nci-cidc-schemas 0.27.22__py2.py3-none-any.whl → 0.27.24__py2.py3-none-any.whl
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- cidc_schemas/__init__.py +1 -1
- cidc_schemas/prism/constants.py +48 -0
- cidc_schemas/schemas/artifacts/artifact_html.json +51 -0
- cidc_schemas/schemas/artifacts/artifact_mtx.json +51 -0
- cidc_schemas/schemas/artifacts/artifact_out.json +51 -0
- cidc_schemas/schemas/artifacts/artifact_rds.json +51 -0
- cidc_schemas/schemas/artifacts/artifact_stats.json +51 -0
- cidc_schemas/schemas/artifacts/artifact_tab.json +51 -0
- cidc_schemas/schemas/artifacts/artifact_tiff.json +51 -0
- cidc_schemas/schemas/artifacts/artifact_txt.json +51 -0
- cidc_schemas/schemas/assays/components/available_assays.json +11 -0
- cidc_schemas/schemas/assays/components/available_ngs_analyses.json +22 -0
- cidc_schemas/schemas/assays/components/visium_input.json +60 -0
- cidc_schemas/schemas/assays/components/visium_preamble.json +27 -0
- cidc_schemas/schemas/assays/scrnaseq_analysis.json +102 -0
- cidc_schemas/schemas/assays/visium_analysis.json +62 -0
- cidc_schemas/schemas/assays/visium_assay.json +68 -0
- cidc_schemas/schemas/templates/analyses/scrnaseq_analysis_template.json +232 -0
- cidc_schemas/schemas/templates/analyses/visium_analysis_template.json +103 -0
- cidc_schemas/schemas/templates/assays/visium_template.json +150 -0
- {nci_cidc_schemas-0.27.22.dist-info → nci_cidc_schemas-0.27.24.dist-info}/METADATA +1 -1
- {nci_cidc_schemas-0.27.22.dist-info → nci_cidc_schemas-0.27.24.dist-info}/RECORD +26 -10
- {nci_cidc_schemas-0.27.22.dist-info → nci_cidc_schemas-0.27.24.dist-info}/WHEEL +0 -0
- {nci_cidc_schemas-0.27.22.dist-info → nci_cidc_schemas-0.27.24.dist-info}/entry_points.txt +0 -0
- {nci_cidc_schemas-0.27.22.dist-info → nci_cidc_schemas-0.27.24.dist-info}/licenses/LICENSE +0 -0
- {nci_cidc_schemas-0.27.22.dist-info → nci_cidc_schemas-0.27.24.dist-info}/top_level.txt +0 -0
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{
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"$schema": "metaschema/strict_meta_schema.json#",
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"$id": "scrnaseq_analysis",
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"title": "Analysis for Assay of scRNA",
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"definitions": {
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"entry": {
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"type": "object",
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"mergeStrategy": "objectMerge",
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"description": "A single analysis record from scRNA analysis.",
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"additionalProperties": false,
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"required": [
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"cimac_id",
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"clustering_rds",
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"report_html",
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"star_sorted_by_coord_bam",
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"star_sorted_by_coord_bam_bai",
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"star_log_final_out",
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"star_log_out",
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"star_log_progress_out",
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"star_sj_out",
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"star_barcode_stats",
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"star_gene_features_stats",
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"star_gene_summary_csv",
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"star_gene_umi_per_cell_sorted",
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"star_gene_filtered_features_tsv",
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"star_gene_filtered_barcodes",
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"star_gene_filtered_matrix",
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"star_gene_raw_features_tsv",
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"star_gene_raw_barcodes",
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"star_gene_raw_matrix"
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],
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"properties": {
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"cimac_id": {"$ref": "assays/components/ngs/ngs_assay_record.json#properties/cimac_id"},
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"clustering_rds": { "$ref": "artifacts/artifact_rds.json"},
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"report_html": { "$ref": "artifacts/artifact_html.json"},
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"star_sorted_by_coord_bam": { "$ref": "artifacts/artifact_bam.json"},
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"star_sorted_by_coord_bam_bai": { "$ref": "artifacts/artifact_bam_bai.json"},
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"star_log_final_out": { "$ref": "artifacts/artifact_out.json"},
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"star_log_out": { "$ref": "artifacts/artifact_out.json"},
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"star_log_progress_out": { "$ref": "artifacts/artifact_out.json"},
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"star_sj_out": { "$ref": "artifacts/artifact_tab.json"},
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"star_barcode_stats": { "$ref": "artifacts/artifact_stats.json"},
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"star_gene_features_stats": { "$ref": "artifacts/artifact_stats.json"},
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"star_gene_summary_csv": { "$ref": "artifacts/artifact_csv.json"},
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"star_gene_umi_per_cell_sorted": { "$ref": "artifacts/artifact_txt.json"},
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"star_gene_filtered_features_tsv": { "$ref": "artifacts/artifact_tsv.json"},
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"star_gene_filtered_barcodes": { "$ref": "artifacts/artifact_tsv.json"},
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"star_gene_filtered_matrix": { "$ref": "artifacts/artifact_mtx.json"},
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"star_gene_raw_features_tsv": { "$ref": "artifacts/artifact_tsv.json"},
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"star_gene_raw_barcodes": { "$ref": "artifacts/artifact_tsv.json"},
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"star_gene_raw_matrix": { "$ref": "artifacts/artifact_mtx.json"},
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"comments": {
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"type": "string",
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"description": "Comments on the scRNA analysis run."
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}
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}
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}
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},
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"type": "object",
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"additionalProperties": false,
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"required": [
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"records",
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"samples_metadata_csv",
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"config_yaml",
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"r_package_versions",
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"integration_rds",
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"integration_heatmap_plots",
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"integration_markers_zip",
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"integration_split_percent_plots",
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"integration_split_umap_plots",
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"integration_umap_plots",
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"batch_id"
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],
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"properties": {
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"batch_id":{
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"$ref": "assays/scrnaseq_assay.json#properties/batch_id"
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},
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"records": {
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"type": "array",
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"mergeStrategy": "arrayMergeById",
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"mergeOptions": { "idRef": "/cimac_id" },
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"items": {
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"$ref": "assays/scrnaseq_analysis.json#definitions/entry"
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}
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},
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"excluded_samples": {
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"$ref": "assays/components/excluded_samples.json"
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},
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"samples_metadata_csv": { "$ref": "artifacts/artifact_csv.json"},
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"config_yaml": { "$ref": "artifacts/artifact_yaml.json"},
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"r_package_versions": { "$ref": "artifacts/artifact_csv.json"},
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"integration_rds": { "$ref": "artifacts/artifact_rds.json"},
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"integration_heatmap_plots": { "$ref": "artifacts/artifact_zip.json"},
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"integration_markers_zip": { "$ref": "artifacts/artifact_zip.json"},
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"integration_split_percent_plots": { "$ref": "artifacts/artifact_zip.json"},
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"integration_split_umap_plots": { "$ref": "artifacts/artifact_zip.json"},
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"integration_umap_plots": { "$ref": "artifacts/artifact_zip.json"}
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}
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}
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{
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"$schema": "metaschema/strict_meta_schema.json#",
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"$id": "visium_analysis",
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"title": "Analysis for Assay of visium",
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"definitions": {
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"entry": {
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"type": "object",
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"mergeStrategy": "objectMerge",
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"description": "A single analysis record from visium analysis.",
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"additionalProperties": false,
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"required": [
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"cimac_id",
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"spatial_variable_features_rds",
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"report_html",
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"visium_spaceranger_output_zip"
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],
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"properties": {
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"cimac_id": {"$ref": "assays/components/ngs/ngs_assay_record.json#properties/cimac_id"},
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"spatial_variable_features_rds": { "$ref": "artifacts/artifact_rds.json"},
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"report_html": { "$ref": "artifacts/artifact_html.json"},
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"visium_spaceranger_output_zip": { "$ref": "artifacts/artifact_zip.json"},
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"comments": {
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"type": "string",
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"description": "Comments on the visium analysis run."
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}
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}
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}
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},
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"type": "object",
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"additionalProperties": false,
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"required": [
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"records",
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"samples_metadata_csv",
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"config_yaml",
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"r_package_versions",
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"merged_rds",
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"batch_id"
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],
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"properties": {
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"batch_id":{
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"$ref": "assays/scrnaseq_assay.json#properties/batch_id"
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},
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"records": {
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"type": "array",
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"mergeStrategy": "arrayMergeById",
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"mergeOptions": { "idRef": "/cimac_id" },
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"items": {
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"$ref": "assays/visium_analysis.json#definitions/entry"
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}
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},
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"excluded_samples": {
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"$ref": "assays/components/excluded_samples.json"
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},
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"samples_metadata_csv": { "$ref": "artifacts/artifact_csv.json"},
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"config_yaml": { "$ref": "artifacts/artifact_yaml.json"},
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"r_package_versions": { "$ref": "artifacts/artifact_csv.json"},
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"merged_rds": { "$ref": "artifacts/artifact_rds.json"}
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}
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}
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{
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"$schema": "metaschema/strict_meta_schema.json#",
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"$id": "visium_assay",
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"title": "Visium Assay",
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"type": "object",
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"$comment": "description used in docs/index.html and docs/assays.visium.html",
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"description": "Visium assay",
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"additionalProperties": false,
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"definitions": {
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"record": {
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"type": "object",
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"mergeStrategy": "objectMerge",
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"description": "A single data record from a Visium assay.",
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"additionalProperties": false,
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"required": [
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"cimac_id",
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"details"
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],
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"properties": {
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"cimac_id": {
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"description": "Id of an sample within this clinical trial, that this assay record is based upon.",
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"$ref": "sample.json#properties/cimac_id"
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},
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"details": {
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"$ref": "assays/components/visium_input.json"
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}
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}
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}
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},
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"properties": {
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"assay_creator": {
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"$ref": "assays/components/assay_core.json#properties/assay_creator"
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},
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"batch_id": {
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"description": "Batch identification number. Unique to every upload.",
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"type": "string"
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},
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"azimuth_reference": {
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"$ref": "assays/components/scrnaseq_preamble.json#properties/azimuth_reference"
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},
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"tabula_sapiens_reference": {
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"$ref": "assays/components/scrnaseq_preamble.json#properties/tabula_sapiens_reference"
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},
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"spatial_gene_expression_platform": {
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"$ref": "assays/components/visium_preamble.json#properties/spatial_gene_expression_platform"
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},
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"human_transcriptome_probe_set_version": {
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"$ref": "assays/components/visium_preamble.json#properties/human_transcriptome_probe_set_version"
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},
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"samples_metadata_csv": {"$ref": "artifacts/artifact_csv.json"},
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"records": {
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"type": "array",
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"description": "A single data record from a visium assay.",
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"items": {
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"$ref": "assays/visium_assay.json#definitions/record"
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"mergeStrategy": "append"
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}
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},
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"required": [
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"assay_creator",
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"samples_metadata_csv",
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]
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}
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{
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"title": "scRNAseq analysis template",
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"description": "Assay by scRNA analysis submission.",
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"prism_template_root_object_schema": "assays/scrnaseq_analysis.json",
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"prism_template_root_object_pointer": "/analysis/scrnaseq_analysis/0",
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"properties": {
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"worksheets": {
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"scRNAseq Analysis": {
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"preamble_rows": {
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"protocol identifier": {
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"merge_pointer": "3/protocol_identifier",
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"type_ref": "clinical_trial.json#properties/protocol_identifier"
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},
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"folder": {
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"do_not_merge": true,
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"type": "string",
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"allow_empty": true
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},
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"batch id": {
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"merge_pointer": "0/batch_id",
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"type_ref": "assays/scrnaseq_assay.json#properties/batch_id"
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},
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"samples metadata csv": {
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"merge_pointer": "0/samples_metadata_csv",
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"type_ref": "assays/components/local_file.json#properties/file_path",
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"gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/samples_metadata.csv",
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"is_artifact": 1
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},
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"config yaml": {
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"merge_pointer": "0/config_yaml",
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"type_ref": "assays/components/local_file.json#properties/file_path",
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"gcs_uri_format": "{protocol identifier}/scrnaseq_analysis/{batch id}/config.yaml",
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"is_artifact": 1
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},
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"r package versions": {
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"merge_pointer": "0/r_package_versions",
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@@ -0,0 +1,103 @@
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{
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"title": "Visium analysis template",
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"description": "Assay by visium analysis submission.",
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"prism_template_root_object_schema": "assays/visium_analysis.json",
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"prism_template_root_object_pointer": "/analysis/visium_analysis/0",
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"worksheets": {
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"preamble_rows": {
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"samples metadata csv": {
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"gcs_uri_format": "{protocol identifier}/visium_analysis/{batch id}/config.yaml",
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"r package versions": {
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"type_ref": "assays/components/local_file.json#properties/file_path",
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"gcs_uri_format": "{protocol identifier}/visium_analysis/{batch id}/R_package_versions.csv",
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"is_artifact": 1
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"merged rds": {
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"type_ref": "assays/components/local_file.json#properties/file_path",
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"gcs_uri_format": "{protocol identifier}/visium_analysis/{batch id}/merged.rds",
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"prism_data_object_pointer": "/records/-",
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"data_columns": {
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"visium Runs": {
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"cimac id": {
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"merge_pointer": "/cimac_id",
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"process_as": [
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"parse_through": "lambda id: f'{folder or \"\"}spatial_variable_features/{id}_spatial_variable_features.rds'",
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"merge_pointer": "0/spatial_variable_features_rds",
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"gcs_uri_format": "{protocol identifier}/visium_analysis/{batch id}/{cimac id}/spatial_variable_features.rds",
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"parse_through": "lambda id: f'{folder or \"\"}report/{id}_report.html'",
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"gcs_uri_format": "{protocol identifier}/visium_analysis/{batch id}/{cimac id}/report.html",
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|
+
"merge_pointer": "0/visium_spaceranger_output_zip",
|
|
72
|
+
"gcs_uri_format": "{protocol identifier}/visium_analysis/{batch id}/{cimac id}/visium_spaceranger_output.zip",
|
|
73
|
+
"type_ref": "assays/components/local_file.json#properties/file_path",
|
|
74
|
+
"is_artifact": 1
|
|
75
|
+
}
|
|
76
|
+
]
|
|
77
|
+
},
|
|
78
|
+
"comments": {
|
|
79
|
+
"type_ref": "assays/scrnaseq_analysis.json#definitions/entry/properties/comments",
|
|
80
|
+
"merge_pointer": "0/comments",
|
|
81
|
+
"allow_empty": true
|
|
82
|
+
}
|
|
83
|
+
}
|
|
84
|
+
}
|
|
85
|
+
},
|
|
86
|
+
"Excluded Samples": {
|
|
87
|
+
"prism_data_object_pointer": "/excluded_samples/-",
|
|
88
|
+
"data_columns": {
|
|
89
|
+
"Samples Excluded From Analysis": {
|
|
90
|
+
"cimac id": {
|
|
91
|
+
"type_ref": "sample.json#properties/cimac_id",
|
|
92
|
+
"merge_pointer": "0/cimac_id"
|
|
93
|
+
},
|
|
94
|
+
"reason": {
|
|
95
|
+
"type_ref": "assays/components/excluded_samples.json#items/properties/reason_excluded",
|
|
96
|
+
"merge_pointer": "0/reason_excluded"
|
|
97
|
+
}
|
|
98
|
+
}
|
|
99
|
+
}
|
|
100
|
+
}
|
|
101
|
+
}
|
|
102
|
+
}
|
|
103
|
+
}
|