nci-cidc-schemas 0.27.21__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/sample.json +1 -1
- 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
- cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json +2 -1
- {nci_cidc_schemas-0.27.21.dist-info → nci_cidc_schemas-0.27.24.dist-info}/METADATA +1 -1
- {nci_cidc_schemas-0.27.21.dist-info → nci_cidc_schemas-0.27.24.dist-info}/RECORD +28 -12
- {nci_cidc_schemas-0.27.21.dist-info → nci_cidc_schemas-0.27.24.dist-info}/WHEEL +0 -0
- {nci_cidc_schemas-0.27.21.dist-info → nci_cidc_schemas-0.27.24.dist-info}/entry_points.txt +0 -0
- {nci_cidc_schemas-0.27.21.dist-info → nci_cidc_schemas-0.27.24.dist-info}/licenses/LICENSE +0 -0
- {nci_cidc_schemas-0.27.21.dist-info → nci_cidc_schemas-0.27.24.dist-info}/top_level.txt +0 -0
cidc_schemas/__init__.py
CHANGED
cidc_schemas/prism/constants.py
CHANGED
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@@ -27,6 +27,7 @@ SUPPORTED_ASSAYS = [
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"microbiome",
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"mihc",
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"scrnaseq",
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"visium",
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]
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SUPPORTED_SHIPPING_MANIFESTS = [
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"tcr_analysis",
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"wes_analysis",
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"wes_tumor_only_analysis",
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"scrnaseq_analysis",
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"visium_analysis",
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]
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"""
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Since most of the definitions are json files which don't allow comments, I'm putting
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our scrnaseq_analysis documentation here. These are the files (and folder structure) that are expected in the gcloud
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directory to fully create a record for scRNA analysis:
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./sample_metadata.csv
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./config.yaml
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./R_package_versions.csv
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./clustering/SRR8318954_clustering.rds
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./integration/integrated.rds
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./integration/heatmap_plots.zip
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./integration/markers.zip
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./integration/split_percent_plots.zip
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./integration/split_umap_plots.zip
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./integration/umap_plots.zip
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./report/SRR8318954_report.html
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./star/SRR8318954.Aligned.sortedByCoord.out.bam
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./star/SRR8318954.Aligned.sortedByCoord.out.bam.bai
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./star/SRR8318954.Log.final.out
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./star/SRR8318954.Log.out
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./star/SRR8318954.Log.progress.out
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./star/SRR8318954.SJ.out.tab
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./star/SRR8318954.Solo.out/Barcodes.stats
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./star/SRR8318954.Solo.out/Gene/Features.stats
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./star/SRR8318954.Solo.out/Gene/Summary.csv
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./star/SRR8318954.Solo.out/Gene/UMIperCellSorted.txt
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./star/SRR8318954.Solo.out/Gene/filtered/features.tsv
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./star/SRR8318954.Solo.out/Gene/filtered/barcodes.tsv
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./star/SRR8318954.Solo.out/Gene/filtered/matrix.mtx
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./star/SRR8318954.Solo.out/Gene/raw/features.tsv
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./star/SRR8318954.Solo.out/Gene/raw/barcodes.tsv
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./star/SRR8318954.Solo.out/Gene/raw/matrix.mtx
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These are the files required for visium analysis:
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./sample_metadata.csv
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./config.yaml
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./R_package_versions.csv
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./spatial_variable_features/{id}_spatial_variable_features.rds
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./report/{id}_report.html
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./merge/merged.rds
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./{id}_spaceranger.zip
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"""
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SUPPORTED_TEMPLATES = SUPPORTED_ASSAYS + SUPPORTED_MANIFESTS + SUPPORTED_ANALYSES
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# provide a way to get file-path prefix for each upload_type
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"olink",
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"mihc",
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"scrnaseq",
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"scrnaseq_analysis",
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"visium",
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"visium_analysis",
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]
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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": "html_artifact",
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"title": "HTML Artifact",
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"type": "object",
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"description": "Information about a HTML file.",
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"additionalProperties": false,
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"properties": {
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"data_format": {
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"description": "Data format.",
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"const": "HTML"
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},
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"upload_placeholder": {
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"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
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},
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"artifact_creator": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
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},
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
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"file_name": {
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"$ref": "artifacts/artifact_core.json#properties/file_name"
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},
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"object_url": {
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"$ref": "artifacts/artifact_core.json#properties/object_url"
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},
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"uploaded_timestamp": {
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"$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
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},
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"file_size_bytes": {
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"$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
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},
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"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
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"crc32c_hash": {
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
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},
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
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"artifact_category": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
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},
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"facet_group": {
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"$ref": "artifacts/artifact_core.json#properties/facet_group"
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}
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},
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"allOf": [
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{
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"$ref": "artifacts/artifact_core.json"
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}
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],
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"mergeStrategy": "objectMerge"
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}
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{
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"$schema": "metaschema/strict_meta_schema.json#",
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"$id": "mtx_artifact",
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"title": "MTX Artifact",
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"type": "object",
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"description": "Information about a MTX file.",
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"additionalProperties": false,
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"properties": {
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"data_format": {
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"description": "Data format.",
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"const": "MTX"
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},
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"upload_placeholder": {
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"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
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},
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"artifact_creator": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
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},
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
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"file_name": {
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"$ref": "artifacts/artifact_core.json#properties/file_name"
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},
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"object_url": {
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"$ref": "artifacts/artifact_core.json#properties/object_url"
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},
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"uploaded_timestamp": {
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"$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
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},
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"file_size_bytes": {
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"$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
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},
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"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
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"crc32c_hash": {
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
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},
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
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"artifact_category": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
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},
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"facet_group": {
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"$ref": "artifacts/artifact_core.json#properties/facet_group"
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}
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},
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"allOf": [
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"$ref": "artifacts/artifact_core.json"
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}
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],
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"mergeStrategy": "objectMerge"
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}
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{
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"$schema": "metaschema/strict_meta_schema.json#",
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"$id": "out_artifact",
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"title": "OUT Artifact",
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"type": "object",
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"description": "Information about a OUT file.",
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"additionalProperties": false,
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"properties": {
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"data_format": {
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"const": "OUT"
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},
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"upload_placeholder": {
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"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
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},
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"artifact_creator": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
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},
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
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"file_name": {
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"$ref": "artifacts/artifact_core.json#properties/file_name"
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},
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"object_url": {
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"$ref": "artifacts/artifact_core.json#properties/object_url"
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},
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"uploaded_timestamp": {
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},
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"file_size_bytes": {
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},
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"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
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"crc32c_hash": {
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
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},
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
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"artifact_category": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
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},
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"facet_group": {
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}
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},
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}
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"$id": "rds_artifact",
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"title": "RDS Artifact",
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"description": "Information about a rds file.",
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"artifact_creator": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
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"file_name": {
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},
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"object_url": {
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"$ref": "artifacts/artifact_core.json#properties/object_url"
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},
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"uploaded_timestamp": {
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"$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
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},
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"file_size_bytes": {
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"$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
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},
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"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
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"crc32c_hash": {
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
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},
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
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"artifact_category": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
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},
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"facet_group": {
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"$ref": "artifacts/artifact_core.json#properties/facet_group"
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"allOf": [
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@@ -0,0 +1,51 @@
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{
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"$schema": "metaschema/strict_meta_schema.json#",
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"$id": "stats_artifact",
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"title": "Stats Artifact",
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"type": "object",
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"description": "Information about a STATS file.",
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"additionalProperties": false,
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"properties": {
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"data_format": {
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"const": "STATS"
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"upload_placeholder": {
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"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
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"file_name": {
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"$ref": "artifacts/artifact_core.json#properties/file_name"
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"object_url": {
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"uploaded_timestamp": {
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"file_size_bytes": {
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"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
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"crc32c_hash": {
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
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"artifact_category": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
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"facet_group": {
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@@ -0,0 +1,51 @@
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"$id": "tab_artifact",
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"title": "TAB Artifact",
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"type": "object",
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"description": "Information about a TAB file.",
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"additionalProperties": false,
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"properties": {
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"data_format": {
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"description": "Data format.",
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"const": "TAB"
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"upload_placeholder": {
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"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
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"artifact_creator": {
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
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"file_name": {
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"$ref": "artifacts/artifact_core.json#properties/file_name"
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"object_url": {
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"uploaded_timestamp": {
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"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
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"crc32c_hash": {
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
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"artifact_category": {
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
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},
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"facet_group": {
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"$ref": "artifacts/artifact_core.json#properties/facet_group"
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"allOf": [
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@@ -0,0 +1,51 @@
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{
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"$schema": "metaschema/strict_meta_schema.json#",
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"$id": "tiff_artifact",
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"title": "Tiff Artifact",
|
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"type": "object",
|
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|
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"description": "Information about a tiff file.",
|
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|
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"additionalProperties": false,
|
|
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|
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"properties": {
|
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|
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"data_format": {
|
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"description": "Data format.",
|
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"const": "TIFF"
|
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},
|
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"upload_placeholder": {
|
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"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
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},
|
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"artifact_creator": {
|
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"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
|
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},
|
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"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
|
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"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
|
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"file_name": {
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"$ref": "artifacts/artifact_core.json#properties/file_name"
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},
|
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"object_url": {
|
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"$ref": "artifacts/artifact_core.json#properties/object_url"
|
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},
|
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"uploaded_timestamp": {
|
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"$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
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},
|
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"file_size_bytes": {
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"$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
|
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},
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"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
|
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|
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"crc32c_hash": {
|
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"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
|
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},
|
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
|
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"artifact_category": {
|
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"$ref": "artifacts/artifact_core.json#properties/artifact_category"
|
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},
|
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"facet_group": {
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"$ref": "artifacts/artifact_core.json#properties/facet_group"
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}
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},
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"allOf": [
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{
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"$ref": "artifacts/artifact_core.json"
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}
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],
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"mergeStrategy": "objectMerge"
|
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|
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}
|
|
@@ -0,0 +1,51 @@
|
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|
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{
|
|
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|
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"$schema": "metaschema/strict_meta_schema.json#",
|
|
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|
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"$id": "txt_artifact",
|
|
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|
+
"title": "Txt Artifact",
|
|
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|
+
"type": "object",
|
|
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|
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"description": "Information about a txt file.",
|
|
7
|
+
"additionalProperties": false,
|
|
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|
+
"properties": {
|
|
9
|
+
"data_format": {
|
|
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|
+
"description": "Data format.",
|
|
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|
+
"const": "TXT"
|
|
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|
+
},
|
|
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|
+
"upload_placeholder": {
|
|
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|
+
"$ref": "artifacts/artifact_core.json#properties/upload_placeholder"
|
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|
+
},
|
|
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|
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"artifact_creator": {
|
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|
+
"$ref": "artifacts/artifact_core.json#properties/artifact_creator"
|
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|
+
},
|
|
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|
+
"uploader": { "$ref": "artifacts/artifact_core.json#properties/uploader" },
|
|
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|
+
"uuid": { "$ref": "artifacts/artifact_core.json#properties/uuid" },
|
|
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|
+
"file_name": {
|
|
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|
+
"$ref": "artifacts/artifact_core.json#properties/file_name"
|
|
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|
+
},
|
|
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|
+
"object_url": {
|
|
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|
+
"$ref": "artifacts/artifact_core.json#properties/object_url"
|
|
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|
+
},
|
|
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|
+
"uploaded_timestamp": {
|
|
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|
+
"$ref": "artifacts/artifact_core.json#properties/uploaded_timestamp"
|
|
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|
+
},
|
|
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|
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"file_size_bytes": {
|
|
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|
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"$ref": "artifacts/artifact_core.json#properties/file_size_bytes"
|
|
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|
+
},
|
|
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|
+
"md5_hash": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
|
|
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|
+
"crc32c_hash": {
|
|
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|
+
"$ref": "artifacts/artifact_core.json#properties/crc32c_hash"
|
|
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|
+
},
|
|
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|
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"visible": { "$ref": "artifacts/artifact_core.json#properties/visible" },
|
|
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|
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"artifact_category": {
|
|
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|
+
"$ref": "artifacts/artifact_core.json#properties/artifact_category"
|
|
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|
+
},
|
|
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|
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"facet_group": {
|
|
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|
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"$ref": "artifacts/artifact_core.json#properties/facet_group"
|
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|
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}
|
|
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|
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},
|
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|
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"allOf": [
|
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{
|
|
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"$ref": "artifacts/artifact_core.json"
|
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|
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}
|
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|
+
],
|
|
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|
+
"mergeStrategy": "objectMerge"
|
|
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|
+
}
|
|
@@ -141,6 +141,17 @@
|
|
|
141
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|
"idRef": "batch_id"
|
|
142
142
|
}
|
|
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143
|
},
|
|
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|
+
"visium": {
|
|
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|
+
"type": "array",
|
|
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|
+
"description": "Visium",
|
|
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|
+
"items": {
|
|
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|
+
"$ref": "assays/visium_assay.json"
|
|
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|
+
},
|
|
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|
+
"mergeStrategy": "arrayMergeById",
|
|
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|
+
"mergeOptions": {
|
|
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|
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"idRef": "batch_id"
|
|
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|
+
}
|
|
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|
+
},
|
|
144
155
|
"nanostring": {
|
|
145
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|
"type": "array",
|
|
146
157
|
"description": "Nanostring",
|
|
@@ -35,6 +35,28 @@
|
|
|
35
35
|
"mergeOptions": {
|
|
36
36
|
"idRef": "batch_id"
|
|
37
37
|
}
|
|
38
|
+
},
|
|
39
|
+
"scrnaseq_analysis": {
|
|
40
|
+
"type": "array",
|
|
41
|
+
"description": "Analysis for Assay for scRNA.",
|
|
42
|
+
"items": {
|
|
43
|
+
"$ref": "assays/scrnaseq_analysis.json"
|
|
44
|
+
},
|
|
45
|
+
"mergeStrategy": "arrayMergeById",
|
|
46
|
+
"mergeOptions": {
|
|
47
|
+
"idRef": "batch_id"
|
|
48
|
+
}
|
|
49
|
+
},
|
|
50
|
+
"visium_analysis": {
|
|
51
|
+
"type": "array",
|
|
52
|
+
"description": "Analysis for Assay for visium.",
|
|
53
|
+
"items": {
|
|
54
|
+
"$ref": "assays/visium_analysis.json"
|
|
55
|
+
},
|
|
56
|
+
"mergeStrategy": "arrayMergeById",
|
|
57
|
+
"mergeOptions": {
|
|
58
|
+
"idRef": "batch_id"
|
|
59
|
+
}
|
|
38
60
|
}
|
|
39
61
|
}
|
|
40
62
|
}
|
|
@@ -0,0 +1,60 @@
|
|
|
1
|
+
{
|
|
2
|
+
"$schema": "metaschema/strict_meta_schema.json#",
|
|
3
|
+
"$id": "visium_input",
|
|
4
|
+
"title": "Visium Input Files and Data",
|
|
5
|
+
"type": "object",
|
|
6
|
+
"description": "Visium assay input files and data",
|
|
7
|
+
"inheritableBase": true,
|
|
8
|
+
"properties": {
|
|
9
|
+
"lane": {
|
|
10
|
+
"description": "Lane used for this run from 1-9",
|
|
11
|
+
"type": "integer",
|
|
12
|
+
"exclusiveMinimum": 0,
|
|
13
|
+
"maximum": 9
|
|
14
|
+
},
|
|
15
|
+
"read_1_fastq_gz": {
|
|
16
|
+
"$ref": "artifacts/artifact_gz.json"
|
|
17
|
+
},
|
|
18
|
+
"read_2_fastq_gz": {
|
|
19
|
+
"$ref": "artifacts/artifact_gz.json"
|
|
20
|
+
},
|
|
21
|
+
"loupe_alignment_file": {
|
|
22
|
+
"$ref": "artifacts/artifact_json.json"
|
|
23
|
+
},
|
|
24
|
+
"slide_serial_code": {
|
|
25
|
+
"type": "string",
|
|
26
|
+
"description": "Visium slide serial number"
|
|
27
|
+
},
|
|
28
|
+
"slide_capture_area": {
|
|
29
|
+
"type": "string",
|
|
30
|
+
"description": "Visium capture area identifier"
|
|
31
|
+
},
|
|
32
|
+
"library_yield_ng": {
|
|
33
|
+
"description": "Resulting yield (in ng) from library construction.",
|
|
34
|
+
"type": "number"
|
|
35
|
+
},
|
|
36
|
+
"dv200": {
|
|
37
|
+
"description": "The percentage of fragments > 200 nucleotides. (0-1)",
|
|
38
|
+
"type": "number",
|
|
39
|
+
"minimum": 0,
|
|
40
|
+
"maximum": 1
|
|
41
|
+
},
|
|
42
|
+
"brightfield_image": { "$ref": "artifacts/artifact_tiff.json"},
|
|
43
|
+
"dark_image": { "$ref": "artifacts/artifact_tiff.json"},
|
|
44
|
+
"colorized_image": { "$ref": "artifacts/artifact_tiff.json"},
|
|
45
|
+
"cytassist_image": { "$ref": "artifacts/artifact_tiff.json"},
|
|
46
|
+
"dapi_index": {
|
|
47
|
+
"type": "integer",
|
|
48
|
+
"description": "Index of DAPI channel (1-indexed) of fluorescence image."
|
|
49
|
+
},
|
|
50
|
+
"comments": {
|
|
51
|
+
"type": "string",
|
|
52
|
+
"description": "Comments on visium run"
|
|
53
|
+
}
|
|
54
|
+
},
|
|
55
|
+
"required": [
|
|
56
|
+
"lane",
|
|
57
|
+
"read_1_fastq_gz",
|
|
58
|
+
"read_2_fastq_gz"
|
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59
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+
]
|
|
60
|
+
}
|
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@@ -0,0 +1,27 @@
|
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1
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+
{
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|
2
|
+
"$schema": "metaschema/strict_meta_schema.json#",
|
|
3
|
+
"$id": "visium_preamble",
|
|
4
|
+
"title": "Visium Preamble",
|
|
5
|
+
"description": "Preamble information in a visium assay",
|
|
6
|
+
"type": "object",
|
|
7
|
+
"inheritableBase": true,
|
|
8
|
+
"properties": {
|
|
9
|
+
"spatial_gene_expression_platform": {
|
|
10
|
+
"description": "Visium spatial gene expression platform",
|
|
11
|
+
"type": "string",
|
|
12
|
+
"enum": [
|
|
13
|
+
"Visium Spatial Gene Expression for FFPE",
|
|
14
|
+
"Visium CytAssist Spatial Gene Expression for FFPE",
|
|
15
|
+
"Visium HD Spatial Gene Expression for FFPE"
|
|
16
|
+
]
|
|
17
|
+
},
|
|
18
|
+
"human_transcriptome_probe_set_version": {
|
|
19
|
+
"description": "Visium human transcriptome probe set version",
|
|
20
|
+
"type": "string",
|
|
21
|
+
"enum": [
|
|
22
|
+
"Visium Human Transcriptome Probe Set v1.0",
|
|
23
|
+
"Visium Human Transcriptome Probe Set v2.0"
|
|
24
|
+
]
|
|
25
|
+
}
|
|
26
|
+
}
|
|
27
|
+
}
|