Merge pull request #14 from PATH-Global-Health/fml-wip

FHIR Mapping Language Tutorial

input/maps/HIVObservationHIVCondition.http

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+### @host = http://localhost:8080/matchboxv3/fhir
+@host = https://test.ahdis.ch/matchbox/fhir
+
+
+### Convert FML to StructureMap
+POST {{host}}/StructureMap/$convert HTTP/1.1
+Content-Type: text/fhir-mapping
+Accept: application/fhir+json
+
+
+< ./HIVObservationHIVCondition.map
+
+
+### Put it
+PUT {{host}}/StructureMap/HIVObservationHIVCondition HTTP/1.1
+Content-Type: application/fhir+json
+Accept: application/fhir+JSON
+
+< ./StructureMap-HIVObservationHIVCondition.json
+
+
+# Or, just do this one...
+
+### PUT FML to StructureMap (combined previous 2 steps in one)
+PUT {{host}}/StructureMap/HIVObservationHIVCondition HTTP/1.1
+Content-Type: text/fhir-mapping
+Accept: application/fhir+json
+
+< ./HIVObservationHIVCondition.map
+
+
+# Then...
+
+
+### Verify StructureMap is created
+GET {{host}}/StructureMap/HIVObservationHIVCondition HTTP/1.1
+Accept: application/fhir+JSON
+
+
+
+### Transforms
+POST {{host}}/StructureMap/$transform?source=https://path-global-health.github.io/MERindicators/StructureMap/HIVObservationHIVCondition
+Accept: application/fhir+json;fhirVersion=4.0
+Content-Type: application/fhir+json;fhirVersion=4.0
+
+< ./test-data1.json
+
+
+
+### Transforms
+POST {{host}}/StructureMap/$transform?source=https://path-global-health.github.io/MERindicators/StructureMap/HIVObservationHIVCondition
+Accept: application/fhir+json;fhirVersion=4.0
+Content-Type: application/fhir+json;fhirVersion=4.0
+
+< ./test-data2.json
+

input/maps/HIVObservationHIVCondition.map

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+map "https://path-global-health.github.io/MERindicators/StructureMap/HIVObservationHIVCondition" = "HIVObservationHIVCondition"
+
+uses "http://hl7.org/fhir/StructureDefinition/Bundle" alias bund as source
+uses "http://hl7.org/fhir/StructureDefinition/Bundle" alias output as target
+
+
+
+group HIVObservationHIVCondition(
+    source src: bund,
+    target tgt: output
+) {
+
+    src -> tgt.type = 'collection' "setBundleType";
+
+    src.entry as entry -> tgt.entry as tentry then {
+      entry.resource : Patient as patient -> tentry.resource = patient then {
+
+        src.entry as obsentry where resource.is(Observation) and resource.subject.exists(reference=("Patient/" & patient.id)) and resource.code.exists(coding.exists(system='https://openconceptlab.org/orgs/CIEL/sources/CIEL' and code='160540')) 
+            -> tgt.entry as newentry, newentry.resource = create("Condition") as cond, uuid() as cid then {
+          obsentry.resource as obs -> newentry.fullUrl = ( "urn:uuid:" & cid ) then {
+            //obsentry -> newentry.resource = cond, cond.id = cid "setConditionRes";
+            obsentry -> cond.id = cid "setCId";
+            patient -> cond.subject as subject then {
+              patient -> subject.reference = reference(patient) "setSubjectRef";
+            } "setSubject";
+            obsentry -> cond.code as ccode then {
+              obsentry -> ccode.coding as coding then {
+                obsentry -> coding.code = '86406008', 
+                            coding.display = "HIV Condition Positive", 
+                            coding.system = 'http://snomed.info/sct' "setCondSystemCode";
+              } "setCondCoding";
+            } "SetCondCode";
+            obs -> tgt.entry as pentry, pentry.resource = create("Provenance") as prov, uuid() as pid then {
+              obs -> prov.id = pid "setPId";
+              obs -> pentry.fullUrl = ( "urn:uuid:" & pid ) "setFullUrl";
+              obs -> prov.target as ptarg then {
+                obs -> ptarg.reference = reference(cond) "setTargetRef";
+              } "setTarget";
+              obs -> prov.entity as entity then {
+                obs -> entity.role = "source" "setRole";
+                obs -> entity.what as pwhat then {
+                  obs -> pwhat.reference = reference(obs) "setWhatRef";
+                } "setWhat";
+              } "setEntity";
+            } "setProvenance";
+          } "setCondition";
+         } "getObservation";
+      } "patientResource";
+    } "copyPatient";
+
+  }
+
+

input/maps/README.md

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+# How to use this folder
+
+This folder is standalone and dependent on the IG it is in.
+
+Follow the directions below then open `input/maps/HIVObservationHIVCondition.http` in VS Code. Click on:
+* Convert FML to StructureMap and Put it or...
+* PUT FML to StructureMap which combines the two operations. This converts FML (.map) files to FHIR StructureMaps and PUTs it on the server.
+* Verify StructureMap is created
+* Transform
+
+The $transform operation will transform the bundle in the payload to an output bundle. In production, the returned bundle would be put on a FHIR server.
+
+## Setup
+
+* The operations use a publicly available server. Please setup a private server with the usual protections before transforming patient data. The open source server used here is the publicly available hosted [Matchbox](https://github.com/ahdis/matchbox) server which is a version of HAPI FHIR Server with additional operations. Standard HAPI FHIR JPA Server does not have the operations needed for this demo.
+
+* Do not post real data. Please use the de-identified examples.
+
+* Install REST Client if using VS Code. Otherwise, use an extension in other editors that can execute .http files.
+[VS Marketplace](https://marketplace.visualstudio.com/items?itemName=humao.rest-client)
+
+* It's recommended to install the FHIR Mapping Language extension if using VS Code [VS Marketplace](https://marketplace.visualstudio.com/items?itemName=HealexSystems.fhir-mapping-language-support)
+

input/maps/_convert.sh

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+#!/usr/bin/env bash
+
+export HEADER1="content-type:application/fhir+json"
+export HEADER2="content-type:text/fhir-mapping"
+export ACCEPT="accept:application/fhir+json"
+
+export FHIR="https://test.ahdis.ch/matchbox/fhir"
+export CONVERT="${FHIR}/StructureMap/$convert"
+export MAP="${FHIR}/StructureMap"
+
+# curl --request POST -H 'accept: application/fhir+json' -H 'content-type: text/fhir-mapping' --data-binary @HIVObservationHIVCondition.map --url 'https://test.ahdis.ch/matchbox/fhir/StructureMap/$convert'
+
+function convertput {
+    # curl -s -X POST -H ${ACCEPT} -H ${HEADER2} --data-binary @${1}.map --url ${CONVERT} | \
+    # curl -s -X PUT -H ${HEADER1} --data-binary @- --url "${MAP}/${1}" | \
+    # curl -s -X GET -H ${ACCEPT} --url "${MAP}/${1}" | \
+    # jq .
+
+    curl -s -X POST -H ${ACCEPT} -H ${HEADER2} --data-binary @${1}.map --url ${CONVERT} | jq . > StructureMap-${1}.json
+    printf "StructureMap created\n"
+
+    curl -s -X PUT -H ${HEADER1} --data-binary @StructureMap-${1}.json --url "${MAP}/${1}" | jq .
+    printf "StructureMap loaded on server\n"
+
+    curl -s -X GET -H ${ACCEPT} --url "${MAP}/${1}" | jq .
+    printf "Confirm StructureMap loaded on server\n"
+}
+
+convertput HIVObservationHIVCondition
+

input/maps/_transform.sh

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+#!/usr/bin/env bash
+
+export HEADER1="content-type:application/fhir+json"
+export ACCEPT="accept:application/fhir+json"
+
+export FHIR="https://test.ahdis.ch/matchbox/fhir"
+export TRANSFORM="${FHIR}/StructureMap/${1}/$transform"
+
+
+
+curl --request POST "https://test.ahdis.ch/matchbox/fhir/StructureMap/\$transform?source=https://path-global-health.github.io/MERindicators/StructureMap/HIVObservationHIVCondition" \
+     --data-binary @test-data1.json  \
+      -H "Accept: application/fhir+json"  -H "Content-Type: application/fhir+json"
+
+
+
+# curl --request POST -H 'accept: application/fhir+json' -H 'content-type: text/fhir+json' --data-binary @test-data1.json --url 'https://test.ahdis.ch/matchbox/fhir/StructureMap/HIVObservationHIVCondition/$transform'
+
+function transform {
+    curl -s -X POST -H ${ACCEPT} -H ${HEADER1} --data-binary @${2} --url ${TRANSFORM} | jq .
+}
+
+transform HIVObservationHIVCondition test-data1.json
+# transform HIVObservationHIVCondition test-data2.json
+