Revert config to defaults

.github/workflows/test.yml

@@ -134,7 +134,7 @@ jobs:
           SERVICE_ACCOUNT_CREDS: ${{ secrets.SERVICE_ACCOUNT_CREDS }}
         run: >
           poetry run pytest --durations=0 --cov-append --cov-report=term --cov-report=html:htmlcov --cov-report=xml:coverage.xml --cov=schematic/
-          -m "not (rule_benchmark or single_process_execution or slow_test)" --reruns 4 -n 8 --ignore=tests/unit
+          -m "not (rule_benchmark or single_process_execution)" --reruns 4 -n 8 --ignore=tests/unit
 
       - name: Run integration tests single process
         if: ${{ contains(fromJSON('["3.10"]'), matrix.python-version) }}

pytest.ini

@@ -2,7 +2,7 @@
 python_files = test_*.py
 asyncio_mode = auto
 asyncio_default_fixture_loop_scope = session
-log_cli = True
+log_cli = False
 log_cli_level = INFO
 markers =
     google_credentials_needed: marks tests requiring Google credentials (skipped on GitHub CI)

tests/data/mock_manifests/mock_example_biospecimen_manifest.csv

@@ -1,2 +1,2 @@
 Sample ID,Patient ID,Tissue Status,Component
-1,1,Healthy,Biospecimen
+1,1,Healthy,Biospecimen

tests/data/mock_manifests/mock_example_bulkrnaseq_manifest.csv

@@ -1,2 +1,2 @@
 Filename,Sample ID,File Format,Component,Genome Build,Genome FASTA,entityId
-Manifest Submission - Manual test - file-based manifest submission/test-dataset/sample A.txt,1,FASTQ,BulkRNA-seqAssay,,,syn63561932
+Manifest Submission - Manual test - file-based manifest submission/test-dataset/sample A.txt,1,FASTQ,BulkRNA-seqAssay,,,syn63561932

tests/integration/test_manifest_generation.py

@@ -14,6 +14,7 @@
 from openpyxl import load_workbook
 
 from tests.conftest import ConfigurationForTesting
+from schematic.configuration.configuration import CONFIG
 
 LIGHT_BLUE = "FFEAF7F9"  # Required cell
 GRAY = "FFE0E0E0"  # Header cell
@@ -280,26 +281,33 @@ def test_single_manifest_generation_google_sheet_with_annotations(
         - When File Format = "FASTQ", [Genome Build] is White (Optional)
         """
         # GIVEN a valid example manifest to generate
-        url = f"{testing_config.schematic_api_server_url}/v1/manifest/generate"
-        params = {
-            "schema_url": "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld",
-            "title": "Example",
-            "data_type": "BulkRNA-seqAssay",
-            "use_annotations": "true",
-            "dataset_id": "syn63561056",
-            "asset_view": "syn63561086",
-            "output_format": "google_sheet",
-            "strict_validation": "true",
-            "data_model_labels": "class_label",
-        }
-        headers = {"accept": "application/json", "Authorization": f"Bearer {syn_token}"}
-
-        # WHEN we make a request to the Schematic API
-        response = (
-            requests.get(url, headers=headers, params=params, timeout=300)
-            if testing_config.use_deployed_schematic_api_server
-            else flask_client.get(url, query_string=params, headers=headers)
-        )
+        try:
+            url = f"{testing_config.schematic_api_server_url}/v1/manifest/generate"
+            params = {
+                "schema_url": "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld",
+                "title": "Example",
+                "data_type": "BulkRNA-seqAssay",
+                "use_annotations": "true",
+                "dataset_id": "syn63561056",
+                "asset_view": "syn63561086",
+                "output_format": "google_sheet",
+                "strict_validation": "true",
+                "data_model_labels": "class_label",
+            }
+            headers = {
+                "accept": "application/json",
+                "Authorization": f"Bearer {syn_token}",
+            }
+            # WHEN we make a request to the Schematic API
+            response = (
+                requests.get(url, headers=headers, params=params, timeout=300)
+                if testing_config.use_deployed_schematic_api_server
+                else flask_client.get(url, query_string=params, headers=headers)
+            )
+        finally:
+            # Resets the config to its default state
+            # TODO: remove with https://sagebionetworks.jira.com/browse/SCHEMATIC-202
+            CONFIG.load_config("config_example.yml")
 
         # THEN we expect a successful response
         assert response.status_code == 200
@@ -558,26 +566,34 @@ def test_single_manifest_generation_google_sheet_no_annotations(
         - When File Format = "CRAM", [Genome Build, Genome FASTA] is Light Blue (Required)
         - When File Format = "FASTQ", [Genome Build] is White (Optional)
         """
-        url = f"{testing_config.schematic_api_server_url}/v1/manifest/generate"
-        # GIVEN a valid request to the Schematic API to generate a Google Sheet manifest without annotations
-        params = {
-            "schema_url": "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld",
-            "title": "Example",
-            "data_type": "BulkRNA-seqAssay",
-            "use_annotations": "false",
-            "dataset_id": "syn63561056",
-            "asset_view": "syn63561086",
-            "output_format": "google_sheet",
-            "strict_validation": "true",
-            "data_model_labels": "class_label",
-        }
-        headers = {"accept": "application/json", "Authorization": f"Bearer {syn_token}"}
-        # WHEN we make a request to the Schematic API
-        response = (
-            requests.get(url, headers=headers, params=params, timeout=300)
-            if testing_config.use_deployed_schematic_api_server
-            else flask_client.get(url, query_string=params, headers=headers)
-        )
+        try:
+            url = f"{testing_config.schematic_api_server_url}/v1/manifest/generate"
+            # GIVEN a valid request to the Schematic API to generate a Google Sheet manifest without annotations
+            params = {
+                "schema_url": "https://raw.githubusercontent.com/Sage-Bionetworks/schematic/develop/tests/data/example.model.jsonld",
+                "title": "Example",
+                "data_type": "BulkRNA-seqAssay",
+                "use_annotations": "false",
+                "dataset_id": "syn63561056",
+                "asset_view": "syn63561086",
+                "output_format": "google_sheet",
+                "strict_validation": "true",
+                "data_model_labels": "class_label",
+            }
+            headers = {
+                "accept": "application/json",
+                "Authorization": f"Bearer {syn_token}",
+            }
+            # WHEN we make a request to the Schematic API
+            response = (
+                requests.get(url, headers=headers, params=params, timeout=300)
+                if testing_config.use_deployed_schematic_api_server
+                else flask_client.get(url, query_string=params, headers=headers)
+            )
+        finally:
+            # Resets the config to its default state
+            # TODO: remove with https://sagebionetworks.jira.com/browse/SCHEMATIC-202
+            CONFIG.load_config("config_example.yml")
 
         # THEN we expect a successful response
         assert response.status_code == 200