nci-cidc-schemas 0.26.36__py2.py3-none-any.whl → 0.26.38__py2.py3-none-any.whl

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Files changed (13) hide show
  1. cidc_schemas/__init__.py +1 -1
  2. cidc_schemas/json_validation.py +1 -1
  3. cidc_schemas/schemas/assays/components/hande_local_file.json +16 -0
  4. cidc_schemas/schemas/assays/ctdna_assay.json +2 -4
  5. cidc_schemas/schemas/templates/assays/ctdna_template.json +4 -2
  6. cidc_schemas/schemas/templates/assays/hande_template.json +6 -4
  7. cidc_schemas/unprism.py +4 -0
  8. {nci_cidc_schemas-0.26.36.dist-info → nci_cidc_schemas-0.26.38.dist-info}/METADATA +1 -1
  9. {nci_cidc_schemas-0.26.36.dist-info → nci_cidc_schemas-0.26.38.dist-info}/RECORD +13 -12
  10. {nci_cidc_schemas-0.26.36.dist-info → nci_cidc_schemas-0.26.38.dist-info}/WHEEL +1 -1
  11. {nci_cidc_schemas-0.26.36.dist-info → nci_cidc_schemas-0.26.38.dist-info}/LICENSE +0 -0
  12. {nci_cidc_schemas-0.26.36.dist-info → nci_cidc_schemas-0.26.38.dist-info}/entry_points.txt +0 -0
  13. {nci_cidc_schemas-0.26.36.dist-info → nci_cidc_schemas-0.26.38.dist-info}/top_level.txt +0 -0
cidc_schemas/__init__.py CHANGED
@@ -2,4 +2,4 @@
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  __author__ = """NCI"""
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  __email__ = "nci-cidc-tools-admin@mail.nih.gov"
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- __version__ = "0.26.36"
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+ __version__ = "0.26.38"
cidc_schemas/json_validation.py CHANGED
@@ -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":
cidc_schemas/schemas/assays/components/hande_local_file.json ADDED
@@ -0,0 +1,16 @@
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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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+ "$id": "local_file_path",
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+ "type": "string",
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+ "description": "Path to file, relative to the intake bucket. One of image file or annotated file is required."
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+ }
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+ },
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+ "required": []
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+ }
cidc_schemas/schemas/assays/ctdna_assay.json CHANGED
@@ -22,10 +22,8 @@
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  "bias_qc_plots",
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  "optimal_solution",
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  "other_solutions",
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- "fraction_cna_subclonal",
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  "fraction_genome_subclonal",
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  "gc_map_correction_mad",
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- "subclone_fraction",
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  "tumor_fraction",
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  "tumor_ploidy"
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  ],
@@ -46,7 +44,7 @@
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  "on_premise_rdata_file": {"$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. Accepts NaN. (0-1)",
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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": {
@@ -60,7 +58,7 @@
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  "type": "number"
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  },
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  "subclone_fraction": {
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- "description": "Fraction of tumor-derived DNA that is subclonal. Accepts NA. (0-1)",
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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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  },
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  "tumor_fraction": {
cidc_schemas/schemas/templates/assays/ctdna_template.json CHANGED
@@ -59,7 +59,8 @@
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  },
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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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  },
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  "fraction genome subclonal": {
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  "merge_pointer": "0/fraction_genome_subclonal",
@@ -87,7 +88,8 @@
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  },
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  "subclone fraction": {
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  "merge_pointer": "0/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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  },
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  "tumor fraction": {
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  "merge_pointer": "0/tumor_fraction",
cidc_schemas/schemas/templates/assays/hande_template.json CHANGED
@@ -33,8 +33,9 @@
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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/local_file.json#properties/file_path",
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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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  },
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  "annotated file type": {
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  "do_not_merge": true,
@@ -46,8 +47,9 @@
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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/local_file.json#properties/file_path",
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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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  },
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  "tumor tissue (% total area)": {
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  "merge_pointer": "0/tumor_tissue_percentage",
cidc_schemas/unprism.py CHANGED
@@ -3,6 +3,7 @@
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  from io import StringIO, BytesIO
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  from typing import Callable, Dict, List, NamedTuple, Optional, Union
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+ import math
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  import pandas as pd
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  from . import prism
@@ -332,6 +333,9 @@ def _cytof_analysis_derivation(context: DeriveFilesContext) -> DeriveFilesResult
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  res_df = pd.DataFrame()
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  for index, row in cell_counts_analysis_csvs.iterrows():
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  obj_url = row[f"output_files.{combined_f_kind}.object_url"]
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+ if isinstance(obj_url, float) and math.isnan(obj_url):
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+ # output file does not exist - continue (don't fail when a cytof assay is not included in analysis)
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+ continue
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  cell_counts_csv = context.fetch_artifact(obj_url, True)
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{nci_cidc_schemas-0.26.36.dist-info → nci_cidc_schemas-0.26.38.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: nci_cidc_schemas
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- Version: 0.26.36
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+ Version: 0.26.38
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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
{nci_cidc_schemas-0.26.36.dist-info → nci_cidc_schemas-0.26.38.dist-info}/RECORD RENAMED
@@ -1,12 +1,12 @@
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- cidc_schemas/__init__.py,sha256=PyjN4BhZxDfIvvKNqCcz38xDv5i4Np3N29vZJJZUFGw,136
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+ cidc_schemas/__init__.py,sha256=9Df5WbWCck9fRAaOji8IQO8BZvV88vXOvtUNUoYYB1c,136
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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=SyZSW7AAS-qlYLUUV_ri4393utkNsDexcWB73rEmFLs,20035
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+ cidc_schemas/json_validation.py,sha256=81Dql5LAw4t-0t1cYKpCNQqiUok9rQvGxSk-9VxyILA,20047
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  cidc_schemas/migrations.py,sha256=Amg_T4cFgMzySD7yNnT_PWpqP7hwlTWGeHlI_RSXuRI,14766
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  cidc_schemas/template.py,sha256=gM6Xp1fOZaF8wOLzY5HGdxi4p8cEYhYXRpqRPncYua0,49865
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  cidc_schemas/template_reader.py,sha256=xXtLRKu1y4FrPj8RgyGOmB2hlsCDXcuvMBWami2_jV8,13119
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  cidc_schemas/template_writer.py,sha256=faOhvSDTp4nuPhOtVQR_J7YNnFzx-vh7oyNpFdee1mY,18236
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- cidc_schemas/unprism.py,sha256=5EeqNKedVEf15CJiMQ-ImXd1wIbNnzihv21rAMClZyc,13325
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+ cidc_schemas/unprism.py,sha256=TOD3CSGkgNnTtT-OeCCE3Ihlam84lr8XGOmtdSy2lL8,13545
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  cidc_schemas/util.py,sha256=ZCQ--ROZyXYVB034fHHmxZXb5F0G2GwzPwSfyfegtGk,4348
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  cidc_schemas/metaschema/strict_meta_schema.json,sha256=3FiS0r2dAXgfPsruJwZYbQoQnHhC_yl-3mclX8gfiQU,6428
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  cidc_schemas/pipeline_configs/rna_level1_analysis_config.yaml.j2,sha256=6no9sFqwzb1T61RZGD-owDt2K5R8G_fPTzflV4fOroo,2832
@@ -61,7 +61,7 @@ cidc_schemas/schemas/artifacts/artifact_xlsx.json,sha256=PmQ3NY_8ywS3iFa4vvLzcXb
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  cidc_schemas/schemas/artifacts/artifact_yaml.json,sha256=Eey5T68k4jXqiFXfgWTVi3ZoiY5EZxc75rWCEvaZscE,1657
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  cidc_schemas/schemas/artifacts/artifact_zip.json,sha256=L9TyKfKm2j0jUo7ED7Lb43Z6VRHP7hEirC349viEBhQ,1653
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  cidc_schemas/schemas/assays/atacseq_assay.json,sha256=5ezVeJmrwOWuXLtf9-gH8iYKhLCys9Ii2VamezNI_hM,2547
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- cidc_schemas/schemas/assays/ctdna_assay.json,sha256=1AwUYiE93XEVDg_FPFyV2OgaD7Ry7pWoD4AH2DAXasA,3503
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+ cidc_schemas/schemas/assays/ctdna_assay.json,sha256=NjsS0htltMIN_sGoissbnkCZCQIbNdNF1YNfWAU_Unk,3421
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  cidc_schemas/schemas/assays/cytof_assay.json,sha256=rf0vebcoHY_dS4wlqkoBY9rclSAE3CRdxeGLXAbhScM,3659
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  cidc_schemas/schemas/assays/cytof_assay_core.json,sha256=Vwg3RmEEdCpZtDDaVAWBDCKTMnSxagsdqSJq4AiDu9w,8828
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  cidc_schemas/schemas/assays/elisa_assay.json,sha256=YHeoxYmgdpefLWkBXNg60JUig2Ccqg8thWZ5M5q3hyw,2233
@@ -89,6 +89,7 @@ cidc_schemas/schemas/assays/components/composite_image.json,sha256=k9EaBG3y9j-lv
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  cidc_schemas/schemas/assays/components/controls.json,sha256=_Wxz7W2msTGJ2Ei4XZg0Qy1t8A5_rLSHNvdPurC073E,458
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  cidc_schemas/schemas/assays/components/enrichment_core.json,sha256=zC5G7q-QyNrdynCOoPCCSfOuSKq8TiDH-Pl6gITNfVQ,813
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  cidc_schemas/schemas/assays/components/excluded_samples.json,sha256=BAuh31ZTGLBEQkGxTkZQQo05CGD4OeHwFOVyVZgdkHI,663
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+ cidc_schemas/schemas/assays/components/hande_local_file.json,sha256=0fMiJo3DMIzL6CVm0JCKdgJqT3-L7ppUHNjtLdVQpcU,454
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  cidc_schemas/schemas/assays/components/image.json,sha256=1llHvtKct7EfgVRibufHf6mfB8HPScPe8-vCoQQzKDA,1260
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  cidc_schemas/schemas/assays/components/imaging_data.json,sha256=pFMGY03w6VkA4RGvx9YFeT969oLGWxEmjvPe01mk3FU,926
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  cidc_schemas/schemas/assays/components/local_file.json,sha256=NWBTV1FIr8KQXFNFiUwxe68ZRiCKxx8Z2rPcMZLp5ug,405
@@ -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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  cidc_schemas/schemas/templates/assays/clinical_data_template.json,sha256=1luQXzyqbAKKiNVwVQFeZ4dwzVpnTeGAropzd_mYmx4,2193
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- cidc_schemas/schemas/templates/assays/ctdna_template.json,sha256=kNDDyRDz_521Snxo21GmhbYLJgGIzM6axRKsbK3JR74,6077
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+ cidc_schemas/schemas/templates/assays/ctdna_template.json,sha256=KDyOPbBh0dytlZRJVKNuaGEB8MAyq6Ls1CvI8d2wF3o,6151
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  cidc_schemas/schemas/templates/assays/cytof_template.json,sha256=YGaLt7DKsz32o3na8NDs-bXteVnAPMiF1hLH643f6kY,13328
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  cidc_schemas/schemas/templates/assays/elisa_template.json,sha256=Q8cv5ZpaRZUfvr6e4PC4uvMqhhaDGLdvVMN_s8Uiajw,2259
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- cidc_schemas/schemas/templates/assays/hande_template.json,sha256=BNMQO4JpBrjuD8ITH1x7cJfkqI4bgKZilvN9yqavaqs,4293
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+ cidc_schemas/schemas/templates/assays/hande_template.json,sha256=EtFvoEtXZelqQPYuJKRbo2127MUek6wGnMcOvMMr3Os,4391
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  cidc_schemas/schemas/templates/assays/ihc_template.json,sha256=lOSP6v24FMk-WN7Za4IYQkM94R-1TEvrnllRopEEYa4,7341
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  cidc_schemas/schemas/templates/assays/mibi_template.json,sha256=T5gAgsmWpUkkO6CI7aFpyD4efSTZsNmbsLLBrHXpNzg,7787
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  cidc_schemas/schemas/templates/assays/microbiome_template.json,sha256=2qaTB8W-tG6NhbSJ3KAEIacp1E4g-cFBGMOMc5zTafo,3578
@@ -153,9 +154,9 @@ cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=Y3951
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  cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json,sha256=lVJrGb28n-vyfjGBzhrzjn1lMKw1b4HXXmWtwA603v0,2797
154
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  cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json,sha256=-CC7Hg-qzZ7e5QrrnkybrS1Vrfq2zlgtxU4kRnR5is8,13472
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  cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=uPiiEo1xEde6MDhQDapLIjL8XcghgeoCEDdZTzGYFBA,12617
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- nci_cidc_schemas-0.26.36.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
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- 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
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- nci_cidc_schemas-0.26.36.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
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- nci_cidc_schemas-0.26.36.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
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- nci_cidc_schemas-0.26.36.dist-info/RECORD,,
157
+ nci_cidc_schemas-0.26.38.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
158
+ nci_cidc_schemas-0.26.38.dist-info/METADATA,sha256=V5e4z-bRTKL8HvnOEW6TP3CoX7Xiphp1lwfXqxOo1NY,4314
159
+ nci_cidc_schemas-0.26.38.dist-info/WHEEL,sha256=0VNUDWQJzfRahYI3neAhz2UVbRCtztpN5dPHAGvmGXc,109
160
+ nci_cidc_schemas-0.26.38.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
161
+ nci_cidc_schemas-0.26.38.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
162
+ nci_cidc_schemas-0.26.38.dist-info/RECORD,,
{nci_cidc_schemas-0.26.36.dist-info → nci_cidc_schemas-0.26.38.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (72.1.0)
2
+ Generator: setuptools (75.5.0)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py2-none-any
5
5
  Tag: py3-none-any