nci-cidc-schemas 0.26.35__py2.py3-none-any.whl → 0.26.37__py2.py3-none-any.whl
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- cidc_schemas/__init__.py +1 -1
- cidc_schemas/json_validation.py +1 -1
- cidc_schemas/schemas/assays/components/hande_local_file.json +16 -0
- cidc_schemas/schemas/assays/ctdna_assay.json +2 -4
- cidc_schemas/schemas/templates/assays/ctdna_template.json +4 -2
- cidc_schemas/schemas/templates/assays/hande_template.json +6 -4
- cidc_schemas/schemas/templates/manifests/h_and_e_template.json +2 -1
- cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json +2 -1
- cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json +8 -4
- cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json +8 -4
- cidc_schemas/schemas/templates/manifests/pbmc_template.json +2 -1
- cidc_schemas/schemas/templates/manifests/plasma_template.json +2 -1
- cidc_schemas/schemas/templates/manifests/tissue_slide_template.json +2 -1
- cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json +8 -4
- cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json +2 -1
- {nci_cidc_schemas-0.26.35.dist-info → nci_cidc_schemas-0.26.37.dist-info}/METADATA +1 -2
- {nci_cidc_schemas-0.26.35.dist-info → nci_cidc_schemas-0.26.37.dist-info}/RECORD +21 -20
- {nci_cidc_schemas-0.26.35.dist-info → nci_cidc_schemas-0.26.37.dist-info}/WHEEL +1 -1
- {nci_cidc_schemas-0.26.35.dist-info → nci_cidc_schemas-0.26.37.dist-info}/LICENSE +0 -0
- {nci_cidc_schemas-0.26.35.dist-info → nci_cidc_schemas-0.26.37.dist-info}/entry_points.txt +0 -0
- {nci_cidc_schemas-0.26.35.dist-info → nci_cidc_schemas-0.26.37.dist-info}/top_level.txt +0 -0
cidc_schemas/__init__.py
CHANGED
cidc_schemas/json_validation.py
CHANGED
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@@ -497,7 +497,7 @@ def convert(fmt: str, value: str) -> str:
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elif fmt == "date":
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reformatter = _to_date
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elif fmt == "string":
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reformatter = lambda n: n and str(n)
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reformatter = lambda n: (n or n == 0) and str(n)
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elif fmt == "integer":
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reformatter = lambda n: n and int(n)
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elif fmt == "boolean":
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{
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"$schema": "metaschema/strict_meta_schema.json#",
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"$id": "local_file",
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"title": "Local file type",
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"type": "object",
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"description": "A type to store local file paths.",
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"additionalProperties": false,
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"properties": {
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"file_path": {
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"$id": "local_file_path",
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"type": "string",
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"description": "Path to file, relative to the intake bucket. One of image file or annotated file is required."
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}
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},
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"required": []
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}
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"bias_qc_plots",
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"optimal_solution",
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"other_solutions",
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"fraction_cna_subclonal",
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"fraction_genome_subclonal",
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"gc_map_correction_mad",
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"subclone_fraction",
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"tumor_fraction",
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"tumor_ploidy"
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],
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"on_premise_rdata_file": {"$ref": "artifacts/artifact_rdata.json"},
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"fraction_cna_subclonal": {
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"description": "Fraction of copy number altered bins that are subclonal
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"description": "Fraction of copy number altered bins that are subclonal (0-1)",
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"type": ["number", "string"]
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},
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"fraction_genome_subclonal": {
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"type": "number"
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"subclone_fraction": {
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"description": "Fraction of tumor-derived DNA that is subclonal
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"description": "Fraction of tumor-derived DNA that is subclonal (0-1)",
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"type": ["number", "string"]
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"fraction cna subclonal": {
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"merge_pointer": "0/fraction_cna_subclonal",
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"type_ref": "assays/ctdna_assay.json#definitions/entry/properties/fraction_cna_subclonal"
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"type_ref": "assays/ctdna_assay.json#definitions/entry/properties/fraction_cna_subclonal",
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"allow_empty": true
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"fraction genome subclonal": {
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"merge_pointer": "0/fraction_genome_subclonal",
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},
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"subclone fraction": {
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"type_ref": "assays/ctdna_assay.json#definitions/entry/properties/subclone_fraction"
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"type_ref": "assays/ctdna_assay.json#definitions/entry/properties/subclone_fraction",
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"allow_empty": true
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"tumor fraction": {
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"merge_pointer": "0/tumor_fraction",
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"merge_pointer": "0/files/image_file",
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"is_artifact": 1,
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"gcs_uri_format": "{protocol identifier}/hande/{cimac id}/image_file.{file type}",
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"type_ref": "assays/components/
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"allow_empty": true
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"type_ref": "assays/components/hande_local_file.json#properties/file_path",
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"allow_empty": true,
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"type": "string"
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"annotated file type": {
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"merge_pointer": "0/files/annotated_image",
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"is_artifact": 1,
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"gcs_uri_format": "{protocol identifier}/hande/{cimac id}/annotated_image.{annotated file type}",
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"type_ref": "assays/components/
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"allow_empty": true
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"type_ref": "assays/components/hande_local_file.json#properties/file_path",
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"allow_empty": true,
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"type": "string"
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"tumor tissue (% total area)": {
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},
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"cohort name": {
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"type_ref": "participant.json#properties/cohort_name"
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"type_ref": "participant.json#properties/cohort_name",
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"participant ID": {
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"cohort name": {
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"type_ref": "participant.json#properties/cohort_name"
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"type_ref": "participant.json#properties/cohort_name",
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"DNA quality": {
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"din value": {
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Metadata-Version: 2.1
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Name: nci_cidc_schemas
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Version: 0.26.
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Version: 0.26.37
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Summary: The CIDC data model and tools for working with it.
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Home-page: https://github.com/NCI-CIDC/cidc-schemas
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Author: NCI
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- **`docs/`** - the most recent build of the data model documentation, along with templates and scripts for re-generating the documentation.
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- **`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.
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- **`tests/`** - tests for the `cidc_schemas` module.
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- **`.githooks/`** - git hooks, e.g. for auto-generating `.csv`s in `template_examples/` and `.html` documentation files.
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### Developer Setup
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3
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cidc_schemas/constants.py,sha256=RULs7pGuBAVq1teXymrfbVsK23ZowJvLuZlv0KcjL-Y,698
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4
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-
cidc_schemas/json_validation.py,sha256=
|
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4
|
+
cidc_schemas/json_validation.py,sha256=81Dql5LAw4t-0t1cYKpCNQqiUok9rQvGxSk-9VxyILA,20047
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5
5
|
cidc_schemas/migrations.py,sha256=Amg_T4cFgMzySD7yNnT_PWpqP7hwlTWGeHlI_RSXuRI,14766
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6
6
|
cidc_schemas/template.py,sha256=gM6Xp1fOZaF8wOLzY5HGdxi4p8cEYhYXRpqRPncYua0,49865
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|
7
7
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cidc_schemas/template_reader.py,sha256=xXtLRKu1y4FrPj8RgyGOmB2hlsCDXcuvMBWami2_jV8,13119
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@@ -61,7 +61,7 @@ cidc_schemas/schemas/artifacts/artifact_xlsx.json,sha256=PmQ3NY_8ywS3iFa4vvLzcXb
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61
61
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cidc_schemas/schemas/artifacts/artifact_yaml.json,sha256=Eey5T68k4jXqiFXfgWTVi3ZoiY5EZxc75rWCEvaZscE,1657
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62
62
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cidc_schemas/schemas/artifacts/artifact_zip.json,sha256=L9TyKfKm2j0jUo7ED7Lb43Z6VRHP7hEirC349viEBhQ,1653
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63
63
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cidc_schemas/schemas/assays/atacseq_assay.json,sha256=5ezVeJmrwOWuXLtf9-gH8iYKhLCys9Ii2VamezNI_hM,2547
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64
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-
cidc_schemas/schemas/assays/ctdna_assay.json,sha256=
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64
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+
cidc_schemas/schemas/assays/ctdna_assay.json,sha256=NjsS0htltMIN_sGoissbnkCZCQIbNdNF1YNfWAU_Unk,3421
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65
65
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cidc_schemas/schemas/assays/cytof_assay.json,sha256=rf0vebcoHY_dS4wlqkoBY9rclSAE3CRdxeGLXAbhScM,3659
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66
66
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cidc_schemas/schemas/assays/cytof_assay_core.json,sha256=Vwg3RmEEdCpZtDDaVAWBDCKTMnSxagsdqSJq4AiDu9w,8828
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67
67
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cidc_schemas/schemas/assays/elisa_assay.json,sha256=YHeoxYmgdpefLWkBXNg60JUig2Ccqg8thWZ5M5q3hyw,2233
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@@ -89,6 +89,7 @@ cidc_schemas/schemas/assays/components/composite_image.json,sha256=k9EaBG3y9j-lv
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89
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cidc_schemas/schemas/assays/components/controls.json,sha256=_Wxz7W2msTGJ2Ei4XZg0Qy1t8A5_rLSHNvdPurC073E,458
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90
90
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cidc_schemas/schemas/assays/components/enrichment_core.json,sha256=zC5G7q-QyNrdynCOoPCCSfOuSKq8TiDH-Pl6gITNfVQ,813
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91
91
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cidc_schemas/schemas/assays/components/excluded_samples.json,sha256=BAuh31ZTGLBEQkGxTkZQQo05CGD4OeHwFOVyVZgdkHI,663
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92
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+
cidc_schemas/schemas/assays/components/hande_local_file.json,sha256=0fMiJo3DMIzL6CVm0JCKdgJqT3-L7ppUHNjtLdVQpcU,454
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92
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cidc_schemas/schemas/assays/components/image.json,sha256=1llHvtKct7EfgVRibufHf6mfB8HPScPe8-vCoQQzKDA,1260
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93
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cidc_schemas/schemas/assays/components/imaging_data.json,sha256=pFMGY03w6VkA4RGvx9YFeT969oLGWxEmjvPe01mk3FU,926
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94
95
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cidc_schemas/schemas/assays/components/local_file.json,sha256=NWBTV1FIr8KQXFNFiUwxe68ZRiCKxx8Z2rPcMZLp5ug,405
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@@ -126,10 +127,10 @@ cidc_schemas/schemas/templates/analyses/wes_analysis_template.json,sha256=V5RRZ3
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cidc_schemas/schemas/templates/analyses/wes_tumor_only_analysis_template.json,sha256=oHQ89pnzqGWE2sfb5sYGYhyknyd0pr0dTEGTYn2y_tQ,16240
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cidc_schemas/schemas/templates/assays/atacseq_fastq_template.json,sha256=7WygawkxnhFu5xBAuIhSOBD8TwCqDgINjC-HIYeCf4Q,3928
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128
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cidc_schemas/schemas/templates/assays/clinical_data_template.json,sha256=1luQXzyqbAKKiNVwVQFeZ4dwzVpnTeGAropzd_mYmx4,2193
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129
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-
cidc_schemas/schemas/templates/assays/ctdna_template.json,sha256=
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130
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+
cidc_schemas/schemas/templates/assays/ctdna_template.json,sha256=KDyOPbBh0dytlZRJVKNuaGEB8MAyq6Ls1CvI8d2wF3o,6151
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130
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cidc_schemas/schemas/templates/assays/cytof_template.json,sha256=YGaLt7DKsz32o3na8NDs-bXteVnAPMiF1hLH643f6kY,13328
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131
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cidc_schemas/schemas/templates/assays/elisa_template.json,sha256=Q8cv5ZpaRZUfvr6e4PC4uvMqhhaDGLdvVMN_s8Uiajw,2259
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132
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-
cidc_schemas/schemas/templates/assays/hande_template.json,sha256=
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133
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+
cidc_schemas/schemas/templates/assays/hande_template.json,sha256=EtFvoEtXZelqQPYuJKRbo2127MUek6wGnMcOvMMr3Os,4391
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133
134
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cidc_schemas/schemas/templates/assays/ihc_template.json,sha256=lOSP6v24FMk-WN7Za4IYQkM94R-1TEvrnllRopEEYa4,7341
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134
135
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cidc_schemas/schemas/templates/assays/mibi_template.json,sha256=T5gAgsmWpUkkO6CI7aFpyD4efSTZsNmbsLLBrHXpNzg,7787
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135
136
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cidc_schemas/schemas/templates/assays/microbiome_template.json,sha256=2qaTB8W-tG6NhbSJ3KAEIacp1E4g-cFBGMOMc5zTafo,3578
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@@ -143,19 +144,19 @@ cidc_schemas/schemas/templates/assays/tcr_adaptive_template.json,sha256=Hb8ngxw6
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143
144
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cidc_schemas/schemas/templates/assays/tcr_fastq_template.json,sha256=7Qq4ssI8ErDrHy5RIxjPcNiDf2IBHG42JcngDFKxqlE,3457
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144
145
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cidc_schemas/schemas/templates/assays/wes_bam_template.json,sha256=nxbb_lNPi-5cdAlwmSBvn7cS_8gMjROOz7wBWk6ev0Y,2724
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145
146
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cidc_schemas/schemas/templates/assays/wes_fastq_template.json,sha256=vuwuIpqXyqpGxCunpjbHKaBQhfKFnr2R-wMkXDiJdKM,3143
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146
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-
cidc_schemas/schemas/templates/manifests/h_and_e_template.json,sha256=
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147
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-
cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json,sha256=
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-
cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json,sha256=
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cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json,sha256=
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-
cidc_schemas/schemas/templates/manifests/pbmc_template.json,sha256=
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cidc_schemas/schemas/templates/manifests/plasma_template.json,sha256=
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-
cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=
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147
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+
cidc_schemas/schemas/templates/manifests/h_and_e_template.json,sha256=PiCpfbWd5I29wwYWCQHjQh10g9l84dligYTVvMcJHgM,12524
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148
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+
cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json,sha256=u1QPL83DUvPMcMdYbwmmgT0nSOqkbjQR-asXZ_6p0CY,11878
|
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149
|
+
cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json,sha256=JudTPeQBjTttX4OXMrVl9DTRM73KgZN3jbtC3lcuQsA,13542
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150
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+
cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json,sha256=xCE0pTXRlKOd0dPMKcDIBKXRa81Ka_H5f6OGE1TNmhw,13185
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151
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+
cidc_schemas/schemas/templates/manifests/pbmc_template.json,sha256=c0F9xu9za95i2RSVl_9wjiZIUxczOFNWJaXRy8pJhOg,17579
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152
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+
cidc_schemas/schemas/templates/manifests/plasma_template.json,sha256=43bizjQ7zJt5mQHtUfFHDA_f3L4DxBo4XqgHnFvNPbw,15148
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153
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+
cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=Y3951-HNUVfvOK4fjUxGJt2gtmGhKZxWiXVLxyZghn8,11073
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153
154
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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
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-
cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=
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-
nci_cidc_schemas-0.26.
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nci_cidc_schemas-0.26.
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nci_cidc_schemas-0.26.
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nci_cidc_schemas-0.26.
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nci_cidc_schemas-0.26.
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nci_cidc_schemas-0.26.
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+
cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json,sha256=-CC7Hg-qzZ7e5QrrnkybrS1Vrfq2zlgtxU4kRnR5is8,13472
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156
|
+
cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=uPiiEo1xEde6MDhQDapLIjL8XcghgeoCEDdZTzGYFBA,12617
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157
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+
nci_cidc_schemas-0.26.37.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
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158
|
+
nci_cidc_schemas-0.26.37.dist-info/METADATA,sha256=Mt2qQfxGcS3Gk4DCRwnghKWQtfC99WAQb2ypxD3gbmw,4314
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159
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+
nci_cidc_schemas-0.26.37.dist-info/WHEEL,sha256=TJ49d73sNs10F0aze1W_bTW2P_X7-F4YXOlBqoqA-jY,109
|
|
160
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+
nci_cidc_schemas-0.26.37.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
|
|
161
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+
nci_cidc_schemas-0.26.37.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
|
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162
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+
nci_cidc_schemas-0.26.37.dist-info/RECORD,,
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|
File without changes
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File without changes
|
|
File without changes
|