diff --git a/server/api/tests/projects/experiments_and_analysis/conftest.py b/server/api/tests/projects/experiments_and_analysis/conftest.py
index 207dd381246d621ea266acec1c802db8195712b5..81fee03cccb2682df66d7cddf84e486694178f59 100644
--- a/server/api/tests/projects/experiments_and_analysis/conftest.py
+++ b/server/api/tests/projects/experiments_and_analysis/conftest.py
@@ -131,11 +131,11 @@ def mock_analysis_wf(mocker):
def mock_run_analysis(*args, **kwargs):
return {"history_id": "history_id", "workflow_id": "workflow_id", "id": "id"}
- def mock_load_results(*args, **kwargs):
- print("fake load analyis results")
+ # def mock_load_results(*args, **kwargs):
+ # print("fake load analyis results")
mocker.patch("api.serializers.run_analyis", mock_run_analysis)
- mocker.patch("api.serializers.load_results", mock_load_results)
+ # mocker.patch("api.serializers.load_results", mock_load_results)
yield mocker
@@ -217,6 +217,13 @@ def analysis_tool_params():
@pytest.fixture
+def workflow_id():
+ yield "657f009ad32a3f27"
+
+
+@pytest.fixture(
+ params=["657f009ad32a3f27"], ids=["v0.22_11"],
+)
def analysis_created_from_api_response(
api_client,
user_created_with_api,
@@ -226,7 +233,8 @@ def analysis_created_from_api_response(
user_password,
analysis_tool_params,
mock_analysis_wf,
- mock_get_history_status_in_model
+ mock_get_history_status_in_model,
+ request,
):
client = authenticate(api_client, user_created_with_api, user_password)
@@ -238,6 +246,7 @@ def analysis_created_from_api_response(
"galaxy_history_id": "",
"experiments": [experiment_created_from_api.id],
"toolsParams": analysis_tool_params,
+ "galaxy_workflow_id": request.param,
},
format="json",
)
@@ -261,15 +270,17 @@ def lodscores_created_from_task_result(
mock_show_history_factory({"name": "xxxx_lod.csv", "id": "lodscores.csv"})
mock_download_dataset_factory()
yield load_lod_score(
- analysis_created_from_api.name, analysis_created_from_api.galaxy_history_id
+ (
+ analysis_created_from_api.id,
+ analysis_created_from_api.galaxy_history_id,
+ "",
+ )
)
@pytest.fixture
def lodscores_created_from_task(lodscores_created_from_task_result):
- lodscore = LodScore.objects.get(
- id=lodscores_created_from_task_result["lodscores_id"]
- )
+ lodscore = LodScore.objects.get(id=lodscores_created_from_task_result[2])
yield lodscore
@@ -285,13 +296,13 @@ def peaks_created_from_task_result(
mock_show_history_factory({"name": "xxxx_refine-peaks.csv", "id": "peaks.csv"})
mock_download_dataset_factory()
yield load_refine_peaks(
- analysis_created_from_api.name, analysis_created_from_api.galaxy_history_id
+ (analysis_created_from_api.id, analysis_created_from_api.galaxy_history_id, "",)
)
@pytest.fixture
def peaks_created_from_task(peaks_created_from_task_result):
- peaks = Peak.objects.filter(id__in=peaks_created_from_task_result["peak_ids"])
+ peaks = Peak.objects.filter(id__in=peaks_created_from_task_result[2])
yield peaks
@@ -313,15 +324,13 @@ def coefficients_created_from_task_result(
)
mock_download_dataset_factory()
yield load_coefficient(
- analysis_created_from_api.name, analysis_created_from_api.galaxy_history_id
+ (analysis_created_from_api.id, analysis_created_from_api.galaxy_history_id, "")
)
@pytest.fixture
def coefficient_created_from_task(coefficients_created_from_task_result):
- coeff = Coefficient.objects.get(
- id=coefficients_created_from_task_result["coefficient_id"]
- )
+ coeff = Coefficient.objects.get(id=coefficients_created_from_task_result[2])
yield coeff
@@ -343,13 +352,14 @@ def haplotypes_created_from_task_result(
)
mock_download_dataset_factory()
yield load_haplotypes(
- analysis_created_from_api.name, analysis_created_from_api.galaxy_history_id
+ (analysis_created_from_api.id, analysis_created_from_api.galaxy_history_id, "")
)
@pytest.fixture
def haplotypes_created_from_task(haplotypes_created_from_task_result):
- haplo = Haplotypes.objects.get(id=haplotypes_created_from_task_result["id"])
+ print(haplotypes_created_from_task_result[2])
+ haplo = Haplotypes.objects.get(id=haplotypes_created_from_task_result[2])
yield haplo
@@ -371,13 +381,13 @@ def snps_assoc_created_from_task_result(
)
mock_download_dataset_factory()
yield load_snps_association(
- analysis_created_from_api.name, analysis_created_from_api.galaxy_history_id
+ (analysis_created_from_api.id, analysis_created_from_api.galaxy_history_id, "",)
)
@pytest.fixture
def snps_assoc_created_from_task(snps_assoc_created_from_task_result):
- snps = SnpsAssociation.objects.get(id=snps_assoc_created_from_task_result["id"])
+ snps = SnpsAssociation.objects.get(id=snps_assoc_created_from_task_result[2])
yield snps
@@ -400,13 +410,13 @@ def top_snps_created_from_task_result(
)
mock_download_dataset_factory()
yield load_top_snps(
- analysis_created_from_api.name, analysis_created_from_api.galaxy_history_id
+ (analysis_created_from_api.id, analysis_created_from_api.galaxy_history_id, "",)
)
@pytest.fixture
def top_snps_created_from_task(top_snps_created_from_task_result):
- snps = TopSnps.objects.get(id=top_snps_created_from_task_result["id"])
+ snps = TopSnps.objects.get(id=top_snps_created_from_task_result[2])
yield snps
@@ -426,7 +436,7 @@ def significance_threshold_created_from_task_result(
)
mock_download_dataset_factory()
yield load_significance_threshold(
- analysis_created_from_api.name, analysis_created_from_api.galaxy_history_id
+ (analysis_created_from_api.id, analysis_created_from_api.galaxy_history_id, "",)
)
@@ -435,7 +445,7 @@ def significance_threshold_created_from_task(
significance_threshold_created_from_task_result,
):
thresholds = LodScoreSignificanceThreshold.objects.filter(
- id__in=significance_threshold_created_from_task_result["ids"]
+ id__in=significance_threshold_created_from_task_result[2]
)
yield thresholds
diff --git a/server/api/tests/projects/experiments_and_analysis/test_analysis.py b/server/api/tests/projects/experiments_and_analysis/test_analysis.py
index 985f6c3990a6918b3df18a6feb6a2966f05feeea..691778ddbd873531209ec024279da6597806edfb 100644
--- a/server/api/tests/projects/experiments_and_analysis/test_analysis.py
+++ b/server/api/tests/projects/experiments_and_analysis/test_analysis.py
@@ -26,6 +26,7 @@ def test_analysis_permissions(
analysis_tool_params,
mock_delete_history,
mock_get_history_status_in_model,
+ workflow_id,
):
role_param = project_with_members_response[1]
@@ -54,6 +55,7 @@ def test_analysis_permissions(
"galaxy_history_id": "",
"experiments": [experiment_created_from_api.id],
"toolsParams": analysis_tool_params,
+ "galaxy_workflow_id": workflow_id,
},
format="json",
)
diff --git a/server/api/tests/projects/experiments_and_analysis/test_coefficients.py b/server/api/tests/projects/experiments_and_analysis/test_coefficients.py
index 421612686cee5c2af29814bc6cba3525b7010509..906a4061b819c20a80af59afc75d6cb962903068 100644
--- a/server/api/tests/projects/experiments_and_analysis/test_coefficients.py
+++ b/server/api/tests/projects/experiments_and_analysis/test_coefficients.py
@@ -3,8 +3,10 @@ from api.tests.utils import authenticate
@pytest.mark.django_db
-def test_coefficient_creation(coefficients_created_from_task_result):
- assert coefficients_created_from_task_result["status"] == "ok"
+def test_coefficient_creation(
+ analysis_created_from_api, coefficients_created_from_task_result
+):
+ assert coefficients_created_from_task_result[0] == analysis_created_from_api.id
@pytest.mark.django_db
diff --git a/server/api/tests/projects/experiments_and_analysis/test_haplotype.py b/server/api/tests/projects/experiments_and_analysis/test_haplotype.py
index 904cbcfcb7aa806fe12f5dc376763a877700c16e..2b806f413a9592f874e29230791cc831221c0d88 100644
--- a/server/api/tests/projects/experiments_and_analysis/test_haplotype.py
+++ b/server/api/tests/projects/experiments_and_analysis/test_haplotype.py
@@ -3,8 +3,10 @@ from api.tests.utils import authenticate
@pytest.mark.django_db
-def test_haplotype_creation(haplotypes_created_from_task_result):
- assert haplotypes_created_from_task_result["status"] == "ok"
+def test_haplotype_creation(
+ analysis_created_from_api, haplotypes_created_from_task_result
+):
+ assert haplotypes_created_from_task_result[0] == analysis_created_from_api.id
@pytest.mark.django_db
diff --git a/server/api/tests/projects/experiments_and_analysis/test_significance_thresholds.py b/server/api/tests/projects/experiments_and_analysis/test_significance_thresholds.py
index 4642eebe07dfc77d2a00ac17b89da88013b560e4..e69e13d19f6879e7997db9e3c638804395de8154 100644
--- a/server/api/tests/projects/experiments_and_analysis/test_significance_thresholds.py
+++ b/server/api/tests/projects/experiments_and_analysis/test_significance_thresholds.py
@@ -4,9 +4,12 @@ from api.tests.utils import authenticate
@pytest.mark.django_db
def test_significance_thresholds_creation(
- significance_threshold_created_from_task_result,
+ analysis_created_from_api, significance_threshold_created_from_task_result,
):
- assert significance_threshold_created_from_task_result["status"] == "ok"
+ assert (
+ significance_threshold_created_from_task_result[0]
+ == analysis_created_from_api.id
+ )
@pytest.mark.django_db
@@ -16,7 +19,6 @@ def test_significance_thresholds_permissions(
project_created_from_api,
project_with_members_response,
analysis_created_from_api,
-
user_password,
significance_threshold_created_from_task,
):
diff --git a/server/api/tests/projects/experiments_and_analysis/test_snps_associations.py b/server/api/tests/projects/experiments_and_analysis/test_snps_associations.py
index d07eaf786a9c0104aeb8c7213ca247886081f18f..a19bf272f6cc188b0de94677c2ef40d3e8045566 100644
--- a/server/api/tests/projects/experiments_and_analysis/test_snps_associations.py
+++ b/server/api/tests/projects/experiments_and_analysis/test_snps_associations.py
@@ -3,8 +3,10 @@ from api.tests.utils import authenticate
@pytest.mark.django_db
-def test_snps_assoc_creation(snps_assoc_created_from_task_result):
- assert snps_assoc_created_from_task_result["status"] == "ok"
+def test_snps_assoc_creation(
+ analysis_created_from_api, snps_assoc_created_from_task_result
+):
+ assert snps_assoc_created_from_task_result[2] == analysis_created_from_api.id
@pytest.mark.django_db
diff --git a/server/api/tests/projects/experiments_and_analysis/test_top_snps.py b/server/api/tests/projects/experiments_and_analysis/test_top_snps.py
index 13aadde9ffa622722ebc8545f89d3a0d14f91f8d..edec14110c5c8a3b41a09e94bdc17b885ca60a80 100644
--- a/server/api/tests/projects/experiments_and_analysis/test_top_snps.py
+++ b/server/api/tests/projects/experiments_and_analysis/test_top_snps.py
@@ -3,8 +3,10 @@ from api.tests.utils import authenticate
@pytest.mark.django_db
-def test_top_snps_creation(top_snps_created_from_task_result):
- assert top_snps_created_from_task_result["status"] == "ok"
+def test_top_snps_creation(
+ analysis_created_from_api, top_snps_created_from_task_result
+):
+ assert top_snps_created_from_task_result[2] == analysis_created_from_api.id
@pytest.mark.django_db
diff --git a/server/api/tests/test_tasks.py b/server/api/tests/test_tasks.py
index ee5f8007f67474027002748b849e0eb3ace2b196..4697b33b09ab155928085c84900181bdf1097022 100644
--- a/server/api/tests/test_tasks.py
+++ b/server/api/tests/test_tasks.py
@@ -37,14 +37,26 @@ def mock_show_dataset(mocker):
yield mocker
+@pytest.fixture
+def mock_rmtree(mocker):
+ def _mock_rmtree(*args, **kwargs):
+ print("mocking rmtree")
+
+ mocker.patch("api.tasks.shutil.rmtree", _mock_rmtree)
+ yield mocker
+
+
def test_celery_raw_fixtures(
mock_show_job,
mock_upload_file,
mock_show_dataset,
+ mock_rmtree,
upload_data_id
# celery_app,
# celery_session_worker,
):
- res = upload_file_to_galaxy("/toto", "history_id", "auto")
- assert res == upload_data_id
+ analysis_id = 1
+ history_id = "history_id"
+ res = upload_file_to_galaxy((analysis_id, history_id), "/fake-folder", "auto")
+ assert res[2] == upload_data_id