nci-cidc-schemas 0.28.2__py2.py3-none-any.whl → 0.28.3__py2.py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- cidc_schemas/__init__.py +1 -1
- cidc_schemas/prism/constants.py +2 -0
- cidc_schemas/schemas/assays/components/available_assays.json +11 -0
- cidc_schemas/schemas/assays/components/nulisa_input.json +46 -0
- cidc_schemas/schemas/assays/nulisa_assay.json +63 -0
- cidc_schemas/schemas/templates/assays/nulisa_template.json +88 -0
- {nci_cidc_schemas-0.28.2.dist-info → nci_cidc_schemas-0.28.3.dist-info}/METADATA +1 -1
- {nci_cidc_schemas-0.28.2.dist-info → nci_cidc_schemas-0.28.3.dist-info}/RECORD +12 -9
- {nci_cidc_schemas-0.28.2.dist-info → nci_cidc_schemas-0.28.3.dist-info}/WHEEL +0 -0
- {nci_cidc_schemas-0.28.2.dist-info → nci_cidc_schemas-0.28.3.dist-info}/entry_points.txt +0 -0
- {nci_cidc_schemas-0.28.2.dist-info → nci_cidc_schemas-0.28.3.dist-info}/licenses/LICENSE +0 -0
- {nci_cidc_schemas-0.28.2.dist-info → nci_cidc_schemas-0.28.3.dist-info}/top_level.txt +0 -0
cidc_schemas/__init__.py
CHANGED
cidc_schemas/prism/constants.py
CHANGED
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@@ -28,6 +28,7 @@ SUPPORTED_ASSAYS = [
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"mihc",
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"scrnaseq",
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"visium",
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"nulisa",
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]
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SUPPORTED_SHIPPING_MANIFESTS = [
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@@ -143,6 +144,7 @@ ASSAY_TO_FILEPATH: Dict[str, str] = {
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"scrnaseq_analysis",
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"visium",
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"visium_analysis",
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"nulisa",
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]
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},
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}
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@@ -167,6 +167,17 @@
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"$ref": "assays/microbiome_assay.json"
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},
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"mergeStrategy": "append"
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},
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"nulisa": {
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"type": "array",
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"description": "NULISA",
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"items": {
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"$ref": "assays/nulisa_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": "nulisa_input",
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"title": "NULISA Input Files and Data",
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"type": "object",
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"description": "NULISA assay input files and data",
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"inheritableBase": true,
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"properties": {
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"ic_median": {
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"description": "Percentage sample IC reads relative to the median (within +/- 40% of the plate median)",
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"type": "number"
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},
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"detectability": {
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"description": "Percentage of targets with reads above the Limit of Detection (LOD) (Minimum threshold = plasma-90%, serum-90%, csf-70%, other-0%)",
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"type": "number"
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},
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"ic_reads": {
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"description": "Number of Internal Control (IC) reads within a sample (Minimum threshold = 1,000)",
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"type": "integer"
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},
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"qc_status": {
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"description": "Status",
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"type": "string",
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"enum": [
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"warning",
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"passed",
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"NA"
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]
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},
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"reads": {
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"description": "Number of reads within a sample (Minimum threshold = 500,000)",
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"type": "integer"
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},
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"auto_well_position": {
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"description": "Auto well position label",
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"type": "string"
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}
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},
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"required": [
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"ic_median",
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"ic_reads",
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"qc_status",
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"reads",
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"auto_well_position"
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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": "nulisa_assay",
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"title": "NULISA Assay",
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"type": "object",
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"$comment": "description used in docs/index.html and docs/assays.nulisa.html",
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"description": "Nucleic acid Linked Immuno-Sandwich Assay (NULISA) assay",
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"additionalProperties": false,
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"definitions": {
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"record": {
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"type": "object",
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"mergeStrategy": "objectMerge",
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"description": "A single data record from a NULISA assay.",
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"additionalProperties": false,
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"required": [
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"cimac_id",
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"details"
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],
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"properties": {
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"cimac_id": {
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"description": "Id of an sample within this clinical trial, that this assay record is based upon.",
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"$ref": "sample.json#properties/cimac_id"
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},
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"details": {
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"$ref": "assays/components/nulisa_input.json"
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}
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}
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}
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},
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"properties": {
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"assay_creator": {
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"$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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"npq_file": {
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"$ref": "artifacts/artifact_csv.json"
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},
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"raw_counts_file": {
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"$ref": "artifacts/artifact_csv.json"
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},
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"metadata_csv": {"$ref": "artifacts/artifact_csv.json"},
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"records": {
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"type": "array",
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"description": "A single data record from a NULISA assay.",
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"items": {
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"$ref": "assays/nulisa_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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"npq_file",
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"raw_counts_file",
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"records"
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]
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}
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{
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"title": "NULISA assay template",
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"description": "NULISA submission.",
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"prism_template_root_object_schema": "assays/nulisa_assay.json",
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"prism_template_root_object_pointer": "/assays/nulisa/0",
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"properties":
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{
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"worksheets":
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{
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"NULISA":
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{
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"preamble_rows":
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{
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"protocol identifier":
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{
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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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"assay creator":
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{
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"merge_pointer": "0/assay_creator",
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"type_ref": "assays/scrnaseq_assay.json#properties/assay_creator"
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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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"npq file": {
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"merge_pointer": "0/npq_file",
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"gcs_uri_format": "{protocol identifier}/nulisa/{batch id}/npq_file.csv",
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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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"raw counts file": {
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"merge_pointer": "0/raw_counts_file",
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"gcs_uri_format": "{protocol identifier}/nulisa/{batch id}/raw_counts_file.csv",
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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 csv": {
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"merge_pointer": "0/metadata_csv",
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"gcs_uri_format": "{protocol identifier}/nulisa/{batch id}/metadata.csv",
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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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"prism_data_object_pointer": "/records/-",
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"data_columns":
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{
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"Samples":
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{
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"Cimac ID":
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{
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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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"IC Median": {
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"merge_pointer": "0/details/ic_median",
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"type": "number"
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},
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"Detectability": {
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"merge_pointer": "0/details/detectability",
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"type": "number",
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"allow_empty": true
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},
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"IC Reads": {
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"merge_pointer": "0/details/ic_reads",
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"type": "integer"
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},
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"QC Status": {
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"merge_pointer": "0/details/qc_status",
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"type": "string"
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},
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"Reads": {
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"merge_pointer": "0/details/reads",
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"type": "integer"
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},
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"AUTO_WELLPOSITION": {
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"merge_pointer": "0/details/auto_well_position",
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"type": "string"
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}
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}
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}
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}
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}
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}
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cidc_schemas/__init__.py,sha256=
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cidc_schemas/__init__.py,sha256=ZhhU8G6vhZDwCRTjZUSvsWDgfM9KmaaVdhcContfbVo,135
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cidc_schemas/cli.py,sha256=gWiktRlraNH8Q0zNUae9dohKjPwBmcY0BJwdcQ_fIic,4099
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cidc_schemas/constants.py,sha256=RULs7pGuBAVq1teXymrfbVsK23ZowJvLuZlv0KcjL-Y,698
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cidc_schemas/json_validation.py,sha256=4UxcYrofXlDT-Lz6uiQGO1Jwz5bRs0mN_UH4p_A84ks,23262
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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/prism/__init__.py,sha256=J5Tj0X7Di6cyxAjaduOUp2aVyvl8UI67bgxEkgttvcU,530
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cidc_schemas/prism/constants.py,sha256=
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cidc_schemas/prism/constants.py,sha256=5Gr6xD_XrJpR7g6WC-twIEzaSnG7Oa1p09kDNWvDx5c,4124
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cidc_schemas/prism/core.py,sha256=tXDCCHurvcrxfU11meH3NRAVo9niklup0dpLRoIXwPk,20242
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cidc_schemas/prism/extra_metadata.py,sha256=2qs2PCvWRknZk56GrnRCjQ2hifAQz2YcJ8qXeMlG-Zg,8769
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cidc_schemas/prism/merger.py,sha256=36CKBPVoWecHuvGp3oT9a2d4jWIkvKuS_UofKTEpMYs,13065
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cidc_schemas/schemas/assays/mihc_assay.json,sha256=OgcklPvtUoCB-Gdvg4DF9fHFI15h9oalGW9lB4SL4xc,3104
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cidc_schemas/schemas/assays/misc_data.json,sha256=R6q-B8E-fIihlDNbe34gy7_aQeU1eIL9R_Yolg8SotU,2005
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cidc_schemas/schemas/assays/nanostring_assay.json,sha256=XAL6n80sxaAwUcNrx-pgA_YC5tyOlJrHOi8ID2vnFBo,2599
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cidc_schemas/schemas/assays/nulisa_assay.json,sha256=CMiAr-TsqRB6R6UcfWjjMrilN9vAQNSBcnv-vo3gPfk,2004
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cidc_schemas/schemas/assays/olink_assay.json,sha256=kQrUPjDKLKYyWpXoauiNDa0FANxPH_1bOfHeQEY-qAQ,5193
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cidc_schemas/schemas/assays/rna_assay-v0.json,sha256=skNGXbVVDY-6RpPosTHweQYtLntvo0bAiXcOxVSeh1s,3043
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cidc_schemas/schemas/assays/rna_assay.json,sha256=Gh47rRWYJSUIoLK3vvOb8_kFXhlISScrtA7nWasoBZI,409
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cidc_schemas/schemas/assays/wes_tumor_only_analysis.json,sha256=dU3oaeBbPnEv2Xjym7ikWr5ywwolnVbWDu1Weq2m8Wg,2018
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cidc_schemas/schemas/assays/components/antibody.json,sha256=vfLxXkXIcaJ1BXeUjCaJehrRCdVrBW3gxibwrD7zzd4,960
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cidc_schemas/schemas/assays/components/assay_core.json,sha256=QGuLiArVb7lEF2t1Ml4Qt7g4SXY58WuGBPFVgvOLI5w,485
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cidc_schemas/schemas/assays/components/available_assays.json,sha256=
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cidc_schemas/schemas/assays/components/available_assays.json,sha256=A6Spi-U_YsAknrrmKbOQuZQ0HRxWhP7oWpgLAaqSUuM,4528
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cidc_schemas/schemas/assays/components/available_ngs_analyses.json,sha256=Y_CL6A5hg4w57En9q1TsLH5ZBdlFeEpE6ggb3-dIIDk,1732
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cidc_schemas/schemas/assays/components/composite_image.json,sha256=k9EaBG3y9j-lvg3nQNZbfVpo9fK_gUz1-9iTwjlTDfE,733
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120
121
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cidc_schemas/schemas/assays/components/controls.json,sha256=_Wxz7W2msTGJ2Ei4XZg0Qy1t8A5_rLSHNvdPurC073E,458
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@@ -132,6 +133,7 @@ cidc_schemas/schemas/assays/components/mihc_input.json,sha256=KozUg3J_0PgQm3b5EE
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132
133
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cidc_schemas/schemas/assays/components/multiple_local_files.json,sha256=VVG6Yvz9yEchgFO9FHQLm7nwM_BcPMjYIecWMnRKp00,480
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133
134
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cidc_schemas/schemas/assays/components/ngs_assay_core.json,sha256=jqJbrnSPZV6pmJLM6J9YAxniwqGJ_pkTLak_m9zG3nY,1229
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134
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cidc_schemas/schemas/assays/components/ngs_assay_record.json,sha256=DwHKyRNDQ6h8PUz0KdBfmcd0Pz1Q1rOeqWpKfUIwjZM,615
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136
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+
cidc_schemas/schemas/assays/components/nulisa_input.json,sha256=Wu_Vx2TfwBXSaB9e9ngA7FJpcqycxwaFeyxJzosYS54,1271
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135
137
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cidc_schemas/schemas/assays/components/reads_core.json,sha256=p5RWN2TEGefenpz6pZlOG6MZ6tTAviKUx1bLCZtsNLk,1139
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136
138
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cidc_schemas/schemas/assays/components/reads_with_index.json,sha256=pg3wMQYMawCb1ZxJwiH_yCH3TAYu29EIZnB18AevzmM,1091
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137
139
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cidc_schemas/schemas/assays/components/scrnaseq_input.json,sha256=fIvV_xJPXDCoYajbsu21ISdhLaQVYjbPg_3nR_Jo7cE,1003
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@@ -176,6 +178,7 @@ cidc_schemas/schemas/templates/assays/mif_template.json,sha256=ozyMdziNxtAReTL7g
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cidc_schemas/schemas/templates/assays/mihc_template.json,sha256=BvlRCTC3R6Z6QCzqR0sH_lKuSjsd-69HWhT236aAuQQ,10974
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177
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cidc_schemas/schemas/templates/assays/misc_data_template.json,sha256=88GBWq7hrALrYmmgfqStrhocNtPWWYOMeUk9i8_uFRg,1896
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178
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cidc_schemas/schemas/templates/assays/nanostring_template.json,sha256=XFbf72EHNspsOUD014WDYjMSmIEz4LpCaY3iP3im2KQ,3214
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|
181
|
+
cidc_schemas/schemas/templates/assays/nulisa_template.json,sha256=usOvwb-6nCGv31vblQgnrv7bnsxZvRmxcHdtFF9sWY8,3749
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179
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cidc_schemas/schemas/templates/assays/olink_template.json,sha256=3YqkeVF9PnXUeETkf0RfEB14jprNPMWWwY4GTALfuWY,6335
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180
183
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cidc_schemas/schemas/templates/assays/rna_bam_template.json,sha256=l2OLgb8hx3fAupUvdWWtn_QbOiyicYE2u4diVz7C5cg,3084
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181
184
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cidc_schemas/schemas/templates/assays/rna_fastq_template.json,sha256=ZSKfzQ38SkpeKTK-xT9YAz0tRafCjo-IUZsr8GBYLOM,3344
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@@ -195,9 +198,9 @@ cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=q2GmO
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195
198
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cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json,sha256=lVJrGb28n-vyfjGBzhrzjn1lMKw1b4HXXmWtwA603v0,2797
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196
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cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json,sha256=LpaoDXDS11NCa-Dv37N-tzEGomswQrx5fypkUcG7xJk,18956
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|
197
200
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cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=-gww6NCHbtbI5z7UmNSmKyPK3IqKCE8F6n4XwTAb_gk,18101
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198
|
-
nci_cidc_schemas-0.28.
|
|
199
|
-
nci_cidc_schemas-0.28.
|
|
200
|
-
nci_cidc_schemas-0.28.
|
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201
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-
nci_cidc_schemas-0.28.
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202
|
-
nci_cidc_schemas-0.28.
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|
203
|
-
nci_cidc_schemas-0.28.
|
|
201
|
+
nci_cidc_schemas-0.28.3.dist-info/licenses/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
|
|
202
|
+
nci_cidc_schemas-0.28.3.dist-info/METADATA,sha256=3GZ-RW1G6XvGLo2b3FQxSM_zIajyDBEUJSBCm4uBdDk,5008
|
|
203
|
+
nci_cidc_schemas-0.28.3.dist-info/WHEEL,sha256=JNWh1Fm1UdwIQV075glCn4MVuCRs0sotJIq-J6rbxCU,109
|
|
204
|
+
nci_cidc_schemas-0.28.3.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
|
|
205
|
+
nci_cidc_schemas-0.28.3.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
|
|
206
|
+
nci_cidc_schemas-0.28.3.dist-info/RECORD,,
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|
File without changes
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|
File without changes
|
|
File without changes
|
|
File without changes
|