Quick Start Guide

In this guide we will clone and build the product, and then use it to transform a COSD 9.0.1 archive to OMOP.

Prerequisites

Build

Clone the repository.

git clone https://github.com/answerdigital/oxford-omop-data-mapper.git

Build the product targeting the windows-x64 platform to the publish directory. Include .NET runtime with the product. (Avoding the need to install the runtime on the location where the tool is used)

Build for Windows x64 

dotnet publish -r win-x64 --self-contained true -o ./publish

Build for other platforms 

dotnet publish -r PLATFORMRID --self-contained true -o ./publish

Replace PLATFORMRID with a platform RID, e.g linux-x64. See full list of supported RIDs

Configure the tool

Update the connection string in appsettings.json to point to your OMOP database. See ConnectionString examples.

Transform a COSD 9.0.1 archive.

Stage the COSD submission file December 2020 Submission.zip.

.\omop.exe stage --type cosd load "COSD\December 2020 Submission.zip"

Output

info: Microsoft.Hosting.Lifetime[0]
      Application started. Press Ctrl+C to shut down.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD data.
info: Microsoft.Hosting.Lifetime[0]
      Hosting environment: Production
info: Microsoft.Hosting.Lifetime[0]
      Content root path: C:\Code\oxford-omop-transformer\publish
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Found 14 entries.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(BA)_RTH_2020-12-01_2020-12-31_2021-02-05T09_54_21.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(BR)_RTH_2020-12-01_2020-12-31_2021-02-05T10_03_55.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(CO)_RTH_2020-12-01_2020-12-31_2021-02-05T10_08_09.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(CT)_RTH_2020-12-01_2020-12-31_2021-02-05T10_13_49.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(GY)_RTH_2020-12-01_2020-12-31_2021-02-05T10_19_30.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(HA)_RTH_2020-12-01_2020-12-31_2021-02-05T10_23_37.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(HN)_RTH_2020-12-01_2020-12-31_2021-02-05T10_25_33.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(LU)_RTH_2020-12-01_2020-12-31_2021-02-05T10_27_26.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(LV)_RTH_2020-12-01_2020-12-31_2021-02-05T10_30_19.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(SA)_RTH_2020-12-01_2020-12-31_2021-02-05T10_32_06.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(SK)_RTH_2020-12-01_2020-12-31_2021-02-05T10_33_11.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(UG)_RTH_2020-12-01_2020-12-31_2021-02-05T10_36_24.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(UR)_RTH_2020-12-01_2020-12-31_2021-02-05T10_38_39.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging COSD_INFOFLEX(CR)_RTH_2020-12-01_2020-12-31_2021-02-05T10_10_53.xml.
info: OmopTransformer.COSD.Staging.CosdStaging[0]
      Staging complete.
info: Microsoft.Hosting.Lifetime[0]
      Application is shutting down...

Transform the staged data.

.\omop.exe transform --type cosd

Output

info: Microsoft.Hosting.Lifetime[0]
      Application started. Press Ctrl+C to shut down.
info: Microsoft.Hosting.Lifetime[0]
      Hosting environment: Production
info: OmopTransformer.Transformation.IRecordTransformer[0]
      Transforming COSD Person.
info: Microsoft.Hosting.Lifetime[0]
      Content root path: C:\Code\oxford-omop-transformer\publish
info: OmopTransformer.RecordProvider[0]
      Querying OmopTransformer.COSD.Demographics.CosdDemographics
info: OmopTransformer.Transformation.IRecordTransformer[0]
      Extracted 3849 COSD Person in 1 seconds.
info: OmopTransformer.Omop.Person.PersonRecorder[0]
      Recording 3849 persons.
info: OmopTransformer.Omop.Person.PersonRecorder[0]
      Batch 1 of 1 completed in 2717ms.
info: OmopTransformer.Omop.Person.PersonRecorder[0]
      procedure occurrences completed in 2.7180059 seconds.
info: OmopTransformer.Transformation.IRecordTransformer[0]
      Transformation took 2922ms.
info: OmopTransformer.Transformation.IRecordTransformer[0]
      Transforming COSD Location.
info: OmopTransformer.RecordProvider[0]
      Querying OmopTransformer.COSD.Demographics.CosdDemographics
info: OmopTransformer.Transformation.IRecordTransformer[0]
      Extracted 3849 COSD Location in 1 seconds.
info: OmopTransformer.Omop.Location.LocationRecorder[0]
      Recording 3849 locations.
info: OmopTransformer.Omop.Location.LocationRecorder[0]
      Batch 1 of 1 completed in 690ms.
info: OmopTransformer.Omop.Location.LocationRecorder[0]
      locations completed in 0.6902594 seconds.
info: OmopTransformer.Transformation.IRecordTransformer[0]
      Transformation took 869ms.
info: Microsoft.Hosting.Lifetime[0]
      Application is shutting down...

Then clear the staging tables.

.\omop.exe stage clear --type cosd

Output

info: Microsoft.Hosting.Lifetime[0]
      Application started. Press Ctrl+C to shut down.
info: Microsoft.Hosting.Lifetime[0]
      Hosting environment: Production
info: Microsoft.Hosting.Lifetime[0]
      Content root path: C:\Code\oxford-omop-transformer\publish
info: OmopTransformer.COSD.Staging.CosdStagingSchema[0]
      Clearing staging tables.
info: Microsoft.Hosting.Lifetime[0]
      Application is shutting down...

View the transformed patients and their locations.

select *
from cdm.person p
	inner join cdm.location l
		on p.location_id = l.location_id;

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