diff --git a/build.gradle b/build.gradle index 302a51c1d9..d2826621e9 100644 --- a/build.gradle +++ b/build.gradle @@ -58,6 +58,11 @@ dependencies { implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-dstu2:6.1.0' implementation 'ca.uhn.hapi.fhir:hapi-fhir-structures-r4:6.1.0' implementation 'ca.uhn.hapi.fhir:hapi-fhir-client:6.1.0' + + implementation 'ca.uhn.hapi.fhir:hapi-fhir-validation:6.1.0' + implementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4:6.1.0' + implementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu3:6.1.0' + implementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu2:6.1.0' // C-CDA export uses Apache FreeMarker templates implementation 'org.freemarker:freemarker:2.3.31' @@ -123,10 +128,6 @@ dependencies { testImplementation 'org.powermock:powermock-module-junit4:2.0.9' testImplementation 'org.powermock:powermock-api-mockito2:2.0.9' testImplementation 'com.github.tomakehurst:wiremock-jre8:2.33.2' - testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation:6.1.0' - testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-r4:6.1.0' - testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu3:6.1.0' - testImplementation 'ca.uhn.hapi.fhir:hapi-fhir-validation-resources-dstu2:6.1.0' testImplementation 'com.helger:ph-schematron:5.6.5' testImplementation 'com.helger:ph-commons:9.5.5' testImplementation 'com.squareup.okhttp3:mockwebserver:4.10.0' @@ -178,6 +179,7 @@ task graphviz(type: JavaExec) { mainClass = "Graphviz" } + task rifMinimize(type: JavaExec) { group 'Application' description 'Filter exported RIF files to produce minimal set that covers all claim types' @@ -229,6 +231,19 @@ shadowJar { task uberJar() { } +task flexporter(type: JavaExec) { + group 'Application' + description 'Apply transformations to FHIR' + classpath sourceSets.main.runtimeClasspath + mainClass = "RunFlexporter" + // args are called "arams" because they are called with -P, + // ex. gradle run -Params="['arg1', 'args2']" + // see https://stackoverflow.com/questions/27604283/gradle-task-pass-arguments-to-java-application + if (project.hasProperty("arams")) { + args Eval.me(arams) + } +} + task concepts(type: JavaExec) { group 'Application' description 'Create a list of simulated concepts' diff --git a/run_flexporter b/run_flexporter new file mode 100755 index 0000000000..015c5d137f --- /dev/null +++ b/run_flexporter @@ -0,0 +1,18 @@ +#!/usr/bin/env sh + +############################################################################## +## +## Flexporter launcher for UN*X +## +############################################################################## + +ARGS= + +for arg in "$@" +do + ARGS=$ARGS\'$arg\', + # Trailing comma ok, don't need to remove it +done + +./gradlew flexporter -Params="[$ARGS]" + diff --git a/src/main/java/RunFlexporter.java b/src/main/java/RunFlexporter.java new file mode 100644 index 0000000000..74d07ab503 --- /dev/null +++ b/src/main/java/RunFlexporter.java @@ -0,0 +1,147 @@ +import java.io.File; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.nio.file.DirectoryStream; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.StandardOpenOption; +import java.util.Arrays; +import java.util.LinkedList; +import java.util.Queue; + +import org.hl7.fhir.r4.model.Bundle; +import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; +import org.hl7.fhir.r4.model.Resource; +import org.mitre.synthea.export.flexporter.Actions; +import org.mitre.synthea.export.flexporter.FhirPathUtils; +import org.mitre.synthea.export.flexporter.Mapping; + +import ca.uhn.fhir.parser.IParser; + + +public class RunFlexporter { + public static void main(String[] args) throws Exception { + Queue argsQ = new LinkedList(Arrays.asList(args)); + + File igDirectory = null; + File sourceFile = null; + File mappingFile = null; + + while (!argsQ.isEmpty()) { + String currArg = argsQ.poll(); + + if (currArg.equals("-ig")) { + String value = argsQ.poll(); + + if (value == null) { + throw new FileNotFoundException("No implementation guide directory provided"); + } + + igDirectory = new File(value); + + if (!igDirectory.isDirectory()) { + throw new FileNotFoundException(String.format( + "Specified implementation guide directory (%s) does not exist or is not a directory", + value)); + } else if (isDirEmpty(igDirectory.toPath())) { + throw new FileNotFoundException( + String.format("Specified implementation guide directory (%s) is empty", value)); + } + } + + else if (currArg.equals("-m")) { + String value = argsQ.poll(); + + if (value == null) { + throw new FileNotFoundException("No mapping file provided"); + } + + mappingFile = new File(value); + + if (!mappingFile.exists()) { + throw new FileNotFoundException( + String.format("Specified mapping file (%s) does not exist", value)); + } + } + + else if (currArg.equals("-s")) { + String value = argsQ.poll(); + sourceFile = new File(value); + + if (value == null) { + throw new FileNotFoundException("No Synthea source FHIR provided"); + } + + if (!sourceFile.exists()) { + throw new FileNotFoundException( + String.format("Specified Synthea source FHIR (%s) does not exist", value)); + } + } + } + + if (mappingFile == null || sourceFile == null) { + usage(); + System.exit(1); + } + + convertFhir(mappingFile, igDirectory, sourceFile); + } + + public static void convertFhir(File mappingFile, File igDirectory, File sourceFhir) + throws IOException { + + Mapping mapping = Mapping.parseMapping(mappingFile); + + IParser parser = FhirPathUtils.FHIR_CTX.newJsonParser().setPrettyPrint(true); + + if (sourceFhir.isDirectory()) { + + // TODO + + } else { + String fhirJson = new String(Files.readAllBytes(sourceFhir.toPath())); + Bundle bundle = parser.parseResource(Bundle.class, fhirJson); + + for (BundleEntryComponent bec : bundle.getEntry()) { + Resource r = bec.getResource(); + if (r.getId().startsWith("urn:uuid:")) { + // HAPI does some weird stuff with IDs + // by default in Synthea they are just plain UUIDs + // and the entry.fullUrl is urn:uuid:(id) + // but somehow when they get parsed back in, the id is urn:uuid:etc + // which then doesn't get written back out at the end + // so this removes the "urn:uuid:" bit if it got added + r.setId(r.getId().substring(9)); + } + } + + // bundle is modified in-place + convertFhir(bundle, mapping); + + String bundleJson = parser.encodeResourceToString(bundle); + + File outFile = + new File("./output/" + System.currentTimeMillis() + "_" + sourceFhir.getName()); + + Files.write(outFile.toPath(), bundleJson.getBytes(), StandardOpenOption.CREATE_NEW); + + System.out.println("Wrote " + outFile); + } + } + + public static Bundle convertFhir(Bundle bundle, Mapping mapping) { + Actions.applyMapping(bundle, mapping, null); + + return bundle; + } + + private static boolean isDirEmpty(final Path directory) throws IOException { + try (DirectoryStream dirStream = Files.newDirectoryStream(directory)) { + return !dirStream.iterator().hasNext(); + } + } + + private static void usage() { + System.out.println("Usage: run_flexporter -m MAPPING_FILE -s SOURCE_FHIR [-i IG_FOLDER]"); + } +} diff --git a/src/main/java/org/mitre/synthea/export/Exporter.java b/src/main/java/org/mitre/synthea/export/Exporter.java index ca3e9f8852..7e35107317 100644 --- a/src/main/java/org/mitre/synthea/export/Exporter.java +++ b/src/main/java/org/mitre/synthea/export/Exporter.java @@ -1,7 +1,6 @@ package org.mitre.synthea.export; import ca.uhn.fhir.parser.IParser; - import java.io.BufferedWriter; import java.io.File; import java.io.FileWriter; @@ -24,6 +23,8 @@ import org.apache.commons.lang3.tuple.Pair; import org.mitre.synthea.engine.Generator; +import org.mitre.synthea.export.flexporter.Actions; +import org.mitre.synthea.export.flexporter.Mapping; import org.mitre.synthea.export.rif.BB2RIFExporter; import org.mitre.synthea.helpers.Config; import org.mitre.synthea.helpers.Utilities; @@ -68,6 +69,7 @@ public static class ExporterRuntimeOptions { !Config.get("generate.terminology_service_url", "").isEmpty(); private BlockingQueue recordQueue; private SupportedFhirVersion fhirVersion; + private List flexporterMappings; public ExporterRuntimeOptions() { yearsOfHistory = Integer.parseInt(Config.get("exporter.years_of_history")); @@ -227,9 +229,18 @@ private static boolean exportRecord(Person person, String fileTag, long stopTime } if (Config.getAsBoolean("exporter.fhir.export")) { File outDirectory = getOutputFolder("fhir", person); + org.hl7.fhir.r4.model.Bundle bundle = FhirR4.convertToFHIR(person, stopTime); + + if (options.flexporterMappings != null) { + for (Mapping mapping : options.flexporterMappings) { + // flexport on the bundle here + Actions.applyMapping(bundle, mapping, person); + } + } + + IParser parser = FhirR4.getContext().newJsonParser(); if (Config.getAsBoolean("exporter.fhir.bulk_data")) { - org.hl7.fhir.r4.model.Bundle bundle = FhirR4.convertToFHIR(person, stopTime); - IParser parser = FhirR4.getContext().newJsonParser().setPrettyPrint(false); + parser.setPrettyPrint(false); for (org.hl7.fhir.r4.model.Bundle.BundleEntryComponent entry : bundle.getEntry()) { String filename = entry.getResource().getResourceType().toString() + ".ndjson"; Path outFilePath = outDirectory.toPath().resolve(filename); @@ -237,7 +248,8 @@ private static boolean exportRecord(Person person, String fileTag, long stopTime appendToFile(outFilePath, entryJson); } } else { - String bundleJson = FhirR4.convertToFHIRJson(person, stopTime); + parser.setPrettyPrint(true); + String bundleJson = parser.encodeResourceToString(bundle); Path outFilePath = outDirectory.toPath().resolve(filename(person, fileTag, "json")); writeNewFile(outFilePath, bundleJson); } diff --git a/src/main/java/org/mitre/synthea/export/flexporter/Actions.java b/src/main/java/org/mitre/synthea/export/flexporter/Actions.java new file mode 100644 index 0000000000..bc07cd36d5 --- /dev/null +++ b/src/main/java/org/mitre/synthea/export/flexporter/Actions.java @@ -0,0 +1,353 @@ +package org.mitre.synthea.export.flexporter; + +import java.util.Collections; +import java.util.HashMap; +import java.util.HashSet; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.UUID; + +import org.apache.commons.lang3.StringUtils; +import org.hl7.fhir.r4.model.Base; +import org.hl7.fhir.r4.model.Bundle; +import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; +import org.hl7.fhir.r4.model.Bundle.BundleEntryRequestComponent; +import org.hl7.fhir.r4.model.Bundle.BundleType; +import org.hl7.fhir.r4.model.Bundle.HTTPVerb; +import org.hl7.fhir.r4.model.Meta; +import org.hl7.fhir.r4.model.Resource; +import org.mitre.synthea.world.agents.Person; + +// For now +@SuppressWarnings("unchecked") +public abstract class Actions { + + public static void applyMapping(Bundle bundle, Mapping mapping, Person person) { + mapping.actions.forEach(action -> applyAction(bundle, action, person)); + } + + public static void applyAction(Bundle bundle, Map action, Person person) { + // TODO: this could be handled better but for now just key off a specific field in the action + + if (action.containsKey("profiles")) { + applyProfiles(bundle, (List>) action.get("profiles")); + } else if (action.containsKey("set_values")) { + setValues(bundle, (List>) action.get("set_values"), person); + } else if (action.containsKey("keep_resources")) { + keepResources(bundle, (List) action.get("keep_resources")); + } else if (action.containsKey("delete_resources")) { + deleteResources(bundle, (List) action.get("delete_resources")); + } else if (action.containsKey("create_resource")) { + createResource(bundle, (List>) action.get("create_resource"), person); + } + } + + + public static void applyProfiles(Bundle bundle, List> items) { + // TODO: might it be faster to loop over all the resources + // and check applicability for each item only once? + for (Map item : items) { + String applicability = item.get("applicability"); + String profile = item.get("profile"); + + List matchingResources = FhirPathUtils.evaluateBundle(bundle, applicability, true); + + for (Base match : matchingResources) { + if (match instanceof Resource) { + applyProfile((Resource) match, profile); + } + } + } + } + + private static void applyProfile(Resource resource, String profileURL) { + Meta meta = resource.getMeta(); + if (meta == null) { + meta = new Meta(); + resource.setMeta(meta); + } + if (!meta.hasProfile(profileURL)) { + meta.addProfile(profileURL); + } + } + + public static void setValues(Bundle bundle, List> items, Person person) { + for (Map entry : items) { + String applicability = (String) entry.get("applicability"); + List> fields = (List>) entry.get("fields"); + + List matchingResources = FhirPathUtils.evaluateBundle(bundle, applicability, true); + + for (Base match : matchingResources) { + if (match instanceof Resource) { + Map fhirPathMapping = + createFhirPathMapping(fields, bundle, (Resource) match, person); + + CustomFHIRPathResourceGeneratorR4 fhirPathgenerator = + new CustomFHIRPathResourceGeneratorR4<>(FhirPathUtils.FHIR_CTX); + fhirPathgenerator.setMapping(fhirPathMapping); + fhirPathgenerator.setResource((Resource) match); + + fhirPathgenerator.generateResource((Class) match.getClass()); + } + } + } + } + + + public static void createResource(Bundle bundle, List> resourcesToCreate, + Person person) { + // TODO: this is fundamentally similar to setValues, so extract common logic + + for (Map newResourceDef : resourcesToCreate) { + + String resourceType = (String) newResourceDef.get("resourceType"); + String basedOnPath = (String) newResourceDef.get("based_on"); + List profiles = (List) newResourceDef.get("profiles"); + + List basedOnResources; + List> writeback; + + if (basedOnPath == null) { + basedOnResources = Collections.singletonList(null); + writeback = null; + } else { + basedOnResources = FhirPathUtils.evaluateBundle(bundle, basedOnPath, true); + // this may return empty list, in which no new resources will be created + + writeback = (List>) newResourceDef.get("writeback"); + } + + List> fields = (List>) newResourceDef.get("fields"); + + for (Base basedOnItem : basedOnResources) { + // IMPORTANT: basedOnItem may be null + + Map fhirPathMapping = + createFhirPathMapping(fields, bundle, (Resource) basedOnItem, person); + + CustomFHIRPathResourceGeneratorR4 fhirPathgenerator = + new CustomFHIRPathResourceGeneratorR4<>(FhirPathUtils.FHIR_CTX); + fhirPathgenerator.setMapping(fhirPathMapping); + + try { + Class resourceClass = + (Class) Class.forName("org.hl7.fhir.r4.model." + resourceType); + + Resource createdResource = fhirPathgenerator.generateResource(resourceClass); + + // ensure the new resource has an ID + // seems like this should work as part of the fhirpathgenerator, but it didn't + // this might be easier anyway + createdResource.setId(UUID.randomUUID().toString()); + if (profiles != null) { + profiles.forEach(p -> applyProfile(createdResource, p)); + } + + // TODO: see if there's a good way to add the resource after the based-on resource + BundleEntryComponent newEntry = bundle.addEntry(); + + newEntry.setResource(createdResource); + + if (bundle.getType().equals(BundleType.TRANSACTION)) { + BundleEntryRequestComponent request = newEntry.getRequest(); + // as of now everything in synthea is POST to resourceType. + request.setMethod(HTTPVerb.POST); + request.setUrl(resourceType); + } + + if (writeback != null && !writeback.isEmpty()) { + Map writebackMapping = + createFhirPathMapping(writeback, bundle, createdResource, person); + + CustomFHIRPathResourceGeneratorR4 writebackGenerator = + new CustomFHIRPathResourceGeneratorR4<>(FhirPathUtils.FHIR_CTX); + writebackGenerator.setMapping(writebackMapping); + writebackGenerator.setResource((Resource) basedOnItem); + + writebackGenerator.generateResource((Class) basedOnItem.getClass()); + } + + } catch (ClassNotFoundException e) { + e.printStackTrace(); + } + } + } + } + + + private static Map createFhirPathMapping(List> fields, + Bundle sourceBundle, Resource sourceResource, Person person) { + Map fhirPathMapping = new HashMap<>(); + + for (Map field : fields) { + String location = field.get("location"); + String valueDef = field.get("value"); + String transform = field.get("transform"); + + if (valueDef == null || valueDef.isEmpty() || valueDef.equals("null")) { + valueDef = null; + } else if (valueDef.startsWith("$")) { + valueDef = getValue(sourceBundle, valueDef, sourceResource, person); + } // else - assume it's a raw value + + // TODO: consider a "skip-resource-if-null" kind of thing + // or "don't create this resource if the referenced field on the source resource is missing" + + if (transform != null) { + valueDef = ValueTransforms.apply(valueDef, transform); + } + + // TODO: the $getField option allows copying a single primitive value + // do we want to allow copying an entire object somehow? + + fhirPathMapping.put(location, valueDef); + } + + return fhirPathMapping; + } + + public static void keepResources(Bundle bundle, List list) { + // TODO: make this FHIRPath instead of just straight resource types + + Set resourceTypesToKeep = new HashSet<>(list); + + Set deletedResourceIDs = new HashSet<>(); + + Iterator itr = bundle.getEntry().iterator(); + + while (itr.hasNext()) { + BundleEntryComponent entry = itr.next(); + + Resource resource = entry.getResource(); + String resourceType = resource.getResourceType().toString(); + if (!resourceTypesToKeep.contains(resourceType)) { + deletedResourceIDs.add(resource.getId()); + itr.remove(); + } + } + + // TODO: additional passes for deleted resource IDs + } + + + public static void deleteResources(Bundle bundle, List list) { + // TODO: make this FHIRPath instead of just straight resource types + + Set resourceTypesToDelete = new HashSet<>(list); + + Set deletedResourceIDs = new HashSet<>(); + + Iterator itr = bundle.getEntry().iterator(); + + while (itr.hasNext()) { + BundleEntryComponent entry = itr.next(); + + Resource resource = entry.getResource(); + String resourceType = resource.getResourceType().toString(); + if (resourceTypesToDelete.contains(resourceType)) { + deletedResourceIDs.add(resource.getId()); + itr.remove(); + } + } + + // TODO: additional passes for deleted resource IDs + } + + + private static String getValue(Bundle bundle, String valueDef, Resource currentResource, + Person person) { + // The flag has the format of $flagName([flagValue1, flagValue2, ..., flagValueN]) + + String flag = StringUtils.substringBetween(valueDef, "$", "("); + String flagValue = StringUtils.substringBetween(valueDef, "([", "])"); + String[] flagValues = flagValue.split(","); + + + // basic naming scheme here is "set" and "get" refer to a particular resource + // (ie, the current one, or the resource a new one is being based on) + // and "find" refers to searching the entire bundle + if (flag.equals("setRef")) { + return setReference(currentResource, flagValues); + } else if (flag.equals("getField")) { + return getField(currentResource, flagValues); + } else if (flag.equals("findRef")) { + return findReference(bundle, flagValues); + } else if (flag.equals("findValue")) { + return findValues(bundle, flagValues); + } else if (flag.equals("getAttribute")) { + return getAttribute(person, flagValues); + } + + return null; + } + + private static String getAttribute(Person person, String... flagValues) { + // flagValues[0] = attribute name + // TODO: how to handle types that aren't just strings? + + // TODO: helpful error message if person == null + Object attribute = person.attributes.get(flagValues[0]); + + if (attribute == null) { + return null; + } + + return String.valueOf(attribute); + } + + private static String setReference(Resource currentResource, String... args) { + return createReference(currentResource); + } + + private static String createReference(Resource resource) { + // ids in FHIR are a little weird + // from some testing, ids in HAPI also seem to be a little flaky + String id = resource.getId(); + + if (id.startsWith("urn:uuid:")) + return id; + + return resource.getResourceType().toString() + "/" + id; + } + + private static String getField(Resource currentResource, String... args) { + // args[0] = FHIRPath, from this resource + // args[1] = how to disambiguate if there are multiple? TODO + + List fieldValues = FhirPathUtils.evaluateResource(currentResource, args[0]); + + if (fieldValues.isEmpty()) + return null; + + return fieldValues.get(0).primitiveValue(); + } + + + private static String findReference(Bundle bundle, String... flagValues) { + // args[0] = FHIRPath, find a resource in the bundle + // args[1] = how to disambiguate. ex "same-encounter" TODO + // note the challenge will be how to pick the "encounter" field on arbitrary resources + // when in doubt, use more fhirpath? + + List matchingResources = FhirPathUtils.evaluateBundle(bundle, flagValues[0], true); + + if (matchingResources.isEmpty()) + return null; + + return createReference((Resource) matchingResources.get(0)); + } + + private static String findValues(Bundle bundle, String... args) { + // args[0] = FHIRPath, from this resource + // args[1] = how to disambiguate if there are multiple? TODO + List fieldValues = FhirPathUtils.evaluateBundle(bundle, args[0], false); + + if (fieldValues.isEmpty()) + return null; + + return fieldValues.get(0).primitiveValue(); + } +} diff --git a/src/main/java/org/mitre/synthea/export/flexporter/CustomFHIRPathResourceGeneratorR4.java b/src/main/java/org/mitre/synthea/export/flexporter/CustomFHIRPathResourceGeneratorR4.java new file mode 100644 index 0000000000..220608116f --- /dev/null +++ b/src/main/java/org/mitre/synthea/export/flexporter/CustomFHIRPathResourceGeneratorR4.java @@ -0,0 +1,685 @@ +package org.mitre.synthea.export.flexporter; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Stack; + +import org.hl7.fhir.r4.utils.FHIRPathEngine; +import org.hl7.fhir.instance.model.api.IBase; +import org.hl7.fhir.instance.model.api.ICompositeType; +import org.hl7.fhir.instance.model.api.IPrimitiveType; +import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext; +import org.hl7.fhir.r4.model.ExpressionNode; +import org.hl7.fhir.r4.model.ExpressionNode.Kind; +import org.hl7.fhir.r4.model.Resource; + +import ca.uhn.fhir.context.BaseRuntimeChildDefinition; +import ca.uhn.fhir.context.BaseRuntimeElementDefinition; +import ca.uhn.fhir.context.FhirContext; +import ca.uhn.fhir.context.RuntimeCompositeDatatypeDefinition; +import ca.uhn.fhir.context.RuntimePrimitiveDatatypeDefinition; +import ca.uhn.fhir.context.RuntimeResourceBlockDefinition; + +/** + * This class can be used to generate resources using FHIRPath expressions. + * + * Note that this is an experimental feature and the API is expected to change. Ideally this will be + * made version independent and moved out of the validation module in a future release. + * + * Modified for the Flexporter: + * -- allow adding to an existing resource + * -- add support for BackboneElements + * -- swapped constructors, pass in a FhirContext to avoid recreating it for each resource + * -- add support for extensions on primitives + * -- more advanced java generics (some functions now take in Class instead of just T + * -- reformatted per Synthea style guidelines + * + * Original: + * https://github.com/hapifhir/hapi-fhir/blob/master/hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/validator/FHIRPathResourceGeneratorR4.java + * + * + * @author Marcel Parciak + * + */ +public class CustomFHIRPathResourceGeneratorR4 { + + private FhirContext ctx; + private FHIRPathEngine engine; + private Map pathMapping; + private T resource = null; + + private String valueToSet = null; + private Stack nodeStack = null; + + /** + * The GenerationTier summarizes some variables that are needed to create FHIR elements later on. + */ + class GenerationTier { + // The RuntimeDefinition of nodes + public BaseRuntimeElementDefinition nodeDefinition = null; + // The actual nodes, i.e. the instances that hold the values + public List nodes = new ArrayList<>(); + // The ChildDefinition applied to the parent (i.e. one of the nodes from a lower + // GenerationTier) to create nodes + public BaseRuntimeChildDefinition childDefinition = null; + // The path segment name of nodes + public String fhirPathName = null; + + public GenerationTier() {} + + public GenerationTier(BaseRuntimeElementDefinition nodeDef, IBase firstNode) { + this.nodeDefinition = nodeDef; + this.nodes.add(firstNode); + } + } + + /** + * Constructor without parameters, needs a call to `setMapping` later on in order to generate any + * Resources. + */ + public CustomFHIRPathResourceGeneratorR4() { + this(FhirContext.forR4()); + } + + public CustomFHIRPathResourceGeneratorR4(FhirContext fhirCtx) { + this.ctx = fhirCtx; + this.pathMapping = new HashMap(); + this.engine = new FHIRPathEngine(new HapiWorkerContext(ctx, ctx.getValidationSupport())); + } + + /** + * Setter for the FHIRPath mapping Map instance. + * + * @param mapping Map a mapping of FHIRPath to value Strings that will be used to + * create a Resource. + */ + public void setMapping(Map mapping) { + this.pathMapping = mapping; + } + + /** + * Getter for a generated Resource. null if no Resource has been generated yet. + * + * @return T the generated Resource or null. + */ + public T getResource() { + return this.resource; + } + + /** + * Getter for a generated Resource. null if no Resource has been generated yet. + * + * @return T the generated Resource or null. + */ + public void setResource(T resource) { + this.resource = resource; + } + + /** + * Prepares the internal state prior to generating a FHIR Resource. Called once upon generation at + * the start. + * + * @param resourceClass Class The class of the Resource that shall be created (an empty + * Resource will be created in this method). + */ + @SuppressWarnings("unchecked") + private void prepareInternalState(Class resourceClass) { + if (this.resource == null) { + this.resource = (T) this.ctx.getResourceDefinition(resourceClass).newInstance(); + } + } + + /** + * The generation method that yields a new instance of class `resourceClass` with every value set + * in the FHIRPath mapping. + * + * @param resourceClass Class The class of the Resource that shall be created. + * @return T a new FHIR Resource instance of class `resourceClass`. + */ + public T generateResource(Class resourceClass) { + this.prepareInternalState(resourceClass); + + for (String fhirPath : this.sortedPaths()) { + // prepare the next fhirPath iteration: create a new nodeStack and set the value + this.nodeStack = new Stack<>(); + this.nodeStack + .push(new GenerationTier(this.ctx.getResourceDefinition(this.resource), this.resource)); + this.valueToSet = this.pathMapping.get(fhirPath); + + // pathNode is the part of the FHIRPath we are processing + ExpressionNode pathNode = this.engine.parse(fhirPath); + while (pathNode != null) { + switch (pathNode.getKind()) { + case Name: + this.handleNameNode(pathNode); + break; + case Function: + this.handleFunctionNode(pathNode); + break; + case Constant: + case Group: + case Unary: + // TODO: unimplmemented, what to do? + break; + } + pathNode = pathNode.getInner(); + } + } + + this.nodeStack = null; + return this.resource; + } + + /* + * Handling Named nodes + */ + + /** + * Handles a named node, either adding a new layer to the `nodeStack` when reaching a Composite + * Node or adding the value for Primitive Nodes. + * + * @param fhirPath String the FHIRPath section for the next GenerationTier. + * @param value String the value that shall be set upon reaching a PrimitiveNode. + */ + private void handleNameNode(ExpressionNode fhirPath) { + BaseRuntimeChildDefinition childDef = + this.nodeStack.peek().nodeDefinition.getChildByName(fhirPath.getName()); + if (childDef == null) { + // nothing to do + return; + } + + // identify the type of named node we need to handle here by getting the runtime + // definition type + switch (childDef.getChildByName(fhirPath.getName()).getChildType()) { + case COMPOSITE_DATATYPE: + handleCompositeNode(fhirPath); + break; + + case PRIMITIVE_DATATYPE: + handlePrimitiveNode(fhirPath); + break; + + case RESOURCE_BLOCK: + // TODO: this appears to be where BackboneElements get handled + handleResourceBlock(fhirPath); + break; + + case ID_DATATYPE: + case RESOURCE: + case CONTAINED_RESOURCE_LIST: + case CONTAINED_RESOURCES: + case EXTENSION_DECLARED: + case PRIMITIVE_XHTML: + case PRIMITIVE_XHTML_HL7ORG: + case UNDECL_EXT: + // TODO: not implemented. What to do? + } + } + + /** + * Handles primitive nodes with regards to the current latest tier of the nodeStack. Sets a + * primitive value to all nodes. + * + * @param fhirPath ExpressionNode segment of the fhirPath that specifies the primitive value to + * set. + */ + private void handlePrimitiveNode(ExpressionNode fhirPath) { + // Flexporter modification: check if the fhirPath is just the primitive, in which case just set + // it but if there is more (ie, an extension) then don't set a value and push a generation tier + GenerationTier nextTier = new GenerationTier(); + // get the name of the FHIRPath for the next tier + nextTier.fhirPathName = fhirPath.getName(); + // get the child definition from the parent nodePefinition + nextTier.childDefinition = + this.nodeStack.peek().nodeDefinition.getChildByName(fhirPath.getName()); + // create a nodeDefinition for the next tier + nextTier.nodeDefinition = nextTier.childDefinition.getChildByName(nextTier.fhirPathName); + + + + // Get the primitive type definition from the childDeftinion + RuntimePrimitiveDatatypeDefinition primitiveTarget = + (RuntimePrimitiveDatatypeDefinition) nextTier.childDefinition + .getChildByName(fhirPath.getName()); + for (IBase nodeElement : this.nodeStack.peek().nodes) { + // add the primitive value to each parent node + + IPrimitiveType primitive; + + List existingValues = nextTier.childDefinition.getAccessor().getValues(nodeElement); + + if (fhirPath.getInner() != null && fhirPath.getInner().getKind() == Kind.Name + && !existingValues.isEmpty()) { + // there is an extension on this (possibly other scenarios too?) + // and already a value set, so don't set a new one + primitive = (IPrimitiveType) existingValues.get(0); + + } else { + primitive = + primitiveTarget.newInstance(nextTier.childDefinition.getInstanceConstructorArguments()); + primitive.setValueAsString(this.valueToSet); + nextTier.childDefinition.getMutator().addValue(nodeElement, primitive); + } + + + nextTier.nodes.add(primitive); + } + + // push the created nextTier to the nodeStack + this.nodeStack.push(nextTier); + } + + /** + * Handles a composite node with regards to the current latest tier of the nodeStack. Creates a + * new node based on fhirPath if none are available. + * + * @param fhirPath ExpressionNode the segment of the FHIRPath that is being handled right now. + */ + private void handleCompositeNode(ExpressionNode fhirPath) { + GenerationTier nextTier = new GenerationTier(); + // get the name of the FHIRPath for the next tier + nextTier.fhirPathName = fhirPath.getName(); + // get the child definition from the parent nodePefinition + nextTier.childDefinition = + this.nodeStack.peek().nodeDefinition.getChildByName(fhirPath.getName()); + // create a nodeDefinition for the next tier + nextTier.nodeDefinition = nextTier.childDefinition.getChildByName(nextTier.fhirPathName); + + RuntimeCompositeDatatypeDefinition compositeTarget = + (RuntimeCompositeDatatypeDefinition) nextTier.nodeDefinition; + // iterate through all parent nodes + for (IBase nodeElement : this.nodeStack.peek().nodes) { + List containedNodes = nextTier.childDefinition.getAccessor().getValues(nodeElement); + if (containedNodes.size() > 0) { + // check if sister nodes are already available + nextTier.nodes.addAll(containedNodes); + } else { + // if not nodes are available, create a new node + ICompositeType compositeNode = + compositeTarget.newInstance(nextTier.childDefinition.getInstanceConstructorArguments()); + nextTier.childDefinition.getMutator().addValue(nodeElement, compositeNode); + nextTier.nodes.add(compositeNode); + } + } + // push the created nextTier to the nodeStack + this.nodeStack.push(nextTier); + } + + private void handleResourceBlock(ExpressionNode fhirPath) { + GenerationTier nextTier = new GenerationTier(); + // get the name of the FHIRPath for the next tier + nextTier.fhirPathName = fhirPath.getName(); + // get the child definition from the parent nodePefinition + nextTier.childDefinition = + this.nodeStack.peek().nodeDefinition.getChildByName(fhirPath.getName()); + // create a nodeDefinition for the next tier + nextTier.nodeDefinition = nextTier.childDefinition.getChildByName(nextTier.fhirPathName); + + RuntimeResourceBlockDefinition compositeTarget = + (RuntimeResourceBlockDefinition) nextTier.nodeDefinition; + // iterate through all parent nodes + for (IBase nodeElement : this.nodeStack.peek().nodes) { + List containedNodes = nextTier.childDefinition.getAccessor().getValues(nodeElement); + if (containedNodes.size() > 0) { + // check if sister nodes are already available + nextTier.nodes.addAll(containedNodes); + } else { + // if not nodes are available, create a new node + IBase compositeNode = + compositeTarget.newInstance(nextTier.childDefinition.getInstanceConstructorArguments()); + nextTier.childDefinition.getMutator().addValue(nodeElement, compositeNode); + nextTier.nodes.add(compositeNode); + } + } + // push the created nextTier to the nodeStack + this.nodeStack.push(nextTier); + } + + /* + * Handling Function Nodes + */ + + /** + * Handles a function node of a FHIRPath. + * + * @param fhirPath ExpressionNode the segment of the FHIRPath that is being handled right now. + */ + private void handleFunctionNode(ExpressionNode fhirPath) { + switch (fhirPath.getFunction()) { + case Where: + this.handleWhereFunctionNode(fhirPath); + case Aggregate: + case Alias: + case AliasAs: + case All: + case AllFalse: + case AllTrue: + case AnyFalse: + case AnyTrue: + case As: + case Check: + case Children: + case Combine: + case ConformsTo: + case Contains: + case ConvertsToBoolean: + case ConvertsToDateTime: + case ConvertsToDecimal: + case ConvertsToInteger: + case ConvertsToQuantity: + case ConvertsToString: + case ConvertsToTime: + case Count: + case Custom: + case Descendants: + case Distinct: + case Empty: + case EndsWith: + case Exclude: + case Exists: + case Extension: + case First: + case HasValue: + case HtmlChecks: + case Iif: + case IndexOf: + case Intersect: + case Is: + case IsDistinct: + case Item: + case Last: + case Length: + case Lower: + case Matches: + case MemberOf: + case Not: + case Now: + case OfType: + case Repeat: + case Replace: + case ReplaceMatches: + case Resolve: + case Select: + case Single: + case Skip: + case StartsWith: + case SubsetOf: + case Substring: + case SupersetOf: + case Tail: + case Take: + case ToBoolean: + case ToChars: + case ToDateTime: + case ToDecimal: + case ToInteger: + case ToQuantity: + case ToString: + case ToTime: + case Today: + case Trace: + case Type: + case Union: + case Upper: + default: + // TODO: unimplemented, what to do? + } + } + + /** + * Handles a function node of a `where`-function. Iterates through all params and handle where + * functions for primitive datatypes (others are not implemented and yield errors.) + * + * @param fhirPath ExpressionNode the segment of the FHIRPath that contains the where function + */ + private void handleWhereFunctionNode(ExpressionNode fhirPath) { + // iterate through all where parameters + for (ExpressionNode param : fhirPath.getParameters()) { + BaseRuntimeChildDefinition wherePropertyChild = + this.nodeStack.peek().nodeDefinition.getChildByName(param.getName()); + BaseRuntimeElementDefinition wherePropertyDefinition = + wherePropertyChild.getChildByName(param.getName()); + + // only primitive nodes can be checked using the where function + switch (wherePropertyDefinition.getChildType()) { + case PRIMITIVE_DATATYPE: + this.handleWhereFunctionParam(param); + break; + case COMPOSITE_DATATYPE: + case CONTAINED_RESOURCES: + case CONTAINED_RESOURCE_LIST: + case EXTENSION_DECLARED: + case ID_DATATYPE: + case PRIMITIVE_XHTML: + case PRIMITIVE_XHTML_HL7ORG: + case RESOURCE: + case RESOURCE_BLOCK: + case UNDECL_EXT: + default: + // TODO: unimplemented. What to do? + } + } + } + + /** + * Filter the latest nodeStack tier using `param`. + * + * @param param ExpressionNode parameter type ExpressionNode that provides the where clause that + * is used to filter nodes from the nodeStack. + */ + private void handleWhereFunctionParam(ExpressionNode param) { + BaseRuntimeChildDefinition wherePropertyChild = + this.nodeStack.peek().nodeDefinition.getChildByName(param.getName()); + BaseRuntimeElementDefinition wherePropertyDefinition = + wherePropertyChild.getChildByName(param.getName()); + + String matchingValue = param.getOpNext().getConstant().toString(); + List matchingNodes = new ArrayList<>(); + List unlabeledNodes = new ArrayList<>(); + // sort all nodes from the nodeStack into matching nodes and unlabeled nodes + for (IBase node : this.nodeStack.peek().nodes) { + List operationValues = wherePropertyChild.getAccessor().getValues(node); + if (operationValues.size() == 0) { + unlabeledNodes.add(node); + } else { + for (IBase operationValue : operationValues) { + IPrimitiveType primitive = (IPrimitiveType) operationValue; + switch (param.getOperation()) { + case Equals: + if (primitive.getValueAsString().equals(matchingValue)) { + matchingNodes.add(node); + } + break; + case NotEquals: + if (!primitive.getValueAsString().equals(matchingValue)) { + matchingNodes.add(node); + } + break; + case And: + case As: + case Concatenate: + case Contains: + case Div: + case DivideBy: + case Equivalent: + case Greater: + case GreaterOrEqual: + case Implies: + case In: + case Is: + case LessOrEqual: + case LessThan: + case MemberOf: + case Minus: + case Mod: + case NotEquivalent: + case Or: + case Plus: + case Times: + case Union: + case Xor: + // TODO: unimplemented, what to do? + } + } + } + } + + if (matchingNodes.size() == 0) { + if (unlabeledNodes.size() == 0) { + // no nodes were matched and no unlabeled nodes are available. We need to add a + // sister node to the nodeStack + GenerationTier latestTier = this.nodeStack.pop(); + GenerationTier previousTier = this.nodeStack.peek(); + this.nodeStack.push(latestTier); + + RuntimeCompositeDatatypeDefinition compositeTarget = + (RuntimeCompositeDatatypeDefinition) latestTier.nodeDefinition; + ICompositeType compositeNode = compositeTarget + .newInstance(latestTier.childDefinition.getInstanceConstructorArguments()); + latestTier.childDefinition.getMutator().addValue(previousTier.nodes.get(0), compositeNode); + unlabeledNodes.add(compositeNode); + } + + switch (param.getOperation()) { + case Equals: + // if we are checking for equality, we need to set the property we looked for on + // the unlabeled node(s) + RuntimePrimitiveDatatypeDefinition equalsPrimitive = + (RuntimePrimitiveDatatypeDefinition) wherePropertyDefinition; + IPrimitiveType primitive = + equalsPrimitive.newInstance(wherePropertyChild.getInstanceConstructorArguments()); + primitive.setValueAsString(param.getOpNext().getConstant().toString()); + for (IBase node : unlabeledNodes) { + wherePropertyChild.getMutator().addValue(node, primitive); + matchingNodes.add(node); + } + break; + case NotEquals: + // if we are checking for inequality, we need to pass all unlabeled (or created + // if none were available) + matchingNodes.addAll(unlabeledNodes); + break; + case And: + case As: + case Concatenate: + case Contains: + case Div: + case DivideBy: + case Equivalent: + case Greater: + case GreaterOrEqual: + case Implies: + case In: + case Is: + case LessOrEqual: + case LessThan: + case MemberOf: + case Minus: + case Mod: + case NotEquivalent: + case Or: + case Plus: + case Times: + case Union: + case Xor: + // TODO: need to implement above first + } + } + + // set the nodes to the filtered ones + this.nodeStack.peek().nodes = matchingNodes; + } + + /** + * Creates a list all FHIRPaths from the mapping ordered by paths with where equals, where + * unequals and the rest. + * + * @return List a List of FHIRPaths ordered by the type. + */ + private List sortedPaths() { + List whereEquals = new ArrayList(); + List whereUnequals = new ArrayList(); + List withoutWhere = new ArrayList(); + + for (String fhirPath : this.pathMapping.keySet()) { + switch (this.getTypeOfFhirPath(fhirPath)) { + case WHERE_EQUALS: + whereEquals.add(fhirPath); + break; + case WHERE_UNEQUALS: + whereUnequals.add(fhirPath); + break; + case WITHOUT_WHERE: + withoutWhere.add(fhirPath); + break; + } + } + + List ret = new ArrayList(); + ret.addAll(whereEquals); + ret.addAll(whereUnequals); + ret.addAll(withoutWhere); + return ret; + } + + /** + * Returns the type of path based on the FHIRPath String. + * + * @param fhirPath String representation of a FHIRPath. + * @return PathType the type of path supplied as `fhirPath`. + */ + private PathType getTypeOfFhirPath(String fhirPath) { + ExpressionNode fhirPathExpression = this.engine.parse(fhirPath); + while (fhirPathExpression != null) { + if (fhirPathExpression.getKind() == ExpressionNode.Kind.Function) { + if (fhirPathExpression.getFunction() == ExpressionNode.Function.Where) { + for (ExpressionNode params : fhirPathExpression.getParameters()) { + switch (params.getOperation()) { + case Equals: + return PathType.WHERE_EQUALS; + case NotEquals: + return PathType.WHERE_UNEQUALS; + case And: + case As: + case Concatenate: + case Contains: + case Div: + case DivideBy: + case Equivalent: + case Greater: + case GreaterOrEqual: + case Implies: + case In: + case Is: + case LessOrEqual: + case LessThan: + case MemberOf: + case Minus: + case Mod: + case NotEquivalent: + case Or: + case Plus: + case Times: + case Union: + case Xor: + // TODO: need to implement above first + } + } + } + } + fhirPathExpression = fhirPathExpression.getInner(); + } + return PathType.WITHOUT_WHERE; + } + + /** + * A simple enum to diffirentiate between types of FHIRPaths in the special use case of generating + * FHIR Resources. + */ + public enum PathType { + WHERE_EQUALS, WHERE_UNEQUALS, WITHOUT_WHERE + } +} diff --git a/src/main/java/org/mitre/synthea/export/flexporter/FhirPathUtils.java b/src/main/java/org/mitre/synthea/export/flexporter/FhirPathUtils.java new file mode 100644 index 0000000000..c112efc1bc --- /dev/null +++ b/src/main/java/org/mitre/synthea/export/flexporter/FhirPathUtils.java @@ -0,0 +1,81 @@ +package org.mitre.synthea.export.flexporter; + +import java.util.ArrayList; +import java.util.List; + +import org.hl7.fhir.r4.hapi.fluentpath.FhirPathR4; +import org.hl7.fhir.r4.model.Base; +import org.hl7.fhir.r4.model.BooleanType; +import org.hl7.fhir.r4.model.Bundle; +import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; +import org.hl7.fhir.r4.model.Resource; +import org.hl7.fhir.r4.model.StringType; + +import ca.uhn.fhir.context.FhirContext; + +public abstract class FhirPathUtils { + public static final FhirContext FHIR_CTX = FhirContext.forR4(); + + private static final FhirPathR4 FHIRPATH = new FhirPathR4(FHIR_CTX); + + public static List evaluateResource(Resource resource, String fhirpath) { + return FHIRPATH.evaluate(resource, fhirpath, Base.class); + } + + public static List evaluateBundle(Bundle bundle, String fhirpath, boolean returnResources) { + if (fhirpath.startsWith("Bundle")) { + // run it on the entire bundle + + // NOTE: this doesn't check returnResources -- would that be useful here? + return evaluateResource(bundle, fhirpath); + } else { + // the fhirpath doesn't start with "Bundle" + // so we'll apply it to each resource within the bundle + List results = new ArrayList<>(); + + for (BundleEntryComponent entry : bundle.getEntry()) { + List resourceResults = evaluateResource(entry.getResource(), fhirpath); + + if (returnResources) { + if (isTruthy(resourceResults)) { + results.add(entry.getResource()); + } + } else { + results.addAll(resourceResults); + } + } + + return results; + } + } + + public static boolean appliesToResource(Resource resource, String fhirpath) { + return isTruthy(evaluateResource(resource, fhirpath)); + } + + public static boolean appliesToBundle(Bundle bundle, String fhirpath) { + return isTruthy(evaluateBundle(bundle, fhirpath, false)); + } + + static boolean isTruthy(Base result) { + if (result == null) { + return false; + } else if (result instanceof StringType) { + StringType str = ((StringType) result); + return !str.isEmpty() && !str.getValue().isEmpty(); + } else if (result instanceof BooleanType) { + BooleanType bool = ((BooleanType) result); + return !bool.isEmpty() && bool.booleanValue(); + } + + return true; + } + + static boolean isTruthy(List result) { + if (result == null || result.isEmpty()) { + return false; + } + + return result.stream().anyMatch(i -> isTruthy(i)); + } +} diff --git a/src/main/java/org/mitre/synthea/export/flexporter/Mapping.java b/src/main/java/org/mitre/synthea/export/flexporter/Mapping.java new file mode 100644 index 0000000000..490165d66e --- /dev/null +++ b/src/main/java/org/mitre/synthea/export/flexporter/Mapping.java @@ -0,0 +1,28 @@ +package org.mitre.synthea.export.flexporter; + +import java.io.File; +import java.io.FileInputStream; +import java.io.FileNotFoundException; +import java.io.InputStream; +import java.util.List; +import java.util.Map; + +import org.yaml.snakeyaml.Yaml; + +public class Mapping { + public String name; + public String applicability; + + /** + * Each action is a Map. Nested fields within the YAML become ArrayLists and + * LinkedHashMaps. + */ + public List> actions; + + public static Mapping parseMapping(File mappingFile) throws FileNotFoundException { + InputStream selectorInputSteam = new FileInputStream(mappingFile); + Yaml yaml = new Yaml(new org.yaml.snakeyaml.constructor.Constructor(Mapping.class)); + + return yaml.loadAs(selectorInputSteam, Mapping.class); + } +} diff --git a/src/main/java/org/mitre/synthea/export/flexporter/ValueTransforms.java b/src/main/java/org/mitre/synthea/export/flexporter/ValueTransforms.java new file mode 100644 index 0000000000..1156238af9 --- /dev/null +++ b/src/main/java/org/mitre/synthea/export/flexporter/ValueTransforms.java @@ -0,0 +1,110 @@ +package org.mitre.synthea.export.flexporter; + +import java.time.LocalDate; +import java.time.LocalDateTime; +import java.time.ZoneId; +import java.time.ZonedDateTime; +import java.time.format.DateTimeFormatter; + +public abstract class ValueTransforms { + + public static String apply(String originalValue, String transformName) { + if (transformName == null) { + return originalValue; + } + + String newValue; + + switch (transformName) { + case "toInstant": + newValue = toInstant(originalValue); + break; + + case "toDateTime": + newValue = toDateTime(originalValue); + break; + + case "toDate": + newValue = toDate(originalValue); + break; + + case "toTime": + newValue = toTime(originalValue); + break; + + default: + throw new IllegalArgumentException("Unrecognized transform name: " + transformName); + } + + return newValue; + } + + + public static String toInstant(String src) { + if (src == null) { + return null; + } + + ZonedDateTime dateTime = parse(src); + + return dateTime.toInstant().toString(); + } + + public static String toDateTime(String src) { + ZonedDateTime dateTime = parse(src); + + return dateTime.toInstant().toString(); + } + + public static String toDate(String src) { + if (src == null) { + return null; + } + + ZonedDateTime dateTime = parse(src); + + return DateTimeFormatter.ISO_LOCAL_DATE.format(dateTime); + } + + public static String toTime(String src) { + if (src == null) + return null; + ZonedDateTime dateTime = parse(src); + + return DateTimeFormatter.ISO_LOCAL_TIME.format(dateTime); + } + + private static DateTimeFormatter YEAR = DateTimeFormatter.ofPattern("yyyy"); + + private static DateTimeFormatter YEAR_MONTH = DateTimeFormatter.ofPattern("yyyy-MM"); + + private static ZonedDateTime parse(String src) { + // assume src is one of the four formats already + + // instant: YYYY-MM-DDThh:mm:ss.sss+zz:zz + // date: YYYY, YYYY-MM, or YYYY-MM-DD + // dateTime: YYYY, YYYY-MM, YYYY-MM-DD or YYYY-MM-DDThh:mm:ss+zz:zz + // time: hh:mm:ss + + switch (src.length()) { + case 4: + // YYYY + return LocalDate.parse(src, YEAR).atStartOfDay(ZoneId.systemDefault()); + case 7: + // YYYY-MM + return LocalDate.parse(src, YEAR_MONTH).atStartOfDay(ZoneId.systemDefault()); + case 8: + // hh:mm:ss + return LocalDateTime.parse(src, DateTimeFormatter.ISO_LOCAL_TIME) + .atZone(ZoneId.systemDefault()); + case 10: + // YYYY-MM-DD + return LocalDate.parse(src, DateTimeFormatter.ISO_LOCAL_DATE) + .atStartOfDay(ZoneId.systemDefault()); + default: + // TODO: make sure this actually works -- the docs are weird + return ZonedDateTime.parse(src, DateTimeFormatter.ISO_ZONED_DATE_TIME); + } + } + +} diff --git a/src/test/java/org/mitre/synthea/export/flexporter/ActionsTest.java b/src/test/java/org/mitre/synthea/export/flexporter/ActionsTest.java new file mode 100644 index 0000000000..da7c4b255a --- /dev/null +++ b/src/test/java/org/mitre/synthea/export/flexporter/ActionsTest.java @@ -0,0 +1,340 @@ +package org.mitre.synthea.export.flexporter; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertTrue; + +import ca.uhn.fhir.parser.IParser; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.nio.file.Files; +import java.util.Arrays; +import java.util.HashMap; +import java.util.HashSet; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.stream.Collectors; + +import org.hl7.fhir.r4.model.BooleanType; +import org.hl7.fhir.r4.model.Bundle; +import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; +import org.hl7.fhir.r4.model.Bundle.BundleType; +import org.hl7.fhir.r4.model.DateTimeType; +import org.hl7.fhir.r4.model.DateType; +import org.hl7.fhir.r4.model.HumanName; +import org.hl7.fhir.r4.model.Immunization; +import org.hl7.fhir.r4.model.InstantType; +import org.hl7.fhir.r4.model.Observation; +import org.hl7.fhir.r4.model.Patient; +import org.hl7.fhir.r4.model.Resource; +import org.hl7.fhir.r4.model.ResourceType; +import org.hl7.fhir.r4.model.ServiceRequest; +import org.hl7.fhir.r4.model.Type; +import org.junit.AfterClass; +import org.junit.BeforeClass; +import org.junit.Test; +import org.mitre.synthea.world.agents.Person; + +public class ActionsTest { + + private static Map buildApplyProfileAction(String profile, String applicability) { + Map map = new HashMap<>(); + map.put("profile", profile); + map.put("applicability", applicability); + return map; + } + + private static Mapping testMapping; + + @BeforeClass + public static void setupClass() throws FileNotFoundException { + ClassLoader classLoader = ActionsTest.class.getClassLoader(); + File file = new File(classLoader.getResource("flexporter/test_mapping.yaml").getFile()); + + testMapping = Mapping.parseMapping(file); + } + + @AfterClass + public static void tearDown() { + testMapping = null; + } + + private static Map getActionByName(String name) { + return testMapping.actions.stream().filter(a -> a.get("name").equals(name)).findFirst().get(); + } + + private static Bundle loadFixtureBundle(String filename) throws IOException { + IParser parser = FhirPathUtils.FHIR_CTX.newJsonParser().setPrettyPrint(true); + ClassLoader classLoader = ActionsTest.class.getClassLoader(); + File file = new File(classLoader.getResource("flexporter/" + filename).getFile()); + + String fhirJson = new String(Files.readAllBytes(file.toPath())); + return parser.parseResource(Bundle.class, fhirJson); + } + + + + @Test + public void testApplyProfiles() { + Patient p = new Patient(); + p.addName().addGiven("Bobby").setFamily("Brown"); + + Bundle b = new Bundle(); + b.addEntry().setResource(p); + + List> actions = + Arrays.asList(buildApplyProfileAction("http://example.com/Patient", "Patient"), + buildApplyProfileAction("http://example.com/Observation", "Observation")); + + Actions.applyProfiles(b, actions); + + assertNotNull(p.getMeta()); + assertNotNull(p.getMeta().getProfile()); + assertEquals(1, p.getMeta().getProfile().size()); + assertEquals("http://example.com/Patient", p.getMeta().getProfile().get(0).getValueAsString()); + } + + + @Test + public void testApplyProfilesNoMatch() { + Patient p = new Patient(); + p.addName().addGiven("Willie").setFamily("White"); + + Bundle b = new Bundle(); + b.addEntry().setResource(p); + + List> actions = + Arrays.asList(buildApplyProfileAction("http://example.com/Observation", "Observation")); + + Actions.applyProfiles(b, actions); + + assertTrue(p.getMeta() == null || p.getMeta().getProfile() == null + || p.getMeta().getProfile().size() == 0); + } + + + @Test + public void testApplyProfilesComplexFhirPath() { + Patient p = new Patient(); + p.addName().addGiven("Barry").setFamily("Black"); + p.setDeceased(new BooleanType(true)); + + Bundle b = new Bundle(); + b.addEntry().setResource(p); + + List> actions = + Arrays.asList(buildApplyProfileAction("http://example.com/Patient", "Patient"), + buildApplyProfileAction("http://example.com/DeceasedPatient", + "(Patient.deceased as boolean) = true")); + + Actions.applyProfiles(b, actions); + + assertNotNull(p.getMeta()); + assertNotNull(p.getMeta().getProfile()); + assertEquals(2, p.getMeta().getProfile().size()); + assertEquals("http://example.com/Patient", p.getMeta().getProfile().get(0).getValueAsString()); + assertEquals("http://example.com/DeceasedPatient", + p.getMeta().getProfile().get(1).getValueAsString()); + } + + + @Test + public void testSetValues() { + Patient p = new Patient(); + p.addName().addGiven("Gary").setFamily("Green"); + + Bundle b = new Bundle(); + b.addEntry().setResource(p); + + Map action = getActionByName("testSetValues"); + + Actions.applyAction(b, action, null); + + assertEquals("1987-06-05", p.getBirthDateElement().getValueAsString()); + } + + + @Test + public void testSetValues_getField() { + Immunization i = new Immunization(); + + DateTimeType date = new DateTimeType(); + date.fromStringValue("2022-02-22"); + i.setOccurrence(date); + + Bundle b = new Bundle(); + b.addEntry().setResource(i); + + Map action = getActionByName("testSetValues_getField"); + + Actions.applyAction(b, action, null); + + assertEquals("2022-02-22", i.getRecordedElement().getValueAsString()); + } + + @Test + public void testSetValues_overwrite() { + Observation o = new Observation(); + + DateTimeType date = new DateTimeType(); + date.fromStringValue("2009-10-26T06:44:52-04:00"); + o.setEffective(date); + + Bundle b = new Bundle(); + b.addEntry().setResource(o); + + Map action = getActionByName("testSetValues_overwrite"); + + Actions.applyAction(b, action, null); + + Type effective = o.getEffective(); + + assertTrue(effective instanceof InstantType); + + InstantType effectiveInstant = (InstantType) effective; + + assertEquals("2009-10-26T06:44:52-04:00", effectiveInstant.getValueAsString()); + } + + @Test + public void testSetValues_transform() { + Patient p = new Patient(); + p.addName().addGiven("Cristina").setFamily("Crimson"); + DateType date = new DateType(); + date.fromStringValue("1999-09-29"); + p.setBirthDateElement(date); + + Bundle b = new Bundle(); + b.addEntry().setResource(p); + + Map action = getActionByName("testSetValues_transform"); + + Actions.applyAction(b, action, null); + + // NOTE: this expected value may change if we ever add randomness to the date -> dateTime + // transform + assertEquals("1999-09-29T04:00:00Z", + ((DateTimeType) date.getExtension().get(0).getValue()).getValueAsString()); + } + + @Test + public void testKeepResources() throws Exception { + Bundle b = loadFixtureBundle("sample_complete_patient.json"); + + + Map action = getActionByName("testKeepResources"); + + Actions.applyAction(b, action, null); + + Set expectedResourceTypes = + new HashSet<>(Arrays.asList("Patient", "Encounter", "Condition")); + + for (BundleEntryComponent bec : b.getEntry()) { + Resource resource = bec.getResource(); + String resourceType = resource.getResourceType().toString(); + assertTrue(resourceType, expectedResourceTypes.contains(resourceType)); + } + } + + @Test + public void testDeleteResources() throws Exception { + Bundle b = loadFixtureBundle("sample_complete_patient.json"); + + long countProvenance = b.getEntry().stream() + .filter(bec -> bec.getResource().getResourceType() == ResourceType.Provenance).count(); + + // this is just making sure the fixture actually contains the thing we want to delete + assertEquals(1, countProvenance); + Map action = getActionByName("testDeleteResources"); + + Actions.applyAction(b, action, null); + + countProvenance = b.getEntry().stream() + .filter(bec -> bec.getResource().getResourceType() == ResourceType.Provenance).count(); + + assertEquals(0, countProvenance); + + } + + @Test + public void testCreateResources_createSingle() throws Exception { + Bundle b = loadFixtureBundle("sample_complete_patient.json"); + + long countSR = b.getEntry().stream() + .filter(bec -> bec.getResource().getResourceType() == ResourceType.ServiceRequest).count(); + assertEquals(0, countSR); + + + Map action = getActionByName("testCreateResources_createSingle"); + + Actions.applyAction(b, action, null); + + List serviceRequests = b.getEntry().stream() + .filter(bec -> bec.getResource().getResourceType() == ResourceType.ServiceRequest) + .map(bec -> bec.getResource()).collect(Collectors.toList()); + + assertEquals(1, serviceRequests.size()); + + ServiceRequest createdSR = (ServiceRequest) serviceRequests.get(0); + + assertEquals("http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-servicerequest", + createdSR.getMeta().getProfile().get(0).getValue()); + + assertEquals("active", createdSR.getStatus().toCode()); + + Patient p = (Patient) b.getEntryFirstRep().getResource(); + assertEquals(p.getId(), createdSR.getSubject().getReference()); + } + + @Test + public void testCreateResources_createBasedOn() throws Exception { + Bundle b = loadFixtureBundle("sample_complete_patient.json"); + + long countSR = b.getEntry().stream() + .filter(bec -> bec.getResource().getResourceType() == ResourceType.ServiceRequest).count(); + assertEquals(0, countSR); + + long countProc = b.getEntry().stream() + .filter(bec -> bec.getResource().getResourceType() == ResourceType.Procedure).count(); + assertTrue(countProc > 0); + + Map action = getActionByName("testCreateResources_createBasedOn"); + + Actions.applyAction(b, action, null); + + // there should now be one ServiceRequest per Procedure + countSR = b.getEntry().stream() + .filter(bec -> bec.getResource().getResourceType() == ResourceType.ServiceRequest).count(); + assertEquals(countProc, countSR); + + // TODO: fill out the rest of this test, check the "writeback" + + } + + @Test + public void testGetAttribute() throws Exception { + Bundle b = new Bundle(); + b.setType(BundleType.COLLECTION); + Person p = new Person(0L); + + String firstName = "Robert"; + String lastName = "Rainbow"; + p.attributes.put(Person.FIRST_NAME, firstName); + p.attributes.put(Person.LAST_NAME, lastName); + p.attributes.put(Person.NAME, firstName + " " + lastName); + Map action = getActionByName("testCreateResources_getAttribute"); + + Actions.applyAction(b, action, p); + + Patient patient = (Patient) b.getEntryFirstRep().getResource(); + HumanName name = patient.getNameFirstRep(); + + assertEquals("Robert", name.getGivenAsSingleString()); + assertEquals("Rainbow", name.getFamily()); + assertEquals("Robert Rainbow", name.getText()); + } + +} diff --git a/src/test/java/org/mitre/synthea/export/flexporter/CustomFHIRPathResourceGeneratorR4Test.java b/src/test/java/org/mitre/synthea/export/flexporter/CustomFHIRPathResourceGeneratorR4Test.java new file mode 100644 index 0000000000..0638985935 --- /dev/null +++ b/src/test/java/org/mitre/synthea/export/flexporter/CustomFHIRPathResourceGeneratorR4Test.java @@ -0,0 +1,188 @@ +package org.mitre.synthea.export.flexporter; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; + +import ca.uhn.fhir.context.FhirContext; + +import java.util.Date; +import java.util.HashMap; +import java.util.List; +import java.util.Map; + +import org.hl7.fhir.r4.model.Address; +import org.hl7.fhir.r4.model.DateType; +import org.hl7.fhir.r4.model.Extension; +import org.hl7.fhir.r4.model.HumanName; +import org.hl7.fhir.r4.model.HumanName.NameUse; +import org.hl7.fhir.r4.model.Patient; +import org.hl7.fhir.r4.model.StringType; +import org.junit.Ignore; +import org.junit.Test; + + +public class CustomFHIRPathResourceGeneratorR4Test { + + // share a context because these are slow to create + private static final FhirContext CTX = FhirContext.forR4(); + + private static void logPatientJson(Patient p) { + String patientJson = CTX.newJsonParser().setPrettyPrint(true).encodeResourceToString(p); + + System.out.println(patientJson); + } + + private Patient createPatient(Map fhirPathMapping) { + CustomFHIRPathResourceGeneratorR4 fhirPathGenerator = + new CustomFHIRPathResourceGeneratorR4<>(CTX); + fhirPathGenerator.setMapping(fhirPathMapping); + return fhirPathGenerator.generateResource(Patient.class); + } + + private void updatePatient(Patient p, Map fhirPathMapping) { + CustomFHIRPathResourceGeneratorR4 fhirPathGenerator = + new CustomFHIRPathResourceGeneratorR4<>(CTX); + fhirPathGenerator.setResource(p); + fhirPathGenerator.setMapping(fhirPathMapping); + fhirPathGenerator.generateResource(Patient.class); + } + + @Test + public void testSimpleField() { + Map fhirPathMapping = new HashMap<>(); + fhirPathMapping.put("Patient.deceasedBoolean", "false"); + Patient patient = createPatient(fhirPathMapping); + + assertFalse(patient.getDeceasedBooleanType().booleanValue()); + } + + @Test + public void testArray1() { + Map fhirPathMapping = new HashMap<>(); + + fhirPathMapping.put("Patient.name.given[0]", "Billy"); + fhirPathMapping.put("Patient.name.given[1]", "Bob"); + + Patient patient = createPatient(fhirPathMapping); + + List given = patient.getNameFirstRep().getGiven(); + + assertEquals(2, given.size()); + assertEquals("Billy", given.get(0).getValueAsString()); + assertEquals("Bob", given.get(1).getValueAsString()); + } + + + @Ignore + @Test + public void testArray2() { + Map fhirPathMapping = new HashMap<>(); + + fhirPathMapping.put("Patient.name[0].given", "Billy"); + fhirPathMapping.put("Patient.name[1].given", "Bob"); + + // TODO: for some reason Patient.name.given[0] and given[1] work as expected (2 name strings in + // the 'given' array) + // but Patient.name[0].given and .name[1].given do not (same result, expected was 2 HumanName + // objects in the name array) + + Patient patient = createPatient(fhirPathMapping); + + List name = patient.getName(); + assertEquals(2, name.size()); + + assertEquals("Billy", name.get(0).getGivenAsSingleString()); + assertEquals("Bob", name.get(1).getGivenAsSingleString()); + } + + @Test + public void testArray3() { + Map fhirPathMapping = new HashMap<>(); + + fhirPathMapping.put("Patient.name.where(use='official').given", "Billy"); + fhirPathMapping.put("Patient.name.where(use='usual').given", "Bob"); + + Patient patient = createPatient(fhirPathMapping); + List name = patient.getName(); + assertEquals(2, name.size()); + + // we don't necessarily know which order these will be in + HumanName first = name.get(0); + HumanName second = name.get(1); + + HumanName official; + HumanName usual; + + if (first.getUse() == NameUse.OFFICIAL) { + official = first; + usual = second; + } else { + usual = first; + official = second; + } + + assertEquals("Billy", official.getGivenAsSingleString()); + assertEquals("Bob", usual.getGivenAsSingleString()); + } + + @Test + public void testExtension() { + Map fhirPathMapping = new HashMap<>(); + fhirPathMapping.put( + "Patient.extension.where(url='http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName').valueString", + "Donita707 Langosh790"); + + fhirPathMapping.put( + "Patient.extension.where(url='http://hl7.org/fhir/StructureDefinition/patient-birthPlace').valueAddress.city", + "Watertown"); + fhirPathMapping.put( + "Patient.extension.where(url='http://hl7.org/fhir/StructureDefinition/patient-birthPlace').valueAddress.state", + "Massachusetts"); + fhirPathMapping.put( + "Patient.extension.where(url='http://hl7.org/fhir/StructureDefinition/patient-birthPlace').valueAddress.country", + "US"); + + Patient patient = createPatient(fhirPathMapping); + + assertEquals(2, patient.getExtension().size()); + + Extension mothersMaidenName = patient + .getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName"); + assertEquals("Donita707 Langosh790", + mothersMaidenName.getValueAsPrimitive().getValueAsString()); + + + Extension birthPlace = + patient.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/patient-birthPlace"); + + Address address = (Address) birthPlace.getValue(); + + assertEquals("Watertown", address.getCity()); + assertEquals("Massachusetts", address.getState()); + assertEquals("US", address.getCountry()); + } + + @Test + public void testExtensionOnPrimitive() { + Map fhirPathMapping = new HashMap<>(); + + // fhirPathMapping.put("Patient.birthDate", "2021-12-15"); + fhirPathMapping.put( + "Patient.birthDate.extension.where(url='http://hl7.org/fhir/StructureDefinition/patient-birthTime').valueDateTime", + "2021-12-15T17:57:28-05:00"); + + Patient patient = new Patient(); + patient.setBirthDate(new Date(123456789L)); // translates into 1970-01-02 + + updatePatient(patient, fhirPathMapping); + + assertEquals(0, patient.getExtension().size()); + + DateType birthdate = patient.getBirthDateElement(); + assertEquals("1970-01-02", birthdate.getValueAsString()); + + Extension birthTime = + birthdate.getExtensionByUrl("http://hl7.org/fhir/StructureDefinition/patient-birthTime"); + assertEquals("2021-12-15T17:57:28-05:00", birthTime.getValueAsPrimitive().getValueAsString()); + } +} diff --git a/src/test/java/org/mitre/synthea/export/flexporter/FhirPathUtilsTest.java b/src/test/java/org/mitre/synthea/export/flexporter/FhirPathUtilsTest.java new file mode 100644 index 0000000000..c6eefb0d19 --- /dev/null +++ b/src/test/java/org/mitre/synthea/export/flexporter/FhirPathUtilsTest.java @@ -0,0 +1,103 @@ +package org.mitre.synthea.export.flexporter; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertTrue; + +import java.util.List; + +import org.hl7.fhir.r4.model.Base; +import org.hl7.fhir.r4.model.BooleanType; +import org.hl7.fhir.r4.model.Bundle; +import org.hl7.fhir.r4.model.Patient; +import org.hl7.fhir.r4.model.StringType; +import org.junit.Test; + + +public class FhirPathUtilsTest { + + @Test + public void testEvaluateResource() { + Patient p = new Patient(); + p.addName().addGiven("John").setFamily("Smith"); + + List result = FhirPathUtils.evaluateResource(p, "Patient.name.given"); + assertEquals(1, result.size()); + assertTrue(result.get(0) instanceof StringType); + assertEquals("John", ((StringType) result.get(0)).getValue()); + + result = FhirPathUtils.evaluateResource(p, "Patient.name.suffix"); + assertEquals(0, result.size()); + } + + @Test + public void testEvaluateBundle() { + Patient p = new Patient(); + p.addName().addGiven("Jessica").setFamily("Jones"); + + Bundle b = new Bundle(); + b.addEntry().setResource(p); + + List result = FhirPathUtils.evaluateBundle(b, "Patient.name.given", false); + assertEquals(1, result.size()); + assertTrue(result.get(0) instanceof StringType); + assertEquals("Jessica", ((StringType) result.get(0)).getValue()); + + // now do the same thing with returnResource = true, + // so we expect the resource that this was true for + result = FhirPathUtils.evaluateBundle(b, "Patient.name.given", true); + assertEquals(1, result.size()); + assertEquals(p, result.get(0)); + + // now try some bundle-specific fhirpath + result = FhirPathUtils.evaluateBundle(b, + "Bundle.entry.resource.ofType(Patient).first().name.given = 'Jessica'", false); + assertEquals(1, result.size()); + assertTrue(result.get(0) instanceof BooleanType); + assertTrue(((BooleanType) result.get(0)).booleanValue()); + + result = FhirPathUtils.evaluateBundle(b, + "Bundle.entry.resource.ofType(Patient).first().name.given = 'Julianna'", false); + assertEquals(1, result.size()); + assertTrue(result.get(0) instanceof BooleanType); + assertFalse(((BooleanType) result.get(0)).booleanValue()); + } + + @Test + public void testAppliesToResource() { + Patient p = new Patient(); + p.addName().addGiven("Jane").setFamily("Shepard"); + + assertTrue(FhirPathUtils.appliesToResource(p, "Patient.name.given")); + assertTrue(FhirPathUtils.appliesToResource(p, "Patient.name.given = 'Jane'")); + assertFalse(FhirPathUtils.appliesToResource(p, "Patient.name.given = 'John'")); + assertFalse(FhirPathUtils.appliesToResource(p, "Patient.name.suffix")); + } + + @Test + public void testAppliesToBundle() { + Patient p = new Patient(); + p.addName().addGiven("Jack").setFamily("Black"); + + Bundle b = new Bundle(); + b.addEntry().setResource(p); + + // fhirpath not starting with "Bundle" implies + // "is there any resource in the bundle that this applies to" + assertTrue(FhirPathUtils.appliesToBundle(b, "Patient.name.given")); + assertTrue(FhirPathUtils.appliesToBundle(b, "Patient.name.given = 'Jack'")); + assertFalse(FhirPathUtils.appliesToBundle(b, "Patient.name.given = 'Jerametrius'")); + assertFalse(FhirPathUtils.appliesToBundle(b, "Patient.name.suffix")); + + // fhirpath starting with "Bundle" implies + // "is this truthy in the context of the bundle resource itself" + assertTrue(FhirPathUtils.appliesToBundle(b, + "Bundle.entry.resource.ofType(Patient).first().name.given")); + assertTrue(FhirPathUtils.appliesToBundle(b, + "Bundle.entry.resource.ofType(Patient).first().name.given = 'Jack'")); + assertFalse(FhirPathUtils.appliesToBundle(b, + "Bundle.entry.resource.ofType(Patient).first().name.given = 'Jerametrius'")); + assertFalse( + FhirPathUtils.appliesToBundle(b, "Bundle.entry.resource.ofType(Patient).name.suffix")); + } +} diff --git a/src/test/resources/flexporter/sample_complete_patient.json b/src/test/resources/flexporter/sample_complete_patient.json new file mode 100644 index 0000000000..b17bc0a071 --- /dev/null +++ b/src/test/resources/flexporter/sample_complete_patient.json @@ -0,0 +1,24158 @@ +{ + "resourceType": "Bundle", + "type": "transaction", + "entry": [ { + "fullUrl": "urn:uuid:d5582579-7193-4866-5560-a01e723b6552", + "resource": { + "resourceType": "Patient", + "id": "d5582579-7193-4866-5560-a01e723b6552", + "meta": { + "profile": [ "http://hl7.org/fhir/us/core/StructureDefinition/us-core-patient", "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-patient" ] + }, + "text": { + "status": "generated", + "div": "
Generated by Synthea.Version identifier: master-branch-latest-108-g7542338a\n . Person seed: 3457288435413077439 Population seed: 1625926618830
" + }, + "extension": [ { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race", + "extension": [ { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2106-3", + "display": "White" + } + }, { + "url": "text", + "valueString": "White" + } ] + }, { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity", + "extension": [ { + "url": "ombCategory", + "valueCoding": { + "system": "urn:oid:2.16.840.1.113883.6.238", + "code": "2186-5", + "display": "Non Hispanic or Latino" + } + }, { + "url": "text", + "valueString": "Non Hispanic or Latino" + } ] + }, { + "url": "http://hl7.org/fhir/StructureDefinition/patient-mothersMaidenName", + "valueString": "Kittie678 Doyle959" + }, { + "url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-birthsex", + "valueCode": "M" + }, { + "url": "http://hl7.org/fhir/StructureDefinition/patient-birthPlace", + "valueAddress": { + "city": "Wayland", + "state": "Massachusetts", + "country": "US" + } + }, { + "url": "http://synthetichealth.github.io/synthea/disability-adjusted-life-years", + "valueDecimal": 2.0028929627142285 + }, { + "url": "http://synthetichealth.github.io/synthea/quality-adjusted-life-years", + "valueDecimal": 67.99710703728577 + } ], + "identifier": [ { + "system": "https://github.com/synthetichealth/synthea", + "value": "d5582579-7193-4866-5560-a01e723b6552" + }, { + "type": { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "MR", + "display": "Medical Record Number" + } ], + "text": "Medical Record Number" + }, + "system": "http://hospital.smarthealthit.org", + "value": "d5582579-7193-4866-5560-a01e723b6552" + }, { + "type": { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "SS", + "display": "Social Security Number" + } ], + "text": "Social Security Number" + }, + "system": "http://hl7.org/fhir/sid/us-ssn", + "value": "999-34-2070" + }, { + 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Care Plan for Infectious disease care plan (record artifact).
Activities:
  • Infectious disease care plan (record artifact)
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Care plan is meant to treat Suspected COVID-19.
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"2021-07-13T12:44:52.558-04:00", + "agent": [ { + "type": { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/provenance-participant-type", + "code": "author", + "display": "Author" + } ], + "text": "Author" + }, + "who": { + "reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999999559", + "display": "Dr. Leigh689 Rutherford999" + }, + "onBehalfOf": { + "reference": "Organization?identifier=https://github.com/synthetichealth/synthea|dd406540-fa97-3a90-858e-0a0ea61cf07b", + "display": "PCP74147" + } + }, { + "type": { + "coding": [ { + "system": "http://hl7.org/fhir/us/core/CodeSystem/us-core-provenance-participant-type", + "code": "transmitter", + "display": "Transmitter" + } ], + "text": "Transmitter" + }, + "who": { + "reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999999559", + "display": "Dr. Leigh689 Rutherford999" + }, + "onBehalfOf": { + "reference": "Organization?identifier=https://github.com/synthetichealth/synthea|dd406540-fa97-3a90-858e-0a0ea61cf07b", + "display": "PCP74147" + } + } ] + }, + "request": { + "method": "POST", + "url": "Provenance" + } + } ] +} \ No newline at end of file diff --git a/src/test/resources/flexporter/test_mapping.yaml b/src/test/resources/flexporter/test_mapping.yaml new file mode 100644 index 0000000000..d04374ad5f --- /dev/null +++ b/src/test/resources/flexporter/test_mapping.yaml @@ -0,0 +1,135 @@ +--- +# name is just a friendly name for this mapping +name: Random Testing + +# applicability determines whether this mapping applies to a given file. +# for now the assumption is 1 file = 1 synthea patient bundle. +applicability: true + +actions: + - name: Apply Profiles + # v1: define specific profiles and an applicability statement on when to apply them + # v1.1: allow specifying a field from the profile to key off of (ex. mCode TNMPrimaryTumorCategory.code) + # maybe v2 will automatically infer? + # some of the challenges to keep in mind: + # - what if the resource doesn't conform to the profile yet? + # we should make sure we can take other actions before applying profiles, + # or manually specify where to apply profiles so that we can apply other fixes based on profile later. + profiles: + - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-patient + applicability: Patient + - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-encounter + applicability: Encounter + # - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-condition + # applicability: Condition + # - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-observation + # applicability: Observation + # - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-procedure + # applicability: Procedure + # - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medicationrequest + # applicability: MedicationRequest + # - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-immunization + # applicability: Immunization + # - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-careplan + # applicability: CarePlan + # - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-imagingstudy + # applicability: ImagingStudy + # - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-device + # applicability: Device + # - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-practitioner + # applicability: Practitioner + # - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-allergyintolerance + # applicability: AllergyIntolerance + # - profile: http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-claim + # applicability: Claim + + + - name: testSetValues + set_values: + - applicability: Patient + fields: + - location: Patient.birthDate + value: !!str "1987-06-05" + + + - name: testSetValues_getField + set_values: + - applicability: Immunization + fields: + - location: Immunization.recorded + value: $getField([Immunization.occurrence]) + # TODO: occurrence is a choice type, + # it would be nice to put "occurrenceDateTime" here + # since that's what's actually in the JSON + # but that doesn't seem to work with HAPI's FhirPath + + - name: testSetValues_overwrite + set_values: + - applicability: Observation + fields: + - location: Observation.effectiveInstant + value: $getField([Observation.effective]) + # - location: Observation.referenceRange.text + # value: sample reference range text + # - location: Observation.valueString + # value: string value here + # - location: Observation.derivedFrom.reference + # value: $findRef([Observation]) + + - name: testSetValues_transform + set_values: + - applicability: Patient + fields: + - location: Patient.birthDate.extension.where(url='http://hl7.org/fhir/StructureDefinition/patient-birthTime').valueDateTime + value: $getField([Patient.birthDate]) + transform: toDateTime + + - name: testCreateResources_createSingle + create_resource: + - resourceType: ServiceRequest + profiles: + - http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-servicerequest + fields: + - location: ServiceRequest.status + value: active + - location: ServiceRequest.subject.reference + value: $findRef([Patient]) + + + - name: testCreateResources_createBasedOn + create_resource: + - resourceType: ServiceRequest + based_on: Procedure + fields: + - location: ServiceRequest.intent + value: plan + - location: ServiceRequest.encounter.reference + value: $getField([Procedure.encounter.reference]) + # TODO: is "writeback" the best term here? + writeback: + - location: Procedure.basedOn.reference + value: $setRef([ServiceRequest]) + + - name: testCreateResources_getAttribute + create_resource: + - resourceType: Patient + fields: + - location: Patient.name.text + value: $getAttribute([name]) + - location: Patient.name.given + value: $getAttribute([first_name]) + - location: Patient.name.family + value: $getAttribute([last_name]) + + + +# TODO: on keep/delete, check for references to removed items!! + - name: testKeepResources + keep_resources: + - Patient + - Encounter + - Condition + + - name: testDeleteResources + delete_resources: + - Provenance