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Merge pull request #627 from hubmapconsortium/jpuerto/visium-dir-sche…
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…ma-updates

Jpuerto/visium dir schema updates
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@yuanzhou
yuanzhou authored Sep 9, 2024
2 parents 8ce3156 + 04713eb commit c903530
Showing 1 changed file with 31 additions and 7 deletions.
38 changes: 31 additions & 7 deletions src/routes/assayclassifier/testing_rule_chain.json
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,12 @@
"value": "{'version': 0}",
"rule_description": "Cover default schema version = 0 for non-DCWG metadata"
},
{
"type": "note",
"match": "creation_action == 'External Process' or (parent_dataset_id != null and derived_dataset_type != null)",
"value": "{'is_epic': true}",
"rule_description": "Preamble rule identifying EPIC"
},
{
"type": "match",
"match": "not_dcwg and is_primary and assay_type in ['AF']",
Expand Down Expand Up @@ -302,7 +308,7 @@
{
"type": "match",
"match": "not_dcwg and is_primary and assay_type in ['SNARE-RNAseq2', 'SNARE2-RNAseq']",
"value": "{'assaytype': 'SNARE-RNAseq2', 'dir-schema': 'scrnaseq-v0', 'tbl-schema': 'scrnaseq-v'+version.to_str, 'vitessce-hints': [], 'contains-pii': true, 'primary': true, 'description': 'snRNAseq (10x Genomics v3)', 'dataset-type': 'RNAseq' }",
"value": "{'assaytype': 'SNARE-RNAseq2', 'dir-schema': 'scrnaseq-v0', 'tbl-schema': 'scrnaseq-v'+version.to_str, 'vitessce-hints': [], 'contains-pii': true, 'primary': true, 'description': 'snRNAseq (SNAREseq2)', 'dataset-type': 'RNAseq' }",
"rule_description": "non-DCWG primary SNARE-RNAseq2"
},
{
Expand Down Expand Up @@ -506,13 +512,13 @@
{
"type": "match",
"match": "is_dcwg and is_primary and dataset_type == 'Visium (no probes)'",
"value": "{'assaytype': 'visium-no-probes', 'vitessce-hints': [], 'dir-schema': 'visium-no-probes-v2', 'description': 'Visium (no probes)', 'contains-pii': true, 'primary': true, 'dataset-type': 'Visium (no probes)', 'must-contain': ['Histology','RNAseq'], 'is-multi-assay': true}",
"value": "{'assaytype': 'visium-no-probes', 'vitessce-hints': [], 'dir-schema': 'visium-no-probes-v3', 'description': 'Visium (no probes)', 'contains-pii': true, 'primary': true, 'dataset-type': 'Visium (no probes)', 'must-contain': ['Histology','RNAseq'], 'is-multi-assay': true}",
"rule_description": "DCWG visium-no-probes"
},
{
"type": "match",
"match": "is_dcwg and is_primary and dataset_type == 'Visium (with probes)'",
"value": "{'assaytype': 'visium-with-probes', 'vitessce-hints': [], 'dir-schema': 'visium-with-probes-v2', 'description': 'Visium (with probes)', 'contains-pii': true, 'primary': true, 'dataset-type': 'Visium (with probes)', 'must-contain': ['Histology','RNAseq (with probes)'], 'is-multi-assay': true}",
"value": "{'assaytype': 'visium-with-probes', 'vitessce-hints': [], 'dir-schema': 'visium-with-probes-v3', 'description': 'Visium (with probes)', 'contains-pii': true, 'primary': true, 'dataset-type': 'Visium (with probes)', 'must-contain': ['Histology','RNAseq (with probes)'], 'is-multi-assay': true}",
"rule_description": "DCWG visium-with-probes"
},
{
Expand Down Expand Up @@ -542,7 +548,7 @@
{
"type": "match",
"match": "is_dcwg and is_primary and dataset_type == 'RNAseq' and assay_input_entity == 'single nucleus' and barcode_read =~~ 'Read 2' and barcode_size == '8,8,8' and barcode_offset == '10,48,86' and umi_read =~~ 'Read 2' and umi_size == 10 and umi_offset == 0",
"value": "{'assaytype': 'SNARE-RNAseq2', 'vitessce-hints': [], 'dir-schema': 'rnaseq-v2', 'contains-pii': true, 'primary': true, 'dataset-type': 'RNAseq', 'description': 'snRNAseq (10x Genomics v3)'}",
"value": "{'assaytype': 'SNARE-RNAseq2', 'vitessce-hints': [], 'dir-schema': 'rnaseq-v2', 'contains-pii': true, 'primary': true, 'dataset-type': 'RNAseq', 'description': 'snRNAseq (SNAREseq2)'}",
"rule_description": "DCWG SNARE-RNAseq2"
},
{
Expand All @@ -553,8 +559,8 @@
},
{
"type": "match",
"match": "is_dcwg and is_primary and dataset_type == 'RNAseq (with probes)' and oligo_probe_panel == '10x Genomics; Visium Human Transcriptome Probe Kit v2 - Small; PN 1000466' and assay_input_entity == 'spot' and barcode_read =~~ 'Read 1' and barcode_size == 16 and barcode_offset == 0 and umi_read =~~ 'Read 1' and umi_size == 12 and umi_offset == 16",
"value": "{'assaytype': 'scRNAseq-visium-with-probes', 'vitessce-hints': [], 'dir-schema': 'rnaseq-with-probes-v2', 'contains-pii': true, 'primary': true, 'dataset-type': 'RNAseq (with probes)', 'description': 'Visium RNAseq with probes'}",
"match": "is_dcwg and is_primary and dataset_type == 'RNAseq (with probes)' and oligo_probe_panel in ['10x Genomics; Visium Human Transcriptome Probe Kit v2 - Small; PN 1000466', '10x Genomics; Visium Human Transcriptome Probe Kit-Small; PN 1000363', '10x Genomics; Visium Human Transcriptome Probe Kit-Large; PN 1000364'] and assay_input_entity == 'spot' and barcode_read =~~ 'Read 1' and barcode_size == 16 and barcode_offset == 0 and umi_read =~~ 'Read 1' and umi_size == 12 and umi_offset == 16",
"value": "{'assaytype': 'scRNAseq-visium-with-probes', 'vitessce-hints': [], 'dir-schema': 'rnaseq-with-probes-v2', 'contains-pii': true, 'primary': true, 'dataset-type': 'RNAseq (with probes)', 'description': 'Visium RNAseq (with probes)'}",
"rule_description": "DCWG scRNAseq-visium-with-probes"
},
{
Expand Down Expand Up @@ -772,5 +778,23 @@
"match": "is_central_processed and data_types[0] in ['phenocycler_deepcell']",
"value": "{'assaytype': 'phenocycler_deepcell', 'vitessce-hints': ['is_image', 'is_tiled', 'sprm', 'anndata'], 'primary': false, 'contains-pii': false, 'description': 'PhenoCycler [DeepCell + SPRM]', 'pipeline-shorthand': 'DeepCell + SPRM'}",
"rule_description": "derived phenocycler"
},
{
"type": "match",
"match": "is_epic and derived_dataset_type == 'Segmentation Mask'",
"value": "{'assaytype': 'segmentation-mask', 'vitessce-hints': [], 'dir-schema': 'segmentation-mask-v2', 'contains-pii': false, 'primary': false, 'dataset-type': 'Segmentation Mask', 'description': 'Segmentation Mask', 'process_state': 'epic'}",
"rule_description": "EPIC dataset segmentation mask"
},
{
"type": "match",
"match": "is_dcwg and is_primary and dataset_type == 'RNAseq (with probes)' and oligo_probe_panel == 'NanoString Technologies; GeoMx Human Whole Transcriptome Atlas, 4 slides; PN GMX-RNA-NGS-HuWTA-4' and assay_input_entity == 'area of interest'",
"value": "{'assaytype': 'geomx-rnaseq-with-probes', 'vitessce-hints': [], 'dir-schema': 'rnaseq-with-probes-v2', 'contains-pii': true, 'primary': true, 'dataset-type': 'RNAseq (with probes)', 'description': 'GeoMx RNAseq (with probes)'}",
"rule_description": "DCWG RNAseq-geomx-with-probes"
},
{
"type": "match",
"match": "is_dcwg and is_primary and dataset_type == 'RNAseq (with probes)' and oligo_probe_panel in ['10X Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit, 64 rxns; PN 1000456', '10X Genomics; Chromium Next GEM Single Cell Fixed RNA Human Transcriptome Probe Kit, 16 rxns; PN 1000420'] and assay_input_entity == 'single cell' and barcode_read =~~ 'Read 1' and barcode_size == 16 and barcode_offset == 0 and umi_read =~~ 'Read 1' and umi_size == 12 and umi_offset == 16",
"value": "{'assaytype': 'scRNAseq-with-probes', 'vitessce-hints': [], 'dir-schema': 'rnaseq-with-probes-v2', 'contains-pii': true, 'primary': true, 'dataset-type': 'RNAseq (with probes)', 'description': 'RNAseq (with probes)'}",
"rule_description": "DCWG scRNAseq-with-probes"
}
]
]

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