nci-cidc-schemas 0.28.3__py2.py3-none-any.whl → 0.28.4__py2.py3-none-any.whl
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- cidc_schemas/__init__.py +1 -1
- cidc_schemas/prism/constants.py +2 -0
- cidc_schemas/schemas/artifacts/artifact_ibd.json +51 -0
- cidc_schemas/schemas/artifacts/artifact_imzml.json +51 -0
- cidc_schemas/schemas/assays/components/available_assays.json +12 -0
- cidc_schemas/schemas/assays/components/maldi_glycan_input.json +28 -0
- cidc_schemas/schemas/assays/maldi_glycan_assay.json +68 -0
- cidc_schemas/schemas/shipping_core.json +1 -0
- cidc_schemas/schemas/templates/assays/maldi_glycan_template.json +139 -0
- {nci_cidc_schemas-0.28.3.dist-info → nci_cidc_schemas-0.28.4.dist-info}/METADATA +10 -4
- {nci_cidc_schemas-0.28.3.dist-info → nci_cidc_schemas-0.28.4.dist-info}/RECORD +15 -10
- {nci_cidc_schemas-0.28.3.dist-info → nci_cidc_schemas-0.28.4.dist-info}/WHEEL +0 -0
- {nci_cidc_schemas-0.28.3.dist-info → nci_cidc_schemas-0.28.4.dist-info}/entry_points.txt +0 -0
- {nci_cidc_schemas-0.28.3.dist-info → nci_cidc_schemas-0.28.4.dist-info}/licenses/LICENSE +0 -0
- {nci_cidc_schemas-0.28.3.dist-info → nci_cidc_schemas-0.28.4.dist-info}/top_level.txt +0 -0
cidc_schemas/__init__.py
CHANGED
cidc_schemas/prism/constants.py
CHANGED
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@@ -29,6 +29,7 @@ SUPPORTED_ASSAYS = [
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"scrnaseq",
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"visium",
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"nulisa",
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"maldi_glycan",
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]
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SUPPORTED_SHIPPING_MANIFESTS = [
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@@ -145,6 +146,7 @@ ASSAY_TO_FILEPATH: Dict[str, str] = {
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"visium",
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"visium_analysis",
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"nulisa",
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"maldi_glycan",
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]
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},
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}
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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": "ibd_artifact",
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"title": "IBD Artifact",
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"type": "object",
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"description": "Information about a IBD 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": "IBD"
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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": "imzml_artifact",
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"title": "IMZML Artifact",
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"type": "object",
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"description": "Information about an IMZML 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": "IMZML"
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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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"mergeOptions": {
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"idRef": "batch_id"
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}
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},
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"maldi_glycan": {
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"type": "array",
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"description": "MALDI Glycan",
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"items": {
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"$ref": "assays/maldi_glycan_assay.json"
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},
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"mergeStrategy": "arrayMergeById",
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"mergeOptions": {
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"idRef": "batch_id"
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}
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}
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}
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}
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{
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"$schema": "metaschema/strict_meta_schema.json#",
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"$id": "maldi_glycan_input",
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"title": "MALDI Glycan Input Files and Data",
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"type": "object",
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"description": "MALDI Glycan assay input files and data",
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"inheritableBase": true,
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"properties": {
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"ibd_file": {
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"$ref": "artifacts/artifact_ibd.json"
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},
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"imzml_file": {
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"$ref": "artifacts/artifact_imzml.json"
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},
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"channels_csv": {
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"$ref": "artifacts/artifact_csv.json"
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},
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"tiff_zip": {
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"$ref": "artifacts/artifact_zip.json"
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}
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},
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"required": [
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"ibd_file",
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"imzml_file",
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"channels_csv",
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"tiff_zip"
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]
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}
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{
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"$schema": "metaschema/strict_meta_schema.json#",
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"$id": "maldi_glycan_assay",
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"title": "MALDI Glycan Assay",
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"type": "object",
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"$comment": "description used in docs/index.html and docs/assays.maldi_glycan.html",
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"description": "MALDI Glycan 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 MALDI Glycan 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/maldi_glycan_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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"$ref": "assays/components/assay_core.json#properties/assay_creator"
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},
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"batch_id": {
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"description": "Batch identification number. Unique to every upload.",
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"type": "string"
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},
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"molecular_assignments_file": {
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"$ref": "artifacts/artifact_tsv.json"
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},
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"metadata_tsv": {"$ref": "artifacts/artifact_tsv.json"},
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"antibodies": {
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"type": "array",
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"items": {
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"$ref": "assays/components/mibi_antibody.json"
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},
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"mergeStrategy": "arrayMergeById",
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"mergeOptions": {
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"idRef": "antibody"
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}
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},
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"records": {
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"type": "array",
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"description": "A single data record from a MALDI Glycan assay.",
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"items": {
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"$ref": "assays/maldi_glycan_assay.json#definitions/record"
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},
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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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"batch_id",
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"molecular_assignments_file",
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"records"
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]
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}
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{
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"title": "MALDI Glycan assay template",
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"description": "MALDI Glycan submission.",
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"prism_template_root_object_schema": "assays/maldi_glycan_assay.json",
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"prism_template_root_object_pointer": "/assays/maldi_glycan/0",
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"properties": {
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"worksheets": {
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"MALDI Glycan": {
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"prism_data_object_pointer": "/records/-",
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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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"batch id": {
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"merge_pointer": "0/batch_id",
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"type_ref": "assays/mibi_assay.json#properties/batch_id"
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},
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"assay creator": {
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"merge_pointer": "0/assay_creator",
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"type_ref": "assays/components/assay_core.json#properties/assay_creator"
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},
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"molecular assignments file": {
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"merge_pointer": "0/molecular_assignments_file",
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"gcs_uri_format": "{protocol identifier}/maldi_glyacn/{batch id}/molecular_assignments.tsv",
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"is_artifact": 1,
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"type_ref": "assays/components/local_file.json#properties/file_path"
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},
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"metadata tsv": {
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"merge_pointer": "0/metadata_tsv",
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"gcs_uri_format": "{protocol identifier}/maldi_glycan/{batch id}/metadata.tsv",
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"is_artifact": 1,
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"type_ref": "assays/components/local_file.json#properties/file_path",
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"allow_empty": true
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}
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},
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"data_columns": {
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"Samples": {
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"cimac id": {
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"merge_pointer": "0/cimac_id",
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"type_ref": "sample.json#properties/cimac_id"
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},
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"ibd file": {
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"merge_pointer": "0/details/ibd_file",
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"is_artifact": 1,
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"gcs_uri_format": "{protocol identifier}/maldi_glyacn/{batch id}/{cimac id}/ibd_file.ibd",
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"type_ref": "assays/components/local_file.json#properties/file_path"
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},
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"imzml file": {
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"merge_pointer": "0/details/imzml_file",
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"is_artifact": 1,
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"gcs_uri_format": "{protocol identifier}/maldi_glyacn/{batch id}/{cimac id}/imzml_file.imzml",
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"type_ref": "assays/components/local_file.json#properties/file_path"
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},
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"channels csv": {
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"merge_pointer": "0/details/channels_csv",
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"is_artifact": 1,
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cidc_schemas/constants.py,sha256=RULs7pGuBAVq1teXymrfbVsK23ZowJvLuZlv0KcjL-Y,698
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cidc_schemas/ngs_pipeline_api/wes/imgs/wes.png,sha256=QQPDqTUSOgaS6s0bLu2g2y_WQgVoujtwDTF9z5xZKCE,403116
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cidc_schemas/pipeline_configs/rna_level1_analysis_config.yaml.j2,sha256=6no9sFqwzb1T61RZGD-owDt2K5R8G_fPTzflV4fOroo,2832
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cidc_schemas/schemas/assays/maldi_glycan_assay.json,sha256=P8ejh4UiLk0Z8nKJm_cwovdtkLc2hV4OcPolFRlFfUc,2218
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cidc_schemas/schemas/assays/components/available_assays.json,sha256=
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cidc_schemas/schemas/assays/components/controls.json,sha256=_Wxz7W2msTGJ2Ei4XZg0Qy1t8A5_rLSHNvdPurC073E,458
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cidc_schemas/schemas/assays/components/maldi_glycan_input.json,sha256=Ic5uY4nCxo3M5nibm3OPelsTUVLx6ZZAcFiSlY8INm0,637
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cidc_schemas/schemas/templates/assays/ihc_template.json,sha256=lOSP6v24FMk-WN7Za4IYQkM94R-1TEvrnllRopEEYa4,7341
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cidc_schemas/schemas/templates/assays/maldi_glycan_template.json,sha256=2TvDdhM9N_HEQ3OkNFOddoRv2TY2nFeJUYaGyJ9ATQ0,7338
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cidc_schemas/schemas/templates/assays/mif_template.json,sha256=ozyMdziNxtAReTL7guFIwTiJGhEWam9Hsb_fOhIYXIY,19272
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cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json,sha256=lVJrGb28n-vyfjGBzhrzjn1lMKw1b4HXXmWtwA603v0,2797
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cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json,sha256=LpaoDXDS11NCa-Dv37N-tzEGomswQrx5fypkUcG7xJk,18956
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cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=-gww6NCHbtbI5z7UmNSmKyPK3IqKCE8F6n4XwTAb_gk,18101
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nci_cidc_schemas-0.28.4.dist-info/licenses/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
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nci_cidc_schemas-0.28.4.dist-info/METADATA,sha256=4pPmMe5SBGo-LKMxS49PQ4L9ZIduvBdEtYTVTtScIc0,5374
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|
+
nci_cidc_schemas-0.28.4.dist-info/WHEEL,sha256=JNWh1Fm1UdwIQV075glCn4MVuCRs0sotJIq-J6rbxCU,109
|
|
209
|
+
nci_cidc_schemas-0.28.4.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
|
|
210
|
+
nci_cidc_schemas-0.28.4.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
|
|
211
|
+
nci_cidc_schemas-0.28.4.dist-info/RECORD,,
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|