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Update ecr schemas to extract the first 10 labs #564

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merged 8 commits into from
May 10, 2023
Merged

Update ecr schemas to extract the first 10 labs #564

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dfeabbf
Add lab 3 to the message parser schema.
DanPaseltiner May 10, 2023
f5f04ba
Labs 1-10 for the message parsing service.
DanPaseltiner May 10, 2023
bca42e9
Update ecr.json
BradySkylight May 10, 2023
b7b2060
trigger CI
DanPaseltiner May 10, 2023
e8d052d
Merge branch 'update-ecr-schemas' of https://github.com/CDCgov/phdi i…
DanPaseltiner May 10, 2023
ec0e753
adding 11-20 labs in the kafka schema
BradySkylight May 10, 2023
0b7eb2a
Merge branch 'update-ecr-schemas' of https://github.com/CDCgov/phdi i…
BradySkylight May 10, 2023
d9f53bc
fixed failing tests
BradySkylight May 10, 2023
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58 changes: 57 additions & 1 deletion containers/kafka-to-delta-table/app/default_schemas/ecr.json
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -40,5 +40,61 @@
"specimen_type_2": "string",
"performing_lab_2": "string",
"specimen_collection_date_2": "timestamp",
"result_date_2": "timestamp"
"result_date_2": "timestamp",
"test_type_3": "string",
"test_result_3": "string",
"test_result_interp_3": "string",
"specimen_type_3": "string",
"performing_lab_3": "string",
"specimen_collection_date_3": "timestamp",
"result_date_3": "timestamp",
"test_type_4": "string",
"test_result_4": "string",
"test_result_interp_4": "string",
"specimen_type_4": "string",
"performing_lab_4": "string",
"specimen_collection_date_4": "timestamp",
"result_date_4": "timestamp",
"test_type_5": "string",
"test_result_5": "string",
"test_result_interp_5": "string",
"specimen_type_5": "string",
"performing_lab_5": "string",
"specimen_collection_date_5": "timestamp",
"result_date_5": "timestamp",
"test_type_6": "string",
"test_result_6": "string",
"test_result_interp_6": "string",
"specimen_type_6": "string",
"performing_lab_6": "string",
"specimen_collection_date_6": "timestamp",
"result_date_6": "timestamp",
"test_type_7": "string",
"test_result_7": "string",
"test_result_interp_7": "string",
"specimen_type_7": "string",
"performing_lab_7": "string",
"specimen_collection_date_7": "timestamp",
"result_date_7": "timestamp",
"test_type_8": "string",
"test_result_8": "string",
"test_result_interp_8": "string",
"specimen_type_8": "string",
"performing_lab_8": "string",
"specimen_collection_date_8": "timestamp",
"result_date_8": "timestamp",
"test_type_9": "string",
"test_result_9": "string",
"test_result_interp_9": "string",
"specimen_type_9": "string",
"performing_lab_9": "string",
"specimen_collection_date_9": "timestamp",
"result_date_9": "timestamp",
"test_type_10": "string",
"test_result_10": "string",
"test_result_interp_10": "string",
"specimen_type_10": "string",
"performing_lab_10": "string",
"specimen_collection_date_10": "timestamp",
"result_date_10": "timestamp"
}
58 changes: 57 additions & 1 deletion containers/message-parser/app/default_schemas/ecr.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -40,5 +40,61 @@
"specimen_type_2": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[1].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen source').valueString",
"performing_lab_2": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[1].performer.display",
"specimen_collection_date_2": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[1].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen collection time').valueDateTime",
"result_date_2": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[1].effectiveDateTime"
"result_date_2": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[1].effectiveDateTime",
"test_type_3": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[2].code.coding.display",
"test_result_3": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[2].valueString",
"test_result_interp_3": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[0].interpretation.coding.display",
"specimen_type_3": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[2].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen source').valueString",
"performing_lab_3": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[2].performer.display",
"specimen_collection_date_3": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[2].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen collection time').valueDateTime",
"result_date_3": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[2].effectiveDateTime",
"test_type_4": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[3].code.coding.display",
"test_result_4": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[3].valueString",
"test_result_interp_4": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[3].interpretation.coding.display",
"specimen_type_4": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[3].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen source').valueString",
"performing_lab_4": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[3].performer.display",
"specimen_collection_date_4": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[3].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen collection time').valueDateTime",
"result_date_4": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[3].effectiveDateTime",
"test_type_5": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[4].code.coding.display",
"test_result_5": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[4].valueString",
"test_result_interp_5": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[4].interpretation.coding.display",
"specimen_type_5": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[4].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen source').valueString",
"performing_lab_5": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[4].performer.display",
"specimen_collection_date_5": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[4].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen collection time').valueDateTime",
"result_date_5": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[4].effectiveDateTime",
"test_type_6": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[5].code.coding.display",
"test_result_6": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[5].valueString",
"test_result_interp_6": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[5].interpretation.coding.display",
"specimen_type_6": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[5].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen source').valueString",
"performing_lab_6": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[5].performer.display",
"specimen_collection_date_6": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[5].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen collection time').valueDateTime",
"result_date_6": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[5].effectiveDateTime",
"test_type_7": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[6].code.coding.display",
"test_result_7": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[6].valueString",
"test_result_interp_7": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[6].interpretation.coding.display",
"specimen_type_7": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[6].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen source').valueString",
"performing_lab_7": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[6].performer.display",
"specimen_collection_date_7": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[6].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen collection time').valueDateTime",
"result_date_7": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[6].effectiveDateTime",
"test_type_8": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[7].code.coding.display",
"test_result_8": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[7].valueString",
"test_result_interp_8": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[7].interpretation.coding.display",
"specimen_type_8": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[7].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen source').valueString",
"performing_lab_8": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[7].performer.display",
"specimen_collection_date_8": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[7].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen collection time').valueDateTime",
"result_date_8": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[7].effectiveDateTime",
"test_type_9": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[8].code.coding.display",
"test_result_9": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[8].valueString",
"test_result_interp_9": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[8].interpretation.coding.display",
"specimen_type_9": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[8].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen source').valueString",
"performing_lab_9": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[8].performer.display",
"specimen_collection_date_9": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[8].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen collection time').valueDateTime",
"result_date_9": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[8].effectiveDateTime",
"test_type_10": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[9].code.coding.display",
"test_result_10": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[9].valueString",
"test_result_interp_10": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[9].interpretation.coding.display",
"specimen_type_10": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[9].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen source').valueString",
"performing_lab_10": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[9].performer.display",
"specimen_collection_date_10": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[9].extension.where(url='http://hl7.org/fhir/R4/specimen.html').extension.where(url='specimen collection time').valueDateTime",
"result_date_10": "Bundle.entry.resource.where(resourceType='Observation').where(category.coding.code='laboratory')[9].effectiveDateTime"
}