", params={"urns": " , "})
    assert response.status_code == 422
    assert response.json()["detail"] == "At least one URN is required"


def test_get_score_sets_with_mixed_valid_and_invalid_urns_returns_404(client, setup_router_db):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    missing_urn = "urn:mavedb:99999999-z-9"

    response = client.get(
        "/api/v1/score-sets/",
        params={"urns": f"{score_set['urn']},{missing_urn}"},
    )
    assert response.status_code == 404
    assert response.json()["detail"] == f"score set with URN '{missing_urn}' not found"


def test_get_score_sets_with_whitespace_around_urns_in_mixed_list_returns_404(client, setup_router_db):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    missing_urn = "urn:mavedb:99999999-z-9"

    response = client.get(
        "/api/v1/score-sets/",
        params={"urns": f"  {score_set['urn']}  ,   {missing_urn}   "},
    )
    assert response.status_code == 404
    assert response.json()["detail"] == f"score set with URN '{missing_urn}' not found"


def test_show_score_sets_anonymous_can_fetch_public_score_sets(
    session, client, setup_router_db, anonymous_app_overrides, data_provider, data_files
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")
    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None):
        published_score_set = publish_score_set(client, score_set["urn"])

    with DependencyOverrider(anonymous_app_overrides):
        response = client.get(
            "/api/v1/score-sets/",
            params={"urns": published_score_set["urn"]},
        )

    assert response.status_code == 200
    response_data = response.json()
    assert len(response_data) == 1
    assert response_data[0]["urn"] == published_score_set["urn"]


def test_show_score_sets_anonymous_cannot_fetch_private_score_sets(session, client, setup_router_db, anonymous_app_overrides):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    # Score set is private (not published); change ownership so it belongs to another user
    change_ownership(session, score_set["urn"], ScoreSetDbModel)

    with DependencyOverrider(anonymous_app_overrides):
        response = client.get(
            "/api/v1/score-sets/",
            params={"urns": score_set["urn"]},
        )

    assert response.status_code == 404
    assert f"score set with URN '{score_set['urn']}' not found" in response.json()["detail"]


def test_show_score_sets_authenticated_user_can_fetch_own_private_score_sets(client, setup_router_db):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])

    response = client.get(
        "/api/v1/score-sets/",
        params={"urns": score_set["urn"]},
    )

    assert response.status_code == 200
    response_data = response.json()
    assert len(response_data) == 1
    assert response_data[0]["urn"] == score_set["urn"]


def test_show_score_sets_authenticated_user_cannot_fetch_other_users_private_score_sets(
    session, client, setup_router_db
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    change_ownership(session, score_set["urn"], ScoreSetDbModel)

    response = client.get(
        "/api/v1/score-sets/",
        params={"urns": score_set["urn"]},
    )

    assert response.status_code == 404
    assert f"score set with URN '{score_set['urn']}' not found" in response.json()["detail"]


def test_show_score_sets_mixed_public_and_private_returns_404(
    session, client, setup_router_db, anonymous_app_overrides, data_provider, data_files
):
    experiment = create_experiment(client)
    public_score_set = create_seq_score_set(client, experiment["urn"])
    public_score_set = mock_worker_variant_insertion(client, session, data_provider, public_score_set, data_files / "scores.csv")
    private_score_set = create_seq_score_set(client, experiment["urn"])
    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None):
        published_score_set = publish_score_set(client, public_score_set["urn"])
    # Make private_score_set belong to a different user to make it inaccessible anonymously
    change_ownership(session, private_score_set["urn"], ScoreSetDbModel)

    with DependencyOverrider(anonymous_app_overrides):
        response = client.get(
            "/api/v1/score-sets/",
            params={"urns": f"{published_score_set['urn']},{private_score_set['urn']}"},
        )

    assert response.status_code == 404
    assert f"score set with URN '{private_score_set['urn']}' not found" in response.json()["detail"]


def test_can_add_contributor_in_both_experiment_and_score_set(session, client, setup_router_db):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    change_ownership(session, score_set["urn"], ScoreSetDbModel)
    change_ownership(session, experiment["urn"], ExperimentDbModel)
    add_contributor(
        session,
        score_set["urn"],
        ScoreSetDbModel,
        TEST_USER["username"],
        TEST_USER["first_name"],
        TEST_USER["last_name"],
    )
    add_contributor(
        session,
        experiment["urn"],
        ExperimentDbModel,
        TEST_USER["username"],
        TEST_USER["first_name"],
        TEST_USER["last_name"],
    )
    score_set_response = client.get(f"/api/v1/score-sets/{score_set['urn']}")
    assert score_set_response.status_code == 200
    ss_response_data = score_set_response.json()
    assert len(ss_response_data["contributors"]) == 1
    assert any(c["orcidId"] == TEST_USER["username"] for c in ss_response_data["contributors"])
    experiment_response = client.get(f"/api/v1/experiments/{experiment['urn']}")
    assert experiment_response.status_code == 200
    exp_response_data = experiment_response.json()
    assert len(exp_response_data["contributors"]) == 1
    assert any(c["orcidId"] == TEST_USER["username"] for c in exp_response_data["contributors"])


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        (
            [
                {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
                {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
            ]
        )
    ],
    indirect=["mock_publication_fetch"],
)
def test_extra_user_can_only_view_published_score_calibrations_in_score_set(
    client, setup_router_db, extra_user_app_overrides, mock_publication_fetch, session, data_provider, data_files
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    create_test_score_calibration_in_score_set_via_client(
        client, published_score_set["urn"], deepcamelize(TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED)
    )
    public_calibration = create_publish_and_promote_score_calibration(
        client,
        published_score_set["urn"],
        deepcamelize(TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED),
    )

    with DependencyOverrider(extra_user_app_overrides):
        response = client.get(f"/api/v1/score-sets/{published_score_set['urn']}")

    assert response.status_code == 200
    response_data = response.json()
    assert len(response_data["scoreCalibrations"]) == 1
    assert response_data["scoreCalibrations"][0]["urn"] == public_calibration["urn"]


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        (
            [
                {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
                {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
            ]
        )
    ],
    indirect=["mock_publication_fetch"],
)
def test_creating_user_can_view_all_score_calibrations_in_score_set(client, setup_router_db, mock_publication_fetch):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    private_calibration = create_test_score_calibration_in_score_set_via_client(
        client, score_set["urn"], deepcamelize(TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED)
    )
    public_calibration = create_publish_and_promote_score_calibration(
        client,
        score_set["urn"],
        deepcamelize(TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED),
    )

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}")

    assert response.status_code == 200
    response_data = response.json()
    assert len(response_data["scoreCalibrations"]) == 2
    urns = [calibration["urn"] for calibration in response_data["scoreCalibrations"]]
    assert private_calibration["urn"] in urns
    assert public_calibration["urn"] in urns


########################################################################################################################
# Adding scores to score set
########################################################################################################################


def test_add_score_set_variants_scores_only_endpoint(client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    scores_csv_path = data_files / "scores.csv"
    with (
        open(scores_csv_path, "rb") as scores_file,
        patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as queue,
    ):
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={"scores_file": (scores_csv_path.name, scores_file, "text/csv")},
        )
        queue.assert_called_once()

    assert response.status_code == 200
    response_data = response.json()
    jsonschema.validate(instance=response_data, schema=ScoreSet.model_json_schema())

    # We test the worker process that actually adds the variant data separately. Here, we take it as
    # fact that it would have succeeded.
    score_set.update({"processingState": "processing"})
    assert score_set == response_data


def test_add_score_set_variants_scores_and_counts_endpoint(session, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    scores_csv_path = data_files / "scores.csv"
    counts_csv_path = data_files / "counts.csv"
    with (
        open(scores_csv_path, "rb") as scores_file,
        open(counts_csv_path, "rb") as counts_file,
        patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as queue,
    ):
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={
                "scores_file": (scores_csv_path.name, scores_file, "text/csv"),
                "counts_file": (counts_csv_path.name, counts_file, "text/csv"),
            },
        )
        queue.assert_called_once()

    assert response.status_code == 200
    response_data = response.json()
    jsonschema.validate(instance=response_data, schema=ScoreSet.model_json_schema())

    # We test the worker process that actually adds the variant data separately. Here, we take it as
    # fact that it would have succeeded.
    score_set.update({"processingState": "processing"})
    assert score_set == response_data


def test_add_score_set_variants_scores_counts_and_column_metadata_endpoint(
    session, client, setup_router_db, data_files
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    scores_csv_path = data_files / "scores.csv"
    counts_csv_path = data_files / "counts.csv"
    score_columns_metadata_path = data_files / "score_columns_metadata.json"
    count_columns_metadata_path = data_files / "count_columns_metadata.json"
    with (
        open(scores_csv_path, "rb") as scores_file,
        open(counts_csv_path, "rb") as counts_file,
        open(score_columns_metadata_path, "rb") as score_columns_metadata_file,
        open(count_columns_metadata_path, "rb") as count_columns_metadata_file,
        patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as queue,
    ):
        score_columns_metadata = json.load(score_columns_metadata_file)
        count_columns_metadata = json.load(count_columns_metadata_file)
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={
                "scores_file": (scores_csv_path.name, scores_file, "text/csv"),
                "counts_file": (counts_csv_path.name, counts_file, "text/csv"),
            },
            data={
                "score_columns_metadata": json.dumps(score_columns_metadata),
                "count_columns_metadata": json.dumps(count_columns_metadata),
            },
        )
        queue.assert_called_once()

    assert response.status_code == 200
    response_data = response.json()
    jsonschema.validate(instance=response_data, schema=ScoreSet.model_json_schema())

    # We test the worker process that actually adds the variant data separately. Here, we take it as
    # fact that it would have succeeded.
    score_set.update({"processingState": "processing"})
    assert score_set == response_data


def test_add_score_set_variants_scores_only_endpoint_utf8_encoded(client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    scores_csv_path = data_files / "scores_utf8_encoded.csv"
    with (
        open(scores_csv_path, "rb") as scores_file,
        patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as queue,
    ):
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={"scores_file": (scores_csv_path.name, scores_file, "text/csv")},
        )
        queue.assert_called_once()

    assert response.status_code == 200
    response_data = response.json()
    jsonschema.validate(instance=response_data, schema=ScoreSet.model_json_schema())

    # We test the worker process that actually adds the variant data separately. Here, we take it as
    # fact that it would have succeeded.
    score_set.update({"processingState": "processing"})
    assert score_set == response_data


def test_add_score_set_variants_scores_and_counts_endpoint_utf8_encoded(session, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    scores_csv_path = data_files / "scores_utf8_encoded.csv"
    counts_csv_path = data_files / "counts_utf8_encoded.csv"
    with (
        open(scores_csv_path, "rb") as scores_file,
        open(counts_csv_path, "rb") as counts_file,
        patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as queue,
    ):
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={
                "scores_file": (scores_csv_path.name, scores_file, "text/csv"),
                "counts_file": (counts_csv_path.name, counts_file, "text/csv"),
            },
        )
        queue.assert_called_once()

    assert response.status_code == 200
    response_data = response.json()
    jsonschema.validate(instance=response_data, schema=ScoreSet.model_json_schema())

    # We test the worker process that actually adds the variant data separately. Here, we take it as
    # fact that it would have succeeded.
    score_set.update({"processingState": "processing"})
    assert score_set == response_data


def test_cannot_add_scores_to_score_set_without_email(session, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    client.put("api/v1/users/me", json={"email": None})
    scores_csv_path = data_files / "scores.csv"
    with open(scores_csv_path, "rb") as scores_file:
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={"scores_file": (scores_csv_path.name, scores_file, "text/csv")},
        )
    assert response.status_code == 403
    response_data = response.json()
    assert response_data["detail"] in "There must be an email address associated with your account to use this feature."


# A user should not be able to add scores to another users' score set. Therefore, they should also not be able
# to add scores and counts. So long as this test passes (a user cannot add scores to another users' score set),
# they necessarily will not be able to add scores and counts-- so omit the test for adding scores + counts.
def test_cannot_add_scores_to_other_user_score_set(session, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    change_ownership(session, score_set["urn"], ScoreSetDbModel)
    scores_csv_path = data_files / "scores.csv"
    with open(scores_csv_path, "rb") as scores_file:
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={"scores_file": (scores_csv_path.name, scores_file, "text/csv")},
        )
    assert response.status_code == 404
    response_data = response.json()
    assert f"score set with URN '{score_set['urn']}' not found" in response_data["detail"]


# A user should not be able to add scores to another users' score set. Therefore, they should also not be able
# to add scores and counts. So long as this test passes (a user cannot add scores to another users' score set),
# they necessarily will not be able to add scores and counts-- so omit the test for adding scores + counts.
def test_anonymous_cannot_add_scores_to_other_user_score_set(
    session, client, setup_router_db, data_files, anonymous_app_overrides
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    change_ownership(session, score_set["urn"], ScoreSetDbModel)
    scores_csv_path = data_files / "scores.csv"

    with open(scores_csv_path, "rb") as scores_file, DependencyOverrider(anonymous_app_overrides):
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={"scores_file": (scores_csv_path.name, scores_file, "text/csv")},
        )

    assert response.status_code == 401
    response_data = response.json()
    assert "Could not validate credentials" in response_data["detail"]


def test_contributor_can_add_scores_to_other_user_score_set(session, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    change_ownership(session, score_set["urn"], ScoreSetDbModel)
    add_contributor(
        session,
        score_set["urn"],
        ScoreSetDbModel,
        TEST_USER["username"],
        TEST_USER["first_name"],
        TEST_USER["last_name"],
    )
    scores_csv_path = data_files / "scores.csv"

    with (
        open(scores_csv_path, "rb") as scores_file,
        patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as queue,
    ):
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={"scores_file": (scores_csv_path.name, scores_file, "text/csv")},
        )
        queue.assert_called_once()

    assert response.status_code == 200
    response_data = response.json()
    jsonschema.validate(instance=response_data, schema=ScoreSet.model_json_schema())

    # We test the worker process that actually adds the variant data separately. Here, we take it as
    # fact that it would have succeeded.
    score_set.update({"processingState": "processing"})
    score_set["contributors"] = [
        {
            "recordType": "Contributor",
            "orcidId": TEST_USER["username"],
            "givenName": TEST_USER["first_name"],
            "familyName": TEST_USER["last_name"],
        }
    ]
    score_set["createdBy"] = {
        "recordType": "User",
        "orcidId": EXTRA_USER["username"],
        "firstName": EXTRA_USER["first_name"],
        "lastName": EXTRA_USER["last_name"],
    }
    score_set["modifiedBy"] = {
        "recordType": "User",
        "orcidId": EXTRA_USER["username"],
        "firstName": EXTRA_USER["first_name"],
        "lastName": EXTRA_USER["last_name"],
    }
    assert score_set == response_data


def test_contributor_can_add_scores_and_counts_to_other_user_score_set(session, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    change_ownership(session, score_set["urn"], ScoreSetDbModel)
    add_contributor(
        session,
        score_set["urn"],
        ScoreSetDbModel,
        TEST_USER["username"],
        TEST_USER["first_name"],
        TEST_USER["last_name"],
    )
    scores_csv_path = data_files / "scores.csv"
    counts_csv_path = data_files / "counts.csv"

    with (
        open(scores_csv_path, "rb") as scores_file,
        open(counts_csv_path, "rb") as counts_file,
        patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as queue,
    ):
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={
                "scores_file": (scores_csv_path.name, scores_file, "text/csv"),
                "counts_file": (counts_csv_path.name, counts_file, "text/csv"),
            },
        )
        queue.assert_called_once()

    assert response.status_code == 200
    response_data = response.json()
    jsonschema.validate(instance=response_data, schema=ScoreSet.model_json_schema())

    # We test the worker process that actually adds the variant data separately. Here, we take it as
    # fact that it would have succeeded.
    score_set.update({"processingState": "processing"})
    score_set["contributors"] = [
        {
            "recordType": "Contributor",
            "orcidId": TEST_USER["username"],
            "givenName": TEST_USER["first_name"],
            "familyName": TEST_USER["last_name"],
        }
    ]
    score_set["createdBy"] = {
        "recordType": "User",
        "orcidId": EXTRA_USER["username"],
        "firstName": EXTRA_USER["first_name"],
        "lastName": EXTRA_USER["last_name"],
    }
    score_set["modifiedBy"] = {
        "recordType": "User",
        "orcidId": EXTRA_USER["username"],
        "firstName": EXTRA_USER["first_name"],
        "lastName": EXTRA_USER["last_name"],
    }
    assert score_set == response_data


def test_admin_can_add_scores_to_other_user_score_set(
    session, client, setup_router_db, data_files, admin_app_overrides
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    scores_csv_path = data_files / "scores.csv"

    with (
        open(scores_csv_path, "rb") as scores_file,
        DependencyOverrider(admin_app_overrides),
        patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as queue,
    ):
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={"scores_file": (scores_csv_path.name, scores_file, "text/csv")},
        )
        queue.assert_called_once()

    assert response.status_code == 200
    response_data = response.json()
    jsonschema.validate(instance=response_data, schema=ScoreSet.model_json_schema())

    # We test the worker process that actually adds the variant data separately. Here, we take it as
    # fact that it would have succeeded.
    score_set.update({"processingState": "processing"})
    assert score_set == response_data


def test_admin_can_add_scores_and_counts_to_other_user_score_set(session, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    scores_csv_path = data_files / "scores.csv"
    counts_csv_path = data_files / "counts.csv"
    with (
        open(scores_csv_path, "rb") as scores_file,
        open(counts_csv_path, "rb") as counts_file,
        patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as queue,
    ):
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={
                "scores_file": (scores_csv_path.name, scores_file, "text/csv"),
                "counts_file": (counts_csv_path.name, counts_file, "text/csv"),
            },
        )
        queue.assert_called_once()

    assert response.status_code == 200
    response_data = response.json()
    jsonschema.validate(instance=response_data, schema=ScoreSet.model_json_schema())

    # We test the worker process that actually adds the variant data separately. Here, we take it as
    # fact that it would have succeeded.
    score_set.update({"processingState": "processing"})
    assert score_set == response_data


########################################################################################################################
# Score set publication
########################################################################################################################


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

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    assert isinstance(MAVEDB_SCORE_SET_URN_RE.fullmatch(published_score_set["urn"]), re.Match)
    assert isinstance(MAVEDB_EXPERIMENT_URN_RE.fullmatch(published_score_set["experiment"]["urn"]), re.Match)

    expected_response = update_expected_response_for_created_resources(
        deepcopy(TEST_MINIMAL_SEQ_SCORESET_RESPONSE), published_score_set["experiment"], published_score_set
    )
    expected_response["experiment"].update({"publishedDate": date.today().isoformat(), "numScoreSets": 1})
    expected_response.update(
        {
            "urn": published_score_set["urn"],
            "publishedDate": date.today().isoformat(),
            "numVariants": 3,
            "private": False,
            "datasetColumns": SAVED_MINIMAL_DATASET_COLUMNS,
            "processingState": ProcessingState.success.name,
        }
    )
    assert sorted(expected_response.keys()) == sorted(published_score_set.keys())

    # refresh score set to post worker state
    score_set = (client.get(f"/api/v1/score-sets/{published_score_set['urn']}")).json()
    for key in expected_response:
        assert (key, expected_response[key]) == (key, score_set[key])

    score_set_variants = session.execute(
        select(VariantDbModel).join(ScoreSetDbModel).where(ScoreSetDbModel.urn == score_set["urn"])
    ).scalars()
    assert all([variant.urn.startswith("urn:mavedb:") for variant in score_set_variants])


def test_publish_multiple_score_sets(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set_1 = create_seq_score_set(client, experiment["urn"])
    score_set_1 = mock_worker_variant_insertion(client, session, data_provider, score_set_1, data_files / "scores.csv")
    score_set_2 = create_seq_score_set(client, experiment["urn"])
    score_set_2 = mock_worker_variant_insertion(client, session, data_provider, score_set_2, data_files / "scores.csv")
    score_set_3 = create_seq_score_set(client, experiment["urn"])
    score_set_3 = mock_worker_variant_insertion(client, session, data_provider, score_set_3, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        pub_score_set_1_data = publish_score_set(client, score_set_1["urn"])
        pub_score_set_2_data = publish_score_set(client, score_set_2["urn"])
        pub_score_set_3_data = publish_score_set(client, score_set_3["urn"])
        worker_queue.assert_called()

    assert pub_score_set_1_data["urn"] == "urn:mavedb:00000001-a-1"
    assert pub_score_set_1_data["title"] == score_set_1["title"]
    assert pub_score_set_1_data["experiment"]["urn"] == "urn:mavedb:00000001-a"
    assert pub_score_set_2_data["urn"] == "urn:mavedb:00000001-a-2"
    assert pub_score_set_2_data["title"] == score_set_2["title"]
    assert pub_score_set_2_data["experiment"]["urn"] == "urn:mavedb:00000001-a"
    assert pub_score_set_3_data["urn"] == "urn:mavedb:00000001-a-3"
    assert pub_score_set_3_data["title"] == score_set_3["title"]
    assert pub_score_set_3_data["experiment"]["urn"] == "urn:mavedb:00000001-a"

    score_set_1_variants = session.execute(
        select(VariantDbModel).join(ScoreSetDbModel).where(ScoreSetDbModel.urn == score_set_1["urn"])
    ).scalars()
    assert all([variant.urn.startswith("urn:mavedb:") for variant in score_set_1_variants])
    score_set_2_variants = session.execute(
        select(VariantDbModel).join(ScoreSetDbModel).where(ScoreSetDbModel.urn == score_set_2["urn"])
    ).scalars()
    assert all([variant.urn.startswith("urn:mavedb:") for variant in score_set_2_variants])
    score_set_3_variants = session.execute(
        select(VariantDbModel).join(ScoreSetDbModel).where(ScoreSetDbModel.urn == score_set_3["urn"])
    ).scalars()
    assert all([variant.urn.startswith("urn:mavedb:") for variant in score_set_3_variants])


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        [
            {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
            {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
        ]
    ],
    indirect=["mock_publication_fetch"],
)
def test_score_calibrations_remain_private_when_score_set_is_published(
    session, data_provider, client, setup_router_db, data_files, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(
        client,
        experiment["urn"],
    )
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")
    create_test_score_calibration_in_score_set_via_client(
        client, score_set["urn"], deepcamelize(TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED)
    )

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    # refresh score set to post worker state
    score_set = (client.get(f"/api/v1/score-sets/{published_score_set['urn']}")).json()

    for score_calibration in score_set["scoreCalibrations"]:
        assert score_calibration["private"] is True


def test_cannot_publish_score_set_without_variants(client, setup_router_db):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        response = client.post(f"/api/v1/score-sets/{score_set['urn']}/publish")
        assert response.status_code == 409
        worker_queue.assert_not_called()
        response_data = response.json()

    assert "cannot publish score set without variant scores" in response_data["detail"]


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

    change_ownership(session, score_set["urn"], ScoreSetDbModel)

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        response = client.post(f"/api/v1/score-sets/{score_set['urn']}/publish")
        assert response.status_code == 404
        worker_queue.assert_not_called()
        response_data = response.json()

    assert f"score set with URN '{score_set['urn']}' not found" in response_data["detail"]


def test_anonymous_cannot_publish_user_private_score_set(
    session, data_provider, client, setup_router_db, data_files, anonymous_app_overrides
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with (
        DependencyOverrider(anonymous_app_overrides),
        patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as queue,
    ):
        response = client.post(f"/api/v1/score-sets/{score_set['urn']}/publish")
        assert response.status_code == 401
        queue.assert_not_called()
        response_data = response.json()

    assert "Could not validate credentials" in response_data["detail"]


def test_contributor_cannot_publish_other_users_score_set(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")
    change_ownership(session, score_set["urn"], ScoreSetDbModel)
    add_contributor(
        session,
        score_set["urn"],
        ScoreSetDbModel,
        TEST_USER["username"],
        TEST_USER["first_name"],
        TEST_USER["last_name"],
    )

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        response = client.post(f"/api/v1/score-sets/{score_set['urn']}/publish")
        assert response.status_code == 403
        worker_queue.assert_not_called()
        response_data = response.json()

    assert f"insufficient permissions on score set with URN '{score_set['urn']}'" in response_data["detail"]


def test_admin_can_publish_other_user_private_score_set(
    session, data_provider, client, admin_app_overrides, setup_router_db, data_files
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with (
        DependencyOverrider(admin_app_overrides),
        patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as queue,
    ):
        response = client.post(f"/api/v1/score-sets/{score_set['urn']}/publish")
        assert response.status_code == 200
        queue.assert_called_once()


########################################################################################################################
# Score set meta-analysis
########################################################################################################################


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

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    meta_score_set = create_seq_score_set(
        client,
        None,
        update={"title": "Test Meta Analysis", "metaAnalyzesScoreSetUrns": [published_score_set["urn"]]},
    )
    meta_score_set = mock_worker_variant_insertion(
        client, session, data_provider, meta_score_set, data_files / "scores.csv"
    )

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


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

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    meta_score_set = create_seq_score_set(
        client,
        None,
        update={"title": "Test Meta Analysis", "metaAnalyzesScoreSetUrns": [score_set["urn"]]},
    )
    meta_score_set = mock_worker_variant_insertion(
        client, session, data_provider, meta_score_set, data_files / "scores.csv"
    )

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        meta_score_set = publish_score_set(client, meta_score_set["urn"])
        worker_queue.assert_called_once()

    assert isinstance(MAVEDB_SCORE_SET_URN_RE.fullmatch(meta_score_set["urn"]), re.Match)
    assert meta_score_set["urn"] == "urn:mavedb:00000001-0-1"


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

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set_1 = publish_score_set(client, score_set_1["urn"])
        published_score_set_2 = publish_score_set(client, score_set_2["urn"])
        worker_queue.assert_called()

    meta_score_set = create_seq_score_set(
        client,
        None,
        update={
            "title": "Test Meta Analysis",
            "metaAnalyzesScoreSetUrns": [published_score_set_1["urn"], published_score_set_2["urn"]],
        },
    )
    meta_score_set = mock_worker_variant_insertion(
        client, session, data_provider, meta_score_set, data_files / "scores.csv"
    )

    published_score_set_1_refresh = (client.get(f"/api/v1/score-sets/{published_score_set_1['urn']}")).json()
    assert meta_score_set["metaAnalyzesScoreSetUrns"] == sorted(
        [published_score_set_1["urn"], published_score_set_2["urn"]]
    )
    assert published_score_set_1_refresh["metaAnalyzedByScoreSetUrns"] == [meta_score_set["urn"]]

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_meta_score_set = publish_score_set(client, meta_score_set["urn"])
        worker_queue.assert_called_once()

    assert isinstance(MAVEDB_SCORE_SET_URN_RE.fullmatch(published_meta_score_set["urn"]), re.Match)
    assert published_meta_score_set["urn"] == "urn:mavedb:00000001-0-1"


def test_multiple_score_set_meta_analysis_multiple_experiment_sets(
    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(client, experiment_1["urn"], update={"title": "Score Set 1"})
    score_set_1 = mock_worker_variant_insertion(client, session, data_provider, score_set_1, data_files / "scores.csv")
    score_set_2 = create_seq_score_set(client, experiment_2["urn"], update={"title": "Score Set 2"})
    score_set_2 = mock_worker_variant_insertion(client, session, data_provider, score_set_2, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set_1 = publish_score_set(client, score_set_1["urn"])
        published_score_set_2 = publish_score_set(client, score_set_2["urn"])
        worker_queue.assert_called()

    meta_score_set = create_seq_score_set(
        client,
        None,
        update={
            "title": "Test Meta Analysis",
            "metaAnalyzesScoreSetUrns": [published_score_set_1["urn"], published_score_set_2["urn"]],
        },
    )
    meta_score_set = mock_worker_variant_insertion(
        client, session, data_provider, meta_score_set, data_files / "scores.csv"
    )
    published_score_set_1_refresh = (client.get(f"/api/v1/score-sets/{published_score_set_1['urn']}")).json()
    assert meta_score_set["metaAnalyzesScoreSetUrns"] == sorted(
        [published_score_set_1["urn"], published_score_set_2["urn"]]
    )
    assert published_score_set_1_refresh["metaAnalyzedByScoreSetUrns"] == [meta_score_set["urn"]]

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_meta_score_set = publish_score_set(client, meta_score_set["urn"])
        worker_queue.assert_called_once()

    assert isinstance(MAVEDB_SCORE_SET_URN_RE.fullmatch(published_meta_score_set["urn"]), re.Match)
    assert published_meta_score_set["urn"] == "urn:mavedb:00000003-0-1"


def test_multiple_score_set_meta_analysis_multiple_experiments(
    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", "experimentSetUrn": experiment_1["experimentSetUrn"]}
    )
    score_set_1 = create_seq_score_set(client, experiment_1["urn"], update={"title": "Score Set 1"})
    score_set_1 = mock_worker_variant_insertion(client, session, data_provider, score_set_1, data_files / "scores.csv")
    score_set_2 = create_seq_score_set(client, experiment_2["urn"], update={"title": "Score Set 2"})
    score_set_2 = mock_worker_variant_insertion(client, session, data_provider, score_set_2, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set_1 = publish_score_set(client, score_set_1["urn"])
        published_score_set_2 = publish_score_set(client, score_set_2["urn"])
        worker_queue.assert_called()

    meta_score_set = create_seq_score_set(
        client,
        None,
        update={
            "title": "Test Meta Analysis",
            "metaAnalyzesScoreSetUrns": [published_score_set_1["urn"], published_score_set_2["urn"]],
        },
    )
    meta_score_set = mock_worker_variant_insertion(
        client, session, data_provider, meta_score_set, data_files / "scores.csv"
    )
    published_score_set_1_refresh = (client.get(f"/api/v1/score-sets/{published_score_set_1['urn']}")).json()
    assert meta_score_set["metaAnalyzesScoreSetUrns"] == sorted(
        [published_score_set_1["urn"], published_score_set_2["urn"]]
    )
    assert published_score_set_1_refresh["metaAnalyzedByScoreSetUrns"] == [meta_score_set["urn"]]

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_meta_score_set = publish_score_set(client, meta_score_set["urn"])
        worker_queue.assert_called_once()

    assert isinstance(MAVEDB_SCORE_SET_URN_RE.fullmatch(published_meta_score_set["urn"]), re.Match)
    assert published_meta_score_set["urn"] == "urn:mavedb:00000001-0-1"


def test_multiple_score_set_meta_analysis_multiple_experiment_sets_different_score_sets(
    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_1 = create_seq_score_set(client, experiment_1["urn"], update={"title": "Score Set 1 exp 1"})
    score_set_1_1 = mock_worker_variant_insertion(
        client, session, data_provider, score_set_1_1, data_files / "scores.csv"
    )
    score_set_2_1 = create_seq_score_set(client, experiment_1["urn"], update={"title": "Score Set 2 exp 1"})
    score_set_2_1 = mock_worker_variant_insertion(
        client, session, data_provider, score_set_2_1, data_files / "scores.csv"
    )
    score_set_1_2 = create_seq_score_set(client, experiment_2["urn"], update={"title": "Score Set 1 exp 2 "})
    score_set_1_2 = mock_worker_variant_insertion(
        client, session, data_provider, score_set_1_2, data_files / "scores.csv"
    )
    score_set_2_2 = create_seq_score_set(client, experiment_2["urn"], update={"title": "Score Set 2 exp 2"})
    score_set_2_2 = mock_worker_variant_insertion(
        client, session, data_provider, score_set_2_2, data_files / "scores.csv"
    )

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set_1_1 = publish_score_set(client, score_set_1_1["urn"])
        published_score_set_1_2 = publish_score_set(client, score_set_1_2["urn"])
        published_score_set_2_1 = publish_score_set(client, score_set_2_1["urn"])
        published_score_set_2_2 = publish_score_set(client, score_set_2_2["urn"])
        worker_queue.assert_called()

    meta_score_set_1 = create_seq_score_set(
        client,
        None,
        update={
            "title": "Test Meta Analysis",
            "metaAnalyzesScoreSetUrns": [published_score_set_1_1["urn"], published_score_set_1_2["urn"]],
        },
    )
    meta_score_set_1 = mock_worker_variant_insertion(
        client, session, data_provider, meta_score_set_1, data_files / "scores.csv"
    )

    published_score_set_1_1_refresh = (client.get(f"/api/v1/score-sets/{published_score_set_1_1['urn']}")).json()
    assert meta_score_set_1["metaAnalyzesScoreSetUrns"] == sorted(
        [published_score_set_1_1["urn"], published_score_set_1_2["urn"]]
    )
    assert published_score_set_1_1_refresh["metaAnalyzedByScoreSetUrns"] == [meta_score_set_1["urn"]]

    meta_score_set_2 = create_seq_score_set(
        client,
        None,
        update={
            "title": "Test Meta Analysis",
            "metaAnalyzesScoreSetUrns": [published_score_set_2_1["urn"], published_score_set_2_2["urn"]],
        },
    )
    meta_score_set_2 = mock_worker_variant_insertion(
        client, session, data_provider, meta_score_set_2, data_files / "scores.csv"
    )
    published_score_set_2_1_refresh = (client.get(f"/api/v1/score-sets/{published_score_set_2_1['urn']}")).json()
    assert meta_score_set_2["metaAnalyzesScoreSetUrns"] == sorted(
        [published_score_set_2_1["urn"], published_score_set_2_2["urn"]]
    )
    assert published_score_set_2_1_refresh["metaAnalyzedByScoreSetUrns"] == [meta_score_set_2["urn"]]

    meta_score_set_3 = create_seq_score_set(
        client,
        None,
        update={
            "title": "Test Meta Analysis",
            "metaAnalyzesScoreSetUrns": [published_score_set_1_1["urn"], published_score_set_2_2["urn"]],
        },
    )
    meta_score_set_3 = mock_worker_variant_insertion(
        client, session, data_provider, meta_score_set_3, data_files / "scores.csv"
    )

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_meta_score_set_1 = publish_score_set(client, meta_score_set_1["urn"])
        published_meta_score_set_2 = publish_score_set(client, meta_score_set_2["urn"])
        published_meta_score_set_3 = publish_score_set(client, meta_score_set_3["urn"])
        worker_queue.assert_called()

    assert isinstance(MAVEDB_SCORE_SET_URN_RE.fullmatch(published_meta_score_set_1["urn"]), re.Match)
    assert isinstance(MAVEDB_SCORE_SET_URN_RE.fullmatch(published_meta_score_set_2["urn"]), re.Match)
    assert isinstance(MAVEDB_SCORE_SET_URN_RE.fullmatch(published_meta_score_set_3["urn"]), re.Match)
    assert published_meta_score_set_1["urn"] == "urn:mavedb:00000003-0-1"
    assert published_meta_score_set_2["urn"] == "urn:mavedb:00000003-0-2"
    assert published_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(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set_1 = mock_worker_variant_insertion(client, session, data_provider, score_set_1, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set_1 = publish_score_set(client, score_set_1["urn"])
        worker_queue.assert_called()

    meta_score_set_1 = create_seq_score_set(
        client,
        None,
        update={"title": "Test Meta Analysis", "metaAnalyzesScoreSetUrns": [published_score_set_1["urn"]]},
    )
    meta_score_set_1 = mock_worker_variant_insertion(
        client, session, data_provider, meta_score_set_1, data_files / "scores.csv"
    )

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        meta_score_set_1 = publish_score_set(client, meta_score_set_1["urn"])
        worker_queue.assert_called()

    assert isinstance(MAVEDB_SCORE_SET_URN_RE.fullmatch(meta_score_set_1["urn"]), re.Match)
    assert meta_score_set_1["urn"] == "urn:mavedb:00000001-0-1"

    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.model_json_schema())

    response = client.post("/api/v1/score-sets/", json=score_set_2)
    response_data = response.json()
    assert response.status_code == 409
    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(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called()

    change_ownership(session, published_score_set["urn"], ScoreSetDbModel)

    meta_score_set = create_seq_score_set(
        client,
        None,
        update={"title": "Test Meta Analysis", "metaAnalyzesScoreSetUrns": [published_score_set["urn"]]},
    )
    meta_score_set = mock_worker_variant_insertion(
        client, session, data_provider, meta_score_set, data_files / "scores.csv"
    )

    published_score_set_refresh = (client.get(f"/api/v1/score-sets/{published_score_set['urn']}")).json()
    assert meta_score_set["metaAnalyzesScoreSetUrns"] == [published_score_set["urn"]]
    assert published_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(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set_1 = mock_worker_variant_insertion(client, session, data_provider, score_set_1, data_files / "scores.csv")
    score_set_2 = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 2"})
    score_set_2 = mock_worker_variant_insertion(client, session, data_provider, score_set_2, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set_1 = publish_score_set(client, score_set_1["urn"])
        published_score_set_2 = publish_score_set(client, score_set_2["urn"])
        worker_queue.assert_called()

    change_ownership(session, published_score_set_2["urn"], ScoreSetDbModel)
    meta_score_set = create_seq_score_set(
        client,
        None,
        update={
            "title": "Test Meta Analysis",
            "metaAnalyzesScoreSetUrns": [published_score_set_1["urn"], published_score_set_2["urn"]],
        },
    )
    meta_score_set = mock_worker_variant_insertion(
        client, session, data_provider, meta_score_set, data_files / "scores.csv"
    )

    published_score_set_1_refresh = (client.get(f"/api/v1/score-sets/{published_score_set_1['urn']}")).json()
    assert meta_score_set["metaAnalyzesScoreSetUrns"] == sorted(
        [published_score_set_1["urn"], published_score_set_2["urn"]]
    )
    assert published_score_set_1_refresh["metaAnalyzedByScoreSetUrns"] == [meta_score_set["urn"]]

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        meta_score_set = publish_score_set(client, meta_score_set["urn"])
        worker_queue.assert_called()

    assert meta_score_set["urn"] == "urn:mavedb:00000001-0-1"
    assert isinstance(MAVEDB_SCORE_SET_URN_RE.fullmatch(meta_score_set["urn"]), re.Match)


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(client, experiment_1["urn"], update={"title": "Score Set 1"})
    score_set_1 = mock_worker_variant_insertion(client, session, data_provider, score_set_1, data_files / "scores.csv")
    score_set_2 = create_seq_score_set(client, experiment_2["urn"], update={"title": "Score Set 2"})
    score_set_2 = mock_worker_variant_insertion(client, session, data_provider, score_set_2, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set_1 = publish_score_set(client, score_set_1["urn"])
        published_score_set_2 = publish_score_set(client, score_set_2["urn"])
        worker_queue.assert_called()

    change_ownership(session, published_score_set_2["urn"], ScoreSetDbModel)
    meta_score_set = create_seq_score_set(
        client,
        None,
        update={
            "title": "Test Meta Analysis",
            "metaAnalyzesScoreSetUrns": [published_score_set_1["urn"], published_score_set_2["urn"]],
        },
    )
    meta_score_set = mock_worker_variant_insertion(
        client, session, data_provider, meta_score_set, data_files / "scores.csv"
    )

    published_score_set_1_refresh = (client.get(f"/api/v1/score-sets/{published_score_set_1['urn']}")).json()
    assert meta_score_set["metaAnalyzesScoreSetUrns"] == sorted(
        [published_score_set_1["urn"], published_score_set_2["urn"]]
    )
    assert published_score_set_1_refresh["metaAnalyzedByScoreSetUrns"] == [meta_score_set["urn"]]

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_meta_score_set = publish_score_set(client, meta_score_set["urn"])
        worker_queue.assert_called()

    assert published_meta_score_set["urn"] == "urn:mavedb:00000003-0-1"
    assert isinstance(MAVEDB_SCORE_SET_URN_RE.fullmatch(published_meta_score_set["urn"]), re.Match)


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


def test_search_private_score_sets_no_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    search_payload = {"text": "fnord"}
    response = client.post("/api/v1/me/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 0
    assert len(response.json()["scoreSets"]) == 0


def test_search_private_score_sets_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Test Fnord Score Set"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    search_payload = {"text": "fnord"}
    response = client.post("/api/v1/me/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 1
    assert len(response.json()["scoreSets"]) == 1
    assert response.json()["scoreSets"][0]["title"] == score_set["title"]


def test_search_private_score_sets_urn_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    search_payload = {"urn": score_set["urn"]}
    response = client.post("/api/v1/me/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 1
    assert len(response.json()["scoreSets"]) == 1
    assert response.json()["scoreSets"][0]["urn"] == score_set["urn"]


# There is space in the end of test urn. The search result returned nothing before.
def test_search_private_score_sets_urn_with_space_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    urn_with_space = score_set["urn"] + "   "
    search_payload = {"urn": urn_with_space}
    response = client.post("/api/v1/me/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 1
    assert len(response.json()["scoreSets"]) == 1
    assert response.json()["scoreSets"][0]["urn"] == score_set["urn"]


def test_search_others_private_score_sets_no_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")
    change_ownership(session, score_set["urn"], ScoreSetDbModel)

    search_payload = {"text": "fnord"}
    response = client.post("/api/v1/me/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 0
    assert len(response.json()["scoreSets"]) == 0


def test_search_others_private_score_sets_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    change_ownership(session, score_set["urn"], ScoreSetDbModel)
    search_payload = {"text": "fnord"}
    response = client.post("/api/v1/me/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 0
    assert len(response.json()["scoreSets"]) == 0


def test_search_others_private_score_sets_urn_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")
    change_ownership(session, score_set["urn"], ScoreSetDbModel)

    search_payload = {"urn": score_set["urn"]}
    response = client.post("/api/v1/me/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 0
    assert len(response.json()["scoreSets"]) == 0


# There is space in the end of test urn. The search result returned nothing before.
def test_search_others_private_score_sets_urn_with_space_match(
    session, data_provider, client, setup_router_db, data_files
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")
    change_ownership(session, score_set["urn"], ScoreSetDbModel)

    urn_with_space = score_set["urn"] + "   "
    search_payload = {"urn": urn_with_space}
    response = client.post("/api/v1/me/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 0
    assert len(response.json()["scoreSets"]) == 0


def test_search_public_score_sets_no_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    search_payload = {"text": "fnord"}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 0
    assert len(response.json()["scoreSets"]) == 0


def test_search_public_score_sets_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Test Fnord Score Set"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    search_payload = {"text": "fnord"}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 1
    assert len(response.json()["scoreSets"]) == 1
    assert response.json()["scoreSets"][0]["title"] == score_set["title"]


def test_cannot_search_public_score_sets_with_published_false(
    session, data_provider, client, setup_router_db, data_files
):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Test Fnord Score Set"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    search_payload = {"text": "fnord", "published": "false"}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    response_data = response.json()
    assert response.status_code == 422
    assert (
        "Cannot search for private score sets except in the context of the current user's data."
        in response_data["detail"]
    )


def test_search_public_score_sets_invalid_limit(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Test Fnord Score Set"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    search_payload = {"text": "fnord", "limit": 101}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    response_data = response.json()
    assert response.status_code == 422
    assert (
        "Cannot search for more than 100 score sets at a time. Please use the offset and limit parameters to run a paginated search."
        in response_data["detail"]
    )


def test_search_public_score_sets_valid_limit(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Test Fnord Score Set"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    search_payload = {"text": "fnord", "limit": 100}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 1
    assert len(response.json()["scoreSets"]) == 1
    assert response.json()["scoreSets"][0]["title"] == score_set["title"]


def test_search_public_score_sets_too_many_publication_identifiers(
    session, data_provider, client, setup_router_db, data_files
):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Test Fnord Score Set"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    publication_identifier_search = [str(20711194 + i) for i in range(41)]
    search_payload = {"text": "fnord", "publication_identifiers": publication_identifier_search}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    response_data = response.json()
    assert response.status_code == 422
    assert (
        "Cannot search for score sets belonging to more than 40 publication identifiers at once."
        in response_data["detail"]
    )


def test_search_public_score_sets_urn_with_space_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    urn_with_space = published_score_set["urn"] + "   "
    search_payload = {"urn": urn_with_space}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 1
    assert len(response.json()["scoreSets"]) == 1
    assert response.json()["scoreSets"][0]["urn"] == published_score_set["urn"]


def test_search_others_public_score_sets_no_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    change_ownership(session, published_score_set["urn"], ScoreSetDbModel)

    search_payload = {"text": "fnord"}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 0
    assert len(response.json()["scoreSets"]) == 0


def test_search_others_public_score_sets_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Test Fnord Score Set"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    change_ownership(session, published_score_set["urn"], ScoreSetDbModel)
    assert session.query(ScoreSetDbModel).filter_by(urn=published_score_set["urn"]).one()

    search_payload = {"text": "fnord"}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 1
    assert len(response.json()["scoreSets"]) == 1
    assert response.json()["scoreSets"][0]["title"] == published_score_set["title"]


def test_search_others_public_score_sets_urn_match(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    change_ownership(session, published_score_set["urn"], ScoreSetDbModel)
    search_payload = {"urn": score_set["urn"]}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 1
    assert len(response.json()["scoreSets"]) == 1
    assert response.json()["scoreSets"][0]["urn"] == published_score_set["urn"]


def test_search_others_public_score_sets_urn_with_space_match(
    session, data_provider, client, setup_router_db, data_files
):
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Score Set 1"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    change_ownership(session, published_score_set["urn"], ScoreSetDbModel)
    urn_with_space = published_score_set["urn"] + "   "
    search_payload = {"urn": urn_with_space}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 1
    assert len(response.json()["scoreSets"]) == 1
    assert response.json()["scoreSets"][0]["urn"] == published_score_set["urn"]


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

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        publish_score_set(client, score_set_1["urn"])
        worker_queue.assert_called_once()

    search_payload = {"published": False}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 422

    response_data = response.json()
    assert (
        "Cannot search for private score sets except in the context of the current user's data."
        in response_data["detail"]
    )


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

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set_1 = publish_score_set(client, score_set_1["urn"])
        worker_queue.assert_called_once()

    search_payload = {"published": True}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 1
    assert len(response.json()["scoreSets"]) == 1
    assert response.json()["scoreSets"][0]["urn"] == published_score_set_1["urn"]


def test_search_published_score_set_not_hidden_by_unpublished_superseding_version(
    session, data_provider, client, setup_router_db, data_files
):
    """A published score set should still appear in search results when its superseding version is unpublished."""
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Test Fnord Score Set"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    # Create an unpublished superseding score set — this should NOT hide the published precursor.
    create_seq_score_set(
        client,
        published_score_set["experiment"]["urn"],
        update={"supersededScoreSetUrn": published_score_set["urn"]},
    )

    search_payload = {"text": "fnord"}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert response.json()["numScoreSets"] == 1
    assert response.json()["scoreSets"][0]["urn"] == published_score_set["urn"]


def test_search_published_score_set_hidden_by_published_superseding_version(
    session, data_provider, client, setup_router_db, data_files
):
    """A published score set should be hidden from search results when its superseding version is also published."""
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"], update={"title": "Test Fnord Score Set"})
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    # Create and publish a superseding score set — this SHOULD hide the precursor.
    superseding = create_seq_score_set(
        client,
        published_score_set["experiment"]["urn"],
        update={"title": "Test Fnord Score Set v2", "supersededScoreSetUrn": published_score_set["urn"]},
    )
    superseding = mock_worker_variant_insertion(client, session, data_provider, superseding, data_files / "scores.csv")
    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_superseding = publish_score_set(client, superseding["urn"])
        worker_queue.assert_called_once()

    search_payload = {"text": "fnord"}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    # Only the superseding version should appear; the precursor should be hidden.
    assert response.json()["numScoreSets"] == 1
    assert response.json()["scoreSets"][0]["urn"] == published_superseding["urn"]


def test_search_filter_options_not_hidden_by_unpublished_superseding_version(
    session, data_provider, client, setup_router_db, data_files
):
    """Filter options should include targets from published score sets even when superseded by unpublished versions."""
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    target_name = published_score_set["targetGenes"][0]["name"]

    # Create an unpublished superseding version.
    create_seq_score_set(
        client,
        published_score_set["experiment"]["urn"],
        update={"supersededScoreSetUrn": published_score_set["urn"]},
    )

    response = client.post("/api/v1/score-sets/search/filter-options", json={})
    assert response.status_code == 200
    target_names = [opt["value"] for opt in response.json()["targetGeneNames"]]
    assert target_name in target_names


def test_search_filter_options_hidden_by_published_superseding_version(
    session, data_provider, client, setup_router_db, data_files
):
    """Filter options should NOT include targets from published score sets when superseded by published versions."""
    experiment = create_experiment(client, {"title": "Experiment 1"})
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    target_name = published_score_set["targetGenes"][0]["name"]

    # Create and publish a superseding version.
    superseding = create_seq_score_set(
        client,
        published_score_set["experiment"]["urn"],
        update={
            "supersededScoreSetUrn": published_score_set["urn"],
            "targetGenes": [
                {
                    "name": "TEST2",
                    "category": "protein_coding",
                    "externalIdentifiers": [],
                    "targetSequence": {
                        "sequenceType": "dna",
                        "sequence": "ACGTTT",
                        "taxonomy": {
                            "code": TEST_SAVED_TAXONOMY["code"],
                            "organismName": TEST_SAVED_TAXONOMY["organism_name"],
                            "commonName": TEST_SAVED_TAXONOMY["common_name"],
                            "rank": TEST_SAVED_TAXONOMY["rank"],
                            "hasDescribedSpeciesName": TEST_SAVED_TAXONOMY["has_described_species_name"],
                            "articleReference": TEST_SAVED_TAXONOMY["article_reference"],
                            "id": TEST_SAVED_TAXONOMY["id"],
                            "url": TEST_SAVED_TAXONOMY["url"],
                        },
                    },
                }
            ],
        },
    )
    superseding = mock_worker_variant_insertion(client, session, data_provider, superseding, data_files / "scores.csv")
    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        publish_score_set(client, superseding["urn"])
        worker_queue.assert_called_once()

    response = client.post("/api/v1/score-sets/search/filter-options", json={})
    assert response.status_code == 200
    target_names = [opt["value"] for opt in response.json()["targetGeneNames"]]
    assert target_name not in target_names


def test_search_score_sets_reports_correct_total_count_with_limit(
    session, data_provider, client, setup_router_db, data_files
):
    """When more published score sets exist than the search limit, num_score_sets should reflect the true total."""
    num_score_sets = 3
    for i in range(num_score_sets):
        experiment = create_experiment(client, {"title": f"Experiment {i}"})
        score_set = create_seq_score_set(client, experiment["urn"], update={"title": f"Score Set {i}"})
        score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

        with patch.object(arq.ArqRedis, "enqueue_job", return_value=None):
            publish_score_set(client, score_set["urn"])

    search_payload = {"limit": 2}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert len(response.json()["scoreSets"]) == 2
    assert response.json()["numScoreSets"] == num_score_sets


def test_search_score_sets_not_affected_by_experiment_metadata(
    session, data_provider, client, setup_router_db, data_files
):
    """Experiments with multiple keywords should not reduce the number of score sets returned by search.

    This is a regression test for a bug where joinedload on one-to-many experiment relationships caused row
    multiplication in the main SQL query. The LIMIT clause was applied to the multiplied rows rather than unique
    score sets, resulting in fewer results than expected.
    """
    num_score_sets = 3
    for i in range(num_score_sets):
        experiment = create_experiment(client, {**TEST_EXPERIMENT_WITH_KEYWORD, "title": f"Experiment {i}"})
        score_set = create_seq_score_set(client, experiment["urn"], update={"title": f"Score Set {i}"})
        score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

        with patch.object(arq.ArqRedis, "enqueue_job", return_value=None):
            publish_score_set(client, score_set["urn"])

    search_payload = {"limit": 2}
    response = client.post("/api/v1/score-sets/search", json=search_payload)
    assert response.status_code == 200
    assert len(response.json()["scoreSets"]) == 2
    assert response.json()["numScoreSets"] == num_score_sets


########################################################################################################################
# Score set deletion
########################################################################################################################


def test_anonymous_cannot_delete_other_users_private_scoreset(
    session, data_provider, client, setup_router_db, data_files, anonymous_app_overrides
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with DependencyOverrider(anonymous_app_overrides):
        response = client.delete(f"/api/v1/score-sets/{score_set['urn']}")

    assert response.status_code == 401
    assert "Could not validate credentials" in response.json()["detail"]


def test_anonymous_cannot_delete_other_users_published_scoreset(
    session, data_provider, client, setup_router_db, data_files, anonymous_app_overrides
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    with DependencyOverrider(anonymous_app_overrides):
        del_response = client.delete(f"/api/v1/score-sets/{published_score_set['urn']}")

    assert del_response.status_code == 401
    del_response_data = del_response.json()
    assert "Could not validate credentials" in del_response_data["detail"]


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

    response = client.delete(f"/api/v1/score-sets/{score_set['urn']}")

    assert response.status_code == 200


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

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    del_response = client.delete(f"/api/v1/score-sets/{published_score_set['urn']}")

    assert del_response.status_code == 403
    del_response_data = del_response.json()
    assert (
        f"insufficient permissions on score set with URN '{published_score_set['urn']}'" in del_response_data["detail"]
    )


def test_contributor_can_delete_other_users_private_scoreset(
    session, data_provider, client, setup_router_db, data_files, admin_app_overrides
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")
    change_ownership(session, score_set["urn"], ScoreSetDbModel)
    add_contributor(
        session,
        score_set["urn"],
        ScoreSetDbModel,
        TEST_USER["username"],
        TEST_USER["first_name"],
        TEST_USER["last_name"],
    )

    response = client.delete(f"/api/v1/score-sets/{score_set['urn']}")

    assert response.status_code == 403
    response_data = response.json()
    assert f"insufficient permissions on score set with URN '{score_set['urn']}'" in response_data["detail"]


def test_admin_can_delete_other_users_private_scoreset(
    session, data_provider, client, setup_router_db, data_files, admin_app_overrides
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with DependencyOverrider(admin_app_overrides):
        response = client.delete(f"/api/v1/score-sets/{score_set['urn']}")

    assert response.status_code == 200


def test_admin_can_delete_other_users_published_scoreset(
    session, data_provider, client, setup_router_db, data_files, admin_app_overrides
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    with DependencyOverrider(admin_app_overrides):
        del_response = client.delete(f"/api/v1/score-sets/{published_score_set['urn']}")
        assert del_response.status_code == 200


########################################################################################################################
# Adding score sets to experiments
########################################################################################################################


def test_can_add_score_set_to_own_private_experiment(session, client, setup_router_db):
    experiment = create_experiment(client)
    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_post_payload["experimentUrn"] = experiment["urn"]
    response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
    assert response.status_code == 200


def test_cannot_add_score_set_to_others_private_experiment(session, client, setup_router_db):
    experiment = create_experiment(client)
    experiment_urn = experiment["urn"]
    change_ownership(session, experiment_urn, ExperimentDbModel)
    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_post_payload["experimentUrn"] = experiment_urn
    response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
    assert response.status_code == 404
    response_data = response.json()
    assert f"experiment with URN '{experiment_urn}' not found" in response_data["detail"]


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

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set_1 = publish_score_set(client, score_set_1["urn"])
        worker_queue.assert_called_once()

    score_set_2 = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_2["experimentUrn"] = published_score_set_1["experiment"]["urn"]
    response = client.post("/api/v1/score-sets/", json=score_set_2)
    assert response.status_code == 200


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

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set_1["urn"])
        worker_queue.assert_called_once()

    published_experiment_urn = published_score_set["experiment"]["urn"]
    change_ownership(session, published_experiment_urn, ExperimentDbModel)
    score_set_2 = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_2["experimentUrn"] = published_experiment_urn
    response = client.post("/api/v1/score-sets/", json=score_set_2)
    assert response.status_code == 200


def test_contributor_can_add_score_set_to_others_private_experiment(session, client, setup_router_db):
    experiment = create_experiment(client)
    change_ownership(session, experiment["urn"], ExperimentDbModel)
    add_contributor(
        session,
        experiment["urn"],
        ExperimentDbModel,
        TEST_USER["username"],
        TEST_USER["first_name"],
        TEST_USER["last_name"],
    )
    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_post_payload["experimentUrn"] = experiment["urn"]
    response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
    assert response.status_code == 200


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

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    published_experiment_urn = published_score_set["experiment"]["urn"]
    change_ownership(session, published_experiment_urn, ExperimentDbModel)
    add_contributor(
        session,
        published_experiment_urn,
        ExperimentDbModel,
        TEST_USER["username"],
        TEST_USER["first_name"],
        TEST_USER["last_name"],
    )
    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_post_payload["experimentUrn"] = published_experiment_urn
    response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
    assert response.status_code == 200


def test_cannot_create_score_set_with_inactive_license(session, client, setup_router_db):
    experiment = create_experiment(client)
    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_post_payload["experimentUrn"] = experiment["urn"]
    score_set_post_payload["licenseId"] = TEST_INACTIVE_LICENSE["id"]
    response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
    assert response.status_code == 409


def test_cannot_modify_score_set_to_inactive_license(session, client, setup_router_db):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set_post_payload = score_set.copy()
    score_set_post_payload.update({"licenseId": TEST_INACTIVE_LICENSE["id"], "urn": score_set["urn"]})
    response = client.put(f"/api/v1/score-sets/{score_set['urn']}", json=score_set_post_payload)
    assert response.status_code == 409


def test_can_modify_metadata_for_score_set_with_inactive_license(session, client, setup_router_db):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    change_to_inactive_license(session, score_set["urn"])
    score_set_post_payload = score_set.copy()
    score_set_post_payload.update({"title": "Update title", "urn": score_set["urn"]})
    response = client.put(f"/api/v1/score-sets/{score_set['urn']}", json=score_set_post_payload)
    assert response.status_code == 200
    response_data = response.json()
    assert ("title", response_data["title"]) == ("title", "Update title")


########################################################################################################################
# Supersede score set
########################################################################################################################


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

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_post_payload["experimentUrn"] = published_score_set["experiment"]["urn"]
    score_set_post_payload["supersededScoreSetUrn"] = published_score_set["urn"]
    superseding_score_set_response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
    assert superseding_score_set_response.status_code == 200


def test_can_view_unpublished_superseding_score_set(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    unpublished_score_set = create_seq_score_set(client, experiment["urn"])
    unpublished_score_set = mock_worker_variant_insertion(
        client, session, data_provider, unpublished_score_set, data_files / "scores.csv"
    )

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, unpublished_score_set["urn"])
        worker_queue.assert_called_once()

    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_post_payload["experimentUrn"] = published_score_set["experiment"]["urn"]
    score_set_post_payload["supersededScoreSetUrn"] = published_score_set["urn"]
    superseding_score_set_response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
    assert superseding_score_set_response.status_code == 200
    superseding_score_set = superseding_score_set_response.json()
    score_set_response = client.get(f"/api/v1/score-sets/{published_score_set['urn']}")
    score_set = score_set_response.json()
    assert score_set_response.status_code == 200
    assert score_set["urn"] == superseding_score_set["supersededScoreSet"]["urn"]
    assert score_set["supersedingScoreSet"]["urn"] == superseding_score_set["urn"]


def test_cannot_view_others_unpublished_superseding_score_set(
    session, data_provider, client, setup_router_db, data_files
):
    experiment = create_experiment(client)
    unpublished_score_set = create_seq_score_set(client, experiment["urn"])
    unpublished_score_set = mock_worker_variant_insertion(
        client, session, data_provider, unpublished_score_set, data_files / "scores.csv"
    )
    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, unpublished_score_set["urn"])
        worker_queue.assert_called_once()

    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_post_payload["experimentUrn"] = published_score_set["experiment"]["urn"]
    score_set_post_payload["supersededScoreSetUrn"] = published_score_set["urn"]
    superseding_score_set_response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
    assert superseding_score_set_response.status_code == 200
    superseding_score_set = superseding_score_set_response.json()
    change_ownership(session, superseding_score_set["urn"], ScoreSetDbModel)
    score_set_response = client.get(f"/api/v1/score-sets/{published_score_set['urn']}")
    score_set = score_set_response.json()
    assert score_set_response.status_code == 200
    assert score_set["urn"] == superseding_score_set["supersededScoreSet"]["urn"]
    # Other users can't view the unpublished superseding score set.
    assert "supersedingScoreSet" not in score_set


def test_can_view_others_published_superseding_score_set(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    unpublished_score_set = create_seq_score_set(client, experiment["urn"])
    unpublished_score_set = mock_worker_variant_insertion(
        client, session, data_provider, unpublished_score_set, data_files / "scores.csv"
    )

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, unpublished_score_set["urn"])
        worker_queue.assert_called_once()

    superseding_score_set = create_seq_score_set(
        client, published_score_set["experiment"]["urn"], update={"supersededScoreSetUrn": published_score_set["urn"]}
    )
    superseding_score_set = mock_worker_variant_insertion(
        client, session, data_provider, superseding_score_set, data_files / "scores.csv"
    )
    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_superseding_score_set = publish_score_set(client, superseding_score_set["urn"])
        worker_queue.assert_called_once()

    change_ownership(session, published_superseding_score_set["urn"], ScoreSetDbModel)

    score_set_response = client.get(f"/api/v1/score-sets/{published_score_set['urn']}")
    assert score_set_response.status_code == 200
    score_set = score_set_response.json()
    assert score_set["urn"] == published_superseding_score_set["supersededScoreSet"]["urn"]
    # Other users can view published superseding score set.
    assert score_set["supersedingScoreSet"]["urn"] == published_superseding_score_set["urn"]


# The superseding score set is unpublished so the newest version to its owner is the unpublished one.
def test_show_correct_score_set_version_with_superseded_score_set_to_its_owner(
    session, data_provider, client, setup_router_db, data_files
):
    experiment = create_experiment(client)
    unpublished_score_set = create_seq_score_set(client, experiment["urn"])
    unpublished_score_set = mock_worker_variant_insertion(
        client, session, data_provider, unpublished_score_set, data_files / "scores.csv"
    )
    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, unpublished_score_set["urn"])
        worker_queue.assert_called_once()

    score_set_post_payload = deepcopy(TEST_MINIMAL_SEQ_SCORESET)
    score_set_post_payload["experimentUrn"] = published_score_set["experiment"]["urn"]
    score_set_post_payload["supersededScoreSetUrn"] = published_score_set["urn"]
    superseding_score_set_response = client.post("/api/v1/score-sets/", json=score_set_post_payload)
    assert superseding_score_set_response.status_code == 200
    superseding_score_set = superseding_score_set_response.json()
    score_set_response = client.get(f"/api/v1/score-sets/{superseding_score_set['urn']}")
    score_set = score_set_response.json()
    assert score_set_response.status_code == 200
    assert score_set["urn"] == superseding_score_set["urn"]


########################################################################################################################
# Score set upload files
########################################################################################################################


# Not sure why scores_non_utf8_encoded.csv file has a wrong encoding problem, but it's good for this test.
def test_upload_a_non_utf8_file(session, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    scores_csv_path = data_files / "scores_non_utf8_encoded.csv"
    with open(scores_csv_path, "rb") as scores_file:
        response = client.post(
            f"/api/v1/score-sets/{score_set['urn']}/variants/data",
            files={"scores_file": (scores_csv_path.name, scores_file, "text/csv")},
        )
    assert response.status_code == 422
    response_data = response.json()
    assert (
        "Error decoding file: 'utf-8' codec can't decode byte 0xdd in position 10: invalid continuation byte. "
        "Ensure the file has correct values." in response_data["detail"]
    )


########################################################################################################################
# Score set download files
########################################################################################################################


@pytest.mark.parametrize(
    "mapped_variant,has_hgvs_g,has_hgvs_p",
    [
        (None, False, False),
        (TEST_MAPPED_VARIANT_WITH_HGVS_G_EXPRESSION, True, False),
        (TEST_MAPPED_VARIANT_WITH_HGVS_P_EXPRESSION, False, True),
    ],
    ids=["without_post_mapped_vrs", "with_post_mapped_hgvs_g", "with_post_mapped_hgvs_p"],
)
def test_download_variants_data_file(
    session, data_provider, client, setup_router_db, data_files, mapped_variant, has_hgvs_g, has_hgvs_p
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")
    if mapped_variant is not None:
        create_mapped_variants_for_score_set(session, score_set["urn"], mapped_variant)

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    download_scores_csv_response = client.get(
        f"/api/v1/score-sets/{published_score_set['urn']}/variants/data?drop_na_columns=true&include_post_mapped_hgvs=true"
    )
    assert download_scores_csv_response.status_code == 200
    download_scores_csv = download_scores_csv_response.text

    reader = csv.DictReader(StringIO(download_scores_csv))
    assert sorted(reader.fieldnames) == sorted(
        [
            "accession",
            "hgvs_nt",
            "hgvs_pro",
            "mavedb.post_mapped_hgvs_g",
            "mavedb.post_mapped_hgvs_p",
            "mavedb.post_mapped_hgvs_c",
            "mavedb.post_mapped_hgvs_at_assay_level",
            "mavedb.post_mapped_vrs_digest",
            "scores.score",
        ]
    )
    rows = list(reader)
    for row in rows:
        if has_hgvs_g:
            assert row["mavedb.post_mapped_hgvs_g"] == mapped_variant["hgvs_g"]
            assert row["mavedb.post_mapped_hgvs_c"] == mapped_variant["hgvs_c"]
            assert row["mavedb.post_mapped_hgvs_p"] == mapped_variant["hgvs_p"]
            assert row["mavedb.post_mapped_hgvs_at_assay_level"] == mapped_variant["hgvs_assay_level"]
        elif has_hgvs_p:
            assert row["mavedb.post_mapped_hgvs_g"] == "NA"
            assert row["mavedb.post_mapped_hgvs_c"] == "NA"
            assert row["mavedb.post_mapped_hgvs_p"] == mapped_variant["hgvs_p"]
            assert row["mavedb.post_mapped_hgvs_at_assay_level"] == mapped_variant["hgvs_assay_level"]
        else:
            assert row["mavedb.post_mapped_hgvs_g"] == "NA"
            assert row["mavedb.post_mapped_hgvs_c"] == "NA"
            assert row["mavedb.post_mapped_hgvs_p"] == "NA"
            assert row["mavedb.post_mapped_hgvs_at_assay_level"] == "NA"


# Test file doesn't have hgvs_splice so its values are all NA.
def test_download_scores_file(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(client, session, data_provider, score_set, data_files / "scores.csv")

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    download_scores_csv_response = client.get(
        f"/api/v1/score-sets/{published_score_set['urn']}/scores?drop_na_columns=true"
    )
    assert download_scores_csv_response.status_code == 200
    download_scores_csv = download_scores_csv_response.text
    csv_header = download_scores_csv.split("\n")[0]
    columns = csv_header.split(",")
    assert "hgvs_nt" in columns
    assert "hgvs_pro" in columns
    assert "hgvs_splice" not in columns


def test_download_counts_file(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(
        client, session, data_provider, score_set, data_files / "scores.csv", data_files / "counts.csv"
    )
    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    download_counts_csv_response = client.get(
        f"/api/v1/score-sets/{published_score_set['urn']}/counts?drop_na_columns=true"
    )
    assert download_counts_csv_response.status_code == 200
    download_counts_csv = download_counts_csv_response.text
    csv_header = download_counts_csv.split("\n")[0]
    columns = csv_header.split(",")
    assert "hgvs_nt" in columns
    assert "hgvs_pro" in columns
    assert "hgvs_splice" not in columns


# Namespace variant CSV export tests.
def test_download_scores_file_in_variant_data_path(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(
        client, session, data_provider, score_set, data_files / "scores.csv", data_files / "counts.csv"
    )
    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    download_scores_csv_response = client.get(
        f"/api/v1/score-sets/{published_score_set['urn']}/variants/data?namespaces=scores&drop_na_columns=true"
    )
    assert download_scores_csv_response.status_code == 200
    download_scores_csv = download_scores_csv_response.text
    reader = csv.reader(StringIO(download_scores_csv))
    columns = next(reader)
    assert "hgvs_nt" in columns
    assert "hgvs_pro" in columns
    assert "hgvs_splice" not in columns
    assert "scores.score" in columns


def test_download_counts_file_in_variant_data_path(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(
        client, session, data_provider, score_set, data_files / "scores.csv", data_files / "counts.csv"
    )
    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    download_counts_csv_response = client.get(
        f"/api/v1/score-sets/{published_score_set['urn']}/variants/data?namespaces=counts&include_custom_columns=true&drop_na_columns=true"
    )
    assert download_counts_csv_response.status_code == 200
    download_counts_csv = download_counts_csv_response.text
    reader = csv.reader(StringIO(download_counts_csv))
    columns = next(reader)
    assert "hgvs_nt" in columns
    assert "hgvs_pro" in columns
    assert "hgvs_splice" not in columns
    assert "counts.c_0" in columns
    assert "counts.c_1" in columns


def test_download_scores_and_counts_file(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(
        client, session, data_provider, score_set, data_files / "scores.csv", data_files / "counts.csv"
    )
    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    download_scores_and_counts_csv_response = client.get(
        f"/api/v1/score-sets/{published_score_set['urn']}/variants/data?namespaces=counts&namespaces=scores&include_custom_columns=true&drop_na_columns=true"
    )
    assert download_scores_and_counts_csv_response.status_code == 200
    download_scores_and_counts_csv = download_scores_and_counts_csv_response.text
    reader = csv.DictReader(StringIO(download_scores_and_counts_csv))
    assert sorted(reader.fieldnames) == sorted(
        ["accession", "hgvs_nt", "hgvs_pro", "scores.score", "scores.s_0", "scores.s_1", "counts.c_0", "counts.c_1"]
    )


@pytest.mark.parametrize(
    "mapped_variant,has_hgvs_g,has_hgvs_p",
    [
        (None, False, False),
        (TEST_MAPPED_VARIANT_WITH_HGVS_G_EXPRESSION, True, False),
        (TEST_MAPPED_VARIANT_WITH_HGVS_P_EXPRESSION, False, True),
    ],
    ids=["without_post_mapped_vrs", "with_post_mapped_hgvs_g", "with_post_mapped_hgvs_p"],
)
def test_download_scores_counts_and_post_mapped_variants_file(
    session, data_provider, client, setup_router_db, data_files, mapped_variant, has_hgvs_g, has_hgvs_p
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(
        client, session, data_provider, score_set, data_files / "scores.csv", data_files / "counts.csv"
    )
    if mapped_variant is not None:
        create_mapped_variants_for_score_set(session, score_set["urn"], mapped_variant)

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    download_multiple_data_csv_response = client.get(
        f"/api/v1/score-sets/{published_score_set['urn']}/variants/data?namespaces=scores&namespaces=counts&include_custom_columns=true&include_post_mapped_hgvs=true&drop_na_columns=true"
    )
    assert download_multiple_data_csv_response.status_code == 200
    download_multiple_data_csv = download_multiple_data_csv_response.text
    reader = csv.DictReader(StringIO(download_multiple_data_csv))
    assert sorted(reader.fieldnames) == sorted(
        [
            "accession",
            "hgvs_nt",
            "hgvs_pro",
            "mavedb.post_mapped_hgvs_c",
            "mavedb.post_mapped_hgvs_g",
            "mavedb.post_mapped_hgvs_p",
            "mavedb.post_mapped_hgvs_at_assay_level",
            "mavedb.post_mapped_vrs_digest",
            "scores.score",
            "scores.s_0",
            "scores.s_1",
            "counts.c_0",
            "counts.c_1",
        ]
    )


# Additional namespace export tests: VEP, ClinGen, gnomAD
def test_download_vep_file_in_variant_data_path(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(
        client, session, data_provider, score_set, data_files / "scores.csv", data_files / "counts.csv"
    )
    # Create mapped variants with VEP consequence populated
    create_mapped_variants_for_score_set(session, score_set["urn"], TEST_MAPPED_VARIANT_WITH_HGVS_G_EXPRESSION)

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    response = client.get(
        f"/api/v1/score-sets/{published_score_set['urn']}/variants/data?namespaces=vep&include_post_mapped_hgvs=true&drop_na_columns=true"
    )
    assert response.status_code == 200
    reader = csv.DictReader(StringIO(response.text))
    assert "vep.vep_functional_consequence" in reader.fieldnames
    # At least one row should contain the test consequence value
    rows = list(reader)
    assert any(row.get("vep.vep_functional_consequence") == "missense_variant" for row in rows)


def test_download_clingen_file_in_variant_data_path(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(
        client, session, data_provider, score_set, data_files / "scores.csv", data_files / "counts.csv"
    )
    # Create mapped variants then set ClinGen allele id for first mapped variant
    create_mapped_variants_for_score_set(session, score_set["urn"], TEST_MAPPED_VARIANT_WITH_HGVS_G_EXPRESSION)
    db_score_set = session.query(ScoreSetDbModel).filter(ScoreSetDbModel.urn == score_set["urn"]).one()
    first_mapped_variant = db_score_set.variants[0].mapped_variants[0]
    first_mapped_variant.clingen_allele_id = VALID_CLINGEN_CA_ID
    session.add(first_mapped_variant)
    session.commit()

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    response = client.get(
        f"/api/v1/score-sets/{published_score_set['urn']}/variants/data?namespaces=clingen&include_post_mapped_hgvs=true&drop_na_columns=true"
    )
    assert response.status_code == 200
    reader = csv.DictReader(StringIO(response.text))
    assert "clingen.clingen_allele_id" in reader.fieldnames
    rows = list(reader)
    assert rows[0].get("clingen.clingen_allele_id") == VALID_CLINGEN_CA_ID


def test_download_gnomad_file_in_variant_data_path(session, data_provider, client, setup_router_db, data_files):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])
    score_set = mock_worker_variant_insertion(
        client, session, data_provider, score_set, data_files / "scores.csv", data_files / "counts.csv"
    )
    # Link a gnomAD variant to the first mapped variant (version may not match export filter)
    score_set = create_seq_score_set_with_mapped_variants(
        client, session, data_provider, experiment["urn"], data_files / "scores.csv"
    )
    link_gnomad_variants_to_mapped_variants(session, score_set)

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as worker_queue:
        published_score_set = publish_score_set(client, score_set["urn"])
        worker_queue.assert_called_once()

    response = client.get(
        f"/api/v1/score-sets/{published_score_set['urn']}/variants/data?namespaces=gnomad&drop_na_columns=true"
    )
    assert response.status_code == 200
    reader = csv.DictReader(StringIO(response.text))
    assert "gnomad.gnomad_af" in reader.fieldnames


########################################################################################################################
# Fetching clinical controls and control options for a score set
########################################################################################################################


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

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/clinical-controls")
    assert response.status_code == 200

    response_data = response.json()
    assert len(response_data) == 2
    for control in response_data:
        mapped_variants = control.pop("mappedVariants")
        assert len(mapped_variants) == 1
        assert all(
            control[k] in (TEST_SAVED_CLINVAR_CONTROL[k], TEST_SAVED_GENERIC_CLINICAL_CONTROL[k])
            for k in TEST_SAVED_CLINVAR_CONTROL.keys()
            if k != "mappedVariants"
        )


@pytest.mark.parametrize("clinical_control", [TEST_SAVED_CLINVAR_CONTROL, TEST_SAVED_GENERIC_CLINICAL_CONTROL])
@pytest.mark.parametrize(
    "parameters", [[("db", "dbName")], [("version", "dbVersion")], [("db", "dbName"), ("version", "dbVersion")]]
)
def test_can_fetch_current_clinical_controls_for_score_set_with_parameters(
    client, setup_router_db, session, data_provider, data_files, clinical_control, parameters
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set_with_mapped_variants(
        client, session, data_provider, experiment["urn"], data_files / "scores.csv"
    )
    link_clinical_controls_to_mapped_variants(session, score_set)

    query_string = "?"
    for param, accessor in parameters:
        query_string += f"{param}={clinical_control[accessor]}&"

    # Remove the last '&' from the query string
    query_string = query_string.strip("&")

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/clinical-controls{query_string}")
    assert response.status_code == 200

    response_data = response.json()
    assert len(response_data)
    for param, accessor in parameters:
        assert all(control[accessor] == clinical_control[accessor] for control in response_data)


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

    response = client.get(f"/api/v1/score-sets/{score_set['urn'] + 'xxx'}/clinical-controls")

    assert response.status_code == 404
    response_data = response.json()
    assert f"score set with URN '{score_set['urn'] + 'xxx'}' not found" in response_data["detail"]


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

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/clinical-controls")

    assert response.status_code == 404
    response_data = response.json()
    assert (
        f"No clinical control variants matching the provided filters associated with score set URN {score_set['urn']} were found"
        in response_data["detail"]
    )


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

    link_clinical_controls_to_mapped_variants(session, score_set)

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/clinical-controls/options")
    assert response.status_code == 200

    response_data = response.json()
    assert len(response_data) == 2
    for control_option in response_data:
        assert len(control_option["availableVersions"]) == 1
        assert control_option["dbName"] in (
            TEST_SAVED_CLINVAR_CONTROL["dbName"],
            TEST_SAVED_GENERIC_CLINICAL_CONTROL["dbName"],
        )
        assert all(
            control_version
            in (TEST_SAVED_CLINVAR_CONTROL["dbVersion"], TEST_SAVED_GENERIC_CLINICAL_CONTROL["dbVersion"])
            for control_version in control_option["availableVersions"]
        )


########################################################################################################################
# Fetching annotated variants for a score set
########################################################################################################################


@pytest.mark.parametrize(
    "annotation_type", ["pathogenicity-evidence-line", "functional-impact-statement", "functional-study-result"]
)
def test_cannot_get_annotated_variants_for_nonexistent_score_set(client, setup_router_db, annotation_type):
    experiment = create_experiment(client)
    score_set = create_seq_score_set(client, experiment["urn"])

    response = client.get(f"/api/v1/score-sets/{score_set['urn'] + 'xxx'}/annotated-variants/{annotation_type}")
    response_data = response.json()

    assert response.status_code == 404
    assert f"score set with URN {score_set['urn'] + 'xxx'} not found" in response_data["detail"]


@pytest.mark.parametrize(
    "annotation_type", ["pathogenicity-evidence-line", "functional-impact-statement", "functional-study-result"]
)
def test_cannot_get_annotated_variants_for_score_set_with_no_mapped_variants(
    client, session, data_provider, data_files, setup_router_db, annotation_type
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set_with_variants(
        client, session, data_provider, experiment["urn"], data_files / "scores.csv"
    )

    with patch.object(arq.ArqRedis, "enqueue_job", return_value=None) as queue:
        publish_score_set_response = client.post(f"/api/v1/score-sets/{score_set['urn']}/publish")
        assert publish_score_set_response.status_code == 200
        queue.assert_called_once()

    publish_score_set = publish_score_set_response.json()

    download_scores_csv_response = client.get(
        f"/api/v1/score-sets/{publish_score_set['urn']}/scores?drop_na_columns=true"
    )
    assert download_scores_csv_response.status_code == 200
    download_scores_csv = download_scores_csv_response.text
    csv_header = download_scores_csv.split("\n")[0]
    columns = csv_header.split(",")
    assert "hgvs_nt" in columns
    assert "hgvs_pro" in columns
    assert "hgvs_splice" not in columns

    response = client.get(f"/api/v1/score-sets/{publish_score_set['urn']}/annotated-variants/{annotation_type}")
    response_data = response.json()

    assert response.status_code == 404
    assert (
        f"No mapped variants associated with score set URN {publish_score_set['urn']} were found"
        in response_data["detail"]
    )


# Tests that annotated variants of the correct type are returned when appropriate. The contents of these
# annotated variants are not tested here, and are tested in more detail via the annotation library tests.


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        [
            {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
            {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
        ]
    ],
    indirect=["mock_publication_fetch"],
)
def test_get_annotated_pathogenicity_evidence_lines_for_score_set(
    client, session, data_provider, data_files, setup_router_db, admin_app_overrides, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set_with_mapped_variants(
        client,
        session,
        data_provider,
        experiment["urn"],
        data_files / "scores.csv",
    )
    create_publish_and_promote_score_calibration(
        client, score_set["urn"], deepcamelize(TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED)
    )

    # The contents of the annotated variants objects should be tested in more detail elsewhere.
    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/pathogenicity-evidence-line")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        variant_urn = annotation_response.get("variant_urn")
        annotated_variant = annotation_response.get("annotation")
        assert f"Pathogenicity evidence line {variant_urn}" in annotated_variant.get("description")


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [({"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"})],
    indirect=["mock_publication_fetch"],
)
def test_nonetype_annotated_pathogenicity_evidence_lines_for_score_set_when_thresholds_not_present(
    client, session, data_provider, data_files, setup_router_db, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set_with_mapped_variants(
        client,
        session,
        data_provider,
        experiment["urn"],
        data_files / "scores.csv",
    )

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/pathogenicity-evidence-line")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        annotated_variant = annotation_response.get("annotation")
        assert annotated_variant is None


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

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/pathogenicity-evidence-line")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        annotated_variant = annotation_response.get("annotation")
        assert annotated_variant is None


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        [
            {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
            {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
        ]
    ],
    indirect=["mock_publication_fetch"],
)
def test_get_annotated_pathogenicity_evidence_lines_for_score_set_when_some_variants_were_not_mapped(
    client, session, data_provider, data_files, setup_router_db, admin_app_overrides, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set_with_mapped_variants(
        client,
        session,
        data_provider,
        experiment["urn"],
        data_files / "scores.csv",
    )
    create_publish_and_promote_score_calibration(
        client, score_set["urn"], deepcamelize(TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED)
    )

    first_var = clear_first_mapped_variant_post_mapped(session, score_set["urn"])

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/pathogenicity-evidence-line")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        variant_urn = annotation_response.get("variant_urn")
        annotated_variant = annotation_response.get("annotation")
        if variant_urn == first_var.urn:
            assert annotated_variant is None
        else:
            assert f"Pathogenicity evidence line {variant_urn}" in annotated_variant.get("description")


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        [
            {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
            {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
        ]
    ],
    indirect=["mock_publication_fetch"],
)
def test_get_annotated_functional_impact_statement_for_score_set(
    client, session, data_provider, data_files, setup_router_db, admin_app_overrides, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set_with_mapped_variants(
        client,
        session,
        data_provider,
        experiment["urn"],
        data_files / "scores.csv",
    )
    create_publish_and_promote_score_calibration(
        client, score_set["urn"], deepcamelize(TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED)
    )

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/functional-impact-statement")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        annotated_variant = annotation_response.get("annotation")
        assert annotated_variant.get("type") == "Statement"


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [({"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"})],
    indirect=["mock_publication_fetch"],
)
def test_nonetype_annotated_functional_impact_statement_for_score_set_when_calibrations_not_present(
    client, session, data_provider, data_files, setup_router_db, admin_app_overrides, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set_with_mapped_variants(
        client,
        session,
        data_provider,
        experiment["urn"],
        data_files / "scores.csv",
        update={
            "secondaryPublicationIdentifiers": [{"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"}],
            "scoreRanges": camelize([TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED, TEST_PATHOGENICITY_SCORE_CALIBRATION]),
        },
    )

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/functional-impact-statement")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        annotated_variant = annotation_response.get("annotation")
        assert annotated_variant is None


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

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/functional-impact-statement")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        annotated_variant = annotation_response.get("annotation")
        assert annotated_variant is None


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [
        [
            {"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"},
            {"dbName": "bioRxiv", "identifier": f"{TEST_BIORXIV_IDENTIFIER}"},
        ]
    ],
    indirect=["mock_publication_fetch"],
)
def test_get_annotated_functional_impact_statement_for_score_set_when_some_variants_were_not_mapped(
    client, session, data_provider, data_files, setup_router_db, admin_app_overrides, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set_with_mapped_variants(
        client,
        session,
        data_provider,
        experiment["urn"],
        data_files / "scores.csv",
    )
    create_publish_and_promote_score_calibration(
        client, score_set["urn"], deepcamelize(TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED)
    )

    first_var = clear_first_mapped_variant_post_mapped(session, score_set["urn"])

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/functional-impact-statement")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        variant_urn = annotation_response.get("variant_urn")
        annotated_variant = annotation_response.get("annotation")
        if variant_urn == first_var.urn:
            assert annotated_variant is None
        else:
            assert annotated_variant.get("type") == "Statement"


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [({"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"})],
    indirect=["mock_publication_fetch"],
)
def test_get_annotated_functional_study_result_for_score_set(
    client, session, data_provider, data_files, setup_router_db, admin_app_overrides, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set_with_mapped_variants(
        client,
        session,
        data_provider,
        experiment["urn"],
        data_files / "scores.csv",
    )

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/functional-study-result")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        annotated_variant = annotation_response.get("annotation")
        assert annotated_variant.get("type") == "ExperimentalVariantFunctionalImpactStudyResult"


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [({"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"})],
    indirect=["mock_publication_fetch"],
)
def test_annotated_functional_study_result_exists_for_score_set_when_thresholds_not_present(
    client, session, data_provider, data_files, setup_router_db, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set_with_mapped_variants(
        client,
        session,
        data_provider,
        experiment["urn"],
        data_files / "scores.csv",
        update={
            "secondaryPublicationIdentifiers": [{"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"}],
            "scoreRanges": camelize([TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED, TEST_PATHOGENICITY_SCORE_CALIBRATION]),
        },
    )

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/functional-study-result")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        annotated_variant = annotation_response.get("annotation")
        assert annotated_variant.get("type") == "ExperimentalVariantFunctionalImpactStudyResult"


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [({"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"})],
    indirect=["mock_publication_fetch"],
)
def test_annotated_functional_study_result_exists_for_score_set_when_ranges_not_present(
    client, session, data_provider, data_files, setup_router_db, admin_app_overrides, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set_with_mapped_variants(
        client,
        session,
        data_provider,
        experiment["urn"],
        data_files / "scores.csv",
        update={
            "secondaryPublicationIdentifiers": [{"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"}],
            "scoreRanges": camelize([TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED, TEST_PATHOGENICITY_SCORE_CALIBRATION]),
        },
    )

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/functional-study-result")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        annotated_variant = annotation_response.get("annotation")
        assert annotated_variant.get("type") == "ExperimentalVariantFunctionalImpactStudyResult"


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

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/functional-study-result")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        annotated_variant = annotation_response.get("annotation")
        assert annotated_variant.get("type") == "ExperimentalVariantFunctionalImpactStudyResult"


@pytest.mark.parametrize(
    "mock_publication_fetch",
    [({"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"})],
    indirect=["mock_publication_fetch"],
)
def test_annotated_functional_study_result_exists_for_score_set_when_some_variants_were_not_mapped(
    client, session, data_provider, data_files, setup_router_db, admin_app_overrides, mock_publication_fetch
):
    experiment = create_experiment(client)
    score_set = create_seq_score_set_with_mapped_variants(
        client,
        session,
        data_provider,
        experiment["urn"],
        data_files / "scores.csv",
        update={
            "secondaryPublicationIdentifiers": [{"dbName": "PubMed", "identifier": f"{TEST_PUBMED_IDENTIFIER}"}],
            "scoreRanges": camelize([TEST_BRNICH_SCORE_CALIBRATION_RANGE_BASED, TEST_PATHOGENICITY_SCORE_CALIBRATION]),
        },
    )

    first_var = clear_first_mapped_variant_post_mapped(session, score_set["urn"])

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/annotated-variants/functional-study-result")
    response_data = parse_ndjson_response(response)

    assert response.status_code == 200
    assert len(response_data) == score_set["numVariants"]

    for annotation_response in response_data:
        variant_urn = annotation_response.get("variant_urn")
        annotated_variant = annotation_response.get("annotation")
        if variant_urn == first_var.urn:
            assert annotated_variant is None
        else:
            assert annotated_variant.get("type") == "ExperimentalVariantFunctionalImpactStudyResult"


########################################################################################################################
# Fetching gnomad variants for a score set
########################################################################################################################


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

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/gnomad-variants")
    assert response.status_code == 200

    response_data = response.json()
    assert len(response_data) == 1
    for gnomad_variant in response_data:
        mapped_variants = gnomad_variant.pop("mappedVariants")
        assert len(mapped_variants) == 1
        gnomad_variant_items = sorted(gnomad_variant.items())
        assert gnomad_variant_items == sorted(TEST_SAVED_GNOMAD_VARIANT.items())


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

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/gnomad-variants?version={TEST_GNOMAD_DATA_VERSION}")
    assert response.status_code == 200

    response_data = response.json()
    assert len(response_data) == 1
    for gnomad_variant in response_data:
        mapped_variants = gnomad_variant.pop("mappedVariants")
        assert len(mapped_variants) == 1
        gnomad_variant_items = sorted(gnomad_variant.items())
        assert gnomad_variant_items == sorted(TEST_SAVED_GNOMAD_VARIANT.items())


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

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/gnomad-variants?version=nonexistent_version")
    assert response.status_code == 404

    response_data = response.json()
    assert "detail" in response_data
    assert (
        response_data["detail"]
        == f"No gnomad variants matching the provided filters associated with score set URN {score_set['urn']} were found"
    )


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

    response = client.get(f"/api/v1/score-sets/{score_set['urn'] + 'xxx'}/gnomad-variants")

    assert response.status_code == 404
    response_data = response.json()
    assert f"score set with URN '{score_set['urn'] + 'xxx'}' not found" in response_data["detail"]


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

    response = client.get(f"/api/v1/score-sets/{score_set['urn']}/gnomad-variants")

    assert response.status_code == 404
    response_data = response.json()
    assert (
        f"No gnomad variants matching the provided filters associated with score set URN {score_set['urn']} were found"
        in response_data["detail"]
    )