nci-cidc-schemas 0.26.37__py2.py3-none-any.whl → 0.27.0__py2.py3-none-any.whl

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Files changed (24) hide show
  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. cidc_schemas/unprism.py +4 -0
  19. {nci_cidc_schemas-0.26.37.dist-info → nci_cidc_schemas-0.27.0.dist-info}/METADATA +27 -16
  20. {nci_cidc_schemas-0.26.37.dist-info → nci_cidc_schemas-0.27.0.dist-info}/RECORD +24 -24
  21. {nci_cidc_schemas-0.26.37.dist-info → nci_cidc_schemas-0.27.0.dist-info}/WHEEL +1 -1
  22. {nci_cidc_schemas-0.26.37.dist-info → nci_cidc_schemas-0.27.0.dist-info}/LICENSE +0 -0
  23. {nci_cidc_schemas-0.26.37.dist-info → nci_cidc_schemas-0.27.0.dist-info}/entry_points.txt +0 -0
  24. {nci_cidc_schemas-0.26.37.dist-info → nci_cidc_schemas-0.27.0.dist-info}/top_level.txt +0 -0
cidc_schemas/schemas/templates/manifests/normal_tissue_dna_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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  },
@@ -129,6 +206,11 @@
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  "type_ref": "sample.json#properties/box_number",
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  "allow_empty": true
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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 location": {
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  "merge_pointer": "/sample_location",
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  "type_ref": "sample.json#properties/sample_location",
@@ -142,12 +224,26 @@
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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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  },
@@ -253,4 +349,4 @@
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  }
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  }
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  }
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- }
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+ }
cidc_schemas/schemas/templates/manifests/pbmc_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",
@@ -66,97 +66,90 @@
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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 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 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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- }
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- },
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-
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- "Essential Patient Data": {
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- "prism_preamble_object_schema": "clinical_trial.json",
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- "prism_preamble_object_pointer": "#",
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- "prism_data_object_pointer": "/participants/0/samples/0",
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- "data_columns": {
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- "Path Concordance Verification": {
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- "entry (#)": {
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- "do_not_merge": true,
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- "allow_empty": true,
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- "type": "string"
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- },
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- "participant ID": {
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- "merge_pointer": "2/participant_id",
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- "type_ref": "participant.json#properties/participant_id"
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- },
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- "CIMAC ID": {
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- "merge_pointer": "/cimac_id",
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- "type_ref": "sample.json#properties/cimac_id",
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- "process_as": [
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- {
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- "merge_pointer": "2/cimac_participant_id",
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- "type_ref": "participant.json#properties/cimac_participant_id",
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- "parse_through": "lambda x: x[:7]"
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- }
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- ]
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- },
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- "surgical pathology report id": {
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- "merge_pointer": "/surgical_pathology_report_id",
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- "type_ref": "sample.json#properties/surgical_pathology_report_id"
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- },
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- "clinical report id": {
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- "merge_pointer": "/clinical_report_id",
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- "type_ref": "sample.json#properties/clinical_report_id"
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- },
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- "collection event name": {
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- "merge_pointer": "/collection_event_name",
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- "type_ref": "sample.json#properties/collection_event_name"
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- },
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- "diagnosis verification": {
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- "merge_pointer": "/diagnosis_verification",
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- "type_ref": "sample.json#properties/diagnosis_verification"
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- }
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  },
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- "ICD-0-3 Code/Description": {
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- "Site Description": {
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- "merge_pointer": "/site_description",
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- "type_ref": "sample.json#properties/site_description"
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- },
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- "Topography Code": {
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- "merge_pointer": "/topography_code",
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- "type_ref": "sample.json#properties/topography_code"
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- },
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- "Topography Description": {
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- "merge_pointer": "/topography_description",
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- "type_ref": "sample.json#properties/topography_description"
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- },
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- "Histology/Behavior": {
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- "merge_pointer": "/histology_behavior",
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- "type_ref": "sample.json#properties/histology_behavior"
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- },
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- "Histology/Behavior Description": {
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- "merge_pointer": "/histology_behavior_description",
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- "type_ref": "sample.json#properties/histology_behavior_description"
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- }
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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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- "Demographics": {
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- "Sex": {
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- "merge_pointer": "2/gender",
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- "type_ref": "participant.json#properties/gender"
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- },
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- "Race": {
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- "merge_pointer": "2/race",
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- "type_ref": "participant.json#properties/race"
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- },
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- "Ethnic Group": {
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- "merge_pointer": "2/ethnicity",
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- "type_ref": "participant.json#properties/ethnicity"
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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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  }
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  },
@@ -168,6 +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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  },
@@ -189,7 +184,6 @@
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  "type_ref": "sample.json#properties/parent_sample_id"
190
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  },
191
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  "processed sample ID": {
192
- "allow_empty": true,
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  "merge_pointer": "/processed_sample_id",
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  "type_ref": "sample.json#properties/processed_sample_id"
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  },
@@ -224,9 +218,19 @@
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  "merge_pointer": "/sample_collection_procedure",
225
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  "type_ref": "sample.json#properties/sample_collection_procedure"
226
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  },
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+ "sample collection procedure other": {
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+ "merge_pointer": "/sample_collection_procedure_other",
223
+ "type_ref": "sample.json#properties/sample_collection_procedure_other",
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+ "allow_empty": true
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+ },
227
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  "type of primary container": {
228
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  "merge_pointer": "0/type_of_primary_container",
229
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  "type_ref": "sample.json#properties/type_of_primary_container"
229
+ },
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+ "type of primary container other": {
231
+ "merge_pointer": "0/type_of_primary_container_other",
232
+ "type_ref": "sample.json#properties/type_of_primary_container_other",
233
+ "allow_empty": true
230
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  },
231
235
  "processed sample type": {
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  "merge_pointer": "/processed_sample_type",
@@ -237,6 +241,11 @@
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  "type_ref": "sample.json#properties/processed_sample_volume",
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  "allow_empty": true
239
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  },
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+ "processed sample quantity": {
245
+ "merge_pointer": "/processed_sample_quantity",
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+ "type_ref": "sample.json#properties/processed_sample_quantity",
247
+ "allow_empty": true
248
+ },
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  "processed sample volume units": {
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  "merge_pointer": "/processed_sample_volume_units",
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  "type_ref": "sample.json#properties/processed_sample_volume_units",
@@ -333,4 +342,4 @@
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  }
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  }
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  }
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- }
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+ }