Merge pull request #205 from mcode/docs-update-2023

Updating docs and README with recent changes

README.md

@@ -108,6 +108,8 @@ To specify which patients the client should extract data for, the configuration
 
 Each extractor uses various methods to gather data and format that data into [mCODE](http://hl7.org/fhir/us/mcode/index.html) profiled resources. The `observation` extractor formats data into a general [FHIR R4](http://hl7.org/fhir/R4) profile. Extractors may require additional configuration items that can be specified in the configuration file.
 
+Post-extraction mapping can be enabled by including a file named `mapper.js` in the `config` folder which exports `resourceMapping` and `variables`. For more information about defining mappers see documentation for the [FHIR Mapper](https://github.com/standardhealth/fhir-mapper)
+
 ### Email Notification
 
 The mCODE Extraction Client supports sending an email using the SMTP protocol when there are errors during data extraction.

docs/appointment.csv

@@ -0,0 +1,4 @@
+mrn,appointmentId,status,serviceCategory,serviceType,appointmentType,specialty,start,end,cancelationCode,description
+mrn-1,exampleId-1,status-code,service-cat,service-type,app-type,specialty-code,YYYY-MM-DD,YYYY-MM-DD,cancel-code,"Example description 1"
+mrn-2,exampleId-2,status-code,service-cat,service-type,app-type,specialty-code,YYYY-MM-DD,YYYY-MM-DD,cancel-code,"Example description 2"
+mrn-2,exampleId-3,status-code,,,,,,,,

docs/cancer-related-medication-request.csv

@@ -1,3 +1,3 @@
-mrn,requestId,code,codeSystem,displayText,treatmentReasonCode,treatmentReasonCodeSystem,treatmentReasonDisplayText,procedureIntent,status,intent,authoredOn,requesterId
-mrn-1,requestId-1,code,code-system,code-text,code,code-system,display-text,procedure-intent-code,status-code,intent-code,YYY-MM-DD,requesterId-1
-mrn-2,requestId-2,code,code-system,code-text,code,code-system,display-text,procedure-intent-code,status-code,intent-code,YYY-MM-DD,requesterId-2
+mrn,requestId,code,codeSystem,displayText,treatmentReasonCode,treatmentReasonCodeSystem,treatmentReasonDisplayText,procedureIntent,status,intent,authoredOn,requesterId,dosageRoute,asNeededCode,doseRateType,doseQuantityValue,doseQuantityUnit,timingCode,timingEvent
+mrn-1,requestId-1,code,code-system,code-text,code,code-system,display-text,procedure-intent-code,status-code,intent-code,YYY-MM-DD,requesterId-1,route-code,needed-code,rate-type,quantity-value,quantity-unit,timing-code,YYYY-MM-DD
+mrn-2,requestId-2,code,code-system,code-text,code,code-system,display-text,procedure-intent-code,status-code,intent-code,YYY-MM-DD,requesterId-2,route-code,needed-code,rate-type,quantity-value,quantity-unit,timing-code,YYYY-MM-DD

docs/clinical-trial-information.csv

@@ -1,3 +1,3 @@
-mrn,trialSubjectID,enrollmentStatus,trialResearchID,trialStatus
-123,subjectId-1,example-status,researchId-1,example-trialStatus
-456,subjectId-2,example-status,researchId-1,example-trialStatus
+mrn,trialSubjectID,enrollmentStatus,trialResearchID,trialStatus,trialResearchSystem,startDate,endDate
+123,subjectId-1,example-status,researchId-1,example-trialStatus,research-system,YYYY-MM-DD,YYYY-MM-DD
+456,subjectId-2,example-status,researchId-1,example-trialStatus,research-system,YYYY-MM-DD,YYYY-MM-DD

docs/encounter.csv

@@ -0,0 +1,4 @@
+mrn,encounterId,status,classCode,classSystem,typeCode,typeSystem,startDate,endDate
+mrn-1,exampleId-1,status-code,class-code,http://terminology.hl7.org/CodeSystem/v3-ActCode,type-code,http://snomed.info/sct,YYYY-MM-DD,YYYY-MM-DD
+mrn-2,exampleId-2,status-code,class-code,http://terminology.hl7.org/CodeSystem/v3-ActCode,type-code,http://snomed.info/sct,YYYY-MM-DD,YYYY-MM-DD
+mrn-3,exampleId-3,status-code,class-code,http://terminology.hl7.org/CodeSystem/v3-ActCode,,,,