nci-cidc-schemas 0.26.38__py2.py3-none-any.whl → 0.27.1__py2.py3-none-any.whl

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Files changed (23) 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. {nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.1.dist-info}/METADATA +27 -16
  19. {nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.1.dist-info}/RECORD +23 -23
  20. {nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.1.dist-info}/WHEEL +1 -1
  21. {nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.1.dist-info}/LICENSE +0 -0
  22. {nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.1.dist-info}/entry_points.txt +0 -0
  23. {nci_cidc_schemas-0.26.38.dist-info → nci_cidc_schemas-0.27.1.dist-info}/top_level.txt +0 -0
cidc_schemas/schemas/templates/manifests/h_and_e_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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  },
@@ -141,16 +218,35 @@
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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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  },
@@ -239,4 +335,4 @@
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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/microbiome_dna_template.json CHANGED
@@ -40,16 +40,16 @@
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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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+ },
53
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  "date shipped": {
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  "merge_pointer": "/date_shipped",
55
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  "type_ref": "shipping_core.json#properties/date_shipped",
@@ -65,14 +65,89 @@
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  "type_ref": "shipping_core.json#properties/quality_of_shipment",
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  "allow_empty": true
67
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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 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": {
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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 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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  }
@@ -84,6 +159,8 @@
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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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  },
@@ -126,6 +203,11 @@
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  "type_ref": "sample.json#properties/box_number",
127
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  "allow_empty": true
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  },
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+ "description of sample": {
207
+ "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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+ },
129
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  "sample location": {
130
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  "merge_pointer": "/sample_location",
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  "type_ref": "sample.json#properties/sample_location",
@@ -139,6 +221,20 @@
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  "merge_pointer": "/sample_collection_procedure",
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  "type_ref": "sample.json#properties/sample_collection_procedure"
141
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  },
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+ "sample collection procedure other": {
225
+ "merge_pointer": "/sample_collection_procedure_other",
226
+ "type_ref": "sample.json#properties/sample_collection_procedure_other",
227
+ "allow_empty": true
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+ },
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+ "type of primary container": {
230
+ "merge_pointer": "/type_of_primary_container",
231
+ "type_ref": "sample.json#properties/type_of_primary_container"
232
+ },
233
+ "type of primary container other": {
234
+ "merge_pointer": "/type_of_primary_container_other",
235
+ "type_ref": "sample.json#properties/type_of_primary_container_other",
236
+ "allow_empty": true
237
+ },
142
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  "processed sample type": {
143
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  "merge_pointer": "/processed_sample_type",
144
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  "type_ref": "sample.json#properties/processed_sample_type"
@@ -199,6 +295,10 @@
199
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  "type_ref": "sample.json#properties/material_storage_condition",
200
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  "allow_empty": true
201
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  },
298
+ "fixation stabilization type": {
299
+ "merge_pointer": "/fixation_stabilization_type",
300
+ "type_ref": "sample.json#properties/fixation_stabilization_type"
301
+ },
202
302
  "quality of sample": {
203
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  "merge_pointer": "/quality_of_sample",
204
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  "type_ref": "sample.json#properties/quality_of_sample",
cidc_schemas/schemas/templates/manifests/normal_blood_dna_template.json CHANGED
@@ -40,16 +40,16 @@
40
40
  "type_ref": "shipping_core.json#properties/tracking_number",
41
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  "allow_empty": true
42
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  },
43
- "account number": {
44
- "merge_pointer": "/account_number",
45
- "type_ref": "shipping_core.json#properties/account_number",
46
- "allow_empty": true
47
- },
48
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  "shipping condition": {
49
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  "merge_pointer": "/shipping_condition",
50
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  "type_ref": "shipping_core.json#properties/shipping_condition",
51
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  "allow_empty": true
52
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  },
48
+ "shipping condition other": {
49
+ "merge_pointer": "/shipping_condition_other",
50
+ "type_ref": "shipping_core.json#properties/shipping_condition_other",
51
+ "allow_empty": true
52
+ },
53
53
  "date shipped": {
54
54
  "merge_pointer": "/date_shipped",
55
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  "type_ref": "shipping_core.json#properties/date_shipped",
@@ -65,14 +65,89 @@
65
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  "type_ref": "shipping_core.json#properties/quality_of_shipment",
66
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  "allow_empty": true
67
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  },
68
- "ship from": {
69
- "merge_pointer": "/ship_from",
70
- "type_ref": "shipping_core.json#properties/ship_from",
68
+ "ship from sender person name": {
69
+ "merge_pointer": "/ship_from_sender_person_name",
70
+ "type_ref": "shipping_core.json#properties/ship_from_sender_person_name",
71
+ "allow_empty": true
72
+ },
73
+ "ship from sender email": {
74
+ "merge_pointer": "/ship_from_sender_email",
75
+ "type_ref": "shipping_core.json#properties/ship_from_sender_email",
76
+ "allow_empty": true
77
+ },
78
+ "ship from sender phone": {
79
+ "merge_pointer": "/ship_from_sender_phone",
80
+ "type_ref": "shipping_core.json#properties/ship_from_sender_phone",
81
+ "allow_empty": true
82
+ },
83
+ "ship from name": {
84
+ "merge_pointer": "/ship_from_name",
85
+ "type_ref": "shipping_core.json#properties/ship_from_name",
86
+ "allow_empty": true
87
+ },
88
+ "ship from street1": {
89
+ "merge_pointer": "/ship_from_street1",
90
+ "type_ref": "shipping_core.json#properties/ship_from_street1",
91
+ "allow_empty": true
92
+ },
93
+ "ship from street2": {
94
+ "merge_pointer": "/ship_from_street2",
95
+ "type_ref": "shipping_core.json#properties/ship_from_street2",
96
+ "allow_empty": true
97
+ },
98
+ "ship from city": {
99
+ "merge_pointer": "/ship_from_city",
100
+ "type_ref": "shipping_core.json#properties/ship_from_city",
101
+ "allow_empty": true
102
+ },
103
+ "ship from state": {
104
+ "merge_pointer": "/ship_from_state",
105
+ "type_ref": "shipping_core.json#properties/ship_from_state",
106
+ "allow_empty": true
107
+ },
108
+ "ship from zip": {
109
+ "merge_pointer": "/ship_from_zip",
110
+ "type_ref": "shipping_core.json#properties/ship_from_zip",
111
+ "allow_empty": true
112
+ },
113
+ "ship from country": {
114
+ "merge_pointer": "/ship_from_country",
115
+ "type_ref": "shipping_core.json#properties/ship_from_country",
116
+ "allow_empty": true
117
+ },
118
+ "ship to name": {
119
+ "merge_pointer": "/ship_to_name",
120
+ "type_ref": "shipping_core.json#properties/ship_to_name",
71
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  "allow_empty": true
72
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  },
73
- "ship to": {
74
- "merge_pointer": "/ship_to",
75
- "type_ref": "shipping_core.json#properties/ship_to",
123
+ "ship to street1": {
124
+ "merge_pointer": "/ship_to_street1",
125
+ "type_ref": "shipping_core.json#properties/ship_to_street1",
126
+ "allow_empty": true
127
+ },
128
+ "ship to street2": {
129
+ "merge_pointer": "/ship_to_street2",
130
+ "type_ref": "shipping_core.json#properties/ship_to_street2",
131
+ "allow_empty": true
132
+ },
133
+ "ship to city": {
134
+ "merge_pointer": "/ship_to_city",
135
+ "type_ref": "shipping_core.json#properties/ship_to_city",
136
+ "allow_empty": true
137
+ },
138
+ "ship to state": {
139
+ "merge_pointer": "/ship_to_state",
140
+ "type_ref": "shipping_core.json#properties/ship_to_state",
141
+ "allow_empty": true
142
+ },
143
+ "ship to zip": {
144
+ "merge_pointer": "/ship_to_zip",
145
+ "type_ref": "shipping_core.json#properties/ship_to_zip",
146
+ "allow_empty": true
147
+ },
148
+ "ship to country": {
149
+ "merge_pointer": "/ship_to_country",
150
+ "type_ref": "shipping_core.json#properties/ship_to_country",
76
151
  "allow_empty": true
77
152
  }
78
153
  }
@@ -84,6 +159,8 @@
84
159
  "data_columns": {
85
160
  "IDs": {
86
161
  "entry (#)": {
162
+ "do_not_merge": true,
163
+ "allow_empty": true,
87
164
  "merge_pointer": "/shipping_entry_number",
88
165
  "type_ref": "sample.json#properties/shipping_entry_number"
89
166
  },
@@ -139,9 +216,18 @@
139
216
  "merge_pointer": "/sample_collection_procedure",
140
217
  "type_ref": "sample.json#properties/sample_collection_procedure"
141
218
  },
219
+ "sample collection procedure other": {
220
+ "merge_pointer": "/sample_collection_procedure_other",
221
+ "type_ref": "sample.json#properties/sample_collection_procedure_other",
222
+ "allow_empty": true
223
+ },
142
224
  "type of primary container": {
143
225
  "merge_pointer": "/type_of_primary_container",
144
- "type_ref": "sample.json#properties/type_of_primary_container",
226
+ "type_ref": "sample.json#properties/type_of_primary_container"
227
+ },
228
+ "type of primary container other": {
229
+ "merge_pointer": "/type_of_primary_container_other",
230
+ "type_ref": "sample.json#properties/type_of_primary_container_other",
145
231
  "allow_empty": true
146
232
  },
147
233
  "processed sample type": {
@@ -231,6 +317,10 @@
231
317
  "type_ref": "sample.json#properties/material_storage_condition",
232
318
  "allow_empty": true
233
319
  },
320
+ "fixation stabilization type": {
321
+ "merge_pointer": "/fixation_stabilization_type",
322
+ "type_ref": "sample.json#properties/fixation_stabilization_type"
323
+ },
234
324
  "quality of sample": {
235
325
  "merge_pointer": "/quality_of_sample",
236
326
  "type_ref": "sample.json#properties/quality_of_sample",