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Coverage Report

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 3 0 0 62% 20-24
biocloudcore/common_slack_functions.py 8 8 0 0 0% 5-22
biocloudcore/common_utility_functions.py 27 17 6 1 39% 31, 44-45, 57-73
biocloudcore/conftest.py 118 11 30 12 84% 47->52, 69, 71, 92, 94, 96, 111->120, 113, 119, 158, 192, 236, 271
biocloudcore/curated/common_dna_functions.py 16 16 0 0 0% 5-180
biocloudcore/curated/crs_harvest_monitor/archive.py 16 16 0 0 0% 1-32
biocloudcore/curated/crs_harvest_monitor/common_harvest_monitor_functions.py 5 5 0 0 0% 5-35
biocloudcore/curated/crs_harvest_monitor/status.py 21 21 0 0 0% 1-54
biocloudcore/curated/dsi/common_dsi_functions.py 20 20 6 0 0% 5-98
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/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/data_lake.py 134 82 16 0 35% 19-26, 37, 41-47, 75-385, 401, 428-433, 440, 444-450, 455-457, 467-475, 485, 494-501, 506-508, 511-512, 517, 522-524, 543-544, 563-570, 575, 587-597, 610-611, 621-622, 635-636, 639
biocloudcore/enriched/common_datamodel_functions.py 30 1 2 1 94% 167
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/material_entity.py 47 1 2 1 96% 116
biocloudcore/enriched/enriched_delta_table.py 23 1 2 1 92% 101
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/sensor.py 37 3 4 1 90% 103-119
biocloudcore/landing_zone/faunabit/api/faunabit_api.py 36 36 4 0 0% 1-76
biocloudcore/landing_zone/faunabit/ingest_faunabit.py 37 37 10 0 0% 1-72
biocloudcore/landing_zone/keycloak/ingest_keycloak.py 18 18 2 0 0% 1-32
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/naturalis_ai_server/api/naturalis_ai_server_api.py 116 116 30 0 0% 1-220
biocloudcore/landing_zone/naturalis_ai_server/ingest_naturalis_ai_server.py 95 95 34 0 0% 1-173
biocloudcore/raw/ada/validators/registrations_validator.py 56 3 8 2 92% 30-31, 89
biocloudcore/raw/common_bucket_functions.py 26 26 6 0 0% 5-90
biocloudcore/raw/common_cleaning_functions.py 34 34 12 0 0% 5-144
biocloudcore/raw/common_s3_functions.py 75 75 14 0 0% 5-215
biocloudcore/raw/common_validator_functions.py 99 71 36 1 21% 27-30, 46-47, 112, 126-127, 143-144, 149-166, 171-198, 231-249, 268-285
biocloudcore/raw/communicator.py 20 20 0 0 0% 1-78
biocloudcore/raw/dsi/algorithm.py 28 28 0 0 0% 1-70
biocloudcore/raw/dsi/analysis_group_result.py 28 28 0 0 0% 1-70
biocloudcore/raw/dsi/analysis_job.py 28 28 0 0 0% 1-70
biocloudcore/raw/dsi/analysis_job_artifact.py 28 28 0 0 0% 1-70
biocloudcore/raw/dsi/project.py 28 28 0 0 0% 1-70
biocloudcore/raw/dsi/sensor.py 28 28 0 0 0% 1-70
biocloudcore/raw/dsi/sensor_deployment.py 28 28 0 0 0% 1-70
biocloudcore/raw/dsi/sensor_media_item.py 28 28 0 0 0% 1-70
biocloudcore/raw/dsi/sensor_model.py 28 28 0 0 0% 1-70
biocloudcore/raw/dsi/sensor_type.py 28 28 0 0 0% 1-70
biocloudcore/raw/dsi/site.py 28 28 0 0 0% 1-70
biocloudcore/raw/faunabit/deployments.py 35 35 4 0 0% 1-123
biocloudcore/raw/faunabit/devices.py 34 34 4 0 0% 1-117
biocloudcore/raw/faunabit/locations.py 35 35 4 0 0% 1-120
biocloudcore/raw/faunabit/projects.py 34 34 4 0 0% 1-117
biocloudcore/raw/faunabit/sensor_media_items.py 85 85 20 0 0% 1-273
biocloudcore/raw/faunabit/validators/deployments_validator.py 9 9 0 0 0% 1-13
biocloudcore/raw/faunabit/validators/devices_validator.py 9 9 0 0 0% 1-13
biocloudcore/raw/faunabit/validators/locations_validator.py 9 9 0 0 0% 1-13
biocloudcore/raw/faunabit/validators/projects_validator.py 9 9 0 0 0% 1-13
biocloudcore/raw/faunabit/validators/sensor_media_items_validator.py 9 9 0 0 0% 1-13
biocloudcore/raw/keycloak/resources.py 35 35 4 0 0% 1-116
biocloudcore/raw/keycloak/users.py 34 34 4 0 0% 1-120
biocloudcore/raw/keycloak/validators/resources_validator.py 7 7 0 0 0% 1-9
biocloudcore/raw/keycloak/validators/users_validator.py 7 7 0 0 0% 1-9
biocloudcore/raw/nanopore/amplicons_deletions.py 28 16 4 0 38% 36-43, 46-83
biocloudcore/raw/nanopore/consensuses.py 31 19 4 0 34% 60-67, 72-130
biocloudcore/raw/nanopore/consensuses_deletions.py 28 16 4 0 38% 36-43, 46-83
biocloudcore/raw/nanopore/sequencing_runs.py 31 19 4 0 34% 59-66, 75-134
biocloudcore/raw/nanopore/validators/amplicons_validator.py 37 2 4 1 93% 36-37
biocloudcore/raw/nanopore/validators/consensuses_validator.py 24 18 4 0 21% 7, 10-47, 59-62
biocloudcore/raw/nanopore/validators/deletions_validator.py 14 10 4 0 22% 6-7, 19-32
biocloudcore/raw/nanopore/validators/sequencing_runs_validator.py 15 9 2 0 35% 7, 10-17, 29-32
biocloudcore/scripts/check_datacontract_version.py 31 31 12 0 0% 3-84
biocloudcore/scripts/update_vault_token.py 27 17 4 0 32% 29-42, 55-74
biocloudcore/scripts/vault_secrets_to_databricks.py 47 47 10 0 0% 8-113
biocloudcore/spark_session.py 56 18 10 3 65% 31-33, 45-48, 55, 59, 73-75, 89-91, 159-162, 167
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/data_quality/soda_quality_checks.py 84 34 12 6 58% 59, 63, 102, 128-149, 259-260, 269-270, 281-300, 318-328, 331-338, 341
biocloudcore/utils/spark_utils.py 320 236 122 11 22% 38-52, 90-124, 147, 156->175, 168, 176-177, 213-224, 227, 250-387, 392, 409-420, 427-442, 453-461, 470-477, 497->499, 500, 507, 540-565, 613-637, 679-688, 735-794, 808-827, 859-866, 880-887, 925-969, 1016->1019, 1020, 1045-1048, 1058-1064, 1082-1095
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 39 31 12 0 16% 19-33, 45-50, 62-89, 101-106
TOTAL 5240 2880 716 45 41%

49 files skipped due to complete coverage.