[FDS-305] Prevent shared snypase resources during integration tests

[BryanFauble]

Problem:

1. For each integration test there are a number of common resource names used for that test. For example overlapping table and folder names. As a result of this any tests that are running against the same set of resources has the potential to cause side affects depending on when and the order of those operations.
2. Trace data and logs were not in a position to be exported when running integration tests.

Solution:

1. Add in some mocking along with UUID for unique resource name generation.
2. Adding in a cleanup mechanism to delete the created resources after test runs.
3. Adding in logic to contest.py to allow exporting logs and traces.

Testing:

1. Using integration test runs to verify changes
2. I tested exporting integration test data to Signoz and verified that we get logs correlated to traces.

[thomasyu888]

🔥 Nicely done here, I know it's still a WIP, but i went ahead and did

docker build -t test -f schematic_api/Dockerfile .

and then I ran schematic profiler

INFO: [2024-08-29 21:31:56] manifest-validate - Monitoring manifest validation
INFO: [2024-08-29 21:31:57] httpx - HTTP Request: POST http://localhost:3001/v1/model/validate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&data_type=Patient&restrict_rules=True "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:31:58] httpx - HTTP Request: POST http://localhost:3001/v1/model/validate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&data_type=Patient "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:32:44] httpx - HTTP Request: POST http://localhost:3001/v1/model/validate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2Fncihtan%2Fdata-models%2Fmain%2FHTAN.model.jsonld&data_type=Biospecimen "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:32:44] manifest-submit - Monitoring manifest submission
INFO: [2024-08-29 21:33:29] httpx - HTTP Request: POST http://localhost:3001/v1/model/submit?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&dataset_id=syn51376664&asset_view=syn51376649&restrict_rules=True&use_schema_label=True&data_model_labels=class_label&table_manipulation=replace&manifest_record_type=table_and_file "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:33:41] httpx - HTTP Request: POST http://localhost:3001/v1/model/submit?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&dataset_id=syn51376664&asset_view=syn51376649&restrict_rules=True&use_schema_label=True&data_model_labels=class_label&table_manipulation=replace&manifest_record_type=file_only "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:33:54] httpx - HTTP Request: POST http://localhost:3001/v1/model/submit?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fdata_flow_config%2Fmain%2FHTAN%2Fdataflow_component.csv&dataset_id=syn51376664&asset_view=syn51376649&restrict_rules=True&use_schema_label=True&data_model_labels=class_label&table_manipulation=replace&manifest_record_type=file_only "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:33:56] manifest-storage - Monitoring storage endpoints
INFO: [2024-08-29 21:34:02] httpx - HTTP Request: GET http://localhost:3001/v1/storage/assets/tables?asset_view=syn23643253&return_type=json "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:34:07] httpx - HTTP Request: GET http://localhost:3001/v1/storage/project/datasets?asset_view=syn23643253&project_id=syn26251192 "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:34:36] httpx - HTTP Request: GET http://localhost:3001/v1/storage/project/datasets?asset_view=syn20446927&project_id=syn32596076 "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:34:36] manifest-generator - Monitoring manifest generation
INFO: [2024-08-29 21:34:49] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&title=example&data_type=Patient "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:35:04] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&title=example&data_type=Patient&output=excel "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:35:25] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&title=example&data_type=Patient&output=excel&dataset_id=syn51078367&asset_view=syn23643253 "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:36:07] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2Fncihtan%2Fdata-models%2Fmain%2FHTAN.model.jsonld&title=example&data_type=Patient "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:36:07] manifest-storage - Monitoring storage endpoints
INFO: [2024-08-29 21:36:13] httpx - HTTP Request: GET http://localhost:3001/v1/storage/assets/tables?asset_view=syn23643253&return_type=json "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:36:19] httpx - HTTP Request: GET http://localhost:3001/v1/storage/project/datasets?asset_view=syn23643253&project_id=syn26251192 "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:36:48] httpx - HTTP Request: GET http://localhost:3001/v1/storage/project/datasets?asset_view=syn20446927&project_id=syn32596076 "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:36:48] manifest-generator - Monitoring manifest generation
INFO: [2024-08-29 21:36:59] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&title=example&data_type=Patient "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:37:11] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&title=example&data_type=Patient&output=excel "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:37:30] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&title=example&data_type=Patient&output=excel&dataset_id=syn51078367&asset_view=syn23643253 "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:38:15] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2Fncihtan%2Fdata-models%2Fmain%2FHTAN.model.jsonld&title=example&data_type=Patient "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:38:15] manifest-submit - Monitoring manifest submission
INFO: [2024-08-29 21:38:59] httpx - HTTP Request: POST http://localhost:3001/v1/model/submit?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&dataset_id=syn51376664&asset_view=syn51376649&restrict_rules=True&use_schema_label=True&data_model_labels=class_label&table_manipulation=replace&manifest_record_type=table_and_file "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:39:12] httpx - HTTP Request: POST http://localhost:3001/v1/model/submit?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&dataset_id=syn51376664&asset_view=syn51376649&restrict_rules=True&use_schema_label=True&data_model_labels=class_label&table_manipulation=replace&manifest_record_type=file_only "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:39:24] httpx - HTTP Request: POST http://localhost:3001/v1/model/submit?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fdata_flow_config%2Fmain%2FHTAN%2Fdataflow_component.csv&dataset_id=syn51376664&asset_view=syn51376649&restrict_rules=True&use_schema_label=True&data_model_labels=class_label&table_manipulation=replace&manifest_record_type=file_only "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:39:26] manifest-validate - Monitoring manifest validation
INFO: [2024-08-29 21:39:26] httpx - HTTP Request: POST http://localhost:3001/v1/model/validate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&data_type=Patient&restrict_rules=True "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:39:27] httpx - HTTP Request: POST http://localhost:3001/v1/model/validate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&data_type=Patient "HTTP/1.1 200 OK"
INFO: [2024-08-29 21:40:05] httpx - HTTP Request: POST http://localhost:3001/v1/model/validate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2Fncihtan%2Fdata-models%2Fmain%2FHTAN.model.jsonld&data_type=Biospecimen "HTTP/1.1 200 OK"

[thomasyu888]

🔥 LGTM! I ran schematic profiler on this after I started the API locally. However, most concurrent API calls made from my account will fail due to my access to hundreds of synapse projects so I had to run these in serial.

INFO: [2024-09-03 20:17:26] manifest-validate - Monitoring manifest validation
INFO: [2024-09-03 20:17:27] httpx - HTTP Request: POST http://localhost:3001/v1/model/validate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&data_type=Patient&restrict_rules=True "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:17:28] httpx - HTTP Request: POST http://localhost:3001/v1/model/validate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&data_type=Patient "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:18:08] httpx - HTTP Request: POST http://localhost:3001/v1/model/validate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2Fncihtan%2Fdata-models%2Fmain%2FHTAN.model.jsonld&data_type=Biospecimen "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:18:08] manifest-submit - Monitoring manifest submission
INFO: [2024-09-03 20:18:54] httpx - HTTP Request: POST http://localhost:3001/v1/model/submit?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&dataset_id=syn51376664&asset_view=syn51376649&restrict_rules=True&use_schema_label=True&data_model_labels=class_label&table_manipulation=replace&manifest_record_type=table_and_file "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:19:07] httpx - HTTP Request: POST http://localhost:3001/v1/model/submit?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&dataset_id=syn51376664&asset_view=syn51376649&restrict_rules=True&use_schema_label=True&data_model_labels=class_label&table_manipulation=replace&manifest_record_type=file_only "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:19:19] httpx - HTTP Request: POST http://localhost:3001/v1/model/submit?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fdata_flow_config%2Fmain%2FHTAN%2Fdataflow_component.csv&dataset_id=syn51376664&asset_view=syn51376649&restrict_rules=True&use_schema_label=True&data_model_labels=class_label&table_manipulation=replace&manifest_record_type=file_only "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:19:21] manifest-storage - Monitoring storage endpoints
INFO: [2024-09-03 20:19:27] httpx - HTTP Request: GET http://localhost:3001/v1/storage/assets/tables?asset_view=syn23643253&return_type=json "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:19:33] httpx - HTTP Request: GET http://localhost:3001/v1/storage/project/datasets?asset_view=syn23643253&project_id=syn26251192 "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:20:01] httpx - HTTP Request: GET http://localhost:3001/v1/storage/project/datasets?asset_view=syn20446927&project_id=syn32596076 "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:20:01] manifest-generator - Monitoring manifest generation
INFO: [2024-09-03 20:20:15] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&title=example&data_type=Patient "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:20:28] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&title=example&data_type=Patient&output=excel "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:20:52] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&title=example&data_type=Patient&output=excel&dataset_id=syn51078367&asset_view=syn23643253 "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:21:37] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2Fncihtan%2Fdata-models%2Fmain%2FHTAN.model.jsonld&title=example&data_type=Patient "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:21:37] manifest-storage - Monitoring storage endpoints
INFO: [2024-09-03 20:21:43] httpx - HTTP Request: GET http://localhost:3001/v1/storage/assets/tables?asset_view=syn23643253&return_type=json "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:21:49] httpx - HTTP Request: GET http://localhost:3001/v1/storage/project/datasets?asset_view=syn23643253&project_id=syn26251192 "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:22:17] httpx - HTTP Request: GET http://localhost:3001/v1/storage/project/datasets?asset_view=syn20446927&project_id=syn32596076 "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:22:17] manifest-generator - Monitoring manifest generation
INFO: [2024-09-03 20:22:30] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&title=example&data_type=Patient "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:22:42] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&title=example&data_type=Patient&output=excel "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:23:04] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&title=example&data_type=Patient&output=excel&dataset_id=syn51078367&asset_view=syn23643253 "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:23:51] httpx - HTTP Request: GET http://localhost:3001/v1/manifest/generate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2Fncihtan%2Fdata-models%2Fmain%2FHTAN.model.jsonld&title=example&data_type=Patient "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:23:51] manifest-submit - Monitoring manifest submission
INFO: [2024-09-03 20:24:35] httpx - HTTP Request: POST http://localhost:3001/v1/model/submit?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&dataset_id=syn51376664&asset_view=syn51376649&restrict_rules=True&use_schema_label=True&data_model_labels=class_label&table_manipulation=replace&manifest_record_type=table_and_file "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:24:48] httpx - HTTP Request: POST http://localhost:3001/v1/model/submit?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&dataset_id=syn51376664&asset_view=syn51376649&restrict_rules=True&use_schema_label=True&data_model_labels=class_label&table_manipulation=replace&manifest_record_type=file_only "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:25:02] httpx - HTTP Request: POST http://localhost:3001/v1/model/submit?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fdata_flow_config%2Fmain%2FHTAN%2Fdataflow_component.csv&dataset_id=syn51376664&asset_view=syn51376649&restrict_rules=True&use_schema_label=True&data_model_labels=class_label&table_manipulation=replace&manifest_record_type=file_only "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:25:04] manifest-validate - Monitoring manifest validation
INFO: [2024-09-03 20:25:05] httpx - HTTP Request: POST http://localhost:3001/v1/model/validate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&data_type=Patient&restrict_rules=True "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:25:06] httpx - HTTP Request: POST http://localhost:3001/v1/model/validate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2FSage-Bionetworks%2Fschematic%2Fdevelop%2Ftests%2Fdata%2Fexample.model.jsonld&data_type=Patient "HTTP/1.1 200 OK"
INFO: [2024-09-03 20:25:44] httpx - HTTP Request: POST http://localhost:3001/v1/model/validate?schema_url=https%3A%2F%2Fraw.githubusercontent.com%2Fncihtan%2Fdata-models%2Fmain%2FHTAN.model.jsonld&data_type=Biospecimen "HTTP/1.1 200 OK"

[sonarqubecloud]

Quality Gate passed

Issues
3 New issues
0 Accepted issues

Measures
0 Security Hotspots
100.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud