nci-cidc-schemas 0.27.8__py2.py3-none-any.whl → 0.27.10__py2.py3-none-any.whl

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Files changed (19) hide show
  1. cidc_schemas/__init__.py +1 -1
  2. cidc_schemas/json_validation.py +16 -3
  3. cidc_schemas/schemas/sample.json +4 -0
  4. cidc_schemas/schemas/shipping_core.json +3 -3
  5. cidc_schemas/schemas/templates/manifests/h_and_e_template.json +5 -0
  6. cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json +5 -0
  7. cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json +5 -0
  8. cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json +5 -0
  9. cidc_schemas/schemas/templates/manifests/pbmc_template.json +5 -0
  10. cidc_schemas/schemas/templates/manifests/plasma_template.json +5 -0
  11. cidc_schemas/schemas/templates/manifests/tissue_slide_template.json +5 -0
  12. cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json +5 -0
  13. cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json +5 -0
  14. {nci_cidc_schemas-0.27.8.dist-info → nci_cidc_schemas-0.27.10.dist-info}/METADATA +1 -1
  15. {nci_cidc_schemas-0.27.8.dist-info → nci_cidc_schemas-0.27.10.dist-info}/RECORD +19 -19
  16. {nci_cidc_schemas-0.27.8.dist-info → nci_cidc_schemas-0.27.10.dist-info}/WHEEL +1 -1
  17. {nci_cidc_schemas-0.27.8.dist-info → nci_cidc_schemas-0.27.10.dist-info}/entry_points.txt +0 -0
  18. {nci_cidc_schemas-0.27.8.dist-info → nci_cidc_schemas-0.27.10.dist-info}/licenses/LICENSE +0 -0
  19. {nci_cidc_schemas-0.27.8.dist-info → nci_cidc_schemas-0.27.10.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__ = "0.27.08"
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+ __version__ = "0.27.10"
cidc_schemas/json_validation.py CHANGED
@@ -106,8 +106,22 @@ class _Validator(jsonschema.Draft7Validator):
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  if "matched_paths" in search:
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  for path in search["matched_paths"]:
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  scope = {"root": self.schema}
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- exec(f"ref_path_pattern = {path}", scope)
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- ref_path_pattern = scope["ref_path_pattern"]
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+ try:
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+ ref_path_pattern = eval(path, scope)
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+ except Exception as e:
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+ raise RuntimeError(
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+ f"Failed to evaluate in_doc_ref_pattern at path '{path}': {e}"
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+ ) from e
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+
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+ # protect against None cache
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+ if self._in_doc_refs_cache is None:
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+ print(f"_in_doc_refs_cache: {self._in_doc_refs_cache}")
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+ print(f"scope '{scope}'")
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+ raise RuntimeError(
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+ "Internal error: _in_doc_refs_cache is None when trying to build cache. "
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+ "This usually means the validation context was improperly set up."
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+ )
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+
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  # If there are no cached values for this ref path pattern, collect them
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  if ref_path_pattern not in self._in_doc_refs_cache:
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  self._in_doc_refs_cache[ref_path_pattern] = (
@@ -116,7 +130,6 @@ class _Validator(jsonschema.Draft7Validator):
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  )
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  )
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- # see: https://docs.python.org/3/library/contextlib.html
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  try:
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  yield
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  finally:
cidc_schemas/schemas/sample.json CHANGED
@@ -154,6 +154,10 @@
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  "Other"
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  ]
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  },
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+ "type_of_sample_other": {
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+ "description": "The description of the sample other.",
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+ "type": "string"
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+ },
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  "description_of_sample": {
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  "description": "The description of the sample.",
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  "type": "string",
cidc_schemas/schemas/shipping_core.json CHANGED
@@ -70,9 +70,9 @@
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  "description": "Type of shipment made.",
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  "type": "string",
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  "enum": [
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- "Frozen_Dry_Ice",
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- "Frozen_Shipper",
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- "Ice_Pack",
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+ "Frozen Dry Ice",
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+ "Frozen Shipper",
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+ "Ice/Cold Pack",
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  "Ambient",
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  "Not Reported",
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  "Other"
cidc_schemas/schemas/templates/manifests/h_and_e_template.json CHANGED
@@ -213,6 +213,11 @@
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  "type of sample": {
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  "merge_pointer": "/type_of_sample",
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  "type_ref": "sample.json#properties/type_of_sample"
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+ },
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+ "type of sample other": {
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+ "merge_pointer": "/type_of_sample_other",
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+ "type_ref": "sample.json#properties/type_of_sample_other",
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+ "allow_empty": true
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  },
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  "type of tumor sample": {
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  "merge_pointer": "/type_of_tumor_sample",
cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json CHANGED
@@ -217,6 +217,11 @@
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  "merge_pointer": "/type_of_sample",
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  "type_ref": "sample.json#properties/type_of_sample"
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  },
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+ "type of sample other": {
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+ "merge_pointer": "/type_of_sample_other",
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+ "type_ref": "sample.json#properties/type_of_sample_other",
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+ "allow_empty": true
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+ },
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  "type of tumor sample": {
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  "merge_pointer": "/type_of_tumor_sample",
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  "type_ref": "sample.json#properties/type_of_tumor_sample"
cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json CHANGED
@@ -212,6 +212,11 @@
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  "merge_pointer": "/type_of_sample",
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  "type_ref": "sample.json#properties/type_of_sample"
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  },
215
+ "type of sample other": {
216
+ "merge_pointer": "/type_of_sample_other",
217
+ "type_ref": "sample.json#properties/type_of_sample_other",
218
+ "allow_empty": true
219
+ },
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  "type of tumor sample": {
216
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  "merge_pointer": "/type_of_tumor_sample",
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  "type_ref": "sample.json#properties/type_of_tumor_sample"
cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json CHANGED
@@ -220,6 +220,11 @@
220
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  "merge_pointer": "/type_of_sample",
221
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  "type_ref": "sample.json#properties/type_of_sample"
222
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  },
223
+ "type of sample other": {
224
+ "merge_pointer": "/type_of_sample_other",
225
+ "type_ref": "sample.json#properties/type_of_sample_other",
226
+ "allow_empty": true
227
+ },
223
228
  "sample collection procedure": {
224
229
  "merge_pointer": "/sample_collection_procedure",
225
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  "type_ref": "sample.json#properties/sample_collection_procedure"
cidc_schemas/schemas/templates/manifests/pbmc_template.json CHANGED
@@ -213,6 +213,11 @@
213
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  "type of sample": {
214
214
  "merge_pointer": "0/type_of_sample",
215
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  "type_ref": "sample.json#properties/type_of_sample"
216
+ },
217
+ "type of sample other": {
218
+ "merge_pointer": "/type_of_sample_other",
219
+ "type_ref": "sample.json#properties/type_of_sample_other",
220
+ "allow_empty": true
216
221
  },
217
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  "sample collection procedure": {
218
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  "merge_pointer": "/sample_collection_procedure",
cidc_schemas/schemas/templates/manifests/plasma_template.json CHANGED
@@ -215,6 +215,11 @@
215
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  "merge_pointer": "/type_of_sample",
216
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  "type_ref": "sample.json#properties/type_of_sample"
217
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  },
218
+ "type of sample other": {
219
+ "merge_pointer": "/type_of_sample_other",
220
+ "type_ref": "sample.json#properties/type_of_sample_other",
221
+ "allow_empty": true
222
+ },
218
223
  "sample collection procedure": {
219
224
  "merge_pointer": "/sample_collection_procedure",
220
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  "type_ref": "sample.json#properties/sample_collection_procedure"
cidc_schemas/schemas/templates/manifests/tissue_slide_template.json CHANGED
@@ -215,6 +215,11 @@
215
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  "merge_pointer": "/type_of_sample",
216
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  "type_ref": "sample.json#properties/type_of_sample"
217
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  },
218
+ "type of sample other": {
219
+ "merge_pointer": "/type_of_sample_other",
220
+ "type_ref": "sample.json#properties/type_of_sample_other",
221
+ "allow_empty": true
222
+ },
218
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  "type of tumor sample": {
219
224
  "merge_pointer": "/type_of_tumor_sample",
220
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  "type_ref": "sample.json#properties/type_of_tumor_sample"
cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json CHANGED
@@ -215,6 +215,11 @@
215
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  "merge_pointer": "/type_of_sample",
216
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  "type_ref": "sample.json#properties/type_of_sample"
217
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  },
218
+ "type of sample other": {
219
+ "merge_pointer": "/type_of_sample_other",
220
+ "type_ref": "sample.json#properties/type_of_sample_other",
221
+ "allow_empty": true
222
+ },
218
223
  "type of tumor sample": {
219
224
  "merge_pointer": "/type_of_tumor_sample",
220
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  "type_ref": "sample.json#properties/type_of_tumor_sample"
cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json CHANGED
@@ -215,6 +215,11 @@
215
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  "merge_pointer": "/type_of_sample",
216
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  "type_ref": "sample.json#properties/type_of_sample"
217
217
  },
218
+ "type of sample other": {
219
+ "merge_pointer": "/type_of_sample_other",
220
+ "type_ref": "sample.json#properties/type_of_sample_other",
221
+ "allow_empty": true
222
+ },
218
223
  "type of tumor sample": {
219
224
  "merge_pointer": "/type_of_tumor_sample",
220
225
  "type_ref": "sample.json#properties/type_of_tumor_sample"
{nci_cidc_schemas-0.27.8.dist-info → nci_cidc_schemas-0.27.10.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: nci_cidc_schemas
3
- Version: 0.27.8
3
+ Version: 0.27.10
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
{nci_cidc_schemas-0.27.8.dist-info → nci_cidc_schemas-0.27.10.dist-info}/RECORD RENAMED
@@ -1,7 +1,7 @@
1
- cidc_schemas/__init__.py,sha256=HA6o44Sv4NZQs2OCEAduOw8sMUj2p0xeMKKIrPLOUAU,136
1
+ cidc_schemas/__init__.py,sha256=CNRBwX2Hba3M5la6V032DEO4wjN3K9NFqIHiehMhU54,136
2
2
  cidc_schemas/cli.py,sha256=gWiktRlraNH8Q0zNUae9dohKjPwBmcY0BJwdcQ_fIic,4099
3
3
  cidc_schemas/constants.py,sha256=RULs7pGuBAVq1teXymrfbVsK23ZowJvLuZlv0KcjL-Y,698
4
- cidc_schemas/json_validation.py,sha256=nHkSfTmBN7EeTrZVdbb8h6A64lWrJe5z0AIHiIy-YB0,22552
4
+ cidc_schemas/json_validation.py,sha256=BcwWg9cjg3aaFkGIDQyXHpYZGB8IRRzPVvurLXlQiVw,23161
5
5
  cidc_schemas/migrations.py,sha256=Amg_T4cFgMzySD7yNnT_PWpqP7hwlTWGeHlI_RSXuRI,14766
6
6
  cidc_schemas/template.py,sha256=uvQNbkvusMq9D_1cnUMxT7j7Rf-iqq7o5nuZUhCaXY0,51428
7
7
  cidc_schemas/template_reader.py,sha256=xXtLRKu1y4FrPj8RgyGOmB2hlsCDXcuvMBWami2_jV8,13119
@@ -20,8 +20,8 @@ cidc_schemas/schemas/aliquot.json,sha256=F24s6xGTeJl-VT6s6wvV8YtMA4O-0BsUCwtD2OE
20
20
  cidc_schemas/schemas/clinical_data.json,sha256=ubt2dqTLCbDuxuOXrBObT_xLHVSArMBx4oASFOAYEas,1474
21
21
  cidc_schemas/schemas/clinical_trial.json,sha256=aUjYgdtlRWDfULk0-apralt4-KrtjriUqt3qNTdL2Rc,4442
22
22
  cidc_schemas/schemas/participant.json,sha256=X72GQSdLqhZl_Vg8OHPqRotblIluNSmiw8N5UeM-di8,2843
23
- cidc_schemas/schemas/sample.json,sha256=culRSM94LahOFAN9B58G1McQ3rWKzhsoVvCcMXwqGmg,21378
24
- cidc_schemas/schemas/shipping_core.json,sha256=OGdcdoFJXoKacD_FoSukX6SXJvcgFXTnWPko9VqOD5o,4234
23
+ cidc_schemas/schemas/sample.json,sha256=4WnxrgJ978CybHg3bQ2JrYgi_0ih0zHyIhr1DwPuDRc,21519
24
+ cidc_schemas/schemas/shipping_core.json,sha256=poCU_gwwXSy997eqkJCBY8TswEHo7rUDIuGszcgYKK8,4239
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
@@ -144,19 +144,19 @@ cidc_schemas/schemas/templates/assays/tcr_adaptive_template.json,sha256=Hb8ngxw6
144
144
  cidc_schemas/schemas/templates/assays/tcr_fastq_template.json,sha256=7Qq4ssI8ErDrHy5RIxjPcNiDf2IBHG42JcngDFKxqlE,3457
145
145
  cidc_schemas/schemas/templates/assays/wes_bam_template.json,sha256=nxbb_lNPi-5cdAlwmSBvn7cS_8gMjROOz7wBWk6ev0Y,2724
146
146
  cidc_schemas/schemas/templates/assays/wes_fastq_template.json,sha256=vuwuIpqXyqpGxCunpjbHKaBQhfKFnr2R-wMkXDiJdKM,3143
147
- cidc_schemas/schemas/templates/manifests/h_and_e_template.json,sha256=ttdf1U9ENF1U6cn4jG6pLB0hqIVignaa8UfmyPwLuTY,17726
148
- cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json,sha256=VavO5lg52VEXbdXS_pqsYRwCdjjk4wQuzrgaIOlwiU8,17566
149
- cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json,sha256=nmr3DCCFzpAT_SdEfSTCWIga48z4PwnoSodBbnZvNAE,18649
150
- cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json,sha256=GUtdrieD8vwoUMRs9ePzDHCrN2sbgDx81-R1K2PBzsI,18387
151
- cidc_schemas/schemas/templates/manifests/pbmc_template.json,sha256=b72ng2fU2tEYTye_Na5bsHv7dxNS9sPciIQqznhHZ7s,18241
152
- cidc_schemas/schemas/templates/manifests/plasma_template.json,sha256=sQR_ayLKgxzrkjC-PC7eCmEyV6dQzQr-boZAtDBgbx8,15856
153
- cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=jwyXOjKnCrHzz1tDF57dYi-Z4QmYrECjSKiQ7g56XG8,16275
147
+ cidc_schemas/schemas/templates/manifests/h_and_e_template.json,sha256=8fbhWxKWhITds1KkbEdQxHHoeoKB2Tm40plzsxz3_FE,18009
148
+ cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json,sha256=POucJzR6ac_ndXgttL8Pm6s7BKtu5tqJz4Y49U8zLj0,17848
149
+ cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json,sha256=13FceWQ4DR09N0hJgBwcN6aO6q94Ru-ys1JZcd_Iefk,18931
150
+ cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json,sha256=yAKMW5KIbQ14O8wXUTRdMM1QFg-hxLNz0y4XncxPpRI,18669
151
+ cidc_schemas/schemas/templates/manifests/pbmc_template.json,sha256=gHxO3dcBMjzHM6PTCg7eZwFnKF4cEbXFZdVeZHfCQG8,18524
152
+ cidc_schemas/schemas/templates/manifests/plasma_template.json,sha256=VNraMcIdpxvPJC5SH4nnUeqOCz5HUuiGiMcKC20Ctso,16138
153
+ cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=q2GmOA2bstMRJmkigOri_uFYKJNHJG3qjVXUjV410Ls,16557
154
154
  cidc_schemas/schemas/templates/manifests/tumor_normal_pairing_template.json,sha256=lVJrGb28n-vyfjGBzhrzjn1lMKw1b4HXXmWtwA603v0,2797
155
- cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json,sha256=eoX_YIl1HfQXiL7Q6ybIuOLs85Nbn7EylJ8dzXKiMZw,18674
156
- cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=HK2Q2VQcDhP8FZDZapk04Qx2-Tji9dCMH1UpkVhU3Vs,17819
157
- nci_cidc_schemas-0.27.8.dist-info/licenses/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
158
- nci_cidc_schemas-0.27.8.dist-info/METADATA,sha256=6f6zUMbzQPgTgZVzhFPs7nwQgf_l1MTBs8eP051ShOY,4553
159
- nci_cidc_schemas-0.27.8.dist-info/WHEEL,sha256=MAQBAzGbXNI3bUmkDsiV_duv8i-gcdnLzw7cfUFwqhU,109
160
- nci_cidc_schemas-0.27.8.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
161
- nci_cidc_schemas-0.27.8.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
162
- nci_cidc_schemas-0.27.8.dist-info/RECORD,,
155
+ cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json,sha256=LpaoDXDS11NCa-Dv37N-tzEGomswQrx5fypkUcG7xJk,18956
156
+ cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=-gww6NCHbtbI5z7UmNSmKyPK3IqKCE8F6n4XwTAb_gk,18101
157
+ nci_cidc_schemas-0.27.10.dist-info/licenses/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
158
+ nci_cidc_schemas-0.27.10.dist-info/METADATA,sha256=M2wECfycUwM55Xfm1hUrueC0IOscCc1zmQhnbEQAObs,4554
159
+ nci_cidc_schemas-0.27.10.dist-info/WHEEL,sha256=AeO2BvogYWm3eGaHCvhzmUYt8ia7KfURiHzO_1atlys,109
160
+ nci_cidc_schemas-0.27.10.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
161
+ nci_cidc_schemas-0.27.10.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
162
+ nci_cidc_schemas-0.27.10.dist-info/RECORD,,
{nci_cidc_schemas-0.27.8.dist-info → nci_cidc_schemas-0.27.10.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (78.1.0)
2
+ Generator: setuptools (79.0.1)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py2-none-any
5
5
  Tag: py3-none-any