Fix tests

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
 

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",
         )

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

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

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,
 ):

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

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

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