PyPI - nci-cidc-schemas - Versions diffs - 0.26.35__tar.gz → 0.26.37__tar.gz - Mend

nci-cidc-schemas 0.26.35tar.gz → 0.26.37tar.gz

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{nci_cidc_schemas-0.26.35/nci_cidc_schemas.egg-info → nci_cidc_schemas-0.26.37}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nci_cidc_schemas
-Version: 0.26.35
+Version: 0.26.37
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI
@@ -56,7 +56,6 @@ pip install nci-cidc-schemas
 - **`docs/`** - the most recent build of the data model documentation, along with templates and scripts for re-generating the documentation.
 - **`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.
 - **`tests/`** - tests for the `cidc_schemas` module.
-- **`.githooks/`** - git hooks, e.g. for auto-generating `.csv`s in `template_examples/` and `.html` documentation files.
 ### Developer Setup

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/README.md RENAMED Viewed

@@ -24,7 +24,6 @@ pip install nci-cidc-schemas
 - **`docs/`** - the most recent build of the data model documentation, along with templates and scripts for re-generating the documentation.
 - **`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.
 - **`tests/`** - tests for the `cidc_schemas` module.
-- **`.githooks/`** - git hooks, e.g. for auto-generating `.csv`s in `template_examples/` and `.html` documentation files.
 ### Developer Setup

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/__init__.py RENAMED Viewed

@@ -2,4 +2,4 @@
 __author__ = """NCI"""
 __email__ = "nci-cidc-tools-admin@mail.nih.gov"
-__version__ = "0.26.35"
+__version__ = "0.26.37"

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/json_validation.py RENAMED Viewed

@@ -497,7 +497,7 @@ def convert(fmt: str, value: str) -> str:
     elif fmt == "date":
         reformatter = _to_date
     elif fmt == "string":
-        reformatter = lambda n: n and str(n)
+        reformatter = lambda n: (n or n == 0) and str(n)
     elif fmt == "integer":
         reformatter = lambda n: n and int(n)
     elif fmt == "boolean":

nci_cidc_schemas-0.26.37/cidc_schemas/schemas/assays/components/hande_local_file.json ADDED Viewed

@@ -0,0 +1,16 @@
+{
+  "$schema": "metaschema/strict_meta_schema.json#",
+  "$id": "local_file",
+  "title": "Local file type",
+  "type": "object",
+  "description": "A type to store local file paths.",
+  "additionalProperties": false,
+  "properties": {
+    "file_path": {
+      "$id": "local_file_path",
+      "type": "string",
+      "description": "Path to file, relative to the intake bucket. One of image file or annotated file is required."
+    }
+  },
+  "required": []
+}

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/schemas/assays/ctdna_assay.json RENAMED Viewed

@@ -22,10 +22,8 @@
 				"bias_qc_plots",
 				"optimal_solution",
 				"other_solutions",
-				"fraction_cna_subclonal",
 				"fraction_genome_subclonal",
 				"gc_map_correction_mad",
-				"subclone_fraction",
 				"tumor_fraction",
 				"tumor_ploidy"
 			],
@@ -46,7 +44,7 @@
 				"on_premise_rdata_file": {"$ref": "artifacts/artifact_rdata.json"},
 				"fraction_cna_subclonal": {
-					"description": "Fraction of copy number altered bins that are subclonal. Accepts NaN. (0-1)",
+					"description": "Fraction of copy number altered bins that are subclonal (0-1)",
 					"type": ["number", "string"]
 				},
 				"fraction_genome_subclonal": {
@@ -60,7 +58,7 @@
 					"type": "number"
 				},
 				"subclone_fraction": {
-					"description": "Fraction of tumor-derived DNA that is subclonal. Accepts NA. (0-1)",
+					"description": "Fraction of tumor-derived DNA that is subclonal (0-1)",
 					"type": ["number", "string"]
 				},
 				"tumor_fraction": {

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/schemas/templates/assays/ctdna_template.json RENAMED Viewed

@@ -59,7 +59,8 @@
             },
             "fraction cna subclonal": {
                 "merge_pointer": "0/fraction_cna_subclonal",
-                "type_ref": "assays/ctdna_assay.json#definitions/entry/properties/fraction_cna_subclonal"
+                "type_ref": "assays/ctdna_assay.json#definitions/entry/properties/fraction_cna_subclonal",
+                "allow_empty": true
             },
             "fraction genome subclonal": {
                 "merge_pointer": "0/fraction_genome_subclonal",
@@ -87,7 +88,8 @@
             },
             "subclone fraction": {
                 "merge_pointer": "0/subclone_fraction",
-                "type_ref": "assays/ctdna_assay.json#definitions/entry/properties/subclone_fraction"
+                "type_ref": "assays/ctdna_assay.json#definitions/entry/properties/subclone_fraction",
+                "allow_empty": true
             },
             "tumor fraction": {
                 "merge_pointer": "0/tumor_fraction",

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/schemas/templates/assays/hande_template.json RENAMED Viewed

@@ -33,8 +33,9 @@
                         "merge_pointer": "0/files/image_file",
                         "is_artifact": 1,
                         "gcs_uri_format": "{protocol identifier}/hande/{cimac id}/image_file.{file type}",
-                        "type_ref": "assays/components/local_file.json#properties/file_path",
-                        "allow_empty": true
+                        "type_ref": "assays/components/hande_local_file.json#properties/file_path",
+                        "allow_empty": true,
+                        "type": "string"
                       },
                       "annotated file type": {
                         "do_not_merge": true,
@@ -46,8 +47,9 @@
                           "merge_pointer": "0/files/annotated_image",
                           "is_artifact": 1,
                           "gcs_uri_format": "{protocol identifier}/hande/{cimac id}/annotated_image.{annotated file type}",
-                          "type_ref": "assays/components/local_file.json#properties/file_path",
-                          "allow_empty": true
+                          "type_ref": "assays/components/hande_local_file.json#properties/file_path",
+                          "allow_empty": true,
+                          "type": "string"
                       },
                       "tumor tissue (% total area)": {
                         "merge_pointer": "0/tumor_tissue_percentage",

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/schemas/templates/manifests/h_and_e_template.json RENAMED Viewed

@@ -95,7 +95,8 @@
                         },
                         "cohort name": {
                             "merge_pointer": "2/cohort_name",
-                            "type_ref": "participant.json#properties/cohort_name"
+                            "type_ref": "participant.json#properties/cohort_name",
+                            "allow_empty": true
                         },
                         "participant ID": {
                             "merge_pointer": "2/participant_id",

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json RENAMED Viewed

@@ -93,7 +93,8 @@
                         },
                         "cohort name": {
                             "merge_pointer": "2/cohort_name",
-                            "type_ref": "participant.json#properties/cohort_name"
+                            "type_ref": "participant.json#properties/cohort_name",
+                            "allow_empty": true
                         },
                         "participant ID": {
                             "merge_pointer": "2/participant_id",

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json RENAMED Viewed

@@ -93,7 +93,8 @@
                         },
                         "cohort name": {
                             "merge_pointer": "2/cohort_name",
-                            "type_ref": "participant.json#properties/cohort_name"
+                            "type_ref": "participant.json#properties/cohort_name",
+                            "allow_empty": true
                         },
                         "participant ID": {
                             "merge_pointer": "2/participant_id",
@@ -190,15 +191,18 @@
                     "DNA quality": {
                         "din value": {
                             "merge_pointer": "/din",
-                            "type_ref": "sample.json#properties/din"
+                            "type_ref": "sample.json#properties/din",
+                            "allow_empty": true
                         },
                         "a260/a280 value": {
                             "merge_pointer": "/a260_a280",
-                            "type_ref": "sample.json#properties/a260_a280"
+                            "type_ref": "sample.json#properties/a260_a280",
+                            "allow_empty": true
                         },
                         "a260/a230 value": {
                             "merge_pointer": "/a260_a230",
-                            "type_ref": "sample.json#properties/a260_a230"
+                            "type_ref": "sample.json#properties/a260_a230",
+                            "allow_empty": true
                         }
                     },
                     "Filled by CIMAC Lab": {

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json RENAMED Viewed

@@ -95,7 +95,8 @@
                         },
                         "cohort name": {
                             "merge_pointer": "2/cohort_name",
-                            "type_ref": "participant.json#properties/cohort_name"
+                            "type_ref": "participant.json#properties/cohort_name",
+                            "allow_empty": true
                         },
                         "participant ID": {
                             "merge_pointer": "2/participant_id",
@@ -187,15 +188,18 @@
                     "DNA quality": {
                         "din value": {
                             "merge_pointer": "/din",
-                            "type_ref": "sample.json#properties/din"
+                            "type_ref": "sample.json#properties/din",
+                            "allow_empty": true
                         },
                         "a260/a280 value": {
                             "merge_pointer": "/a260_a280",
-                            "type_ref": "sample.json#properties/a260_a280"
+                            "type_ref": "sample.json#properties/a260_a280",
+                            "allow_empty": true
                         },
                         "a260/a230 value": {
                             "merge_pointer": "/a260_a230",
-                            "type_ref": "sample.json#properties/a260_a230"
+                            "type_ref": "sample.json#properties/a260_a230",
+                            "allow_empty": true
                         }
                     },
                     "Filled by CIMAC Lab": {

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/schemas/templates/manifests/pbmc_template.json RENAMED Viewed

@@ -177,7 +177,8 @@
                         },
                         "cohort name": {
                             "merge_pointer": "2/cohort_name",
-                            "type_ref": "participant.json#properties/cohort_name"
+                            "type_ref": "participant.json#properties/cohort_name",
+                            "allow_empty": true
                         },
                         "participant ID": {
                             "merge_pointer": "2/participant_id",

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/schemas/templates/manifests/plasma_template.json RENAMED Viewed

@@ -173,7 +173,8 @@
                         },
                         "cohort name": {
                             "merge_pointer": "2/cohort_name",
-                            "type_ref": "participant.json#properties/cohort_name"
+                            "type_ref": "participant.json#properties/cohort_name",
+                            "allow_empty": true
                         },
                         "collection event name": {
                             "merge_pointer": "/collection_event_name",

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/schemas/templates/manifests/tissue_slide_template.json RENAMED Viewed

@@ -95,7 +95,8 @@
                         },
                         "cohort name": {
                             "merge_pointer": "2/cohort_name",
-                            "type_ref": "participant.json#properties/cohort_name"
+                            "type_ref": "participant.json#properties/cohort_name",
+                            "allow_empty": true
                         },
                         "participant ID": {
                             "merge_pointer": "2/participant_id",

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json RENAMED Viewed

@@ -95,7 +95,8 @@
                         },
                         "cohort name": {
                             "merge_pointer": "2/cohort_name",
-                            "type_ref": "participant.json#properties/cohort_name"
+                            "type_ref": "participant.json#properties/cohort_name",
+                            "allow_empty": true
                         },
                         "participant ID": {
                             "merge_pointer": "2/participant_id",
@@ -192,15 +193,18 @@
                     "DNA quality": {
                         "din value": {
                             "merge_pointer": "/din",
-                            "type_ref": "sample.json#properties/din"
+                            "type_ref": "sample.json#properties/din",
+                            "allow_empty": true
                         },
                         "a260/a280 value": {
                             "merge_pointer": "/a260_a280",
-                            "type_ref": "sample.json#properties/a260_a280"
+                            "type_ref": "sample.json#properties/a260_a280",
+                            "allow_empty": true
                         },
                         "a260/a230 value": {
                             "merge_pointer": "/a260_a230",
-                            "type_ref": "sample.json#properties/a260_a230"
+                            "type_ref": "sample.json#properties/a260_a230",
+                            "allow_empty": true
                         }
                     },
                     "Filled by CIMAC Lab": {

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json RENAMED Viewed

@@ -95,7 +95,8 @@
                         },
                         "cohort name": {
                             "merge_pointer": "2/cohort_name",
-                            "type_ref": "participant.json#properties/cohort_name"
+                            "type_ref": "participant.json#properties/cohort_name",
+                            "allow_empty": true
                         },
                         "participant ID": {
                             "merge_pointer": "2/participant_id",

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37/nci_cidc_schemas.egg-info}/PKG-INFO RENAMED Viewed

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: nci_cidc_schemas
-Version: 0.26.35
+Version: 0.26.37
 Summary: The CIDC data model and tools for working with it.
 Home-page: https://github.com/NCI-CIDC/cidc-schemas
 Author: NCI
@@ -56,7 +56,6 @@ pip install nci-cidc-schemas
 - **`docs/`** - the most recent build of the data model documentation, along with templates and scripts for re-generating the documentation.
 - **`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.
 - **`tests/`** - tests for the `cidc_schemas` module.
-- **`.githooks/`** - git hooks, e.g. for auto-generating `.csv`s in `template_examples/` and `.html` documentation files.
 ### Developer Setup

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/nci_cidc_schemas.egg-info/SOURCES.txt RENAMED Viewed

@@ -95,6 +95,7 @@ cidc_schemas/schemas/assays/components/composite_image.json
 cidc_schemas/schemas/assays/components/controls.json
 cidc_schemas/schemas/assays/components/enrichment_core.json
 cidc_schemas/schemas/assays/components/excluded_samples.json
+cidc_schemas/schemas/assays/components/hande_local_file.json
 cidc_schemas/schemas/assays/components/image.json
 cidc_schemas/schemas/assays/components/imaging_data.json
 cidc_schemas/schemas/assays/components/local_file.json

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/tests/prism/cidc_test_data/assay_data.py RENAMED Viewed

@@ -3513,10 +3513,8 @@ def ctdna() -> PrismTestData:
                             "on_premise_rdata_file": {
                                 "upload_placeholder": "4c409c82-dff7-4f78-801c-222ssff"
                             },
-                            "fraction_cna_subclonal": 0.1,
                             "fraction_genome_subclonal": 0.2,
                             "gc_map_correction_mad": 0.04,
-                            "subclone_fraction": 0.15,
                             "tumor_fraction": 0.25,
                             "tumor_ploidy": 2.599,
                         },

{nci_cidc_schemas-0.26.35 → nci_cidc_schemas-0.26.37}/tests/prism/cidc_test_data/manifest_data.py RENAMED Viewed

@@ -1234,9 +1234,6 @@ def tumor_tissue_dna() -> PrismTestData:
                         "sample_derivative_volume_units": "Microliters",
                         "sample_derivative_concentration": 1.0,
                         "sample_derivative_concentration_units": "Nanogram per Microliter",
-                        "din": 9.0,
-                        "a260_a280": 1.8,
-                        "a260_a230": 2.0,
                         "material_used": 1.0,
                         "material_used_units": "Milliliters",
                         "material_remaining": 0.0,
@@ -1300,7 +1297,6 @@ def tumor_tissue_dna() -> PrismTestData:
                         "sample_derivative_volume_units": "Microliters",
                         "sample_derivative_concentration": 3.0,
                         "sample_derivative_concentration_units": "Micrograms per Microliter",
-                        "din": 8.0,
                         "a260_a280": 1.9,
                         "a260_a230": 2.2,
                         "material_used": 1.0,
@@ -1313,7 +1309,6 @@ def tumor_tissue_dna() -> PrismTestData:
                         "residual_sample_use": "Not Reported",
                     },
                 ],
-                "cohort_name": "Arm_A",
                 "participant_id": "test_encrypted('TTTPP5')",
                 "cimac_participant_id": "CTTTP05",
             },
@@ -1340,7 +1335,6 @@ def tumor_tissue_dna() -> PrismTestData:
                         "sample_derivative_concentration": 4.0,
                         "sample_derivative_concentration_units": "Cells per Vial",
                         "din": 9.0,
-                        "a260_a280": 1.8,
                         "a260_a230": 2.0,
                         "material_used": 1.0,
                         "material_used_units": "Milliliters",
@@ -1372,8 +1366,6 @@ def tumor_tissue_dna() -> PrismTestData:
                         "sample_derivative_concentration": 5.0,
                         "sample_derivative_concentration_units": "Not Reported",
                         "din": 9.0,
-                        "a260_a280": 1.7,
-                        "a260_a230": 2.1,
                         "material_used": 1.0,
                         "material_used_units": "Milliliters",
                         "material_remaining": 0.0,
@@ -1403,8 +1395,6 @@ def tumor_tissue_dna() -> PrismTestData:
                         "sample_derivative_volume_units": "Other",
                         "sample_derivative_concentration": 6.0,
                         "sample_derivative_concentration_units": "Other",
-                        "din": 8.0,
-                        "a260_a280": 1.9,
                         "a260_a230": 2.2,
                         "material_used": 1.0,
                         "material_used_units": "Milliliters",
@@ -1792,7 +1782,6 @@ def tumor_tissue_rna() -> PrismTestData:
                         "residual_sample_use": "Not Reported",
                     },
                 ],
-                "cohort_name": "Arm_Z",
                 "participant_id": "test_encrypted('TTTPP6')",
                 "cimac_participant_id": "CTTTP06",
             },