nci-cidc-schemas 0.26.34__py2.py3-none-any.whl → 0.26.36__py2.py3-none-any.whl

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Files changed (28) hide show
  1. cidc_schemas/__init__.py +1 -1
  2. cidc_schemas/prism/constants.py +0 -2
  3. cidc_schemas/schemas/artifacts/artifact_core.json +1 -0
  4. cidc_schemas/schemas/artifacts/artifact_ome_tiff.json +51 -0
  5. cidc_schemas/schemas/assays/components/available_ngs_analyses.json +0 -3
  6. cidc_schemas/schemas/assays/components/mibi_imaging/mibi_files.json +55 -0
  7. cidc_schemas/schemas/assays/components/mibi_imaging/mibi_input.json +56 -0
  8. cidc_schemas/schemas/assays/mibi_assay.json +8 -55
  9. cidc_schemas/schemas/shipping_core.json +2 -1
  10. cidc_schemas/schemas/templates/assays/mibi_template.json +48 -61
  11. cidc_schemas/schemas/templates/manifests/h_and_e_template.json +2 -1
  12. cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json +2 -1
  13. cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json +8 -4
  14. cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json +8 -4
  15. cidc_schemas/schemas/templates/manifests/pbmc_template.json +2 -1
  16. cidc_schemas/schemas/templates/manifests/plasma_template.json +2 -1
  17. cidc_schemas/schemas/templates/manifests/tissue_slide_template.json +2 -1
  18. cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json +8 -4
  19. cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json +2 -1
  20. cidc_schemas/template.py +0 -1
  21. {nci_cidc_schemas-0.26.34.dist-info → nci_cidc_schemas-0.26.36.dist-info}/METADATA +1 -2
  22. {nci_cidc_schemas-0.26.34.dist-info → nci_cidc_schemas-0.26.36.dist-info}/RECORD +26 -25
  23. {nci_cidc_schemas-0.26.34.dist-info → nci_cidc_schemas-0.26.36.dist-info}/WHEEL +1 -1
  24. cidc_schemas/schemas/assays/ctdna_analysis.json +0 -52
  25. cidc_schemas/schemas/templates/analyses/ctdna_analysis_template.json +0 -121
  26. {nci_cidc_schemas-0.26.34.dist-info → nci_cidc_schemas-0.26.36.dist-info}/LICENSE +0 -0
  27. {nci_cidc_schemas-0.26.34.dist-info → nci_cidc_schemas-0.26.36.dist-info}/entry_points.txt +0 -0
  28. {nci_cidc_schemas-0.26.34.dist-info → nci_cidc_schemas-0.26.36.dist-info}/top_level.txt +0 -0
cidc_schemas/__init__.py CHANGED
@@ -2,4 +2,4 @@
2
2
 
3
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  __author__ = """NCI"""
4
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  __email__ = "nci-cidc-tools-admin@mail.nih.gov"
5
- __version__ = "0.26.34"
5
+ __version__ = "0.26.36"
cidc_schemas/prism/constants.py CHANGED
@@ -51,7 +51,6 @@ SUPPORTED_ANALYSES = [
51
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  "tcr_analysis",
52
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  "wes_analysis",
53
53
  "wes_tumor_only_analysis",
54
- "ctdna_analysis",
55
54
  ]
56
55
 
57
56
  SUPPORTED_TEMPLATES = SUPPORTED_ASSAYS + SUPPORTED_MANIFESTS + SUPPORTED_ANALYSES
@@ -63,7 +62,6 @@ ASSAY_TO_FILEPATH: Dict[str, str] = {
63
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  "rna_level1_analysis": "rna/",
64
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  "wes_analysis": "wes/",
65
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  "wes_tumor_only_analysis": "wes_tumor_only/",
66
- "ctdna_analysis": "ctdna/",
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  # assay specifics removed
68
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  "atacseq_fastq": "atacseq/",
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  "rna_bam": "rna/",
cidc_schemas/schemas/artifacts/artifact_core.json CHANGED
@@ -90,6 +90,7 @@
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  "YAML",
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  "PDF",
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  "RDATA",
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+ "OME.TIFF",
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  "[NOT SET]"
94
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  ]
95
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  },
cidc_schemas/schemas/artifacts/artifact_ome_tiff.json ADDED
@@ -0,0 +1,51 @@
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+ {
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+ "$schema": "metaschema/strict_meta_schema.json#",
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+ "$id": "ome_tiff_artifact",
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+ "title": "Ome Tiff Artifact",
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+ "type": "object",
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+ "description": "Information about a ome tiff 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": "OME.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": { "$ref": "artifacts/artifact_core.json#properties/md5_hash" },
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+ "crc32c_hash": {
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+ "$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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+ "$ref": "artifacts/artifact_core.json#properties/facet_group"
43
+ }
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+ },
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+ "allOf": [
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+ {
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+ "$ref": "artifacts/artifact_core.json"
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+ }
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+ ],
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+ "mergeStrategy": "objectMerge"
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+ }
cidc_schemas/schemas/assays/components/available_ngs_analyses.json CHANGED
@@ -13,9 +13,6 @@
13
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  "wes_tumor_only_analysis": {
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  "$ref": "assays/wes_tumor_only_analysis.json"
15
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  },
16
- "ctdna_analysis": {
17
- "$ref": "assays/ctdna_analysis.json"
18
- },
19
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  "wes_analysis_old": {
20
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  "$ref": "assays/wes_analysis.json"
21
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  },
cidc_schemas/schemas/assays/components/mibi_imaging/mibi_files.json ADDED
@@ -0,0 +1,55 @@
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+ {
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+ "$schema": "metaschema/strict_meta_schema.json#",
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+ "$id": "mibi_files",
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+ "description": "A region of interest (ROI) is a portion of an image which has been analyzed using image processing software.",
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+ "type": "object",
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+ "properties": {
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+ "roi_id": {
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+ "description": "Identifier of a region of interest within one mibi slide, e.g. 1, 2, 3 or [123 x 321]",
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+ "type": "string"
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+ },
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+ "dataset": {
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+ "description": "Dataset the record belongs to",
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+ "type": "string"
14
+ },
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+ "mibi_ome_tiff_file_name": {
16
+ "type": "string",
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+ "description": "A (short) name of the file. Do not include the .ome.tiff extension"
18
+ },
19
+ "mibi_ome_tiff_file": {
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+ "description": "Image for MIBI in OME TIFF format",
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+ "$ref": "artifacts/artifact_ome_tiff.json"
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+ },
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+ "roi_description": {
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+ "description": "A text description of this ROI",
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+ "type": "string"
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+ },
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+ "he_file": {
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+ "inheritableBase": true,
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+ "mergeStrategy": "objectMerge",
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+ "anyOf": [
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+ {
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+ "$comment": "Path to the H & E image in SVS format.",
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+ "$ref": "artifacts/artifact_image.json"
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+ },
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+ {
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+ "$comment": "Path to the H & E image in JPG format.",
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+ "$ref": "artifacts/artifact_jpg.json"
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+ }
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+ ]
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+ },
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+ "comment": {
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+ "description": "A text comment regarding this slide.",
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+ "type": "string"
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+ }
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+ },
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+ "inheritableBase": true,
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+ "required": [
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+ "roi_id",
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+ "dataset",
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+ "mibi_ome_tiff_file_name",
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+ "mibi_ome_tiff_file",
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+ "roi_description",
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+ "he_file"
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+ ]
55
+ }
cidc_schemas/schemas/assays/components/mibi_imaging/mibi_input.json ADDED
@@ -0,0 +1,56 @@
1
+ {
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+ "$schema": "metaschema/strict_meta_schema.json#",
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+ "$id": "mibi_input",
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+ "title": "MIBI Input Files",
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+ "type": "object",
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+ "description": "MIBI assay input files.",
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+ "inheritableBase": true,
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+ "properties": {
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+ "roi_id": {
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+ "description": "Identifier of a region of interest within one mibi slide, e.g. 1, 2, 3 or [123 x 321]",
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+ "type": "string"
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+ },
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+ "dataset": {
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+ "description": "Dataset the record belongs to",
15
+ "type": "string"
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+ },
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+ "mibi_ome_tiff_file_name": {
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+ "type": "string",
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+ "description": "A (short) name of the file. Do not include the .ome.tiff extension"
20
+ },
21
+ "mibi_ome_tiff_file": {
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+ "description": "Image for MIBI in OME TIFF format",
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+ "$ref": "artifacts/artifact_ome_tiff.json"
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+ },
25
+ "roi_description": {
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+ "description": "A text description of this ROI",
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+ "type": "string"
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+ },
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+ "he_file": {
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+ "inheritableBase": true,
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+ "mergeStrategy": "objectMerge",
32
+ "anyOf": [
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+ {
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+ "$comment": "Path to the H & E image in SVS format.",
35
+ "$ref": "artifacts/artifact_image.json"
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+ },
37
+ {
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+ "$comment": "Path to the H & E image in JPG format.",
39
+ "$ref": "artifacts/artifact_jpg.json"
40
+ }
41
+ ]
42
+ },
43
+ "comment": {
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+ "description": "A text comment regarding this slide.",
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+ "type": "string"
46
+ }
47
+ },
48
+ "required": [
49
+ "roi_id",
50
+ "dataset",
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+ "mibi_ome_tiff_file_name",
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+ "mibi_ome_tiff_file",
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+ "roi_description",
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+ "he_file"
55
+ ]
56
+ }
cidc_schemas/schemas/assays/mibi_assay.json CHANGED
@@ -6,10 +6,10 @@
6
6
  "$comment": "description used in docs/index.html and docs/assays.mibi.html",
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7
  "description": "Multiplexed Ion Beam Imaging (MIBI) assay",
8
8
  "additionalProperties": false,
9
- "mergeStrategy": "objectMerge",
10
9
  "definitions": {
11
10
  "record": {
12
11
  "type": "object",
12
+ "mergeStrategy": "objectMerge",
13
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  "description": "A single data record from a MIBI assay.",
14
14
  "additionalProperties": false,
15
15
  "properties": {
@@ -17,58 +17,13 @@
17
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  "description": "Id of an sample within this clinical trial, that this assay record is based upon.",
18
18
  "$ref": "sample.json#properties/cimac_id"
19
19
  },
20
- "regions_of_interest": {
21
- "type": "array",
22
- "items": {
23
- "$ref": "assays/mibi_assay.json#definitions/region_of_interest"
24
- },
25
- "mergeStrategy": "arrayMergeById",
26
- "mergeOptions": {
27
- "idRef": "roi_id"
28
- }
20
+ "files": {
21
+ "$ref": "assays/components/mibi_imaging/mibi_input.json"
29
22
  }
30
23
  },
31
24
  "required": [
32
25
  "cimac_id",
33
- "regions_of_interest"
34
- ]
35
- },
36
- "region_of_interest": {
37
- "type": "object",
38
- "description": "A region of interest (ROI) is a portion of an image which has been analyzed using image processing software.",
39
- "additionalProperties": false,
40
- "properties": {
41
- "roi_id": {
42
- "description": "Identifier of a region of interest within one mIF slide, e.g. 1, 2, 3 or [123x321]",
43
- "type": "string"
44
- },
45
- "multichannel_image": {
46
- "description": "Analysis-ready multichannel image in OME TIFF format",
47
- "$ref": "artifacts/artifact_image.json"
48
- },
49
- "cluster_labels": {
50
- "description": "Cluster-labelled image in TIFF format",
51
- "$ref": "artifacts/artifact_image.json"
52
- },
53
- "channel_names": {
54
- "description": "Channel names table in CSV format",
55
- "$ref": "artifacts/artifact_csv.json"
56
- },
57
- "single_cell_table": {
58
- "description": "Single cell data table in CSV format",
59
- "$ref": "artifacts/artifact_csv.json"
60
- },
61
- "roi_description": {
62
- "description": "A text description of this ROI. Eg: decidua",
63
- "type": "string"
64
- },
65
- "comment": {
66
- "description": "A text comment regarding this slide.",
67
- "type": "string"
68
- }
69
- },
70
- "required": [
71
- "roi_id"
26
+ "files"
72
27
  ]
73
28
  }
74
29
  },
@@ -101,15 +56,13 @@
101
56
  "items": {
102
57
  "$ref": "assays/mibi_assay.json#definitions/record"
103
58
  },
104
- "mergeStrategy": "arrayMergeById",
105
- "mergeOptions": {
106
- "idRef": "cimac_id"
107
- }
59
+ "mergeStrategy": "append"
108
60
  }
109
61
  },
110
62
  "required": [
111
63
  "batch_id",
112
64
  "records",
113
- "assay_creator"
65
+ "assay_creator",
66
+ "antibodies"
114
67
  ]
115
- }
68
+ }
cidc_schemas/schemas/shipping_core.json CHANGED
@@ -53,7 +53,8 @@
53
53
  "ATACseq",
54
54
  "ctDNA",
55
55
  "Microbiome",
56
- "Nanostring"
56
+ "Nanostring",
57
+ "MIBI"
57
58
  ]
58
59
  },
59
60
  "courier": {
cidc_schemas/schemas/templates/assays/mibi_template.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "properties": {
7
7
  "worksheets": {
8
8
  "MIBI": {
9
- "prism_data_object_pointer": "/records/0/regions_of_interest/-",
9
+ "prism_data_object_pointer": "/records/-",
10
10
  "preamble_rows": {
11
11
  "protocol identifier": {
12
12
  "merge_pointer": "3/protocol_identifier",
@@ -20,82 +20,59 @@
20
20
  "merge_pointer": "0/assay_creator",
21
21
  "type_ref": "assays/components/assay_core.json#properties/assay_creator"
22
22
  },
23
- "folder": {
24
- "do_not_merge": true,
25
- "type": "string",
26
- "allow_empty": true
27
- },
28
23
  "metadata tsv": {
24
+ "merge_pointer": "0/metadata_tsv",
25
+ "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/metadata.tsv",
26
+ "is_artifact": 1,
29
27
  "type_ref": "assays/components/local_file.json#properties/file_path",
30
- "do_not_merge": true,
31
- "allow_empty": true,
32
- "process_as": [
33
- {
34
- "parse_through": "lambda metadata_tsv: f'{folder or \"\"}{metadata_tsv}'",
35
- "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/metadata.tsv",
36
- "type_ref": "assays/components/local_file.json#properties/file_path",
37
- "merge_pointer": "0/metadata_tsv",
38
- "is_artifact": 1
39
- }
40
- ]
28
+ "allow_empty": true
41
29
  }
42
30
  },
43
31
  "data_columns": {
44
32
  "Samples": {
45
- "Cimac id": {
46
- "merge_pointer": "2/cimac_id",
33
+ "cimac id": {
34
+ "merge_pointer": "0/cimac_id",
47
35
  "type_ref": "sample.json#properties/cimac_id"
48
36
  },
49
- "Roi id": {
50
- "merge_pointer": "0/roi_id",
51
- "type_ref": "assays/mibi_assay.json#definitions/region_of_interest/properties/roi_id"
37
+ "roi id": {
38
+ "merge_pointer": "0/files/roi_id",
39
+ "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/roi_id"
52
40
  },
53
41
  "Dataset": {
42
+ "merge_pointer": "0/files/dataset",
43
+ "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/dataset",
44
+ "allow_empty": true
45
+ },
46
+ "HE file type": {
54
47
  "do_not_merge": true,
55
48
  "type": "string",
56
- "process_as": [
57
- {
58
- "parse_through": "lambda dataset: f'{folder or \"\"}{dataset}/3D_image_stack.ome.tiff'",
59
- "merge_pointer": "/multichannel_image",
60
- "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/multichannel_image.ome.tiff",
61
- "type_ref": "assays/components/local_file.json#properties/file_path",
62
- "is_artifact": 1,
63
- "allow_empty": true
64
- },
65
- {
66
- "parse_through": "lambda dataset: f'{folder or \"\"}{dataset}/Mapping/cluster_labels_image.tif'",
67
- "merge_pointer": "/cluster_labels",
68
- "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/cluster_labels.tif",
69
- "type_ref": "assays/components/local_file.json#properties/file_path",
70
- "is_artifact": 1,
71
- "allow_empty": true
72
- },
73
- {
74
- "parse_through": "lambda dataset: f'{folder or \"\"}{dataset}/mcd/channelnames_report.csv'",
75
- "merge_pointer": "/channel_names",
76
- "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/channel_names.csv",
77
- "type_ref": "assays/components/local_file.json#properties/file_path",
78
- "is_artifact": 1,
79
- "allow_empty": true
80
- },
81
- {
82
- "parse_through": "lambda dataset: f'{folder or \"\"}{dataset}/SingleCellData/cells.csv'",
83
- "merge_pointer": "/single_cell_table",
84
- "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/single_cell_table.csv",
85
- "type_ref": "assays/components/local_file.json#properties/file_path",
86
- "is_artifact": 1,
87
- "allow_empty": true
88
- }
89
- ]
49
+ "enum": ["svs", "jpg"]
50
+ },
51
+ "HE file name": {
52
+ "merge_pointer": "0/files/he_file",
53
+ "is_artifact": 1,
54
+ "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/he_file.{he file type}",
55
+ "type_ref": "assays/components/local_file.json#properties/file_path"
90
56
  },
91
57
  "Roi description": {
92
- "merge_pointer": "0/roi_description",
93
- "type_ref": "assays/mibi_assay.json#definitions/region_of_interest/properties/roi_description",
58
+ "merge_pointer": "0/files/roi_description",
59
+ "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/roi_description",
94
60
  "allow_empty": true
95
61
  },
62
+ "MIBI OME Tiff File": {
63
+ "merge_pointer": "0/files/mibi_ome_tiff_file",
64
+ "type_ref": "assays/components/local_file.json#properties/file_path",
65
+ "is_artifact": 1,
66
+ "gcs_uri_format": "{protocol identifier}/mibi/{batch id}/{cimac id}/{roi id}/{mibi ome tiff file name}.ome.tiff"
67
+ },
68
+ "MIBI OME Tiff File Name": {
69
+ "merge_pointer": "0/files/mibi_ome_tiff_file_name",
70
+ "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/mibi_ome_tiff_file_name"
71
+ },
72
+
96
73
  "Comment": {
97
- "merge_pointer": "0/comment",
98
- "type_ref": "assays/mibi_assay.json#definitions/region_of_interest/properties/comment",
74
+ "merge_pointer": "0/files/comment",
75
+ "type_ref": "assays/components/mibi_imaging/mibi_files.json#properties/comment",
99
76
  "allow_empty": true
100
77
  }
101
78
  }
@@ -115,6 +92,16 @@
115
92
  "merge_pointer": "0/antibody",
116
93
  "type_ref": "assays/components/antibody.json#properties/antibody"
117
94
  },
95
+ "Clone": {
96
+ "merge_pointer": "0/clone",
97
+ "type_ref": "assays/components/antibody.json#properties/clone",
98
+ "allow_empty": true
99
+ },
100
+ "Company": {
101
+ "merge_pointer": "0/company",
102
+ "type_ref": "assays/components/antibody.json#properties/clone",
103
+ "allow_empty": true
104
+ },
118
105
  "Scicrunch rrid": {
119
106
  "merge_pointer": "0/scicrunch_rrid",
120
107
  "type_ref": "assays/components/mibi_antibody.json#properties/scicrunch_rrid",
@@ -160,4 +147,4 @@
160
147
  }
161
148
  }
162
149
  }
163
- }
150
+ }
cidc_schemas/schemas/templates/manifests/h_and_e_template.json CHANGED
@@ -95,7 +95,8 @@
95
95
  },
96
96
  "cohort name": {
97
97
  "merge_pointer": "2/cohort_name",
98
- "type_ref": "participant.json#properties/cohort_name"
98
+ "type_ref": "participant.json#properties/cohort_name",
99
+ "allow_empty": true
99
100
  },
100
101
  "participant ID": {
101
102
  "merge_pointer": "2/participant_id",
cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json CHANGED
@@ -93,7 +93,8 @@
93
93
  },
94
94
  "cohort name": {
95
95
  "merge_pointer": "2/cohort_name",
96
- "type_ref": "participant.json#properties/cohort_name"
96
+ "type_ref": "participant.json#properties/cohort_name",
97
+ "allow_empty": true
97
98
  },
98
99
  "participant ID": {
99
100
  "merge_pointer": "2/participant_id",
cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json CHANGED
@@ -93,7 +93,8 @@
93
93
  },
94
94
  "cohort name": {
95
95
  "merge_pointer": "2/cohort_name",
96
- "type_ref": "participant.json#properties/cohort_name"
96
+ "type_ref": "participant.json#properties/cohort_name",
97
+ "allow_empty": true
97
98
  },
98
99
  "participant ID": {
99
100
  "merge_pointer": "2/participant_id",
@@ -190,15 +191,18 @@
190
191
  "DNA quality": {
191
192
  "din value": {
192
193
  "merge_pointer": "/din",
193
- "type_ref": "sample.json#properties/din"
194
+ "type_ref": "sample.json#properties/din",
195
+ "allow_empty": true
194
196
  },
195
197
  "a260/a280 value": {
196
198
  "merge_pointer": "/a260_a280",
197
- "type_ref": "sample.json#properties/a260_a280"
199
+ "type_ref": "sample.json#properties/a260_a280",
200
+ "allow_empty": true
198
201
  },
199
202
  "a260/a230 value": {
200
203
  "merge_pointer": "/a260_a230",
201
- "type_ref": "sample.json#properties/a260_a230"
204
+ "type_ref": "sample.json#properties/a260_a230",
205
+ "allow_empty": true
202
206
  }
203
207
  },
204
208
  "Filled by CIMAC Lab": {
cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json CHANGED
@@ -95,7 +95,8 @@
95
95
  },
96
96
  "cohort name": {
97
97
  "merge_pointer": "2/cohort_name",
98
- "type_ref": "participant.json#properties/cohort_name"
98
+ "type_ref": "participant.json#properties/cohort_name",
99
+ "allow_empty": true
99
100
  },
100
101
  "participant ID": {
101
102
  "merge_pointer": "2/participant_id",
@@ -187,15 +188,18 @@
187
188
  "DNA quality": {
188
189
  "din value": {
189
190
  "merge_pointer": "/din",
190
- "type_ref": "sample.json#properties/din"
191
+ "type_ref": "sample.json#properties/din",
192
+ "allow_empty": true
191
193
  },
192
194
  "a260/a280 value": {
193
195
  "merge_pointer": "/a260_a280",
194
- "type_ref": "sample.json#properties/a260_a280"
196
+ "type_ref": "sample.json#properties/a260_a280",
197
+ "allow_empty": true
195
198
  },
196
199
  "a260/a230 value": {
197
200
  "merge_pointer": "/a260_a230",
198
- "type_ref": "sample.json#properties/a260_a230"
201
+ "type_ref": "sample.json#properties/a260_a230",
202
+ "allow_empty": true
199
203
  }
200
204
  },
201
205
  "Filled by CIMAC Lab": {
cidc_schemas/schemas/templates/manifests/pbmc_template.json CHANGED
@@ -177,7 +177,8 @@
177
177
  },
178
178
  "cohort name": {
179
179
  "merge_pointer": "2/cohort_name",
180
- "type_ref": "participant.json#properties/cohort_name"
180
+ "type_ref": "participant.json#properties/cohort_name",
181
+ "allow_empty": true
181
182
  },
182
183
  "participant ID": {
183
184
  "merge_pointer": "2/participant_id",
cidc_schemas/schemas/templates/manifests/plasma_template.json CHANGED
@@ -173,7 +173,8 @@
173
173
  },
174
174
  "cohort name": {
175
175
  "merge_pointer": "2/cohort_name",
176
- "type_ref": "participant.json#properties/cohort_name"
176
+ "type_ref": "participant.json#properties/cohort_name",
177
+ "allow_empty": true
177
178
  },
178
179
  "collection event name": {
179
180
  "merge_pointer": "/collection_event_name",
cidc_schemas/schemas/templates/manifests/tissue_slide_template.json CHANGED
@@ -95,7 +95,8 @@
95
95
  },
96
96
  "cohort name": {
97
97
  "merge_pointer": "2/cohort_name",
98
- "type_ref": "participant.json#properties/cohort_name"
98
+ "type_ref": "participant.json#properties/cohort_name",
99
+ "allow_empty": true
99
100
  },
100
101
  "participant ID": {
101
102
  "merge_pointer": "2/participant_id",
cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json CHANGED
@@ -95,7 +95,8 @@
95
95
  },
96
96
  "cohort name": {
97
97
  "merge_pointer": "2/cohort_name",
98
- "type_ref": "participant.json#properties/cohort_name"
98
+ "type_ref": "participant.json#properties/cohort_name",
99
+ "allow_empty": true
99
100
  },
100
101
  "participant ID": {
101
102
  "merge_pointer": "2/participant_id",
@@ -192,15 +193,18 @@
192
193
  "DNA quality": {
193
194
  "din value": {
194
195
  "merge_pointer": "/din",
195
- "type_ref": "sample.json#properties/din"
196
+ "type_ref": "sample.json#properties/din",
197
+ "allow_empty": true
196
198
  },
197
199
  "a260/a280 value": {
198
200
  "merge_pointer": "/a260_a280",
199
- "type_ref": "sample.json#properties/a260_a280"
201
+ "type_ref": "sample.json#properties/a260_a280",
202
+ "allow_empty": true
200
203
  },
201
204
  "a260/a230 value": {
202
205
  "merge_pointer": "/a260_a230",
203
- "type_ref": "sample.json#properties/a260_a230"
206
+ "type_ref": "sample.json#properties/a260_a230",
207
+ "allow_empty": true
204
208
  }
205
209
  },
206
210
  "Filled by CIMAC Lab": {
cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json CHANGED
@@ -95,7 +95,8 @@
95
95
  },
96
96
  "cohort name": {
97
97
  "merge_pointer": "2/cohort_name",
98
- "type_ref": "participant.json#properties/cohort_name"
98
+ "type_ref": "participant.json#properties/cohort_name",
99
+ "allow_empty": true
99
100
  },
100
101
  "participant ID": {
101
102
  "merge_pointer": "2/participant_id",
cidc_schemas/template.py CHANGED
@@ -232,7 +232,6 @@ def _initialize_template_schema(name: str, title: str, pointer: str):
232
232
  "rna": "RNA sequencing Level 1",
233
233
  "wes": "Whole Exome Sequencing (WES) Tumor-Normal Paired",
234
234
  "wes_tumor_only": "Whole Exome Sequencing (WES) Tumor-Only",
235
- "ctDNA": "ctDNA",
236
235
  }[name]
237
236
 
238
237
  # static
{nci_cidc_schemas-0.26.34.dist-info → nci_cidc_schemas-0.26.36.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: nci_cidc_schemas
3
- Version: 0.26.34
3
+ Version: 0.26.36
4
4
  Summary: The CIDC data model and tools for working with it.
5
5
  Home-page: https://github.com/NCI-CIDC/cidc-schemas
6
6
  Author: NCI
@@ -56,7 +56,6 @@ pip install nci-cidc-schemas
56
56
  - **`docs/`** - the most recent build of the data model documentation, along with templates and scripts for re-generating the documentation.
57
57
  - **`template_examples/`** - example populated Excel files for template specifications in `schemas/templates`, and `.csv`s auto-generated from those `.xlsx`s that allow to transparently keep track of changes in them.
58
58
  - **`tests/`** - tests for the `cidc_schemas` module.
59
- - **`.githooks/`** - git hooks, e.g. for auto-generating `.csv`s in `template_examples/` and `.html` documentation files.
60
59
 
61
60
  ### Developer Setup
62
61
 
{nci_cidc_schemas-0.26.34.dist-info → nci_cidc_schemas-0.26.36.dist-info}/RECORD RENAMED
@@ -1,9 +1,9 @@
1
- cidc_schemas/__init__.py,sha256=5VfL7TJUTUC2eX_om5PYcQz83FCUfoSmeQKSu-bPYRA,136
1
+ cidc_schemas/__init__.py,sha256=PyjN4BhZxDfIvvKNqCcz38xDv5i4Np3N29vZJJZUFGw,136
2
2
  cidc_schemas/cli.py,sha256=gWiktRlraNH8Q0zNUae9dohKjPwBmcY0BJwdcQ_fIic,4099
3
3
  cidc_schemas/constants.py,sha256=RULs7pGuBAVq1teXymrfbVsK23ZowJvLuZlv0KcjL-Y,698
4
4
  cidc_schemas/json_validation.py,sha256=SyZSW7AAS-qlYLUUV_ri4393utkNsDexcWB73rEmFLs,20035
5
5
  cidc_schemas/migrations.py,sha256=Amg_T4cFgMzySD7yNnT_PWpqP7hwlTWGeHlI_RSXuRI,14766
6
- cidc_schemas/template.py,sha256=J41S65-2w4VdmpLDVY-icyHWAsbH1Gtg-pMlL_TGo6A,49891
6
+ cidc_schemas/template.py,sha256=gM6Xp1fOZaF8wOLzY5HGdxi4p8cEYhYXRpqRPncYua0,49865
7
7
  cidc_schemas/template_reader.py,sha256=xXtLRKu1y4FrPj8RgyGOmB2hlsCDXcuvMBWami2_jV8,13119
8
8
  cidc_schemas/template_writer.py,sha256=faOhvSDTp4nuPhOtVQR_J7YNnFzx-vh7oyNpFdee1mY,18236
9
9
  cidc_schemas/unprism.py,sha256=5EeqNKedVEf15CJiMQ-ImXd1wIbNnzihv21rAMClZyc,13325
@@ -11,7 +11,7 @@ cidc_schemas/util.py,sha256=ZCQ--ROZyXYVB034fHHmxZXb5F0G2GwzPwSfyfegtGk,4348
11
11
  cidc_schemas/metaschema/strict_meta_schema.json,sha256=3FiS0r2dAXgfPsruJwZYbQoQnHhC_yl-3mclX8gfiQU,6428
12
12
  cidc_schemas/pipeline_configs/rna_level1_analysis_config.yaml.j2,sha256=6no9sFqwzb1T61RZGD-owDt2K5R8G_fPTzflV4fOroo,2832
13
13
  cidc_schemas/prism/__init__.py,sha256=J5Tj0X7Di6cyxAjaduOUp2aVyvl8UI67bgxEkgttvcU,530
14
- cidc_schemas/prism/constants.py,sha256=fFiXfFFMiGqG07mKlt_ejcRZrnMD6g66pwnB6s4Dfgk,2379
14
+ cidc_schemas/prism/constants.py,sha256=b5pgxrzwJvKWWIEE9V72cvKwl_ARRaANPHzKk4yo4M4,2325
15
15
  cidc_schemas/prism/core.py,sha256=PQgsRAEleT6gO3VyE4uFTYa3qK_VXjFcErV1YwWV1nQ,19294
16
16
  cidc_schemas/prism/extra_metadata.py,sha256=wZjhUGKSvfupr6qZ1WuPepKnf_FG1nGfsDai_kBFZ50,8559
17
17
  cidc_schemas/prism/merger.py,sha256=Kf5o9NWT80XqYZASbH0dJsQ0dkwMl3HtoR_p7wqUypI,12431
@@ -21,7 +21,7 @@ cidc_schemas/schemas/clinical_data.json,sha256=ubt2dqTLCbDuxuOXrBObT_xLHVSArMBx4
21
21
  cidc_schemas/schemas/clinical_trial.json,sha256=mqvpCTqWGimKA8-S4F32YMDBoHcJkawpr9iTwUgH56w,4652
22
22
  cidc_schemas/schemas/participant.json,sha256=vCtxbUfVGTjvZ8SPPNLvWJkJIBZUK2NSHpYzJgdoSaY,2991
23
23
  cidc_schemas/schemas/sample.json,sha256=TRWgxQBybtj4WjLBNZAdpoShpbDTGl8iT3FceGx2gD8,16296
24
- cidc_schemas/schemas/shipping_core.json,sha256=MYnULNUnXYmOOHvF6T7oSBfMsT5f1waFdzlgdknnMD0,3299
24
+ cidc_schemas/schemas/shipping_core.json,sha256=ouekd6KNf4EKVz4IsE2yjibvIjpCE8CZBxCRXlJ7p_U,3315
25
25
  cidc_schemas/schemas/artifacts/artifact_bam.json,sha256=nPy3qx07--arLyb9VgfdVK6OJoMPhr6rnp-3AF6o82Q,1653
26
26
  cidc_schemas/schemas/artifacts/artifact_bam_bai.json,sha256=S1LxCZVyN3v-Hxhs7TEDbGcV-y7LVdAoLzGblT9IhEk,1671
27
27
  cidc_schemas/schemas/artifacts/artifact_bed.json,sha256=nGPKiAd2GQGJ6JkdLaqZhfOuyDmsAdUqril1Yao2qmE,1653
@@ -32,7 +32,7 @@ cidc_schemas/schemas/artifacts/artifact_clinical_docx.json,sha256=9Lbq9H0mhPIRDA
32
32
  cidc_schemas/schemas/artifacts/artifact_clinical_xlsx.json,sha256=IOQD7NBS3lvJV2Dts0Z6y0QoyYeB2jc2OLFgjSSTEn4,2232
33
33
  cidc_schemas/schemas/artifacts/artifact_cncf.json,sha256=IrawYPFqZ4HV0bClCKgOpO8Xh6d2GD8rP7tjS5ASv_o,1657
34
34
  cidc_schemas/schemas/artifacts/artifact_cns.json,sha256=R9RItkDV_kqnfLqr-WBa7yJmeDc2kblJg3xx7hNjtAk,1653
35
- cidc_schemas/schemas/artifacts/artifact_core.json,sha256=Fmm6LSnEBzEutpXtTpB3pQgzObCXl4Ymu9BbvN_5aHM,3140
35
+ cidc_schemas/schemas/artifacts/artifact_core.json,sha256=dNVhgD7CYaSjANH6EN_rxatqwAKOtOyEravE6N_-9Ds,3160
36
36
  cidc_schemas/schemas/artifacts/artifact_csv.json,sha256=BPqogQ3DMjyRs9N-sk9c1Q7gKTNumOHhhwwn5gCHbGM,1665
37
37
  cidc_schemas/schemas/artifacts/artifact_elisa_xlsx.json,sha256=1Erw2HG4YJPiNop40hs9LigHr7O66_WRlrZ3wWSQzBs,2216
38
38
  cidc_schemas/schemas/artifacts/artifact_fastq_gz.json,sha256=k8So4mBtC7YWp6-PSeCKNvp3v0MNPNfdPWRQWoASNvA,1683
@@ -47,6 +47,7 @@ cidc_schemas/schemas/artifacts/artifact_log.json,sha256=TvHQLsxAfnB9WbnHt-otYObK
47
47
  cidc_schemas/schemas/artifacts/artifact_maf.json,sha256=MyJOs8A0aHrl8i9l5Q1m4ADm8dqcTyJ_YtUJDS48Bjk,1653
48
48
  cidc_schemas/schemas/artifacts/artifact_narrowPeak.json,sha256=EOGIAmpo46qZdSzZj3Gi7WKLS81OH1xUTJzeu7_I75c,1681
49
49
  cidc_schemas/schemas/artifacts/artifact_npx.json,sha256=I0o8C9ilOrbLBmLpTOQ1ARFyQHyaSd321mPjuJMGUUw,2134
50
+ cidc_schemas/schemas/artifacts/artifact_ome_tiff.json,sha256=wSIQPf2mi00BwikFlz8qL3wmVvtYWhuOxrHLc3ngzS0,1673
50
51
  cidc_schemas/schemas/artifacts/artifact_pdf.json,sha256=t-RR4gftGD-wjB7t40lb1TbnKLosPQCDyP-SL1V5dWc,1674
51
52
  cidc_schemas/schemas/artifacts/artifact_png.json,sha256=cGzHZQg3qbungIkxvLh6TY8iqKjtutBU2XmBnRyiijQ,1653
52
53
  cidc_schemas/schemas/artifacts/artifact_rcc.json,sha256=IyqqsxPdFZjRoFuBpnkBKBLbc-SoWvrQoqFWeNLU_as,1704
@@ -60,14 +61,13 @@ cidc_schemas/schemas/artifacts/artifact_xlsx.json,sha256=PmQ3NY_8ywS3iFa4vvLzcXb
60
61
  cidc_schemas/schemas/artifacts/artifact_yaml.json,sha256=Eey5T68k4jXqiFXfgWTVi3ZoiY5EZxc75rWCEvaZscE,1657
61
62
  cidc_schemas/schemas/artifacts/artifact_zip.json,sha256=L9TyKfKm2j0jUo7ED7Lb43Z6VRHP7hEirC349viEBhQ,1653
62
63
  cidc_schemas/schemas/assays/atacseq_assay.json,sha256=5ezVeJmrwOWuXLtf9-gH8iYKhLCys9Ii2VamezNI_hM,2547
63
- cidc_schemas/schemas/assays/ctdna_analysis.json,sha256=8HTya0iwtxle0myQ4Dj6VaTII0RuqqiR14SUrmPKPAM,1513
64
64
  cidc_schemas/schemas/assays/ctdna_assay.json,sha256=1AwUYiE93XEVDg_FPFyV2OgaD7Ry7pWoD4AH2DAXasA,3503
65
65
  cidc_schemas/schemas/assays/cytof_assay.json,sha256=rf0vebcoHY_dS4wlqkoBY9rclSAE3CRdxeGLXAbhScM,3659
66
66
  cidc_schemas/schemas/assays/cytof_assay_core.json,sha256=Vwg3RmEEdCpZtDDaVAWBDCKTMnSxagsdqSJq4AiDu9w,8828
67
67
  cidc_schemas/schemas/assays/elisa_assay.json,sha256=YHeoxYmgdpefLWkBXNg60JUig2Ccqg8thWZ5M5q3hyw,2233
68
68
  cidc_schemas/schemas/assays/hande_assay.json,sha256=NhLyBiBOgeZ9woeGO4EEIod-y_Wzz6WamsP3ZNzxtS0,3192
69
69
  cidc_schemas/schemas/assays/ihc_assay.json,sha256=g1WuTUrN6M3mmQL7TCURsKL442An8jlmXaxddg2Ayak,6738
70
- cidc_schemas/schemas/assays/mibi_assay.json,sha256=gxUdCKzsNpL5FB8muT8Gq-3cqbOTGiOax-kFjI4myCA,4187
70
+ cidc_schemas/schemas/assays/mibi_assay.json,sha256=0DnK6Tl_DZbzKuLcleaBYMW19OBpI3ociSqqeK0bG04,2164
71
71
  cidc_schemas/schemas/assays/microbiome_assay.json,sha256=4eSEKRylf86yLV7QKCIlMzzjj_XHKMfQpA0njLHBs00,2078
72
72
  cidc_schemas/schemas/assays/mif_assay.json,sha256=IG-s80kl8PUUi4U6FGmJbziG0nJf5Or_WTzfb5d46uQ,2599
73
73
  cidc_schemas/schemas/assays/misc_data.json,sha256=R6q-B8E-fIihlDNbe34gy7_aQeU1eIL9R_Yolg8SotU,2005
@@ -84,7 +84,7 @@ cidc_schemas/schemas/assays/wes_tumor_only_analysis.json,sha256=dU3oaeBbPnEv2Xjy
84
84
  cidc_schemas/schemas/assays/components/antibody.json,sha256=vfLxXkXIcaJ1BXeUjCaJehrRCdVrBW3gxibwrD7zzd4,960
85
85
  cidc_schemas/schemas/assays/components/assay_core.json,sha256=QGuLiArVb7lEF2t1Ml4Qt7g4SXY58WuGBPFVgvOLI5w,485
86
86
  cidc_schemas/schemas/assays/components/available_assays.json,sha256=RiyOd6-awMmELxYj-UbAo5dQxQv_rEMI3TuYAk4TCiU,3540
87
- cidc_schemas/schemas/assays/components/available_ngs_analyses.json,sha256=-827aY2HoYDWc_zjqEBFCqPH6DFgSqFRberrn7E96zc,1237
87
+ cidc_schemas/schemas/assays/components/available_ngs_analyses.json,sha256=dmC10wI7roGVwbf5T8DxIW1geIjks-Sl-GHJkJXc6eQ,1163
88
88
  cidc_schemas/schemas/assays/components/composite_image.json,sha256=k9EaBG3y9j-lvg3nQNZbfVpo9fK_gUz1-9iTwjlTDfE,733
89
89
  cidc_schemas/schemas/assays/components/controls.json,sha256=_Wxz7W2msTGJ2Ei4XZg0Qy1t8A5_rLSHNvdPurC073E,458
90
90
  cidc_schemas/schemas/assays/components/enrichment_core.json,sha256=zC5G7q-QyNrdynCOoPCCSfOuSKq8TiDH-Pl6gITNfVQ,813
@@ -104,6 +104,8 @@ cidc_schemas/schemas/assays/components/imaging/mif_entry.json,sha256=0jYCSMD3j5r
104
104
  cidc_schemas/schemas/assays/components/imaging/mif_export.json,sha256=CVGCpIVcHkTnIQvBibU4HkdYcm2lYzGYu3pXGm4bUa8,1728
105
105
  cidc_schemas/schemas/assays/components/imaging/mif_input.json,sha256=Hf1PKkk6pHRLcGGJrVmkhC6SApOA5pD6XJFRscM9ee0,1000
106
106
  cidc_schemas/schemas/assays/components/imaging/mif_roi.json,sha256=XL80pl3_5xj40Y4fpE0THDjCDNYojtxDpjtatoFcNAA,1112
107
+ cidc_schemas/schemas/assays/components/mibi_imaging/mibi_files.json,sha256=zylVuDxUKxJ2wXPuTphuT1yY8YYl_vm42a80Xpl3tfc,1580
108
+ cidc_schemas/schemas/assays/components/mibi_imaging/mibi_input.json,sha256=JvigxrK5namtAjUHvBm6QVBZWePVLXWTNaORoUH_aBA,1522
107
109
  cidc_schemas/schemas/assays/components/ngs/ngs_assay_record.json,sha256=DwHKyRNDQ6h8PUz0KdBfmcd0Pz1Q1rOeqWpKfUIwjZM,615
108
110
  cidc_schemas/schemas/assays/components/ngs/atacseq/atacseq_analysis.json,sha256=kDhS8GHGLF05v4427J6E73J6MiOh0R8Lh6RHrSD5Ak0,2283
109
111
  cidc_schemas/schemas/assays/components/ngs/rna/fusion.json,sha256=lgGWX9unADhT4xNDGqQD_VbC6cUo1JMgH9Ii7ZBvofQ,392
@@ -117,7 +119,6 @@ cidc_schemas/schemas/assays/components/ngs/rna/salmon.json,sha256=GRJaC4MhupuRrE
117
119
  cidc_schemas/schemas/assays/components/ngs/rna/star.json,sha256=XoL1Ro8YDr-ZQQOmYZC8NnREDW-7qzR6IzJi3tLQ2ks,772
118
120
  cidc_schemas/schemas/assays/components/ngs/rna/trust4.json,sha256=o-fxkTL-1Tho1kPkJ6CcMUp5kE5mnkZU8cdSCzHR5cQ,382
119
121
  cidc_schemas/schemas/templates/analyses/atacseq_analysis_template.json,sha256=7vBdwVD6HEd9Pj8AkEoa34fQjIynztsNaKvfn2KoFFc,5403
120
- cidc_schemas/schemas/templates/analyses/ctdna_analysis_template.json,sha256=WSuNoR4cFoYOH3_VHD0FY0m8TD578Yl6MSESQPMDMQo,7408
121
122
  cidc_schemas/schemas/templates/analyses/cytof_analysis_template.json,sha256=d6qOGbYXXx1c8rb-saM4D_tMuK8n4ydbyW9_xaW6xhk,6381
122
123
  cidc_schemas/schemas/templates/analyses/rna_level1_analysis_template.json,sha256=vMHXSQNZz8sFxwiBUnRXb5o08GxgbKZjMu8ZPjNn4TI,15944
123
124
  cidc_schemas/schemas/templates/analyses/tcr_analysis_template.json,sha256=ai5KUp6q5GGTxDybOHBaseOnvQCVqIRh4SurETz5Vx0,3054
@@ -130,7 +131,7 @@ cidc_schemas/schemas/templates/assays/cytof_template.json,sha256=YGaLt7DKsz32o3n
130
131
  cidc_schemas/schemas/templates/assays/elisa_template.json,sha256=Q8cv5ZpaRZUfvr6e4PC4uvMqhhaDGLdvVMN_s8Uiajw,2259
131
132
  cidc_schemas/schemas/templates/assays/hande_template.json,sha256=BNMQO4JpBrjuD8ITH1x7cJfkqI4bgKZilvN9yqavaqs,4293
132
133
  cidc_schemas/schemas/templates/assays/ihc_template.json,sha256=lOSP6v24FMk-WN7Za4IYQkM94R-1TEvrnllRopEEYa4,7341
133
- cidc_schemas/schemas/templates/assays/mibi_template.json,sha256=wy-LeCZRVYpvkpD7S04GZgL6P8ZvtoGroIzzijpti6M,8984
134
+ cidc_schemas/schemas/templates/assays/mibi_template.json,sha256=T5gAgsmWpUkkO6CI7aFpyD4efSTZsNmbsLLBrHXpNzg,7787
134
135
  cidc_schemas/schemas/templates/assays/microbiome_template.json,sha256=2qaTB8W-tG6NhbSJ3KAEIacp1E4g-cFBGMOMc5zTafo,3578
135
136
  cidc_schemas/schemas/templates/assays/mif_template.json,sha256=ozyMdziNxtAReTL7guFIwTiJGhEWam9Hsb_fOhIYXIY,19272
136
137
  cidc_schemas/schemas/templates/assays/misc_data_template.json,sha256=88GBWq7hrALrYmmgfqStrhocNtPWWYOMeUk9i8_uFRg,1896
@@ -142,19 +143,19 @@ cidc_schemas/schemas/templates/assays/tcr_adaptive_template.json,sha256=Hb8ngxw6
142
143
  cidc_schemas/schemas/templates/assays/tcr_fastq_template.json,sha256=7Qq4ssI8ErDrHy5RIxjPcNiDf2IBHG42JcngDFKxqlE,3457
143
144
  cidc_schemas/schemas/templates/assays/wes_bam_template.json,sha256=nxbb_lNPi-5cdAlwmSBvn7cS_8gMjROOz7wBWk6ev0Y,2724
144
145
  cidc_schemas/schemas/templates/assays/wes_fastq_template.json,sha256=vuwuIpqXyqpGxCunpjbHKaBQhfKFnr2R-wMkXDiJdKM,3143
145
- cidc_schemas/schemas/templates/manifests/h_and_e_template.json,sha256=sgVDCTfdaPFkCN5KGbwfCJYFQnTw6rqk33eY3AAXkSc,12475
146
- cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json,sha256=Zr5ihmNu4Q2jRb55Cn4EFrxrZQJYvJlCIcNHDbsODUw,11829
147
- cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json,sha256=Vk7hS-ji-w5d73CkOqFlSAzcm0ouJBAcdgzxNFFB8jQ,13346
148
- cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json,sha256=jv4JKiVyyvAvsMMLW8NOGrseOZ8eOWbP1mk9us1Qxqk,12989
149
- cidc_schemas/schemas/templates/manifests/pbmc_template.json,sha256=49e5d5WCstjLrLhC2K-82qs1IdwbWjFgR8hFIXRYyKk,17530
150
- cidc_schemas/schemas/templates/manifests/plasma_template.json,sha256=cdLEb6kt_Z7zjcw_Bh-5-PFpRUC0YpViuYIw-hKTyAs,15099
151
- cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=sFPytc04_-QtfetvYIeh4PdlBFtlBiOGZY5HmhOzJTM,11024
146
+ cidc_schemas/schemas/templates/manifests/h_and_e_template.json,sha256=PiCpfbWd5I29wwYWCQHjQh10g9l84dligYTVvMcJHgM,12524
147
+ cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json,sha256=u1QPL83DUvPMcMdYbwmmgT0nSOqkbjQR-asXZ_6p0CY,11878
148
+ cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json,sha256=JudTPeQBjTttX4OXMrVl9DTRM73KgZN3jbtC3lcuQsA,13542
149
+ cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json,sha256=xCE0pTXRlKOd0dPMKcDIBKXRa81Ka_H5f6OGE1TNmhw,13185
150
+ cidc_schemas/schemas/templates/manifests/pbmc_template.json,sha256=c0F9xu9za95i2RSVl_9wjiZIUxczOFNWJaXRy8pJhOg,17579
151
+ cidc_schemas/schemas/templates/manifests/plasma_template.json,sha256=43bizjQ7zJt5mQHtUfFHDA_f3L4DxBo4XqgHnFvNPbw,15148
152
+ cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=Y3951-HNUVfvOK4fjUxGJt2gtmGhKZxWiXVLxyZghn8,11073
152
153
  cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json,sha256=lVJrGb28n-vyfjGBzhrzjn1lMKw1b4HXXmWtwA603v0,2797
153
- cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json,sha256=D4ICMeHQgKXFDwaMOqrcLcUEF-dYGalagGYDUFAploU,13276
154
- cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=MpJTjoaTdIlNBAIIxSfmItVevA5BXnajqu_jaEXxBmo,12568
155
- nci_cidc_schemas-0.26.34.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
156
- nci_cidc_schemas-0.26.34.dist-info/METADATA,sha256=zdG4Fo50hBiDycEaiq1b3xAA6Stq7B90SS6qLjw51cM,4436
157
- nci_cidc_schemas-0.26.34.dist-info/WHEEL,sha256=DZajD4pwLWue70CAfc7YaxT1wLUciNBvN_TTcvXpltE,110
158
- nci_cidc_schemas-0.26.34.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
159
- nci_cidc_schemas-0.26.34.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
160
- nci_cidc_schemas-0.26.34.dist-info/RECORD,,
154
+ cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json,sha256=-CC7Hg-qzZ7e5QrrnkybrS1Vrfq2zlgtxU4kRnR5is8,13472
155
+ cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=uPiiEo1xEde6MDhQDapLIjL8XcghgeoCEDdZTzGYFBA,12617
156
+ nci_cidc_schemas-0.26.36.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
157
+ nci_cidc_schemas-0.26.36.dist-info/METADATA,sha256=0hI13s8gAgLo2Z70NJIV5bt8j3H_CUDgWZNJwW86JYY,4314
158
+ nci_cidc_schemas-0.26.36.dist-info/WHEEL,sha256=XRxW4r1PNiVhMpP4bT9oWtu3HyndxpJ84SkubFgzp_Y,109
159
+ nci_cidc_schemas-0.26.36.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
160
+ nci_cidc_schemas-0.26.36.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
161
+ nci_cidc_schemas-0.26.36.dist-info/RECORD,,
{nci_cidc_schemas-0.26.34.dist-info → nci_cidc_schemas-0.26.36.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: bdist_wheel (0.43.0)
2
+ Generator: setuptools (72.1.0)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py2-none-any
5
5
  Tag: py3-none-any
cidc_schemas/schemas/assays/ctdna_analysis.json DELETED
@@ -1,52 +0,0 @@
1
- {
2
- "$schema": "metaschema/strict_meta_schema.json#",
3
- "$id": "ctdna_analysis",
4
- "title": "ctDNA analysis",
5
- "type": "object",
6
- "description": "Combined analysis files for the ctDNA assay.",
7
-
8
- "definitions": {
9
- "sample_analysis": {
10
- "type": "object",
11
- "description": "ctDNA assay output files for a tumor normal pair of samples.",
12
-
13
- "required": [
14
- "run_id",
15
- "tumor"
16
- ],
17
- "additionalProperties": false,
18
- "properties": {
19
- "run_id": {
20
- "type": "string",
21
- "description": "An id used as if this was a paired analysis run."
22
- },
23
- "error": { "$ref": "assays/wes_core.json#properties/error" },
24
- "tumor": { "$ref": "assays/wes_assay.json#definitions/sample_analysis" },
25
- "comments": {
26
- "type": "string",
27
- "description": "Comments on the tumor-only analysis run."
28
- }
29
- }
30
- }
31
- },
32
-
33
- "required": [],
34
- "additionalProperties": false,
35
- "properties": {
36
- "runs": {
37
- "type": "array",
38
- "items": {
39
- "$ref": "assays/ctdna_analysis.json#definitions/sample_analysis"
40
- },
41
- "mergeStrategy": "arrayMergeById",
42
- "mergeOptions": {
43
- "$comment": "TODO fix to merge by a pair of normal and tumor ids. It requires improvements to the merge strategy code.",
44
- "idRef": "/run_id"
45
- }
46
- },
47
- "batch_id": {"$ref": "assays/tcr_assay.json#properties/batch_id"},
48
- "excluded_samples": {
49
- "$ref": "assays/components/excluded_samples.json"
50
- }
51
- }
52
- }
cidc_schemas/schemas/templates/analyses/ctdna_analysis_template.json DELETED
@@ -1,121 +0,0 @@
1
- {
2
- "title": "ctDNA analysis template",
3
- "description": "ctDNA analysis submission.",
4
- "prism_template_root_object_schema": "assays/ctdna_analysis.json",
5
- "prism_template_root_object_pointer": "/analysis/ctdna_analysis",
6
- "properties": {
7
- "worksheets": {
8
- "ctDNA Analysis": {
9
- "preamble_rows": {
10
- "protocol identifier": {
11
- "merge_pointer": "2/protocol_identifier",
12
- "type_ref": "clinical_trial.json#properties/protocol_identifier"
13
- },
14
- "folder": {
15
- "do_not_merge": true,
16
- "type": "string",
17
- "allow_empty": true
18
- },
19
- "batch id": {
20
- "merge_pointer": "0/batch_id",
21
- "type_ref": "assays/tcr_assay.json#properties/batch_id"
22
- }
23
- },
24
- "prism_data_object_pointer": "/runs/-",
25
- "data_columns": {
26
- "ctDNA Runs": {
27
- "run id": {
28
- "merge_pointer": "/run_id",
29
- "type_ref": "assays/ctdna_analysis.json#definitions/sample_analysis/properties/run_id",
30
- "process_as": [
31
- {
32
- "parse_through": "lambda run: f'{folder or \"\"}analysis/{run}_error.yaml'",
33
- "merge_pointer": "/error",
34
- "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/error.yaml",
35
- "type_ref": "assays/components/local_file.json#properties/file_path",
36
- "is_artifact": 1,
37
- "allow_empty": true
38
- }
39
- ]
40
- },
41
- "cimac id": {
42
- "merge_pointer": "/tumor/cimac_id",
43
- "type_ref": "sample.json#properties/cimac_id",
44
- "process_as": [
45
- {
46
- "parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}.sorted.dedup.bam'",
47
- "merge_pointer": "/tumor/alignment/align_sorted_dedup",
48
- "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/sorted.dedup.bam",
49
- "type_ref": "assays/components/local_file.json#properties/file_path",
50
- "is_artifact": 1
51
- },
52
- {
53
- "parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}.sorted.dedup.bam.bai'",
54
- "merge_pointer": "/tumor/alignment/align_sorted_dedup_index",
55
- "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/sorted.dedup.bam.bai",
56
- "type_ref": "assays/components/local_file.json#properties/file_path",
57
- "is_artifact": 1
58
- },
59
- {
60
- "parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}_recalibrated.bam'",
61
- "merge_pointer": "/tumor/alignment/align_recalibrated",
62
- "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/recalibrated.bam",
63
- "type_ref": "assays/components/local_file.json#properties/file_path",
64
- "is_artifact": 1
65
- },
66
- {
67
- "parse_through": "lambda id: f'{folder or \"\"}analysis/align/{id}/{id}_recalibrated.bam.bai'",
68
- "merge_pointer": "/tumor/alignment/align_recalibrated_index",
69
- "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/recalibrated.bam.bai",
70
- "type_ref": "assays/components/local_file.json#properties/file_path",
71
- "is_artifact": 1
72
- },
73
- {
74
- "parse_through": "lambda id: f'{folder or \"\"}analysis/hlahd/{id}/result/{id}_final.result.txt'",
75
- "merge_pointer": "/tumor/hla/hla_final_result",
76
- "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/hla_final_result.txt",
77
- "type_ref": "assays/components/local_file.json#properties/file_path",
78
- "is_artifact": 1
79
- },
80
- {
81
- "parse_through": "lambda id: f'{folder or \"\"}analysis/optitype/{id}/{id}_result.tsv'",
82
- "merge_pointer": "/tumor/hla/optitype_result",
83
- "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/optitype_result.tsv",
84
- "type_ref": "assays/components/local_file.json#properties/file_path",
85
- "is_artifact": 1
86
- },
87
- {
88
- "parse_through": "lambda id: f'{folder or \"\"}analysis/xhla/{id}/report-{id}-hla.json'",
89
- "merge_pointer": "/tumor/hla/xhla_report_hla",
90
- "gcs_uri_format": "{protocol identifier}/ctdna/{run id}/analysis/tumor/{cimac id}/xhla_report_hla.json",
91
- "type_ref": "assays/components/local_file.json#properties/file_path",
92
- "is_artifact": 1
93
- }
94
- ]
95
- },
96
- "comments": {
97
- "type_ref": "assays/ctdna_analysis.json#definitions/sample_analysis/properties/comments",
98
- "merge_pointer": "0/comments",
99
- "allow_empty": true
100
- }
101
- }
102
- }
103
- },
104
- "Excluded Samples": {
105
- "prism_data_object_pointer": "/excluded_samples/-",
106
- "data_columns": {
107
- "Samples Excluded From Analysis": {
108
- "cimac id": {
109
- "type_ref": "sample.json#properties/cimac_id",
110
- "merge_pointer": "0/cimac_id"
111
- },
112
- "reason": {
113
- "type_ref": "assays/components/excluded_samples.json#items/properties/reason_excluded",
114
- "merge_pointer": "0/reason_excluded"
115
- }
116
- }
117
- }
118
- }
119
- }
120
- }
121
- }