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Added CLI example to README, corrected an omop.json error
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PhilAppleby committed Dec 18, 2024
1 parent 7c57500 commit 1c93b2e
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11 changes: 4 additions & 7 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,9 @@ TODO:
Reduction in complexity over the original CaRROT-CDM version for the Transform part of *ETL* - In practice *Extract* is always
performed by Data Partners, *Load* by database bulk-load software.

Sample command line:
Statistics

`carrot-transform run mapstream \
--rulesfile=${DATASETHOME}/rules/mapping.json \
--person-file=${DATASETHOME/input/Demographics.csv \
--omop-version="5.3" \
--output-dir=${DATASETHOME}/output \
${DATASETHOME}/input`
External libraries imported (approximate)

carrot-cdm 61
carrot-transform 12
6 changes: 6 additions & 0 deletions carrottransform/config/omop.json
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Expand Up @@ -26,6 +26,10 @@
"visit_occurrence": {
"visit_start_datetime": "visit_start_date",
"visit_end_datetime": "visit_end_date"
},
"device_exposure": {
"device_exposure_start_datetime": "device_exposure_start_date",
"device_exposure_end_datetime": "device_exposure_end_date"
}
},
"date_field_components": {
Expand All @@ -46,6 +50,7 @@
"person": "person_id",
"procedure_occurrence": "person_id",
"specimen": "person_id",
"device_exposure": "person_id",
"visit_occurrence": "person_id"
},
"auto_number_field": {
Expand All @@ -56,6 +61,7 @@
"observation": "observation_id",
"procedure_occurrence": "procedure_occurrence_id",
"specimen": "specimen_id",
"device_exposure": "device_exposure_id",
"visit_occurrence": "visit_occurrence_id"
}
}

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