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Merged
merged 3 commits into from
May 13, 2025
Merged

Jpuerto/remove cycif #740

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9d4b78b
Merge pull request #735 from hubmapconsortium/jpuerto/rule-updates
yuanzhou Apr 29, 2025
2190860
Merge pull request #739 from hubmapconsortium/jpuerto/rules-auth-fix
yuanzhou Apr 29, 2025
a5ad756
General: Remove entry for CyCIF
May 9, 2025
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22 changes: 14 additions & 8 deletions src/routes/assayclassifier/testing_rule_chain.json
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Original file line number Diff line number Diff line change
Expand Up @@ -513,7 +513,7 @@
},
{
"type": "match",
"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', '10x Genomics; Visium Mouse Transcriptome Probe Kit - Small; PN 1000365'] 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",
"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', '10x Genomics; Visium Mouse Transcriptome Probe Kit - Small; PN 1000365', '10x Genomics; Visium Mouse Transcriptome Probes v2 - small; PN 1000667'] 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": "{'ubkg_code': 'C200820', '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 @@ -601,12 +601,6 @@
"value": "{'ubkg_code': 'C200960', 'assaytype': 'phenocycler', 'vitessce-hints': [], 'dir-schema': 'phenocycler-v2', 'contains-pii': false, 'primary': true, 'dataset-type': 'PhenoCycler', 'description': 'PhenoCycler'}",
"rule_description": "DCWG phenocycler"
},
{
"type": "match",
"match": "is_dcwg and is_primary and dataset_type == 'CycIF'",
"value": "{'ubkg_code': 'C200970', 'assaytype': 'cycif', 'vitessce-hints': [], 'dir-schema': 'cycif-v2', 'contains-pii': false, 'primary': true, 'dataset-type': 'CycIF', 'description': 'CycIF'}",
"rule_description": "DCWG cycif"
},
{
"type": "match",
"match": "is_dcwg and is_primary and dataset_type == 'MERFISH'",
Expand Down Expand Up @@ -753,7 +747,7 @@
},
{
"type": "match",
"match": "is_dcwg and is_primary and dataset_type == 'Xenium' and oligo_probe_panel in ['10x Genomics; Xenium Human Multi-Tissue and Cancer Panel v1; PN 1000626', '10x Genomics; Xenium Prime 5K Human Pan Tissue & Pathways Panel; PN 1000724']",
"match": "is_dcwg and is_primary and dataset_type == 'Xenium' and oligo_probe_panel in ['10x Genomics; Xenium Human Multi-Tissue and Cancer Panel v1; PN 1000626', '10x Genomics; Xenium Prime 5K Human Pan Tissue & Pathways Panel; PN 1000724', 'Custom']",
"value": "{'ubkg_code': 'C202050', 'assaytype': 'xenium', 'vitessce-hints': [], 'dir-schema': 'xenium-v2', 'contains-pii': true, 'primary': true, 'dataset-type': 'Xenium', 'description': 'Xenium'}",
"rule_description": "DCWG xenium"
},
Expand Down Expand Up @@ -786,6 +780,18 @@
"match": "is_dcwg and is_primary and dataset_type == 'Singular Genomics G4X'",
"value": "{'ubkg_code': 'C202100', 'assaytype': 'singular-genomics-g4x', 'vitessce-hints': [], 'dir-schema': 'singular-genomics-g4x-v2', 'contains-pii': true, 'primary': true, 'dataset-type': 'Singular Genomics G4X', 'description': 'Singular Genomics G4X'}",
"rule_description": "DCWG Singular Genomics G4X"
},
{
"type": "match",
"match": "is_central_processed and data_types[0] in ['geomx']",
"value": "{'ubkg_code': 'C202110', 'assaytype': 'geomx_ngs', 'vitessce-hints': ['geomx', 'is_image', 'pyramid'], 'primary': false, 'contains-pii': false, 'description': 'GeoMx (NGS) [AnnData]', 'pipeline-shorthand': 'AnnData'}",
"rule_description": "derived geomx_ngs"
},
{
"type": "match",
"match": "is_dcwg and is_primary and dataset_type == 'CosMx' and oligo_probe_panel in ['NanoString Technologies; CosMx Human Universal Cell Characterization Panel (RNA, 1000 Plex); PN CMX-H-USCP-1KP-R']",
"value": "{'ubkg_code': 'C202120', 'assaytype': 'cosmx', 'vitessce-hints': [], 'dir-schema': 'cosmx-v2', 'contains-pii': true, 'primary': true, 'dataset-type': 'CosMx', 'description': 'CosMx'}",
"rule_description": "DCWG CosMx"
}
],
"pre":
Expand Down