Coverage Report¶
| Name | Stmts | Miss | Branch | BrPart | Cover | Missing |
|---|---|---|---|---|---|---|
| biocloudcore/cmd_parser.py | 49 | 49 | 24 | 0 | 0% | 1-101 |
| biocloudcore/common_dataframe_functions.py | 8 | 4 | 0 | 0 | 50% | 16-20, 33 |
| biocloudcore/common_slack_functions.py | 8 | 8 | 0 | 0 | 0% | 5-22 |
| biocloudcore/common_utility_functions.py | 28 | 17 | 6 | 1 | 41% | 31, 44-45, 57-73 |
| biocloudcore/conftest.py | 87 | 8 | 24 | 10 | 84% | 47->52, 69, 71, 92, 94, 96, 111->120, 113, 119, 174 |
| biocloudcore/curated/common_dna_functions.py | 16 | 16 | 0 | 0 | 0% | 1-134 |
| biocloudcore/curated/dsi/common_dsi_functions.py | 20 | 20 | 6 | 0 | 0% | 1-94 |
| biocloudcore/curated/dsi/deployment.py | 15 | 15 | 0 | 0 | 0% | 1-69 |
| biocloudcore/curated/dsi/deployment_project.py | 15 | 15 | 0 | 0 | 0% | 1-56 |
| biocloudcore/curated/dsi/media_item.py | 15 | 15 | 0 | 0 | 0% | 1-67 |
| biocloudcore/curated/dsi/project.py | 15 | 15 | 0 | 0 | 0% | 1-60 |
| biocloudcore/curated/dsi/run_deployment.py | 15 | 15 | 2 | 0 | 0% | 1-40 |
| biocloudcore/curated/dsi/run_deployment_project.py | 15 | 15 | 2 | 0 | 0% | 1-40 |
| biocloudcore/curated/dsi/run_dsi_curated_cleanup.py | 13 | 13 | 2 | 0 | 0% | 1-31 |
| biocloudcore/curated/dsi/run_media_item.py | 15 | 15 | 2 | 0 | 0% | 1-40 |
| biocloudcore/curated/dsi/run_project.py | 15 | 15 | 2 | 0 | 0% | 1-40 |
| biocloudcore/curated/dsi/run_sensor.py | 15 | 15 | 2 | 0 | 0% | 1-40 |
| biocloudcore/curated/dsi/sensor.py | 17 | 17 | 0 | 0 | 0% | 1-76 |
| biocloudcore/curated/keycloak/deployment_sync.py | 36 | 36 | 4 | 0 | 0% | 1-154 |
| biocloudcore/curated/keycloak/rights_sync.py | 70 | 70 | 12 | 0 | 0% | 1-273 |
| biocloudcore/curated/keycloak/run_deployment_sync.py | 13 | 13 | 2 | 0 | 0% | 1-29 |
| biocloudcore/curated/keycloak/run_rights_sync.py | 13 | 13 | 2 | 0 | 0% | 1-29 |
| biocloudcore/data_lake.py | 134 | 82 | 16 | 0 | 35% | 20-27, 38, 42-48, 76-386, 402, 437-442, 449, 453-459, 464-466, 476-484, 494, 503-510, 515-517, 520-521, 526, 531-533, 552-553, 572-579, 584, 596-606, 619-620, 630-631, 644-645, 648 |
| biocloudcore/enriched/common_datamodel_functions.py | 30 | 1 | 2 | 1 | 94% | 163 |
| biocloudcore/enriched/dna/amplicon.py | 33 | 2 | 2 | 1 | 91% | 111-118 |
| biocloudcore/enriched/dna/consensus_sequence.py | 33 | 2 | 2 | 1 | 91% | 102-109 |
| biocloudcore/enriched/dna/dags/enriched_csc.py | 35 | 35 | 0 | 0 | 0% | 1-162 |
| biocloudcore/enriched/dna/dags/enriched_dna_identification.py | 20 | 20 | 0 | 0 | 0% | 1-72 |
| biocloudcore/enriched/dna/material_entity.py | 47 | 1 | 2 | 1 | 96% | 116 |
| biocloudcore/enriched/dna/run_additional_number.py | 22 | 22 | 2 | 0 | 0% | 1-41 |
| biocloudcore/enriched/dna/run_amplicon.py | 26 | 26 | 4 | 0 | 0% | 1-52 |
| biocloudcore/enriched/dna/run_consensus_sequence.py | 25 | 25 | 4 | 0 | 0% | 1-51 |
| biocloudcore/enriched/dna/run_dna_extract.py | 22 | 22 | 2 | 0 | 0% | 1-47 |
| biocloudcore/enriched/dna/run_identification_dna.py | 21 | 21 | 2 | 0 | 0% | 1-40 |
| biocloudcore/enriched/dna/run_identification_morphology.py | 22 | 22 | 2 | 0 | 0% | 1-45 |
| biocloudcore/enriched/dna/run_material_entity.py | 22 | 22 | 2 | 0 | 0% | 1-45 |
| biocloudcore/enriched/dna/run_sample_sheet.py | 21 | 21 | 2 | 0 | 0% | 1-43 |
| biocloudcore/enriched/dna/run_sequencing_run.py | 21 | 21 | 2 | 0 | 0% | 1-43 |
| biocloudcore/enriched/enriched_delta_table.py | 23 | 1 | 2 | 1 | 92% | 101 |
| biocloudcore/enriched/keycloak/run_user_permission.py | 24 | 24 | 2 | 0 | 0% | 1-49 |
| biocloudcore/enriched/media/dags/enriched_diopsis.py | 28 | 28 | 0 | 0 | 0% | 1-102 |
| biocloudcore/enriched/media/deployment.py | 35 | 1 | 2 | 1 | 95% | 135 |
| biocloudcore/enriched/media/project.py | 32 | 1 | 2 | 1 | 94% | 101 |
| biocloudcore/enriched/media/run_deployment.py | 24 | 24 | 2 | 0 | 0% | 1-54 |
| biocloudcore/enriched/media/run_deployment_project.py | 24 | 24 | 2 | 0 | 0% | 1-54 |
| biocloudcore/enriched/media/run_media_item.py | 24 | 24 | 2 | 0 | 0% | 1-54 |
| biocloudcore/enriched/media/run_project.py | 22 | 22 | 2 | 0 | 0% | 1-47 |
| biocloudcore/enriched/media/run_sensor.py | 22 | 22 | 2 | 0 | 0% | 1-52 |
| biocloudcore/enriched/media/sensor.py | 37 | 3 | 4 | 1 | 90% | 103-119 |
| biocloudcore/landing_zone/dienekes/dags/lz_metadata_sheets.py | 24 | 24 | 0 | 0 | 0% | 1-97 |
| biocloudcore/landing_zone/dienekes/dags/lz_sample_sheets.py | 21 | 21 | 0 | 0 | 0% | 1-76 |
| biocloudcore/landing_zone/faunabit/api/faunabit_api.py | 36 | 36 | 4 | 0 | 0% | 1-76 |
| biocloudcore/landing_zone/faunabit/dags/lz_faunabit.py | 16 | 16 | 0 | 0 | 0% | 1-59 |
| biocloudcore/landing_zone/faunabit/ingest_faunabit.py | 37 | 37 | 10 | 0 | 0% | 1-72 |
| biocloudcore/landing_zone/faunabit/run_ingest_faunabit.py | 13 | 13 | 2 | 0 | 0% | 1-31 |
| biocloudcore/landing_zone/keycloak/dags/lz_keycloak.py | 16 | 16 | 0 | 0 | 0% | 1-56 |
| biocloudcore/landing_zone/keycloak/ingest_keycloak.py | 18 | 18 | 2 | 0 | 0% | 1-32 |
| biocloudcore/landing_zone/keycloak/run_ingest_keycloak.py | 10 | 10 | 2 | 0 | 0% | 1-23 |
| biocloudcore/landing_zone/nanopore/dags/lz_nanopore.py | 19 | 19 | 0 | 0 | 0% | 1-87 |
| biocloudcore/landing_zone/nanopore/ingest_deletions.py | 32 | 32 | 4 | 0 | 0% | 1-98 |
| biocloudcore/landing_zone/nanopore/ingest_nanopore.py | 32 | 32 | 4 | 0 | 0% | 1-99 |
| biocloudcore/landing_zone/nanopore/run_ingest_deletions.py | 18 | 18 | 2 | 0 | 0% | 1-42 |
| biocloudcore/landing_zone/nanopore/run_ingest_nanopore.py | 18 | 18 | 2 | 0 | 0% | 1-42 |
| biocloudcore/landing_zone/naturalis_ai_server/api/naturalis_ai_server_api.py | 116 | 116 | 30 | 0 | 0% | 1-220 |
| biocloudcore/landing_zone/naturalis_ai_server/dags/lz_naturalis_ai_server.py | 12 | 12 | 0 | 0 | 0% | 1-45 |
| biocloudcore/landing_zone/naturalis_ai_server/ingest_naturalis_ai_server.py | 95 | 95 | 34 | 0 | 0% | 1-173 |
| biocloudcore/landing_zone/naturalis_ai_server/run_ingest_naturalis_ai_server.py | 10 | 10 | 2 | 0 | 0% | 1-30 |
| biocloudcore/raw/common_validator_functions.py | 193 | 108 | 106 | 23 | 43% | 22-25, 41-42, 61-76, 107, 121-122, 138-139, 144-161, 166-193, 226-244, 268, 293, 298->397, 305, 307, 309, 311, 325, 327, 336, 338, 340-343, 349, 352, 366, 370, 372, 374, 378-391, 416-433, 474, 479-480 |
| biocloudcore/scripts/check_datacontract_version.py | 31 | 31 | 12 | 0 | 0% | 3-84 |
| biocloudcore/scripts/vault_secrets_to_databricks.py | 47 | 47 | 10 | 0 | 0% | 8-113 |
| biocloudcore/spark_session.py | 56 | 24 | 10 | 3 | 56% | 31-33, 45-48, 55, 59, 73-75, 89-91, 150, 159-162, 167, 171-178 |
| biocloudcore/utils/airflow/custom_operators.py | 42 | 42 | 12 | 0 | 0% | 1-100 |
| biocloudcore/utils/airflow/dag_config.py | 56 | 56 | 6 | 0 | 0% | 1-286 |
| biocloudcore/utils/airflow/delete_single_dag.py | 58 | 58 | 14 | 0 | 0% | 22-141 |
| biocloudcore/utils/airflow/development_cleanup_dags.py | 101 | 101 | 42 | 0 | 0% | 13-178 |
| biocloudcore/utils/airflow/docker_runner/docker_runner.py | 28 | 28 | 2 | 0 | 0% | 1-39 |
| biocloudcore/utils/clients/clickhouse_client.py | 8 | 8 | 0 | 0 | 0% | 1-22 |
| biocloudcore/utils/clients/keycloak_client.py | 210 | 182 | 62 | 0 | 10% | 9-17, 20-21, 24-25, 28-29, 32-41, 44-53, 65-79, 82-88, 91-96, 99-104, 107-112, 115-121, 124-132, 135-140, 143-145, 148-153, 156-164, 167-169, 172-177, 180-193, 196-212, 215-258, 261-281, 285-290 |
| biocloudcore/utils/clients/nbitk_client.py | 9 | 9 | 0 | 0 | 0% | 1-15 |
| biocloudcore/utils/clients/s3_client.py | 163 | 139 | 20 | 0 | 13% | 15-19, 27, 37, 53-59, 71-78, 82-89, 100-110, 114-121, 125-131, 145-156, 168-182, 191-197, 208-223, 251-293, 306-316, 330-348, 365-382 |
| biocloudcore/utils/spark_utils.py | 321 | 248 | 122 | 8 | 19% | 38-52, 90-124, 147, 156->175, 168, 176-177, 213-224, 227, 250-387, 392, 409-420, 427-442, 453-461, 470-477, 495-512, 540-565, 613-637, 679-688, 735-794, 808-827, 859-866, 880-887, 925-967, 1014->1017, 1018, 1043-1046, 1056-1062, 1080-1093 |
| biocloudcore/utils/test_tools/test_dataset.py | 17 | 5 | 0 | 0 | 71% | 40-42, 58-59 |
| biocloudcore/utils/test_tools/test_functions.py | 51 | 20 | 10 | 0 | 54% | 131-135, 148-155, 166-171, 181-184 |
| biocloudcore/utils/tests/create_dataframe_from_delta_table_test.py | 2 | 2 | 0 | 0 | 0% | 2-9 |
| biocloudcore/utils/tests/delete_records_test.py | 2 | 2 | 0 | 0 | 0% | 2-20 |
| biocloudcore/utils/tests/upsert_dates_no_change_test.py | 2 | 2 | 0 | 0 | 0% | 2-30 |
| biocloudcore/utils/tests/upsert_dates_test.py | 2 | 2 | 0 | 0 | 0% | 2-16 |
| biocloudcore/utils/tests/write_as_delta_table_test.py | 2 | 2 | 0 | 0 | 0% | 2-14 |
| biocloudcore/utils/tests/write_as_parquet_file_test.py | 2 | 2 | 0 | 0 | 0% | 2-19 |
| biocloudcore/vault.py | 36 | 29 | 10 | 0 | 15% | 17-27, 39-44, 56-83, 95-100 |
| TOTAL | 4615 | 2628 | 700 | 53 | 39% |
80 files skipped due to complete coverage.