UNPKG

@hms-dbmi-bgm/react-workflow-viz

Version:

React component for visualizing CWL-like workflows and provenance graphs.

1,154 lines (1,153 loc) 414 kB
[ { "name": 1, "meta": { "@id": "/workflow-runs-awsem/d9b35c06-6911-4b67-ac04-395331a98e55/", "workflow": { "uuid": "ace7324e-2943-435b-ac1d-5565953953d5", "status": "in review", "display_title": "Run granite mpileupCounts - GAPFKJF3DVC7", "@type": [ "Workflow", "Item" ], "@id": "/workflows/ace7324e-2943-435b-ac1d-5565953953d5/", "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } }, "analysis_types": "dummy analysis type" }, "inputs": [ { "name": "input_bam", "source": [ { "name": "input_bams", "for_file": "/files-processed/GAPFIMIARUOB/", "step": 2 } ], "meta": { "global": true, "type": "data file" }, "run_data": { "type": "input", "file": [ { "uuid": "676dd0c1-82c4-41be-9ae7-619ce47e158e", "file_format": { "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@type": [ "FileFormat", "Item" ], "@id": "/file-formats/bam/", "status": "shared", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "display_title": "GAPFIMIARUOB.bam", "file_size": 106616301305, "@type": [ "FileProcessed", "File", "Item" ], "@id": "/files-processed/GAPFIMIARUOB/", "status": "uploaded", "workflow_run_outputs": [ { "status": "shared", "display_title": "workflow_sentieon_dedup-recal v1.0.0 run 2022-04-29 04:25:35.950498", "@type": [ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "@id": "/workflow-runs-awsem/784f3f5f-d3cf-432b-8c0f-3dcd957b2042/", "uuid": "784f3f5f-d3cf-432b-8c0f-3dcd957b2042", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } } ], "quality_metric": { "uuid": "b5978c20-271c-4ac4-8407-8b3fd3c0bb86", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2022-04-29", "@type": [ "QualityMetricBamqc", "QualityMetric", "Item" ], "status": "shared", "@id": "/quality-metrics-bamqc/b5978c20-271c-4ac4-8407-8b3fd3c0bb86/", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } } ], "meta": [ { "ordinal": 1, "dimension": "0", "workflow_argument_name": "input_bam" } ] } }, { "name": "reference", "source": [ { "name": "reference_fa", "for_file": "/files-reference/GAPFIXRDPDK5/" } ], "meta": { "global": true, "type": "reference file" }, "run_data": { "type": "input", "file": [ { "uuid": "1936f246-22e1-45dc-bb5c-9cfd55537fe7", "file_format": { "uuid": "5ced774b-a73e-4d1b-8186-d7fbbde7a3c2", "display_title": "fa", "@type": [ "FileFormat", "Item" ], "@id": "/file-formats/fa/", "status": "shared", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "display_title": "GAPFIXRDPDK5.fa", "file_size": 3263683042, "@type": [ "FileReference", "File", "Item" ], "@id": "/files-reference/GAPFIXRDPDK5/", "status": "uploaded", "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } } ], "meta": [ { "ordinal": 1, "dimension": "0", "workflow_argument_name": "reference" } ] } }, { "name": "regions", "source": [ { "name": "regions", "for_file": "/files-reference/GAPFIBGEOI72/" } ], "meta": { "global": true, "type": "reference file" }, "run_data": { "type": "input", "file": [ { "uuid": "1c07a3aa-e2a3-498c-b838-15991c4a2f28", "file_format": { "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "display_title": "txt", "@type": [ "FileFormat", "Item" ], "@id": "/file-formats/txt/", "status": "shared", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "display_title": "GAPFIBGEOI72.txt", "file_size": 7603, "@type": [ "FileReference", "File", "Item" ], "@id": "/files-reference/GAPFIBGEOI72/", "status": "uploaded", "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } } ], "meta": [ { "ordinal": 1, "dimension": "0", "workflow_argument_name": "regions" } ] } }, { "name": "nthreads", "source": [ { "name": "nthreads" } ], "meta": { "global": true, "type": "parameter" }, "run_data": { "type": "parameter", "value": [ "15" ], "meta": { "ordinal": 1, "dimension": "0", "workflow_argument_name": "nthreads" } } } ], "outputs": [ { "name": "rck", "target": [ { "name": "rck", "for_file": "/files-processed/GAPFI9CNINA2/", "step": 3 } ], "meta": { "type": "data file" }, "run_data": { "type": "output", "file": [ { "status": "uploaded", "display_title": "GAPFI9CNINA2.rck.gz", "uuid": "90d5572a-3cb5-40bd-8cec-68346c28705b", "file_format": { "@type": [ "FileFormat", "Item" ], "status": "shared", "display_title": "rck_gz", "uuid": "20d4d3aa-5f1c-4b75-9e25-73f9f370fefa", "@id": "/file-formats/rck_gz/", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "file_size": 11922164723, "@id": "/files-processed/GAPFI9CNINA2/", "@type": [ "FileProcessed", "File", "Item" ], "workflow_run_inputs": [ { "@type": [ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "uuid": "6fb5a7f0-2156-49e3-bf42-95f4e8decdde", "@id": "/workflow-runs-awsem/6fb5a7f0-2156-49e3-bf42-95f4e8decdde/", "display_title": "workflow_granite-rckTar v1.0.0 run 2022-04-29 21:10:35.118284", "status": "shared", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } } ], "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } } ], "meta": [ { "type": "Output processed file" } ] } } ] }, { "name": 4, "meta": { "@id": "/workflow-runs-awsem/8bca34d8-54c4-4de8-9057-ffb868d44795/", "workflow": { "uuid": "ace7324e-2943-435b-ac1d-5565953953d5", "status": "in review", "display_title": "Run granite mpileupCounts - GAPFKJF3DVC7", "@type": [ "Workflow", "Item" ], "@id": "/workflows/ace7324e-2943-435b-ac1d-5565953953d5/", "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } }, "analysis_types": "dummy analysis type" }, "inputs": [ { "name": "input_bam", "source": [ { "name": "input_bams", "for_file": "/files-processed/GAPFICEE9LEN/", "step": 5 } ], "meta": { "global": true, "type": "data file" }, "run_data": { "type": "input", "file": [ { "uuid": "6d199319-3719-4a42-8883-365072bc13b3", "file_format": { "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@type": [ "FileFormat", "Item" ], "@id": "/file-formats/bam/", "status": "shared", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "display_title": "GAPFICEE9LEN.bam", "file_size": 104992897560, "@type": [ "FileProcessed", "File", "Item" ], "@id": "/files-processed/GAPFICEE9LEN/", "status": "uploaded", "workflow_run_outputs": [ { "status": "shared", "display_title": "workflow_sentieon_dedup-recal v1.0.0 run 2022-04-29 04:25:39.481922", "@type": [ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "@id": "/workflow-runs-awsem/25d04009-a2fe-481b-ada7-da5c1216d52e/", "uuid": "25d04009-a2fe-481b-ada7-da5c1216d52e", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } } ], "quality_metric": { "uuid": "23408f2f-13ca-49d6-b8bf-162623795dd6", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2022-04-29", "@type": [ "QualityMetricBamqc", "QualityMetric", "Item" ], "status": "shared", "@id": "/quality-metrics-bamqc/23408f2f-13ca-49d6-b8bf-162623795dd6/", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } } ], "meta": [ { "ordinal": 1, "dimension": "0", "workflow_argument_name": "input_bam" } ] } }, { "name": "reference", "source": [ { "name": "reference_fa", "for_file": "/files-reference/GAPFIXRDPDK5/" } ], "meta": { "global": true, "type": "reference file" }, "run_data": { "type": "input", "file": [ { "uuid": "1936f246-22e1-45dc-bb5c-9cfd55537fe7", "file_format": { "uuid": "5ced774b-a73e-4d1b-8186-d7fbbde7a3c2", "display_title": "fa", "@type": [ "FileFormat", "Item" ], "@id": "/file-formats/fa/", "status": "shared", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "display_title": "GAPFIXRDPDK5.fa", "file_size": 3263683042, "@type": [ "FileReference", "File", "Item" ], "@id": "/files-reference/GAPFIXRDPDK5/", "status": "uploaded", "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } } ], "meta": [ { "ordinal": 1, "dimension": "0", "workflow_argument_name": "reference" } ] } }, { "name": "regions", "source": [ { "name": "regions", "for_file": "/files-reference/GAPFIBGEOI72/" } ], "meta": { "global": true, "type": "reference file" }, "run_data": { "type": "input", "file": [ { "uuid": "1c07a3aa-e2a3-498c-b838-15991c4a2f28", "file_format": { "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "display_title": "txt", "@type": [ "FileFormat", "Item" ], "@id": "/file-formats/txt/", "status": "shared", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "display_title": "GAPFIBGEOI72.txt", "file_size": 7603, "@type": [ "FileReference", "File", "Item" ], "@id": "/files-reference/GAPFIBGEOI72/", "status": "uploaded", "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } } ], "meta": [ { "ordinal": 1, "dimension": "0", "workflow_argument_name": "regions" } ] } }, { "name": "nthreads", "source": [ { "name": "nthreads" } ], "meta": { "global": true, "type": "parameter" }, "run_data": { "type": "parameter", "value": [ "15" ], "meta": { "ordinal": 1, "dimension": "0", "workflow_argument_name": "nthreads" } } } ], "outputs": [ { "name": "rck", "target": [ { "name": "rck", "for_file": "/files-processed/GAPFID5AE9ME/", "step": 3 } ], "meta": { "type": "data file" }, "run_data": { "type": "output", "file": [ { "status": "uploaded", "display_title": "GAPFID5AE9ME.rck.gz", "uuid": "76111407-5e86-48dd-bd13-f3a167638140", "file_format": { "@type": [ "FileFormat", "Item" ], "status": "shared", "display_title": "rck_gz", "uuid": "20d4d3aa-5f1c-4b75-9e25-73f9f370fefa", "@id": "/file-formats/rck_gz/", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "file_size": 11874191792, "@id": "/files-processed/GAPFID5AE9ME/", "@type": [ "FileProcessed", "File", "Item" ], "workflow_run_inputs": [ { "@type": [ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "uuid": "6fb5a7f0-2156-49e3-bf42-95f4e8decdde", "@id": "/workflow-runs-awsem/6fb5a7f0-2156-49e3-bf42-95f4e8decdde/", "display_title": "workflow_granite-rckTar v1.0.0 run 2022-04-29 21:10:35.118284", "status": "shared", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } } ], "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } } ], "meta": [ { "type": "Output processed file" } ] } } ] }, { "name": 6, "meta": { "@id": "/workflow-runs-awsem/e93fc945-f186-41e0-a0c3-b19a007ce81c/", "workflow": { "uuid": "ace7324e-2943-435b-ac1d-5565953953d5", "status": "in review", "display_title": "Run granite mpileupCounts - GAPFKJF3DVC7", "@type": [ "Workflow", "Item" ], "@id": "/workflows/ace7324e-2943-435b-ac1d-5565953953d5/", "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } }, "analysis_types": "dummy analysis type" }, "inputs": [ { "name": "input_bam", "source": [ { "name": "input_bams", "for_file": "/files-processed/GAPFITNHTOZI/", "step": 7 } ], "meta": { "global": true, "type": "data file" }, "run_data": { "type": "input", "file": [ { "uuid": "222ce0eb-22f8-40e3-87d5-f2708ad18393", "file_format": { "uuid": "d13d06cf-218e-4f61-aaf0-91f226248b3c", "display_title": "bam", "@type": [ "FileFormat", "Item" ], "@id": "/file-formats/bam/", "status": "shared", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "display_title": "GAPFITNHTOZI.bam", "file_size": 111610806810, "@type": [ "FileProcessed", "File", "Item" ], "@id": "/files-processed/GAPFITNHTOZI/", "status": "uploaded", "workflow_run_outputs": [ { "status": "shared", "display_title": "workflow_sentieon_dedup-recal v1.0.0 run 2022-04-29 04:25:46.368031", "@type": [ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "@id": "/workflow-runs-awsem/d4b58584-ecc6-41ad-a0ce-81d4b600b033/", "uuid": "d4b58584-ecc6-41ad-a0ce-81d4b600b033", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } } ], "quality_metric": { "uuid": "5530ced5-5252-42f2-afde-0d14e30a669b", "overall_quality_status": "PASS", "display_title": "QualityMetricBamqc from 2022-04-29", "@type": [ "QualityMetricBamqc", "QualityMetric", "Item" ], "status": "shared", "@id": "/quality-metrics-bamqc/5530ced5-5252-42f2-afde-0d14e30a669b/", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } } ], "meta": [ { "ordinal": 1, "dimension": "0", "workflow_argument_name": "input_bam" } ] } }, { "name": "reference", "source": [ { "name": "reference_fa", "for_file": "/files-reference/GAPFIXRDPDK5/" } ], "meta": { "global": true, "type": "reference file" }, "run_data": { "type": "input", "file": [ { "uuid": "1936f246-22e1-45dc-bb5c-9cfd55537fe7", "file_format": { "uuid": "5ced774b-a73e-4d1b-8186-d7fbbde7a3c2", "display_title": "fa", "@type": [ "FileFormat", "Item" ], "@id": "/file-formats/fa/", "status": "shared", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "display_title": "GAPFIXRDPDK5.fa", "file_size": 3263683042, "@type": [ "FileReference", "File", "Item" ], "@id": "/files-reference/GAPFIXRDPDK5/", "status": "uploaded", "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } } ], "meta": [ { "ordinal": 1, "dimension": "0", "workflow_argument_name": "reference" } ] } }, { "name": "regions", "source": [ { "name": "regions", "for_file": "/files-reference/GAPFIBGEOI72/" } ], "meta": { "global": true, "type": "reference file" }, "run_data": { "type": "input", "file": [ { "uuid": "1c07a3aa-e2a3-498c-b838-15991c4a2f28", "file_format": { "uuid": "0cd4e777-a596-4927-95c8-b07716121aa3", "display_title": "txt", "@type": [ "FileFormat", "Item" ], "@id": "/file-formats/txt/", "status": "shared", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "display_title": "GAPFIBGEOI72.txt", "file_size": 7603, "@type": [ "FileReference", "File", "Item" ], "@id": "/files-reference/GAPFIBGEOI72/", "status": "uploaded", "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED", "remoteuser.INDEXER" ], "edit": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin" ] } } ], "meta": [ { "ordinal": 1, "dimension": "0", "workflow_argument_name": "regions" } ] } }, { "name": "nthreads", "source": [ { "name": "nthreads" } ], "meta": { "global": true, "type": "parameter" }, "run_data": { "type": "parameter", "value": [ "15" ], "meta": { "ordinal": 1, "dimension": "0", "workflow_argument_name": "nthreads" } } } ], "outputs": [ { "name": "rck", "target": [ { "name": "rck", "for_file": "/files-processed/GAPFI5T4QIBP/", "step": 3 } ], "meta": { "type": "data file" }, "run_data": { "type": "output", "file": [ { "status": "uploaded", "display_title": "GAPFI5T4QIBP.rck.gz", "uuid": "87e8832d-9ece-439a-8602-152b1ee74b0f", "file_format": { "@type": [ "FileFormat", "Item" ], "status": "shared", "display_title": "rck_gz", "uuid": "20d4d3aa-5f1c-4b75-9e25-73f9f370fefa", "@id": "/file-formats/rck_gz/", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } }, "file_size": 12086253767, "@id": "/files-processed/GAPFI5T4QIBP/", "@type": [ "FileProcessed", "File", "Item" ], "workflow_run_inputs": [ { "@type": [ "WorkflowRunAwsem", "WorkflowRun", "Item" ], "uuid": "6fb5a7f0-2156-49e3-bf42-95f4e8decdde", "@id": "/workflow-runs-awsem/6fb5a7f0-2156-49e3-bf42-95f4e8decdde/", "display_title": "workflow_granite-rckTar v1.0.0 run 2022-04-29 21:10:35.118284", "status": "shared", "principals_allowed": { "view": [ "system.Authenticated" ], "edit": [ "group.admin" ] } } ], "principals_allowed": { "view": [ "editor_for.12a92962-8265-4fc0-b2f8-cf14f05db58b", "group.admin", "group.read-only-admin", "remoteuser.EMBED",