diff --git a/src/routes/assayclassifier/testing_rule_chain.json b/src/routes/assayclassifier/testing_rule_chain.json index 1e7940e1..2bd2ffb3 100644 --- a/src/routes/assayclassifier/testing_rule_chain.json +++ b/src/routes/assayclassifier/testing_rule_chain.json @@ -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']", @@ -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" }, { @@ -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" }, { @@ -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" }, { @@ -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" }, { @@ -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" } -] \ No newline at end of file +]