nci-cidc-schemas 0.26.38__py2.py3-none-any.whl → 0.27.0__py2.py3-none-any.whl

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  1. cidc_schemas/__init__.py +1 -1
  2. cidc_schemas/json_validation.py +43 -0
  3. cidc_schemas/prism/merger.py +17 -8
  4. cidc_schemas/schemas/clinical_trial.json +3 -7
  5. cidc_schemas/schemas/participant.json +1 -3
  6. cidc_schemas/schemas/sample.json +178 -44
  7. cidc_schemas/schemas/shipping_core.json +74 -34
  8. cidc_schemas/schemas/templates/manifests/h_and_e_template.json +109 -13
  9. cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json +111 -11
  10. cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json +102 -12
  11. cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json +109 -13
  12. cidc_schemas/schemas/templates/manifests/pbmc_template.json +102 -93
  13. cidc_schemas/schemas/templates/manifests/plasma_template.json +101 -91
  14. cidc_schemas/schemas/templates/manifests/tissue_slide_template.json +109 -13
  15. cidc_schemas/schemas/templates/manifests/tumor_tissue_dna_template.json +109 -13
  16. cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json +109 -13
  17. cidc_schemas/template.py +1 -1
  18. {nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.0.dist-info}/METADATA +27 -16
  19. {nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.0.dist-info}/RECORD +23 -23
  20. {nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.0.dist-info}/WHEEL +1 -1
  21. {nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.0.dist-info}/LICENSE +0 -0
  22. {nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.0.dist-info}/entry_points.txt +0 -0
  23. {nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.0.dist-info}/top_level.txt +0 -0
cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json CHANGED
@@ -41,16 +41,16 @@
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  "type_ref": "shipping_core.json#properties/tracking_number",
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  "allow_empty": true
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  },
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- "account number": {
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- "merge_pointer": "/account_number",
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- "type_ref": "shipping_core.json#properties/account_number",
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- "allow_empty": true
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- },
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  "shipping condition": {
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  "merge_pointer": "/shipping_condition",
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  "type_ref": "shipping_core.json#properties/shipping_condition",
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  "allow_empty": true
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  },
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+ "shipping condition other": {
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+ "merge_pointer": "/shipping_condition_other",
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+ "type_ref": "shipping_core.json#properties/shipping_condition_other",
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+ "allow_empty": true
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+ },
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  "date shipped": {
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  "merge_pointer": "/date_shipped",
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  "type_ref": "shipping_core.json#properties/date_shipped",
@@ -66,14 +66,89 @@
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  "type_ref": "shipping_core.json#properties/quality_of_shipment",
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  "allow_empty": true
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  },
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- "ship from": {
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- "merge_pointer": "/ship_from",
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- "type_ref": "shipping_core.json#properties/ship_from",
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+ "ship from sender person name": {
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+ "merge_pointer": "/ship_from_sender_person_name",
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+ "type_ref": "shipping_core.json#properties/ship_from_sender_person_name",
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+ "allow_empty": true
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+ },
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+ "ship from sender email": {
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+ "merge_pointer": "/ship_from_sender_email",
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+ "type_ref": "shipping_core.json#properties/ship_from_sender_email",
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  "allow_empty": true
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  },
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- "ship to": {
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- "merge_pointer": "/ship_to",
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- "type_ref": "shipping_core.json#properties/ship_to",
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+ "ship from sender phone": {
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+ "merge_pointer": "/ship_from_sender_phone",
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+ "type_ref": "shipping_core.json#properties/ship_from_sender_phone",
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+ "allow_empty": true
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+ },
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+ "ship from name": {
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+ "merge_pointer": "/ship_from_name",
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+ "type_ref": "shipping_core.json#properties/ship_from_name",
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+ "allow_empty": true
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+ },
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+ "ship from street1": {
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+ "merge_pointer": "/ship_from_street1",
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+ "type_ref": "shipping_core.json#properties/ship_from_street1",
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+ "allow_empty": true
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+ },
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+ "ship from street2": {
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+ "merge_pointer": "/ship_from_street2",
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+ "type_ref": "shipping_core.json#properties/ship_from_street2",
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+ "allow_empty": true
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+ },
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+ "ship from city": {
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+ "merge_pointer": "/ship_from_city",
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+ "type_ref": "shipping_core.json#properties/ship_from_city",
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+ "allow_empty": true
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+ },
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+ "ship from state": {
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+ "merge_pointer": "/ship_from_state",
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+ "type_ref": "shipping_core.json#properties/ship_from_state",
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+ "allow_empty": true
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+ },
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+ "ship from zip": {
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+ "merge_pointer": "/ship_from_zip",
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+ "type_ref": "shipping_core.json#properties/ship_from_zip",
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+ "allow_empty": true
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+ },
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+ "ship from country": {
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+ "merge_pointer": "/ship_from_country",
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+ "type_ref": "shipping_core.json#properties/ship_from_country",
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+ "allow_empty": true
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+ },
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+ "ship to name": {
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+ "merge_pointer": "/ship_to_name",
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+ "type_ref": "shipping_core.json#properties/ship_to_name",
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+ "allow_empty": true
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+ },
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+ "ship to street1": {
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+ "merge_pointer": "/ship_to_street1",
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+ "type_ref": "shipping_core.json#properties/ship_to_street1",
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+ "allow_empty": true
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+ },
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+ "ship to street2": {
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+ "merge_pointer": "/ship_to_street2",
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+ "type_ref": "shipping_core.json#properties/ship_to_street2",
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+ "allow_empty": true
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+ },
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+ "ship to city": {
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+ "merge_pointer": "/ship_to_city",
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+ "type_ref": "shipping_core.json#properties/ship_to_city",
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+ "allow_empty": true
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+ },
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+ "ship to state": {
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+ "merge_pointer": "/ship_to_state",
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+ "type_ref": "shipping_core.json#properties/ship_to_state",
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+ "allow_empty": true
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+ },
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+ "ship to zip": {
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+ "merge_pointer": "/ship_to_zip",
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+ "type_ref": "shipping_core.json#properties/ship_to_zip",
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+ "allow_empty": true
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+ },
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+ "ship to country": {
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+ "merge_pointer": "/ship_to_country",
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+ "type_ref": "shipping_core.json#properties/ship_to_country",
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  "allow_empty": true
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  }
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  }
@@ -86,6 +161,8 @@
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  "data_columns": {
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  "IDs": {
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  "entry (#)": {
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+ "do_not_merge": true,
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+ "allow_empty": true,
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  "merge_pointer": "/shipping_entry_number",
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  "type_ref": "sample.json#properties/shipping_entry_number"
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  },
@@ -142,16 +219,35 @@
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  "merge_pointer": "/type_of_tumor_sample",
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  "type_ref": "sample.json#properties/type_of_tumor_sample"
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  },
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+ "description of sample": {
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+ "merge_pointer": "/description_of_sample",
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+ "type_ref": "sample.json#properties/description_of_sample",
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+ "allow_empty": true
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+ },
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  "sample collection procedure": {
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  "merge_pointer": "/sample_collection_procedure",
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  "type_ref": "sample.json#properties/sample_collection_procedure"
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  },
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+ "sample collection procedure other": {
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+ "merge_pointer": "/sample_collection_procedure_other",
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+ "type_ref": "sample.json#properties/sample_collection_procedure_other",
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+ "allow_empty": true
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+ },
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+ "type of primary container": {
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+ "merge_pointer": "/type_of_primary_container",
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+ "type_ref": "sample.json#properties/type_of_primary_container"
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+ },
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+ "type of primary container other": {
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+ "merge_pointer": "/type_of_primary_container_other",
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+ "type_ref": "sample.json#properties/type_of_primary_container_other",
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+ "allow_empty": true
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+ },
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  "core number": {
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  "merge_pointer": "/core_number",
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  "type_ref": "sample.json#properties/core_number",
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  "allow_empty": true
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  },
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- "fixation/stabilization type": {
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+ "fixation stabilization type": {
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  "merge_pointer": "/fixation_stabilization_type",
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  "type_ref": "sample.json#properties/fixation_stabilization_type"
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  },
@@ -240,4 +336,4 @@
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  }
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  }
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  }
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- }
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+ }
cidc_schemas/template.py CHANGED
@@ -941,7 +941,7 @@ class Template:
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  worksheets {Dict[str, dict]} -- a mapping from worksheet names to worksheet schemas
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  """
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- ignored_worksheets = ["Legend", "Data Dictionary"]
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+ ignored_worksheets = ["Legend", "Data Dictionary", "Essential Patient Data"]
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  def __init__(self, schema: dict, type: str, schema_root: str = SCHEMA_DIR):
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  """
{nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.0.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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- Metadata-Version: 2.1
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+ Metadata-Version: 2.2
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  Name: nci_cidc_schemas
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- Version: 0.26.38
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+ Version: 0.27.0
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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
@@ -15,20 +15,31 @@ Classifier: Programming Language :: Python :: 3.9
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  Requires-Python: >=3.9,<3.11
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  Description-Content-Type: text/markdown
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  License-File: LICENSE
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- Requires-Dist: dateparser ==1.1.4
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- Requires-Dist: xlsxwriter ==1.1.6
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- Requires-Dist: argparse ==1.1
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- Requires-Dist: pyyaml ==6.0.1
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- Requires-Dist: jsonschema ==3.0.1
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- Requires-Dist: openpyxl ==3.0.7
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- Requires-Dist: jsonmerge ==1.6.1
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- Requires-Dist: deepdiff ~=4.3.0
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- Requires-Dist: jsonpointer ==2.0
27
- Requires-Dist: pandas ==1.5.3
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- Requires-Dist: jinja2 ~=3.1.3
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- Requires-Dist: nci-cidc-ngs-pipeline-api ==0.1.25
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- Requires-Dist: markupsafe ==2.1.5
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- Requires-Dist: regex ==2022.3.2
18
+ Requires-Dist: dateparser==1.1.4
19
+ Requires-Dist: xlsxwriter==1.1.6
20
+ Requires-Dist: argparse==1.1
21
+ Requires-Dist: pyyaml==6.0.1
22
+ Requires-Dist: jsonschema==3.0.1
23
+ Requires-Dist: openpyxl==3.0.7
24
+ Requires-Dist: jsonmerge==1.6.1
25
+ Requires-Dist: deepdiff~=4.3.0
26
+ Requires-Dist: jsonpointer==2.0
27
+ Requires-Dist: pandas==1.5.3
28
+ Requires-Dist: jinja2~=3.1.3
29
+ Requires-Dist: nci-cidc-ngs-pipeline-api==0.1.25
30
+ Requires-Dist: markupsafe==2.1.5
31
+ Requires-Dist: regex==2022.3.2
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+ Dynamic: author
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+ Dynamic: author-email
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+ Dynamic: classifier
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+ Dynamic: description
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+ Dynamic: description-content-type
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+ Dynamic: home-page
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+ Dynamic: keywords
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+ Dynamic: license
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+ Dynamic: requires-dist
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+ Dynamic: requires-python
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+ Dynamic: summary
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  # cidc-schemas
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{nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.0.dist-info}/RECORD RENAMED
@@ -1,9 +1,9 @@
1
- cidc_schemas/__init__.py,sha256=9Df5WbWCck9fRAaOji8IQO8BZvV88vXOvtUNUoYYB1c,136
1
+ cidc_schemas/__init__.py,sha256=hWMDf0YSZahXXxDPePLAjf-v4R28ET5oLvjtC3oVifA,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=81Dql5LAw4t-0t1cYKpCNQqiUok9rQvGxSk-9VxyILA,20047
4
+ cidc_schemas/json_validation.py,sha256=nHkSfTmBN7EeTrZVdbb8h6A64lWrJe5z0AIHiIy-YB0,22552
5
5
  cidc_schemas/migrations.py,sha256=Amg_T4cFgMzySD7yNnT_PWpqP7hwlTWGeHlI_RSXuRI,14766
6
- cidc_schemas/template.py,sha256=gM6Xp1fOZaF8wOLzY5HGdxi4p8cEYhYXRpqRPncYua0,49865
6
+ cidc_schemas/template.py,sha256=0QZNtH9bIzr3felvsoyShtBq0TX2t1-OVkrQQ3gs8TM,49891
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=TOD3CSGkgNnTtT-OeCCE3Ihlam84lr8XGOmtdSy2lL8,13545
@@ -14,14 +14,14 @@ cidc_schemas/prism/__init__.py,sha256=J5Tj0X7Di6cyxAjaduOUp2aVyvl8UI67bgxEkgttvc
14
14
  cidc_schemas/prism/constants.py,sha256=b5pgxrzwJvKWWIEE9V72cvKwl_ARRaANPHzKk4yo4M4,2325
15
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  cidc_schemas/prism/core.py,sha256=PQgsRAEleT6gO3VyE4uFTYa3qK_VXjFcErV1YwWV1nQ,19294
16
16
  cidc_schemas/prism/extra_metadata.py,sha256=wZjhUGKSvfupr6qZ1WuPepKnf_FG1nGfsDai_kBFZ50,8559
17
- cidc_schemas/prism/merger.py,sha256=Kf5o9NWT80XqYZASbH0dJsQ0dkwMl3HtoR_p7wqUypI,12431
17
+ cidc_schemas/prism/merger.py,sha256=4dUOtF8jyZBoU8LL2d9_nStaD3MUCP7NStoFlxnHcz4,13076
18
18
  cidc_schemas/prism/pipelines.py,sha256=x_qxZ2Xq2pX30gSFW_w-hwUlaUz29lQ-hByM8h0_tao,33532
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19
  cidc_schemas/schemas/aliquot.json,sha256=F24s6xGTeJl-VT6s6wvV8YtMA4O-0BsUCwtD2OEx_cY,1943
20
20
  cidc_schemas/schemas/clinical_data.json,sha256=ubt2dqTLCbDuxuOXrBObT_xLHVSArMBx4oASFOAYEas,1474
21
- cidc_schemas/schemas/clinical_trial.json,sha256=mqvpCTqWGimKA8-S4F32YMDBoHcJkawpr9iTwUgH56w,4652
22
- cidc_schemas/schemas/participant.json,sha256=vCtxbUfVGTjvZ8SPPNLvWJkJIBZUK2NSHpYzJgdoSaY,2991
23
- cidc_schemas/schemas/sample.json,sha256=TRWgxQBybtj4WjLBNZAdpoShpbDTGl8iT3FceGx2gD8,16296
24
- cidc_schemas/schemas/shipping_core.json,sha256=ouekd6KNf4EKVz4IsE2yjibvIjpCE8CZBxCRXlJ7p_U,3315
21
+ cidc_schemas/schemas/clinical_trial.json,sha256=aUjYgdtlRWDfULk0-apralt4-KrtjriUqt3qNTdL2Rc,4442
22
+ cidc_schemas/schemas/participant.json,sha256=X72GQSdLqhZl_Vg8OHPqRotblIluNSmiw8N5UeM-di8,2843
23
+ cidc_schemas/schemas/sample.json,sha256=ZND6Vcq2J4GfqY532pFI7dptg8K6vS5VL25JsDwcfI8,20796
24
+ cidc_schemas/schemas/shipping_core.json,sha256=OGdcdoFJXoKacD_FoSukX6SXJvcgFXTnWPko9VqOD5o,4234
25
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  cidc_schemas/schemas/artifacts/artifact_bam.json,sha256=nPy3qx07--arLyb9VgfdVK6OJoMPhr6rnp-3AF6o82Q,1653
26
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  cidc_schemas/schemas/artifacts/artifact_bam_bai.json,sha256=S1LxCZVyN3v-Hxhs7TEDbGcV-y7LVdAoLzGblT9IhEk,1671
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  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
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  cidc_schemas/schemas/templates/assays/wes_bam_template.json,sha256=nxbb_lNPi-5cdAlwmSBvn7cS_8gMjROOz7wBWk6ev0Y,2724
146
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  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=PiCpfbWd5I29wwYWCQHjQh10g9l84dligYTVvMcJHgM,12524
148
- cidc_schemas/schemas/templates/manifests/microbiome_dna_template.json,sha256=u1QPL83DUvPMcMdYbwmmgT0nSOqkbjQR-asXZ_6p0CY,11878
149
- cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json,sha256=JudTPeQBjTttX4OXMrVl9DTRM73KgZN3jbtC3lcuQsA,13542
150
- cidc_schemas/schemas/templates/manifests/normal_tissue_dna_template.json,sha256=xCE0pTXRlKOd0dPMKcDIBKXRa81Ka_H5f6OGE1TNmhw,13185
151
- cidc_schemas/schemas/templates/manifests/pbmc_template.json,sha256=c0F9xu9za95i2RSVl_9wjiZIUxczOFNWJaXRy8pJhOg,17579
152
- cidc_schemas/schemas/templates/manifests/plasma_template.json,sha256=43bizjQ7zJt5mQHtUfFHDA_f3L4DxBo4XqgHnFvNPbw,15148
153
- cidc_schemas/schemas/templates/manifests/tissue_slide_template.json,sha256=Y3951-HNUVfvOK4fjUxGJt2gtmGhKZxWiXVLxyZghn8,11073
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=y88bHiUDoSvpgA1poHSOfwa4K-TLUjemnZ-qghibteY,17333
149
+ cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json,sha256=wuDJrzC-f1jtTWt_tAeamIVd92QqItD24bnnpSj_ZM4,18416
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
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=-CC7Hg-qzZ7e5QrrnkybrS1Vrfq2zlgtxU4kRnR5is8,13472
156
- cidc_schemas/schemas/templates/manifests/tumor_tissue_rna_template.json,sha256=uPiiEo1xEde6MDhQDapLIjL8XcghgeoCEDdZTzGYFBA,12617
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,,
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-0.27.0.dist-info/LICENSE,sha256=zK77-w4rYCZBHAYJEGkcFuPXwKIsP7jMPZ2iQOXjzko,1072
158
+ nci_cidc_schemas-0.27.0.dist-info/METADATA,sha256=4E9ohB5cgcwYAqTTZIHtdMf-sq-W9TUIoYJs-j9xnVw,4531
159
+ nci_cidc_schemas-0.27.0.dist-info/WHEEL,sha256=9Hm2OB-j1QcCUq9Jguht7ayGIIZBRTdOXD1qg9cCgPM,109
160
+ nci_cidc_schemas-0.27.0.dist-info/entry_points.txt,sha256=kSyTzXeJQrJp_2ZX0GS_NnbJR8ceQKLBSgER46PM0hs,55
161
+ nci_cidc_schemas-0.27.0.dist-info/top_level.txt,sha256=Wwb5Cu7QrnbmSJxI2d00e3-Mir36t0jTRnSulmfhi30,13
162
+ nci_cidc_schemas-0.27.0.dist-info/RECORD,,
{nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.0.dist-info}/WHEEL RENAMED
@@ -1,5 +1,5 @@
1
1
  Wheel-Version: 1.0
2
- Generator: setuptools (75.5.0)
2
+ Generator: setuptools (75.8.0)
3
3
  Root-Is-Purelib: true
4
4
  Tag: py2-none-any
5
5
  Tag: py3-none-any