diff --git a/build.gradle b/build.gradle index 4829d1f8e8..e3ecf53a74 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' @@ -66,11 +71,14 @@ dependencies { implementation 'guru.nidi:graphviz-java:0.18.1' // JavaScript engine included for graphviz. It gets used // if someone does not have graphviz installed in their environment - implementation 'org.graalvm.js:js:22.2.0' + implementation 'org.graalvm.js:js:22.3.3' + implementation 'org.graalvm.js:js-scriptengine:22.3.3' + implementation 'org.graalvm.sdk:graal-sdk:22.3.3' + // CSV Stuff implementation 'org.apache.commons:commons-csv:1.9.0' implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-csv:2.13.4' - implementation 'org.yaml:snakeyaml:1.32' + implementation 'org.yaml:snakeyaml:1.33' implementation 'org.apache.commons:commons-math3:3.6.1' implementation 'org.apache.commons:commons-text:1.9' implementation 'commons-validator:commons-validator:1.7' @@ -125,10 +133,6 @@ 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' @@ -180,6 +184,7 @@ 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' @@ -231,6 +236,19 @@ 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/App.java b/src/main/java/App.java index 1d7475bc15..e790479a45 100644 --- a/src/main/java/App.java +++ b/src/main/java/App.java @@ -9,6 +9,8 @@ import org.mitre.synthea.engine.Generator; import org.mitre.synthea.engine.Module; +import org.mitre.synthea.export.Exporter; +import org.mitre.synthea.export.flexporter.Mapping; import org.mitre.synthea.helpers.Config; import org.mitre.synthea.helpers.Utilities; @@ -56,6 +58,7 @@ public static void usage() { */ public static void main(String[] args) throws Exception { Generator.GeneratorOptions options = new Generator.GeneratorOptions(); + Exporter.ExporterRuntimeOptions exportOptions = new Exporter.ExporterRuntimeOptions(); boolean validArgs = true; boolean overrideFutureDateError = false; @@ -199,6 +202,25 @@ public static void main(String[] args) throws Exception { throw new FileNotFoundException(String.format( "Specified keep-patients file (%s) does not exist", value)); } + } else if (currArg.equals("-fm")) { + String value = argsQ.poll(); + File flexporterMappingFile = new File(value); + if (flexporterMappingFile.exists()) { + Mapping mapping = Mapping.parseMapping(flexporterMappingFile); + exportOptions.addFlexporterMapping(mapping); + } else { + throw new FileNotFoundException(String.format( + "Specified flexporter mapping file (%s) does not exist", value)); + } + } else if (currArg.equals("-ig")) { + String value = argsQ.poll(); + File igFile = new File(value); + if (igFile.exists()) { + RunFlexporter.loadIG(igFile); + } else { + throw new FileNotFoundException(String.format( + "Specified IG directory (%s) does not exist", value)); + } } else if (currArg.startsWith("--")) { String configSetting; String value; @@ -230,7 +252,7 @@ public static void main(String[] args) throws Exception { } if (validArgs && validateConfig(options, overrideFutureDateError)) { - Generator generator = new Generator(options); + Generator generator = new Generator(options, exportOptions); generator.run(); } } diff --git a/src/main/java/RunFlexporter.java b/src/main/java/RunFlexporter.java new file mode 100644 index 0000000000..a7918e2dbb --- /dev/null +++ b/src/main/java/RunFlexporter.java @@ -0,0 +1,222 @@ +import ca.uhn.fhir.parser.DataFormatException; +import ca.uhn.fhir.parser.IParser; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; + +import java.io.File; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.nio.charset.Charset; +import java.nio.file.DirectoryStream; +import java.nio.file.Files; +import java.nio.file.Path; +import java.nio.file.StandardOpenOption; +import java.util.ArrayDeque; +import java.util.Arrays; +import java.util.Map; +import java.util.Queue; + +import org.apache.commons.io.FilenameUtils; +import org.hl7.fhir.instance.model.api.IBaseResource; +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.ValueSet; +import org.mitre.synthea.export.FhirR4; +import org.mitre.synthea.export.flexporter.Actions; +import org.mitre.synthea.export.flexporter.FhirPathUtils; +import org.mitre.synthea.export.flexporter.FlexporterJavascriptContext; +import org.mitre.synthea.export.flexporter.Mapping; +import org.mitre.synthea.helpers.RandomCodeGenerator; + +/** + * Entrypoint for the "Flexporter" when run as a standalone gradle task. + * The Flexporter is primarily expected to be used to apply transformations + * to newly generated Synthea patients, but can also be run against existing FHIR bundles. + * These bundles are assumed to have been generated by Synthea, but depending on the mapping, + * they don't necessarily have to be. + */ +public class RunFlexporter { + + /** + * Main method. Invoke the flexporter with given arguments: + * -fm {Flexporter Mapping file path} + * -s {Source FHIR file path} + * -ig {Implementation Guide file path} + * + * @param args Command line args as described above + */ + public static void main(String[] args) throws Exception { + Queue argsQ = new ArrayDeque(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("-fm")) { + 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); + } + + + private static Bundle convertFhir(Bundle bundle, Mapping mapping) { + if (FhirPathUtils.appliesToBundle(bundle, mapping.applicability, mapping.variables)) { + bundle = Actions.applyMapping(bundle, mapping, null, new FlexporterJavascriptContext()); + } + + return bundle; + } + + private static void convertFhir(File mappingFile, File igDirectory, File sourceFhir) + throws IOException { + + Mapping mapping = Mapping.parseMapping(mappingFile); + + if (igDirectory != null) { + loadIG(igDirectory); + } + + IParser parser = FhirR4.getContext().newJsonParser().setPrettyPrint(true); + + handleFile(sourceFhir, mapping, parser); + } + + private static void handleFile(File sourceFhir, Mapping mapping, IParser parser) + throws IOException { + if (sourceFhir.isDirectory()) { + for (File subfile : sourceFhir.listFiles()) { + if (subfile.isDirectory() || subfile.getName().endsWith(".json")) { + handleFile(subfile, mapping, parser); + } + } + + } 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 = convertFhir(bundle, mapping); + + String bundleJson = parser.encodeResourceToString(bundle); + + new File("./output/flexporter/").mkdirs(); + + String outFileName = "" + System.currentTimeMillis() + "_" + sourceFhir.getName(); + + File outFile = + new File("./output/flexporter/" + outFileName); + + Files.write(outFile.toPath(), bundleJson.getBytes(Charset.defaultCharset()), + StandardOpenOption.CREATE_NEW); + + System.out.println("Wrote " + outFile); + } + } + + static void loadIG(File igDirectory) throws IOException { + File[] artifacts = igDirectory.listFiles(); + + for (File artifact : artifacts) { + if (artifact.isFile() && FilenameUtils.getExtension(artifact.toString()).equals("json")) { + + IParser parser = FhirR4.getContext().newJsonParser(); + + String fhirJson = new String(Files.readAllBytes(artifact.toPath())); + IBaseResource resource = null; + + try { + resource = parser.parseResource(fhirJson); + } catch (DataFormatException dfe) { + // why does an IG contain bad data? + System.err.println("Warning: Unable to parse IG artifact " + artifact.getAbsolutePath()); + dfe.printStackTrace(); + } + + if (resource instanceof ValueSet) { + try { + RandomCodeGenerator.loadValueSet(null, (ValueSet)resource); + } catch (Exception e) { + System.err.println("WARNING: Unable to load ValueSet " + artifact.getAbsolutePath()); + e.printStackTrace(); + } + } + } + } + } + + 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 -fm MAPPING_FILE -s SOURCE_FHIR [-ig 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 27d3e73e8e..7d36e2dbf7 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; @@ -21,10 +20,15 @@ import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.LinkedBlockingQueue; import java.util.function.Predicate; + import org.apache.commons.lang3.tuple.ImmutablePair; 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.FhirPathUtils; +import org.mitre.synthea.export.flexporter.FlexporterJavascriptContext; +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; @@ -97,6 +101,7 @@ 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")); @@ -111,6 +116,7 @@ public ExporterRuntimeOptions(ExporterRuntimeOptions init) { terminologyService = init.terminologyService; recordQueue = init.recordQueue; fhirVersion = init.fhirVersion; + flexporterMappings = init.flexporterMappings; } /** @@ -148,6 +154,19 @@ public String getNextRecord() throws InterruptedException { public boolean isRecordQueueEmpty() { return recordQueue == null || recordQueue.size() == 0; } + + /** + * Register a new Flexporter mapping to be applied to Bundles from the FHIR exporter. + * Multiple mappings may be added and will be processed in order. + * @param mapping Flexporter mapping to add to list + */ + public void addFlexporterMapping(Mapping mapping) { + if (this.flexporterMappings == null) { + this.flexporterMappings = new ArrayList<>(); + } + + this.flexporterMappings.add(mapping); + } } /** @@ -256,9 +275,26 @@ 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) { + FlexporterJavascriptContext fjContext = null; + + for (Mapping mapping : options.flexporterMappings) { + if (FhirPathUtils.appliesToBundle(bundle, mapping.applicability, mapping.variables)) { + if (fjContext == null) { + // only set this the first time it is actually used + // TODO: figure out how to silence the truffle warnings + fjContext = new FlexporterJavascriptContext(); + } + bundle = Actions.applyMapping(bundle, mapping, person, fjContext); + } + } + } + + 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); @@ -266,7 +302,8 @@ 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..d9d308aee4 --- /dev/null +++ b/src/main/java/org/mitre/synthea/export/flexporter/Actions.java @@ -0,0 +1,784 @@ +package org.mitre.synthea.export.flexporter; + +import ca.uhn.fhir.parser.IParser; + +import java.time.Duration; +import java.time.LocalDateTime; +import java.time.temporal.TemporalAmount; +import java.util.ArrayList; +import java.util.Collections; +import java.util.Date; +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 java.util.stream.Collectors; + +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.DateTimeType; +import org.hl7.fhir.r4.model.Encounter; +import org.hl7.fhir.r4.model.Meta; +import org.hl7.fhir.r4.model.Period; +import org.hl7.fhir.r4.model.Resource; +import org.mitre.synthea.engine.State; +import org.mitre.synthea.export.FhirR4; +import org.mitre.synthea.export.flexporter.FieldWrapper.DateFieldWrapper; +import org.mitre.synthea.export.flexporter.FieldWrapper.ReferenceFieldWrapper; +import org.mitre.synthea.helpers.RandomCodeGenerator; +import org.mitre.synthea.world.agents.Person; +import org.mitre.synthea.world.concepts.HealthRecord.Code; + +/** + * The Actions class represents the set of all actions the Flexporter can perform. + * The entry point is the applyMapping function which invokes the appropriate method. + * Unlike the State class where each state type is a subclass, this uses a method + * to represent each action. At some point it may be refactored to be more like State. + */ +@SuppressWarnings("unchecked") // For now +public abstract class Actions { + + /** + * Apply the given Mapping to the provided Bundle. + * @param bundle FHIR bundle + * @param mapping Flexporter mapping + * @param person Synthea Person object that was used to create the Bundle. + * This will be null if running the flexporter standalone from the run_flexporter task. + * @param fjContext Flexporter Javascript Context associated with this run + * @return the Bundle after all transformations have been applied. + * Important: in many cases it will be the same Bundle object as passed in, but not always! + */ + public static Bundle applyMapping(Bundle bundle, Mapping mapping, Person person, + FlexporterJavascriptContext fjContext) { + + for (Map action : mapping.actions) { + bundle = applyAction(bundle, action, person, fjContext); + } + + return bundle; + } + + /** + * Apply the given single Action to the provided Bundle. + * @param bundle FHIR bundle + * @param action Flexporter action + * @param person Synthea Person object that was used to create the Bundle. + * This will be null if running the flexporter standalone from the run_flexporter task. + * @param fjContext Flexporter Javascript Context associated with this run + * @return the Bundle after the transformation has been applied. + * Important: in many cases it will be the same Bundle object as passed in, but not always! + */ + public static Bundle applyAction(Bundle bundle, Map action, Person person, + FlexporterJavascriptContext fjContext) { + // TODO: this could be handled better but for now just key off a specific field in the action + + Bundle returnBundle = bundle; + // most actions modify the bundle in-place, but some might return a whole new one + + if (action.containsKey("profiles")) { + applyProfiles(bundle, (List>) action.get("profiles")); + + } else if (action.containsKey("set_values")) { + setValues(bundle, (List>) action.get("set_values"), person, fjContext); + + } 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, + null); + + } else if (action.containsKey("min_date") || action.containsKey("max_date")) { + dateFilter(bundle, (String)action.get("min_date"), (String)action.get("max_date")); + + } else if (action.containsKey("shift_dates")) { + shiftDates(bundle, (String)action.get("shift_dates")); + + } else if (action.containsKey("execute_script")) { + returnBundle = executeScript((List>) action.get("execute_script"), bundle, + fjContext); + } + + return returnBundle; + } + + + /** + * Apply a profile to resources matching certain rules. Note this only adds the profile URL to + * resource.meta.profile, it does not apply any other transformations or checking. + * Resources to apply the profile to are selected by FHIRPath. (Or simply resource type) + * + * @param bundle Bundle to apply profiles to + * @param items List of rule definitions for applying profiles. Each item should have a "profile" + * for the URL and "applicability" for the FHIRPath to select resources. + */ + 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); + } + } + } + } + + /** + * Helper function to add a single profile URL to a resource, + * and set the Meta if not already set. + * + * @param resource FHIR resource + * @param profileURL Profile URL to add, if not already present + */ + public 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); + } + } + + /** + * Set values on existing resources within the Bundle, based on rules. + * + * @param bundle Bundle to apply rules to + * @param items List of rules. Rules include "applicability" to select which resources to apply + * values to, and "fields" which are "location" and "value" pairs defining which field to set + * and what value to put there. + * @param person Synthea person object to fetch values from (e.g, attributes). May be null + * @param fjContext Javascript context for this run + */ + public static void setValues(Bundle bundle, List> items, Person person, + FlexporterJavascriptContext fjContext) { + 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, fjContext); + + CustomFHIRPathResourceGeneratorR4 fhirPathgenerator = + new CustomFHIRPathResourceGeneratorR4<>(); + fhirPathgenerator.setMapping(fhirPathMapping); + fhirPathgenerator.setResource((Resource) match); + + fhirPathgenerator.generateResource((Class) match.getClass()); + } + } + } + } + + /** + * Create new resources to add to the Bundle, either a single resource or a resource based on + * other instances of existing resources. Fields on the resource as well as the "based on" + * resource will be set based on rules. + * + * @param bundle Bundle to add resources to + * @param resourcesToCreate List of rules. Rules include a "resourceType", optionally a "based_on" + * FHIRPath to select resources to base the new one off of, and "fields" which are "location" + * and "value" pairs defining which field to set and what value. + * @param person Synthea person object to fetch values from (e.g, attributes). May be null + * @param fjContext Javascript context for this run + */ + public static void createResource(Bundle bundle, List> resourcesToCreate, + Person person, FlexporterJavascriptContext fjContext) { + // TODO: this is fundamentally similar to setValues, so extract common logic + + for (Map newResourceDef : resourcesToCreate) { + + String resourceType = (String) newResourceDef.get("resourceType"); + + String basedOnPath = null; + String basedOnState = null; + String basedOnModule = null; + Map basedOn = (Map) newResourceDef.get("based_on"); + if (basedOn != null) { + basedOnPath = (String) basedOn.get("resource"); + basedOnState = (String) basedOn.get("state"); + basedOnModule = (String) basedOn.get("module"); + } + + List profiles = (List) newResourceDef.get("profiles"); + List> fields = (List>) newResourceDef.get("fields"); + + List basedOnResources; + List> writeback; + + if (basedOnPath != null) { + basedOnResources = FhirPathUtils.evaluateBundle(bundle, basedOnPath, true); + // this may return empty list, in which no new resources will be created + + writeback = (List>) newResourceDef.get("writeback"); + + } else if (basedOnState != null && basedOnModule != null) { + String moduleKey = String.format("%s Module", basedOnModule); + List moduleHistory = (List)person.attributes.get(moduleKey); + + if (moduleHistory == null) { + + // TODO - maybe throw an exception? + return; + } + final String basedOnStateName = basedOnState; // java weirdness + List instances = moduleHistory.stream() + .filter(s -> s.name.equals(basedOnStateName)) + .collect(Collectors.toList()); + + basedOnResources = new ArrayList<>(); + + for (State instance : instances) { + Long entered = instance.entered; + Long exited = instance.exited; + + // map these to a FHIR type so that we can re-use the existing concepts + + // TODO: not sure Encounter is the best but it gives us a Period + // and a reference to another encounter. + // Parameters could also work if we want more generic things, + // but the FHIRPath to retrieve from it is ugly + Encounter dummyEncounter = new Encounter(); + Period period = new Period(); + if (entered != null) { + period.setStartElement(new DateTimeType(new Date(entered))); + } + if (exited != null) { + period.setEndElement(new DateTimeType(new Date(exited))); + } + dummyEncounter.setPeriod(period); + // TODO: figure out what encounter, if any, was active at this time + // and set the dummy.partOf as a reference to it + // dummyEncounter.setPartOf(new Reference("urn:uuid:" + enc.uuid.toString())); + + basedOnResources.add(dummyEncounter); + } + + if (!basedOnResources.isEmpty()) { + // rewrite "State.entered" to "Encounter.period.start", etc + // so that the end user doesn't have to know we used an Encounter + + for (Map field : fields) { + Object valueDef = field.get("value"); + if (valueDef instanceof String && ((String) valueDef).startsWith("$")) { + String value = (String) valueDef; + if (value.contains("State.")) { + value = value + .replace("State.entered", "Encounter.period.start") + .replace("State.exited", "Encounter.period.end"); + + field.put("value", value); + } + } + } + + } + + writeback = null; + } else { + basedOnResources = Collections.singletonList(null); + writeback = null; + } + + + for (Base basedOnItem : basedOnResources) { + // IMPORTANT: basedOnItem may be null + + Map fhirPathMapping = + createFhirPathMapping(fields, bundle, (Resource) basedOnItem, person, fjContext); + + CustomFHIRPathResourceGeneratorR4 fhirPathgenerator = + new CustomFHIRPathResourceGeneratorR4<>(); + fhirPathgenerator.setMapping(fhirPathMapping); + + Resource createdResource = fhirPathgenerator.generateResource(resourceType); + + // 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()); + // TODO: consistent UUIDs + 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, fjContext); + + CustomFHIRPathResourceGeneratorR4 writebackGenerator = + new CustomFHIRPathResourceGeneratorR4<>(); + writebackGenerator.setMapping(writebackMapping); + writebackGenerator.setResource((Resource) basedOnItem); + + writebackGenerator.generateResource((Class) basedOnItem.getClass()); + } + } + } + } + + + private static Map createFhirPathMapping(List> fields, + Bundle sourceBundle, Resource sourceResource, Person person, + FlexporterJavascriptContext fjContext) { + + Map fhirPathMapping = new HashMap<>(); + + for (Map field : fields) { + String location = (String)field.get("location"); + Object valueDef = field.get("value"); + String transform = (String)field.get("transform"); + + if (valueDef == null) { + // do nothing, leave it null + } else if (valueDef instanceof String) { + String valueString = (String)valueDef; + + if (valueString.startsWith("$")) { + valueDef = getValue(sourceBundle, valueString, sourceResource, person, fjContext); + } // 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" + + // Things are starting to get a little wonky with types. + // What else could we have here? + if (valueDef instanceof Base && ((Base) valueDef).isPrimitive()) { + valueDef = ((Base)valueDef).primitiveValue(); + } + + if (transform != null) { + // TODO: valuetransforms should support objects + valueDef = ValueTransforms.apply((String)valueDef, transform); + } + + if (valueDef instanceof String || valueDef instanceof Base) { + // String may be a raw value from the mapping, or a primitive from FHIR + // Base means we plucked a full FHIR object from somewhere + fhirPathMapping.put(location, valueDef); + + } else if (valueDef instanceof Map) { + Map valueMap = (Map) valueDef; + + populateFhirPathMapping(fhirPathMapping, location, valueMap); + + } else { + // unexpected type here - is it even possible to get anything else? + String type = valueDef == null ? "null" : valueDef.getClass().toGenericString(); + System.err.println("Unhandled type in createFhirPathMapping: " + type); + } + } + + return fhirPathMapping; + } + + private static void populateFhirPathMapping(Map fhirPathMapping, String basePath, + Map valueMap) { + for (Map.Entry entry : valueMap.entrySet()) { + String key = entry.getKey(); + Object value = entry.getValue(); + + String path = basePath + "." + key; + + if (value instanceof String) { + fhirPathMapping.put(path, value); + } else if (value instanceof Map) { + populateFhirPathMapping(fhirPathMapping, path, (Map) value); + } else if (value != null) { + System.err + .println("Unexpected class found in populateFhirPathMapping -- " + value.getClass()); + } + } + } + + /** + * Filter the Bundle by only keeping selected resources. + * + * @param bundle FHIR Bundle to filter + * @param list List of resource types to retain, all other types not listed will be removed + */ + private 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(); + } + } + + if (!deletedResourceIDs.isEmpty()) { + pruneDeletedResources(bundle, deletedResourceIDs); + } + } + + /** + * Shift all dates on all resources in the Bundle. Note this only modifies date/time-type fields + * on resources and cannot modify dates embedded within strings (for example, clinical notes). + * @param bundle FHIR Bundle to shift dates for + * @param amountString Amount to shift in ISO-8601 format, either Period or Duration + */ + private static void shiftDates(Bundle bundle, String amountString) { + if (amountString == null) { + return; + } + + // note: amount can either be <= 1 day with second precision, or > 1 day with day precision + // not both + // (for example you can't shift by a year and 3 hours) + TemporalAmount amount = null; + + if (amountString.contains("Y") || (amountString.indexOf('M') < amountString.indexOf('T'))) { + // ISO-8601 period formats {@code PnYnMnD} + // if we see Y, or M before T, it's a Period + amount = java.time.Period.parse(amountString); + } else { + // ISO-8601 duration format {@code PnDTnHnMn.nS} + amount = Duration.parse(amountString); + } + + for (BundleEntryComponent entry : bundle.getEntry()) { + Resource resource = entry.getResource(); + List dateFieldsOnResource = + FieldWrapper.DATE_FIELDS.get(resource.getResourceType()); + if (dateFieldsOnResource == null) { + continue; + } + + for (DateFieldWrapper dateField : dateFieldsOnResource) { + dateField.shift(resource, amount); + } + } + } + + /** + * Filter the Bundle by date. If any resource has a date outside the provided range + * it will be filtered out. + * TODO: align this with export.years_of_history filter. "active" items outside range? + * @param bundle The Bundle to filter + * @param minDateStr Earliest/start value of the time range, in ISO-8601 format + * @param maxDateStr Latest/stop/end value of the time range, in ISO-8601 format + */ + private static void dateFilter(Bundle bundle, String minDateStr, String maxDateStr) { + if (minDateStr == null && maxDateStr == null) { + return; + } + + // TODO: support dates with or without time + LocalDateTime minDate = null; + LocalDateTime maxDate = null; + + if (minDateStr != null) { + minDate = LocalDateTime.parse(minDateStr); + } + + if (maxDateStr != null) { + maxDate = LocalDateTime.parse(maxDateStr); + } + + Set deletedResourceIDs = new HashSet<>(); + + Iterator itr = bundle.getEntry().iterator(); + + while (itr.hasNext()) { + BundleEntryComponent entry = itr.next(); + + Resource resource = entry.getResource(); + List dateFieldsOnResource = + FieldWrapper.DATE_FIELDS.get(resource.getResourceType()); + + if (dateFieldsOnResource == null) { + continue; + } + + for (DateFieldWrapper dateField : dateFieldsOnResource) { + if (!dateField.valueInRange(resource, minDate, maxDate)) { + deletedResourceIDs.add(resource.getId()); + itr.remove(); + break; + } + } + } + + if (!deletedResourceIDs.isEmpty()) { + pruneDeletedResources(bundle, deletedResourceIDs); + } + } + + /** + * Filter the Bundle by removing selected resources. + * Resources that reference deleted resources will also be deleted, and so on. + * TODO: Support different methods for handling references: + * Cascade (current), Delete reference field but leave object, Do nothing + * + * @param bundle FHIR Bundle to filter + * @param list List of resource types to delete, other types not listed will be kept + */ + 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(); + } + } + + if (!deletedResourceIDs.isEmpty()) { + pruneDeletedResources(bundle, deletedResourceIDs); + } + } + + // TODO: add modes -- cascade delete resources, clear out the one field, etc + private static void pruneDeletedResources(Bundle bundle, Set deletedResourceIDs) { + Iterator itr = bundle.getEntry().iterator(); + + Set deletedIDsThisRound = new HashSet<>(); + + while (itr.hasNext()) { + BundleEntryComponent entry = itr.next(); + + Resource resource = entry.getResource(); + + List references = + FieldWrapper.REFERENCE_FIELDS.get(resource.getResourceType()); + + if (references == null) { + continue; + } + + for (ReferenceFieldWrapper rf : references) { + List referencedIDs = rf.getReferences(resource); + + boolean deleted = false; + for (String referencedID : referencedIDs) { + if (deletedResourceIDs.contains(referencedID)) { + deletedIDsThisRound.add(resource.getId()); + itr.remove(); + deleted = true; + break; + } + } + if (deleted) { + break; + } + } + } + + if (!deletedIDsThisRound.isEmpty()) { + pruneDeletedResources(bundle, deletedIDsThisRound); + } + } + + /** + * Execute scripts against the given Bundle. + * + * @param scripts Script definitions, containing a definition of one or more JS functions, the + * name of the function to invoke, and whether it applies to the bundle as a whole, or to the + * individual resources. + * @param bundle FHIR bundle to apply scripts against + * @param fjContext Javascript context for this run + * @return The new Bundle. IMPORTANT - using the JS context will always result in a new bundle, + * not modify the existing one in-place. + */ + public static Bundle executeScript(List> scripts, Bundle bundle, + FlexporterJavascriptContext fjContext) { + IParser parser = FhirR4.getContext().newJsonParser(); + + String bundleJson = parser.encodeResourceToString(bundle); + + fjContext.loadBundle(bundleJson); + + for (Map scriptDef : scripts) { + + String function = scriptDef.get("function"); + String functionName = scriptDef.get("function_name"); + String applyTo = scriptDef.get("apply_to"); + + fjContext.loadFunction(function); + + if (applyTo.equalsIgnoreCase("bundle")) { + fjContext.applyFunctionToBundle(functionName); + } else if (applyTo.equalsIgnoreCase("resource") || applyTo.equalsIgnoreCase("resources")) { + String resourceType = scriptDef.get("resource_type"); + fjContext.applyFunctionToResources(functionName, resourceType); + } else { + throw new IllegalArgumentException("Unknown option for execute_script.apply_to: '" + applyTo + + "'. Valid options are 'bundle' and 'resources'"); + } + } + + String outBundleJson = fjContext.getBundle(); + + Bundle newBundle = parser.parseResource(Bundle.class, outBundleJson); + + return newBundle; + } + + + private static Object getValue(Bundle bundle, String valueDef, Resource currentResource, + Person person, FlexporterJavascriptContext fjContext) { + // 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, fjContext, flagValues); + } else if (flag.equals("findRef")) { + return findReference(bundle, flagValues); + } else if (flag.equals("findValue")) { + return findValue(bundle, flagValues); + } else if (flag.equals("getAttribute")) { + return getAttribute(person, flagValues); + } else if (flag.equals("randomCode")) { + return randomCode(flagValues[0]); + } + + 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 Object getField(Resource currentResource, FlexporterJavascriptContext fjContext, + 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); + } + + + 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 Base findValue(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); + } + + private static Map randomCode(String valueSetUrl) { + Code code = RandomCodeGenerator.getCode(valueSetUrl, + (int) (Math.random() * Integer.MAX_VALUE)); + Map codeAsMap = Map.of( + "system", code.system, + "code", code.code, + "display", code.display); + return codeAsMap; + } +} 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..71400e5174 --- /dev/null +++ b/src/main/java/org/mitre/synthea/export/flexporter/CustomFHIRPathResourceGeneratorR4.java @@ -0,0 +1,740 @@ +package org.mitre.synthea.export.flexporter; + +import ca.uhn.fhir.context.BaseRuntimeChildDatatypeDefinition; +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; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.Stack; + +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 org.hl7.fhir.r4.utils.FHIRPathEngine; +import org.mitre.synthea.export.FhirR4; + + +/** + * 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 in a future release. + * + *

Modified for the Flexporter: + * -- allow adding to an existing resource + * -- add class lookup by resourceType + * -- 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 {@code 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 marcel.parciak@med.uni-goettingen.de + * + */ +public class CustomFHIRPathResourceGeneratorR4 { + + private FhirContext ctx; + private FHIRPathEngine engine; + private Map pathMapping; + private T resource = null; + + private Object 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); + } + } + + /** + * Default constructor, needs a call to `setMapping` later on in order to generate any + * Resources. + */ + public CustomFHIRPathResourceGeneratorR4() { + this.ctx = FhirR4.getContext(); + this.pathMapping = new HashMap(); + this.engine = new FHIRPathEngine(new HapiWorkerContext(ctx, ctx.getValidationSupport())); + } + + /** + * Setter for the FHIRPath mapping Map instance. + * + * @param mapping {@code Map} a mapping of FHIRPath to objects + * 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; + } + + /** + * Sets the resource to apply FHIRPath changes to. + * If not set, calling generateResource will instantiate a new resource. + */ + 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 {@code 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 the given resourceType + * with every value set in the FHIRPath mapping. + * + * @param resourceType String The class name of the Resource that shall be created. + * @return T a new FHIR Resource instance of the given resource type. + */ + public T generateResource(String resourceType) { + try { + @SuppressWarnings("unchecked") + Class resourceClass = + (Class) Class.forName("org.hl7.fhir.r4.model." + resourceType); + + return generateResource(resourceClass); + } catch (ClassNotFoundException e) { + throw new RuntimeException(e); + } + } + + /** + * The generation method that yields a new instance of class `resourceClass` with every value set + * in the FHIRPath mapping. + * + * @param resourceClass {@code 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: + default: + // 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: + default: + // 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(String.valueOf(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 (nextTier.childDefinition instanceof BaseRuntimeChildDatatypeDefinition + && ((BaseRuntimeChildDatatypeDefinition) nextTier.childDefinition).getDatatype() + .isInstance(this.valueToSet)) { + + // this lets us work with objects that are not trivially strings, e.g. CodeableConcepts + + // TODO: are there any other implications to this? + nextTier.childDefinition.getMutator().setValue(nodeElement, (IBase)this.valueToSet); + + } else { + 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); + break; + // 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: + default: + // 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: + default: + // 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 {@code 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; + default: + // not sure why checkstyle makes this necessary... + // the 3 above are the only options in the enum + } + } + + 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: + default: + // 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 + } + + /** + * Helper function to set a single value on a resource. + * @param resource Resource to set value on + * @param fieldPath Path to set value to. May be a nested field + * @param value Value to set at given path on the resource + */ + public static void setField(T resource, String fieldPath, Object value) { + CustomFHIRPathResourceGeneratorR4 generator = + new CustomFHIRPathResourceGeneratorR4<>(); + generator.setResource(resource); + + HashMap mapping = new HashMap<>(); + mapping.put(fieldPath, value); + generator.setMapping(mapping); + generator.generateResource(resource.getClass()); + } +} 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..3e128a6b86 --- /dev/null +++ b/src/main/java/org/mitre/synthea/export/flexporter/FhirPathUtils.java @@ -0,0 +1,179 @@ +package org.mitre.synthea.export.flexporter; + +import java.util.ArrayList; +import java.util.List; +import java.util.Map; +import java.util.stream.Collectors; + +import org.apache.commons.exec.util.StringUtils; +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 org.mitre.synthea.export.FhirR4; + + +public abstract class FhirPathUtils { + + private static final FhirPathR4 FHIRPATH = new FhirPathR4(FhirR4.getContext()); + + /** + * Execute the given FHIRPath against the given resource and return the results. + * + * @param resource FHIR resource to execute FHIRPath against + * @param fhirpath FHIRPath string + * @return Raw values from FHIRPath engine evaluating the string + */ + public static List evaluateResource(Resource resource, String fhirpath) { + return FHIRPATH.evaluate(resource, fhirpath, Base.class); + } + + /** + * Execute the given FHIRPath against the given Bundle and return the results. There are a few + * different possibilities in how this works. + * - If the FHIRPath string starts with "Bundle" then this will execute the FHIRPath once + * against the Bundle as a whole, otherwise it will be executed against each resource. + * - If "returnResources" is true, then resources from the Bundle + * that return a truthy value will be returned, otherwise the raw value from the FHIRpath engine + * will be returned. + * + * @param bundle FHIR bundle to evaluate FHIRpath against + * @param fhirpath FHIRPath string + * @param returnResources If true, return resources from bundle matching FHIRPath; if false, + * return raw values from FHIRPath engine + * @return Differs based on input - see above + */ + 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; + } + } + + /** + * Execute the given FHIRPath against the given Bundle and return the results. There are a few + * different possibilities in how this works. + * - If the FHIRPath string starts with "Bundle" then this will execute the FHIRPath once + * against the Bundle as a whole, otherwise it will be executed against each resource. + * - If "returnResources" is true, then resources from the Bundle + * that return a truthy value will be returned, otherwise the raw value from the FHIRpath engine + * will be returned. + * This version allows for specifying variables to inject into the FHIRPath. + * + * @param bundle FHIR bundle to evaluate FHIRpath against + * @param fhirpath FHIRPath string + * @param variables FHIRPath variables to inject + * @param returnResources If true, return resources from bundle matching FHIRPath; if false, + * return raw values from FHIRPath engine + * @return Differs based on input - see above + */ + public static List evaluateBundle(Bundle bundle, String fhirpath, + Map variables, boolean returnResources) { + + if (variables != null) { + for (Map.Entry entry : variables.entrySet()) { + Object replacementObj = entry.getValue(); + + String replacement = null; + if (replacementObj instanceof String) { + replacement = (String) replacementObj; + } else if (replacementObj instanceof List) { + List replacementList = (List) replacementObj; + + replacementList = replacementList.stream() + .map(s -> { + if (StringUtils.isQuoted(s)) { + return s; + } + // quoting strings is very difficult in general + // but for now assume this will simple things like codes + // which don't contain nested quotes + if (s.contains("'")) { + return "\"" + s + "\""; + } else { + return "'" + s + "'"; + } + }) + .collect(Collectors.toList()); + + replacement = "(" + String.join(" | ", replacementList) + ")"; + } + + + if (replacement != null) { + fhirpath = fhirpath.replace("%" + entry.getKey(), replacement); + } + } + } + + return evaluateBundle(bundle, fhirpath, returnResources); + } + + + 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)); + } + + public static boolean appliesToBundle(Bundle bundle, String fhirpath, + Map variables) { + return isTruthy(evaluateBundle(bundle, fhirpath, variables, false)); + } + + /** + * Helper function to convert FHIRPath evaluation primitives into a boolean. + * Nulls, empty strings, and boolean false all mean "false" here. Everything else means "true". + */ + 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; + } + + /** + * Helper function to convert FHIRPath evaluation results into a boolean. + * FHIRPath.evaluate returns a {@code List} which is matching pieces of resources. + * This will return false if the list is empty, or if everything in the list is falsy. + */ + 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/FieldWrapper.java b/src/main/java/org/mitre/synthea/export/flexporter/FieldWrapper.java new file mode 100644 index 0000000000..ba44c3c9fa --- /dev/null +++ b/src/main/java/org/mitre/synthea/export/flexporter/FieldWrapper.java @@ -0,0 +1,621 @@ +package org.mitre.synthea.export.flexporter; + +import ca.uhn.fhir.context.BaseRuntimeChildDefinition; +import ca.uhn.fhir.context.RuntimeResourceDefinition; + +import java.time.LocalDate; +import java.time.LocalDateTime; +import java.time.LocalTime; +import java.time.ZoneOffset; +import java.time.ZonedDateTime; +import java.time.temporal.TemporalAmount; +import java.util.Date; +import java.util.HashMap; +import java.util.List; +import java.util.Map; +import java.util.function.BiConsumer; +import java.util.function.Function; +import java.util.stream.Collectors; + +import org.hl7.fhir.instance.model.api.IBase; +import org.hl7.fhir.r4.model.AllergyIntolerance; +import org.hl7.fhir.r4.model.Base; +import org.hl7.fhir.r4.model.CarePlan; +import org.hl7.fhir.r4.model.CareTeam; +import org.hl7.fhir.r4.model.Claim; +import org.hl7.fhir.r4.model.Condition; +import org.hl7.fhir.r4.model.DateTimeType; +import org.hl7.fhir.r4.model.DateType; +import org.hl7.fhir.r4.model.Device; +import org.hl7.fhir.r4.model.DiagnosticReport; +import org.hl7.fhir.r4.model.DocumentReference; +import org.hl7.fhir.r4.model.Encounter; +import org.hl7.fhir.r4.model.ExplanationOfBenefit; +import org.hl7.fhir.r4.model.Goal; +import org.hl7.fhir.r4.model.ImagingStudy; +import org.hl7.fhir.r4.model.Immunization; +import org.hl7.fhir.r4.model.InstantType; +import org.hl7.fhir.r4.model.Media; +import org.hl7.fhir.r4.model.MedicationAdministration; +import org.hl7.fhir.r4.model.MedicationRequest; +import org.hl7.fhir.r4.model.Observation; +import org.hl7.fhir.r4.model.Patient; +import org.hl7.fhir.r4.model.Period; +import org.hl7.fhir.r4.model.Procedure; +import org.hl7.fhir.r4.model.Provenance; +import org.hl7.fhir.r4.model.Reference; +import org.hl7.fhir.r4.model.Resource; +import org.hl7.fhir.r4.model.ResourceType; +import org.hl7.fhir.r4.model.SupplyDelivery; +import org.hl7.fhir.r4.model.TimeType; +import org.mitre.synthea.export.FhirR4; + +public abstract class FieldWrapper { + protected Function> getter; + protected BiConsumer setter; + + /** + * Create a FieldWrapper for the field defined by the given path. + * + * @param fieldPath Path to FHIR field (not FHIRPath). Should be of the form: + * Resource.field.nestedField.nested2... + */ + public FieldWrapper(String fieldPath) { + // split at the first . so we get two items in the array: + // [0] = resource, [1] = field[.nestedField etc] + String[] pathParts = fieldPath.split("\\.", 2); + + try { + String className = "org.hl7.fhir.r4.model." + pathParts[0]; + + @SuppressWarnings("unchecked") + Class clazz = + (Class) Class.forName(className); + init(clazz, pathParts[1]); + } catch (Exception e) { + // means we defined some classname that isn't a resource type + throw new RuntimeException(e); + } + } + + /** + * Create a FieldWrapper for the field on the given resource type defined by the given path. + * + * @param fieldName Path to FHIR field (not FHIRPath). Should not include resourceType and + * should be of the form: field.nestedField.nested2... + */ + public FieldWrapper(Class clazz, String fieldName) { + init(clazz, fieldName); + } + + private void init(Class clazz, String fieldName) { + RuntimeResourceDefinition rd = FhirR4.getContext().getResourceDefinition(clazz); + if (fieldName.contains(".")) { + // the .stream() and everything after it is just turning List into List ugh + this.getter = (resource) -> + FhirPathUtils.evaluateResource(resource, fieldName) + .stream() + .map(b -> (IBase)b) + .collect(Collectors.toList()); + this.setter = (resource, value) -> + CustomFHIRPathResourceGeneratorR4.setField(resource, fieldName, value); + } else { + BaseRuntimeChildDefinition fieldDef = rd.getChildByName(fieldName); + if (fieldDef == null) { + // maybe it's a choice type. + fieldDef = rd.getChildByName(fieldName + "[x]"); + if (fieldDef == null) { + throw new IllegalArgumentException( + "Unknown field " + fieldName + " on resourceType " + clazz.getSimpleName()); + } + + } + this.getter = fieldDef.getAccessor()::getValues; + this.setter = fieldDef.getMutator()::setValue; + } + } + + /** + * Get a single value from the field this FieldWrapper represents from the given resource. + * For fields that may have more than a single value, use getAll(Resource) instead. + * Calling this on a field that has more than one value will return only the first value. + * @param resource Resource to get value from + * @return the value from the field + */ + public IBase getSingle(Resource resource) { + return getAll(resource).stream().findFirst().orElse(null); + } + + /** + * Get the values from the field this FieldWrapper represents from the given resource. + * @param resource Resource to get value from + * @return the list of values from the field + */ + public List getAll(Resource resource) { + return this.getter.apply(resource); + } + + /** + * Set the given value for the field this FieldWrapper represents on the given resource. + * @param resource The resource to set a value on + * @param value The value to set + */ + public void set(Resource resource, IBase value) { + this.setter.accept(resource, value); + } + + + /** + * DateFieldWrapper is used to represent a field on a resource representing a date and/or time. + * This wrapper offers convenience features such as normalizing the various types that a FHIR + * field can be to a LocalDateTime, checking if the value is in a given range, + * and shifting the value by a given amount. + */ + public static class DateFieldWrapper extends FieldWrapper { + public DateFieldWrapper(String fieldPath) { + super(fieldPath); + } + + public DateFieldWrapper(Class clazz, String fieldName) { + super(clazz, fieldName); + } + + /** + * Normalize the given raw date value into a LocalDateTime. FHIR values can be a number of + * different types so this checks which one the value is and converts accordingly. + * @param rawValue Original raw FHIR value + * @return parsed date as LocalDateTime + */ + private static LocalDateTime normalize(IBase rawValue) { + if (!(rawValue instanceof Base)) { + // should never happen, not sure it's possible + // (though this also catches nulls) + return null; + } + + Base rawValueBase = (Base) rawValue; + if (rawValueBase.isPrimitive()) { + + String strValue = rawValueBase.primitiveValue(); + + if (rawValueBase instanceof DateType) { + return LocalDate.parse(strValue).atStartOfDay(); + } else if (rawValueBase instanceof DateTimeType) { + return ZonedDateTime.parse(strValue).toLocalDateTime(); + } else if (rawValueBase instanceof DateType) { + return ZonedDateTime.parse(strValue).toLocalDateTime(); + } else if (rawValueBase instanceof TimeType) { + return ZonedDateTime.parse(strValue).toLocalDateTime(); + } else if (rawValueBase instanceof InstantType) { + return ZonedDateTime.parse(strValue).toLocalDateTime(); + } + } + + // various reasons we arrive here, for example a choice type that includes non-time values + return null; + } + + /** + * Shift the Period by the given TemporalAmount, by shifting both the start and end + * elements of the Period by the given amount. + * @param period Period to shift + * @param amount TemporalAmount to shift by + * @return the shifted Period (note: the same object instance as passed in) + */ + static Period shift(Period period, TemporalAmount amount) { + if (period == null) { + return null; + } + + period.setStartElement(shift(period.getStartElement(), amount)); + period.setEndElement(shift(period.getEndElement(), amount)); + return period; + } + + static DateTimeType shift(DateTimeType dateTime, TemporalAmount amount) { + if (dateTime == null) { + return null; + } + + String s = dateTime.getValueAsString(); + ZonedDateTime shifted = ZonedDateTime.parse(s).plus(amount); + dateTime.setValueAsString(shifted.toString()); + return dateTime; + } + + static DateType shift(DateType date, TemporalAmount amount) { + if (date == null) { + return null; + } + + String s = date.getValueAsString(); + LocalDate shifted = LocalDate.parse(s).plus(amount); + date.setValueAsString(shifted.toString()); + return date; + } + + static TimeType shift(TimeType time, TemporalAmount amount) { + if (time == null) { + return null; + } + if (amount instanceof java.time.Period) { + // trying to shift years/months/days but we only have a time of day + // so just keep it the same + return time; + } + + String t = time.getValue(); + LocalTime localTime = LocalTime.parse(t).plus(amount); + time.setValue(localTime.toString()); + return time; + } + + static InstantType shift(InstantType instant, TemporalAmount amount) { + if (instant == null) { + return null; + } + + String s = instant.getValueAsString(); + + // note that we use ZonedDateTime vs java Instant here + // because Instant doesn't allow shifting by time units > Days + ZonedDateTime shifted = ZonedDateTime.parse(s).plus(amount); + + instant.setValueAsString(shifted.toString()); + + return instant; + } + + /** + * Shift the value of the field represented by this FieldWrapper by the given amount. + * @param resource Resource to modify the value on + * @param amount Amount to shift the date by + */ + public void shift(Resource resource, TemporalAmount amount) { + IBase value = getSingle(resource); + if (value == null) { + return; + } + + IBase newValue; + + if (value instanceof Period) { + newValue = shift((Period) value, amount); + } else if (value instanceof DateTimeType) { + newValue = shift((DateTimeType) value, amount); + } else if (value instanceof DateType) { + newValue = shift((DateType) value, amount); + } else if (value instanceof TimeType) { + newValue = shift((TimeType) value, amount); + } else if (value instanceof InstantType) { + newValue = shift((InstantType) value, amount); + } else { + // many choice fields have both temporal and non-temporal options, + // for example Observation.value + // just do nothing + + return; + } + + set(resource, newValue); + } + + /** + * Tests if the value of the field represented by this FieldWrapper is in the given range. + * At least one or both of min or max is required, an "open range" is possible by + * providing only one. + * @param resource Resource to get the value from + * @param min Earliest/start value of the time range + * @param max Latest/stop/end value of the time range + * @return Whether the value is in the range. + */ + public boolean valueInRange(Resource resource, LocalDateTime min, LocalDateTime max) { + if (min == null && max == null) { + return true; + } + + if (min == null) { + min = LocalDateTime.MIN; + } + + if (max == null) { + max = LocalDateTime.MAX; + } + + IBase value = this.getSingle(resource); + + if (value instanceof Period) { + Period period = (Period) value; + + Date startDt = period.getStart(); + LocalDateTime start = startDt.toInstant().atOffset(ZoneOffset.UTC).toLocalDateTime(); + Date endDt = period.getEnd(); + + if (endDt == null) { + // use the same single value check as if this were not a Period + return (start.isAfter(min) || start.isEqual(min)) + && (start.isBefore(max) || start.isEqual(max)); + } + + LocalDateTime end = endDt.toInstant().atOffset(ZoneOffset.UTC).toLocalDateTime(); + + // https://stackoverflow.com/a/325964 + // (StartA <= EndB) and (EndA >= StartB) + + return (start.isBefore(max) || start.isEqual(max)) + && (end.isAfter(min) || end.isEqual(min)); + + } else if (value != null) { + LocalDateTime myValue = normalize(value); + + if (myValue == null) { + return true; + // probably wasn't actually a temporal value + } + + return (myValue.isAfter(min) || myValue.isEqual(min)) + && (myValue.isBefore(max) || myValue.isEqual(max)); + + } else { + // debatable which way this should go. we have a date field set to null, + // does that mean it's in the given range? + return true; + } + } + } + + public static final Map> DATE_FIELDS = buildDateFields(); + + // TODO: this could instead iterate over all fields on relevant resources, + // which might be cleaner or slower, especially if it means a lot of iteration + // over resource types or fields we never use. + // A human would do it by looking at all fields that are actually present on a resource + // and see if they are dates. But I don't see an easy way to do that here + private static Map> buildDateFields() { + Map> dateFields = new HashMap<>(); + + dateFields.put(ResourceType.Patient, List.of( + new DateFieldWrapper(Patient.class, "birthDate"), + new DateFieldWrapper(Patient.class, "deceased") + )); + + dateFields.put(ResourceType.Encounter, List.of( + new DateFieldWrapper(Encounter.class, "period") + )); + + dateFields.put(ResourceType.Condition, List.of( + new DateFieldWrapper(Condition.class, "onset"), + new DateFieldWrapper(Condition.class, "abatement"), + new DateFieldWrapper(Condition.class, "recordedDate") + )); + + dateFields.put(ResourceType.AllergyIntolerance, List.of( + new DateFieldWrapper(AllergyIntolerance.class, "recordedDate") + )); + + dateFields.put(ResourceType.Procedure, List.of( + new DateFieldWrapper(Procedure.class, "performed") // Period or dateTime + )); + + dateFields.put(ResourceType.Observation, List.of( + new DateFieldWrapper(Observation.class, "effective"), + // new DateFieldWrapper(Observation.class, "value"), + // value could technically be a date but I don't think we ever use that + new DateFieldWrapper(Observation.class, "issued") + )); + + dateFields.put(ResourceType.MedicationRequest, List.of( + new DateFieldWrapper(MedicationRequest.class, "authoredOn") + )); + + dateFields.put(ResourceType.MedicationAdministration, List.of( + new DateFieldWrapper(MedicationAdministration.class, "effective") + )); + + dateFields.put(ResourceType.CarePlan, List.of( + new DateFieldWrapper(CarePlan.class, "period") + )); + + dateFields.put(ResourceType.Goal, List.of( + new DateFieldWrapper(Goal.class, "target.due") + )); + + dateFields.put(ResourceType.CareTeam, List.of( + new DateFieldWrapper(CareTeam.class, "period") + )); + + dateFields.put(ResourceType.ImagingStudy, List.of( + new DateFieldWrapper(ImagingStudy.class, "started"), + new DateFieldWrapper(ImagingStudy.class, "series.started") + )); + + dateFields.put(ResourceType.DiagnosticReport, List.of( + new DateFieldWrapper(DiagnosticReport.class, "effective"), + new DateFieldWrapper(DiagnosticReport.class, "issued") + )); + + dateFields.put(ResourceType.Device, List.of( + new DateFieldWrapper(Device.class, "manufactureDate"), + new DateFieldWrapper(Device.class, "expirationDate") + )); + + dateFields.put(ResourceType.SupplyDelivery, List.of( + new DateFieldWrapper(SupplyDelivery.class, "occurrence") + )); + + dateFields.put(ResourceType.ExplanationOfBenefit, List.of( + new DateFieldWrapper(ExplanationOfBenefit.class, "billablePeriod"), + new DateFieldWrapper(ExplanationOfBenefit.class, "procedure.date") + )); + + dateFields.put(ResourceType.Provenance, List.of( + new DateFieldWrapper(Provenance.class, "recorded") + )); + + return dateFields; + } + + public static class ReferenceFieldWrapper extends FieldWrapper { + public ReferenceFieldWrapper(String fieldPath) { + super(fieldPath); + } + + public ReferenceFieldWrapper(Class clazz, String fieldName) { + super(clazz, fieldName); + } + + /** + * Get a single reference from the field this FieldWrapper represents on the given resource, + * as a string. + * @param resource Resource to get the value from + * @return Reference as string, ex. "Patient/123" or "urn:uuid:98d1c..." + */ + public String getReference(Resource resource) { + IBase referenceObject = getSingle(resource); + if (!(referenceObject instanceof Reference)) { + return null; + } + Reference ref = (Reference)referenceObject; + return ref.getReference(); + } + + /** + * Get all references from the field this FieldWrapper represents on the given resource, + * as a list of strings. + * @param resource Resource to get the value from + * @return References as strings, ex. "Patient/123" or "urn:uuid:98d1c..." + */ + public List getReferences(Resource resource) { + List referenceObjects = getAll(resource); + + return referenceObjects.stream() + .map(ro -> { + if (!(ro instanceof Reference)) { + return null; + } + return ((Reference)ro).getReference(); + }) + .filter(ro -> ro != null) + .collect(Collectors.toList()); + } + } + + public static final Map> REFERENCE_FIELDS = + buildReferenceFields(); + + private static Map> buildReferenceFields() { + Map> refFields = new HashMap<>(); + + refFields.put(ResourceType.Encounter, List.of( + new ReferenceFieldWrapper(Encounter.class, "subject"), + new ReferenceFieldWrapper(Encounter.class, "location.location"), + new ReferenceFieldWrapper(Encounter.class, "participant.individual") + )); + + refFields.put(ResourceType.Condition, List.of( + new ReferenceFieldWrapper(Condition.class, "subject"), + new ReferenceFieldWrapper(Condition.class, "encounter") + )); + + refFields.put(ResourceType.AllergyIntolerance, List.of( + new ReferenceFieldWrapper(AllergyIntolerance.class, "patient") + )); + + refFields.put(ResourceType.Procedure, List.of( + new ReferenceFieldWrapper(Procedure.class, "subject"), + new ReferenceFieldWrapper(Procedure.class, "encounter"), + new ReferenceFieldWrapper(Procedure.class, "reasonReference") + )); + + refFields.put(ResourceType.MedicationRequest, List.of( + new ReferenceFieldWrapper(MedicationRequest.class, "subject"), + new ReferenceFieldWrapper(MedicationRequest.class, "encounter"), + new ReferenceFieldWrapper(MedicationRequest.class, "medication"), + new ReferenceFieldWrapper(MedicationRequest.class, "reasonReference") + )); + + refFields.put(ResourceType.MedicationAdministration, List.of( + new ReferenceFieldWrapper(MedicationAdministration.class, "subject"), + new ReferenceFieldWrapper(MedicationAdministration.class, "context"), + new ReferenceFieldWrapper(MedicationAdministration.class, "reasonReference") + )); + + refFields.put(ResourceType.Observation, List.of( + new ReferenceFieldWrapper(Observation.class, "subject"), + new ReferenceFieldWrapper(Observation.class, "encounter") + )); + + refFields.put(ResourceType.DiagnosticReport, List.of( + new ReferenceFieldWrapper(DiagnosticReport.class, "subject"), + new ReferenceFieldWrapper(DiagnosticReport.class, "encounter"), + new ReferenceFieldWrapper(DiagnosticReport.class, "result") + )); + + refFields.put(ResourceType.CarePlan, List.of( + new ReferenceFieldWrapper(CarePlan.class, "subject"), + new ReferenceFieldWrapper(CarePlan.class, "encounter"), + new ReferenceFieldWrapper(CarePlan.class, "careTeam"), + new ReferenceFieldWrapper(CarePlan.class, "addresses"), + new ReferenceFieldWrapper(CarePlan.class, "activity.detail.reason"), + new ReferenceFieldWrapper(CarePlan.class, "goal") + )); + + refFields.put(ResourceType.Goal, List.of( + new ReferenceFieldWrapper(Goal.class, "subject"), + new ReferenceFieldWrapper(Goal.class, "addresses") + )); + + refFields.put(ResourceType.CareTeam, List.of( + new ReferenceFieldWrapper(CareTeam.class, "subject"), + new ReferenceFieldWrapper(CareTeam.class, "encounter") + )); + + refFields.put(ResourceType.Immunization, List.of( + new ReferenceFieldWrapper(Immunization.class, "patient"), + new ReferenceFieldWrapper(Immunization.class, "encounter") + )); + + refFields.put(ResourceType.Device, List.of( + new ReferenceFieldWrapper(Device.class, "patient") + )); + + refFields.put(ResourceType.SupplyDelivery, List.of( + new ReferenceFieldWrapper(SupplyDelivery.class, "patient") + )); + + refFields.put(ResourceType.ImagingStudy, List.of( + new ReferenceFieldWrapper(ImagingStudy.class, "subject"), + new ReferenceFieldWrapper(ImagingStudy.class, "encounter") + )); + + refFields.put(ResourceType.DocumentReference, List.of( + new ReferenceFieldWrapper(DocumentReference.class, "subject") + )); + + refFields.put(ResourceType.Media, List.of( + new ReferenceFieldWrapper(Media.class, "subject"), + new ReferenceFieldWrapper(Media.class, "encounter") + )); + + refFields.put(ResourceType.Claim, List.of( + new ReferenceFieldWrapper(Claim.class, "patient"), + new ReferenceFieldWrapper(Claim.class, "item.encounter"), + new ReferenceFieldWrapper(Claim.class, "prescription"), + new ReferenceFieldWrapper(Claim.class, "procedure.procedure"), // procedureReference + new ReferenceFieldWrapper(Claim.class, "diagnosis.diagnosis") // diagnosisReference + + )); + + refFields.put(ResourceType.ExplanationOfBenefit, List.of( + new ReferenceFieldWrapper(ExplanationOfBenefit.class, "patient"), + new ReferenceFieldWrapper(ExplanationOfBenefit.class, "claim"), + new ReferenceFieldWrapper(ExplanationOfBenefit.class, "provider") + )); + + refFields.put(ResourceType.Provenance, List.of( + new ReferenceFieldWrapper(Provenance.class, "target") + )); + + return refFields; + } +} diff --git a/src/main/java/org/mitre/synthea/export/flexporter/FlexporterJavascriptContext.java b/src/main/java/org/mitre/synthea/export/flexporter/FlexporterJavascriptContext.java new file mode 100644 index 0000000000..d031c3c19b --- /dev/null +++ b/src/main/java/org/mitre/synthea/export/flexporter/FlexporterJavascriptContext.java @@ -0,0 +1,134 @@ +package org.mitre.synthea.export.flexporter; + +import java.io.IOException; +import java.net.URL; + +import org.apache.commons.lang3.StringUtils; +import org.graalvm.polyglot.Context; +import org.graalvm.polyglot.Source; +import org.graalvm.polyglot.Value; + +public class FlexporterJavascriptContext { + private final Context jsContext; + + private Value workingBundleAsJSObject; + + /** + * Default constructor for a Javascript Context. + */ + public FlexporterJavascriptContext() { + jsContext = Context.create("js"); + // TODO: if we want to add custom libraries like fhirpath or fhir-mapper, do it here + // try { + + // for (String filename : Arrays.asList("fhirpath.js", "fhir-mapper.js") ) { + // String fileText = Files.readString(Path.of()); + // loadFunction(fileText); + + + // loadFile(filename); + // } + // System.out.println("All functions available from Java (as loaded into Bindings) " + // + jsContext.getBindings("js").getMemberKeys()); + // } catch (Exception e) { + // e.printStackTrace(); + // } + } + + /** + * Load the JS file referenced by the given file path into the JS context. + * Globals registered in the given file will be accessible to other loaded functions. + * @param filename Path to a JS file + * @throws IOException if the file doesn't exist, can't be read, or can't be parsed as JS + */ + public void loadFile(String filename) throws IOException { + URL url = FlexporterJavascriptContext.class.getClassLoader().getResource("./lib/" + filename); + + jsContext.eval(Source.newBuilder("js", url).build()); + } + + /** + * Load a JS function from string. + * @param functionDef JavaScript code + */ + public void loadFunction(String functionDef) { + jsContext.eval("js", functionDef); + } + + /** + * Load a Bundle as the JS context's working bundle. + * All executed functions will use the bundle as an argument. + * + * @param bundleAsString Bundle as JSON string + */ + public void loadBundle(String bundleAsString) { + // workingBundleAsJSObject = JSON.parse(bundleAsString) + + Value parseFn = jsContext.eval("js","(bundleString) => JSON.parse(bundleString)"); + + workingBundleAsJSObject = parseFn.execute(bundleAsString); + } + + /** + * Get the current working Bundle as a JSON string. + */ + public String getBundle() { + // return JSON.stringify(workingBundleAsJSObject) + + Value stringifyFn = jsContext.eval("js","(bundle) => JSON.stringify(bundle)"); + + String bundleString = stringifyFn.execute(workingBundleAsJSObject).asString(); + + return bundleString; + } + + /** + * Applies a function to the working Bundle. + * Invoked as `fnName(bundle)` + * The function must have already been loaded by loadFile or loadFunction. + * + * @param fnName Function name to invoke + */ + public void applyFunctionToBundle(String fnName) { + // assumption is the fn has already been loaded by loadFunction. + // good news -- based on testing, if the bundle is modified in-place + // in the JS context then our variable "sees" those updates. + // (the variable maintains a reference to the object within the JS VM) + + Value applyFn = jsContext.getBindings("js").getMember(fnName); + applyFn.execute(workingBundleAsJSObject); + } + + /** + * Applies a function to each resource within the Bundle. + * Invoked as `fnName(resource, bundle)`. + * (i.e., the bundle itself is also passed to the function as context) + * The function must have already been loaded by loadFile or loadFunction. + * + * @param fnName Function name to invoke + * @param resourceType Resource Type to apply the function to, other resources will be ignored + */ + public void applyFunctionToResources(String fnName, String resourceType) { + // assumption is the fn has already been loaded by loadFunction + + Value applyFn = jsContext.getBindings("js").getMember(fnName); + + Value entries = workingBundleAsJSObject.getMember("entry"); + + for (int i = 0; i < entries.getArraySize(); i++) { + Value entry = entries.getArrayElement(i); + Value resource = entry.getMember("resource"); + + if (StringUtils.isNotBlank(resourceType)) { + String type = resource.getMember("resourceType").asString(); + if (!resourceType.equalsIgnoreCase(type)) { + continue; + } + } + + // provide both the resource and the full bundle for context + // (eg, so we can create references to other resources) + applyFn.execute(resource, workingBundleAsJSObject); + } + } +} 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..6920c256e7 --- /dev/null +++ b/src/main/java/org/mitre/synthea/export/flexporter/Mapping.java @@ -0,0 +1,37 @@ +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; +import org.yaml.snakeyaml.constructor.Constructor; + +public class Mapping { + public String name; + public String applicability; + + public Map variables; + + /** + * Each action is a {@code Map>String,?>}. Nested fields within the YAML become ArrayLists and + * LinkedHashMaps. + */ + public List> actions; + + /** + * Read the provided file into a Mapping. + * @param mappingFile Source file to read content from + * @return Mapping object + * @throws FileNotFoundException if the file doesn't exist + */ + public static Mapping parseMapping(File mappingFile) throws FileNotFoundException { + InputStream selectorInputSteam = new FileInputStream(mappingFile); + Yaml yaml = new Yaml(new 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..abf3c86c30 --- /dev/null +++ b/src/main/java/org/mitre/synthea/export/flexporter/ValueTransforms.java @@ -0,0 +1,138 @@ +package org.mitre.synthea.export.flexporter; + +import java.time.LocalDate; +import java.time.ZoneId; +import java.time.ZonedDateTime; +import java.time.format.DateTimeFormatter; + +public abstract class ValueTransforms { + + /** + * Apply the selected Value Transform on the given value. + * + * @param originalValue Source value + * @param transformName Name of the transform to apply + * @return transformed value + */ + 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; + } + + /** + * Convert the given date/time string into an Instant. + * @param src Source date/time string + * @return Input date/time reformatted as an Instant + */ + public static String toInstant(String src) { + if (src == null) { + return null; + } + + ZonedDateTime dateTime = parse(src); + + return dateTime.toInstant().toString(); + } + + /** + * Convert the given date/time string into a DateTime. + * @param src Source date/time string + * @return Input date/time reformatted as a DateTime + */ + public static String toDateTime(String src) { + ZonedDateTime dateTime = parse(src); + + return dateTime.toInstant().toString(); + } + + /** + * Convert the given date/time string into a Date. + * @param src Source date/time string + * @return Input date/time reformatted as a Date + */ + public static String toDate(String src) { + if (src == null) { + return null; + } + + ZonedDateTime dateTime = parse(src); + + return DateTimeFormatter.ISO_LOCAL_DATE.format(dateTime); + } + + /** + * Convert the given date/time string into a Time. + * @param src Source date/time string + * @return Input date/time reformatted as a Time + */ + public static String toTime(String src) { + if (src == null) { + return null; + } + + ZonedDateTime dateTime = parse(src); + + return DateTimeFormatter.ISO_LOCAL_TIME.format(dateTime); + } + + private static final DateTimeFormatter YEAR = DateTimeFormatter.ofPattern("yyyy"); + + private static final DateTimeFormatter YEAR_MONTH = DateTimeFormatter.ofPattern("yyyy-MM"); + + private static final ZoneId UTC = ZoneId.of("UTC"); + + 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 ZonedDateTime.parse(src, DateTimeFormatter.ISO_LOCAL_TIME); + case 10: + // YYYY-MM-DD + return LocalDate.parse(src, DateTimeFormatter.ISO_LOCAL_DATE) + .atStartOfDay(UTC); + default: + // TODO: make sure this actually works -- the docs are weird + return ZonedDateTime.parse(src, DateTimeFormatter.ISO_ZONED_DATE_TIME); + } + } + +} diff --git a/src/main/java/org/mitre/synthea/helpers/RandomCodeGenerator.java b/src/main/java/org/mitre/synthea/helpers/RandomCodeGenerator.java index a585171d06..35b1f83e5e 100644 --- a/src/main/java/org/mitre/synthea/helpers/RandomCodeGenerator.java +++ b/src/main/java/org/mitre/synthea/helpers/RandomCodeGenerator.java @@ -1,16 +1,14 @@ package org.mitre.synthea.helpers; -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.core.type.TypeReference; -import com.fasterxml.jackson.databind.ObjectMapper; +import ca.uhn.fhir.parser.IParser; import java.io.IOException; import java.util.ArrayList; -import java.util.Collection; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.Random; +import java.util.stream.Collectors; import javax.annotation.Nonnull; @@ -20,9 +18,14 @@ import okhttp3.ResponseBody; import org.apache.commons.lang3.StringUtils; import org.apache.commons.validator.routines.UrlValidator; +import org.hl7.fhir.r4.model.ValueSet; +import org.hl7.fhir.r4.model.ValueSet.ConceptReferenceComponent; +import org.hl7.fhir.r4.model.ValueSet.ConceptSetComponent; +import org.hl7.fhir.r4.model.ValueSet.ValueSetComposeComponent; +import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionComponent; +import org.hl7.fhir.r4.model.ValueSet.ValueSetExpansionContainsComponent; +import org.mitre.synthea.export.FhirR4; import org.mitre.synthea.world.concepts.HealthRecord.Code; -import org.slf4j.Logger; -import org.slf4j.LoggerFactory; /** * Generates random codes based upon ValueSet URIs, with the help of a FHIR @@ -36,8 +39,7 @@ public abstract class RandomCodeGenerator { public static String expandBaseUrl = Config.get("generate.terminology_service_url") + "/ValueSet/$expand?url="; - private static final Logger logger = LoggerFactory.getLogger(RandomCodeGenerator.class); - public static Map> codeListCache = new HashMap<>(); + public static Map> codeListCache = new HashMap<>(); public static List selectedCodes = new ArrayList<>(); private static UrlValidator urlValidator = new UrlValidator(UrlValidator.ALLOW_2_SLASHES); private static OkHttpClient client = new OkHttpClient(); @@ -51,65 +53,140 @@ public abstract class RandomCodeGenerator { * a random seed to ensure reproducibility of this result * @return the randomly selected Code */ - @SuppressWarnings("unchecked") public static Code getCode(String valueSetUri, long seed, Code code) { if (urlValidator.isValid(valueSetUri)) { - expandValueSet(valueSetUri); - List codes = codeListCache.get(valueSetUri); - int randomIndex = new Random(seed).nextInt(codes.size()); - Map codeMap = (Map) codes.get(randomIndex); - validateCode(codeMap); - Code newCode = new Code(codeMap.get("system"), codeMap.get("code"), codeMap.get("display")); + Code newCode = getCode(valueSetUri, seed); + if (newCode == null) { + return code; + } + validateCode(newCode); selectedCodes.add(newCode); return newCode; } return code; } - @SuppressWarnings("unchecked") + /** + * Gets a random code from the expansion of a ValueSet. + * + * @param valueSetUri + * the URI of the ValueSet + * @param seed + * a random seed to ensure reproducibility of this result + * @return the randomly selected code + */ + public static Code getCode(String valueSetUri, long seed) { + if (urlValidator.isValid(valueSetUri)) { + expandValueSet(valueSetUri); + List codes = codeListCache.get(valueSetUri); + int randomIndex = new Random(seed).nextInt(codes.size()); + Code code = codes.get(randomIndex); + validateCode(code); + return code; + } + return null; + } + + /** + * Check whether the given code is in the given ValueSet. + * + * @param code Code to check + * @param valueSetUri URI of the ValueSet to check the code for + * @return true if the code is in the given valueset + */ + // TODO: this does not belong here, but this class is where the code cache is + public static boolean codeInValueSet(Code code, String valueSetUri) { + if (urlValidator.isValid(valueSetUri)) { + expandValueSet(valueSetUri); + List cachedCodeList = codeListCache.get(valueSetUri); + return cachedCodeList.contains(code); + } + // TODO?? + return false; + } + + private static synchronized void expandValueSet(String valueSetUri) { if (!codeListCache.containsKey(valueSetUri)) { Request request = new Request.Builder() .url(expandBaseUrl + valueSetUri) .header("Content-Type", "application/json") .build(); - Map valueSet = null; try { Response response = client.newCall(request).execute(); - ObjectMapper objectMapper = new ObjectMapper(); ResponseBody body = response.body(); if (body != null) { - valueSet = objectMapper.readValue(body.byteStream(), - new TypeReference>() { - }); + IParser parser = FhirR4.getContext().newJsonParser(); + ValueSet valueSet = (ValueSet) parser.parseResource(body.charStream()); + loadValueSet(valueSetUri, valueSet); } else { throw new RuntimeException("Value Set Expansion contained no body"); } - } catch (JsonProcessingException e) { - throw new RuntimeException("JsonProcessingException while parsing valueSet response"); } catch (IOException e) { throw new RuntimeException("Issue when expanding the value set", e); } + } + } + + /** + * Load the given value set into our cache. + * @param valueSetUri URI to reference this value set + * @param valueSet Parsed JSON representation of FHIR valueset + */ + public static void loadValueSet(String valueSetUri, ValueSet valueSet) { + if (valueSetUri == null) { + valueSetUri = valueSet.getUrl(); + } - Map expansion = (Map) valueSet.get("expansion"); - validateExpansion(expansion); - codeListCache.put(valueSetUri, (List) expansion.get("contains")); + if (valueSetUri != null && !codeListCache.containsKey(valueSetUri)) { + if (valueSet.hasExpansion()) { + ValueSetExpansionComponent expansion = valueSet.getExpansion(); + + validateExpansion(expansion); + List contains = expansion.getContains(); + List containsCodes = contains.stream() + .map(c -> new Code(c.getSystem(), c.getCode(), c.getDisplay())) + .collect(Collectors.toList()); + codeListCache.put(valueSetUri, containsCodes); + + } else if (valueSet.hasCompose()) { + List codes = new ArrayList<>(); + ValueSetComposeComponent compose = valueSet.getCompose(); + List includeList = compose.getInclude(); + + for (ConceptSetComponent include : includeList) { + String system = include.getSystem(); + + List conceptList = include.getConcept(); + + for (ConceptReferenceComponent concept : conceptList) { + codes.add(new Code(system, concept.getCode(), concept.getDisplay())); + } + } + + if (codes.isEmpty()) { + throw new RuntimeException("ValueSet does not contain any codes defined within compose"); + } + + codeListCache.put(valueSetUri, codes); + } else { + throw new RuntimeException("ValueSet does not contain compose or expansion"); + } + System.out.println("Loaded " + valueSetUri); } } - private static void validateExpansion(@Nonnull Map expansion) { - if (expansion == null) { - throw new RuntimeException("ValueSet does not contain expansion"); - } else if (!expansion.containsKey("contains") - || ((Collection) expansion.get("contains")).isEmpty()) { + private static void validateExpansion(@Nonnull ValueSetExpansionComponent expansion) { + if (expansion.getContains() == null + || expansion.getContains().isEmpty()) { throw new RuntimeException("ValueSet expansion does not contain any codes"); - } else if (!expansion.containsKey("total")) { + } else if (expansion.getTotal() == 0) { throw new RuntimeException("No total element in ValueSet expand result"); } } - private static void validateCode(Map code) { - if (StringUtils.isAnyEmpty(code.get("system"), code.get("code"), code.get("display"))) { + private static void validateCode(Code code) { + if (StringUtils.isAnyEmpty(code.system, code.code, code.display)) { throw new RuntimeException( "ValueSet contains element does not contain system, code and display"); } 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..c8bdecde48 --- /dev/null +++ b/src/test/java/org/mitre/synthea/export/flexporter/ActionsTest.java @@ -0,0 +1,609 @@ +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.time.ZonedDateTime; +import java.util.Arrays; +import java.util.Date; +import java.util.HashMap; +import java.util.HashSet; +import java.util.LinkedList; +import java.util.List; +import java.util.Map; +import java.util.Set; +import java.util.function.Function; +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.Coding; +import org.hl7.fhir.r4.model.DateTimeType; +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.Immunization; +import org.hl7.fhir.r4.model.InstantType; +import org.hl7.fhir.r4.model.MedicationRequest; +import org.hl7.fhir.r4.model.Observation; +import org.hl7.fhir.r4.model.Patient; +import org.hl7.fhir.r4.model.Period; +import org.hl7.fhir.r4.model.Procedure; +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.TimeType; +import org.hl7.fhir.r4.model.Type; +import org.junit.AfterClass; +import org.junit.BeforeClass; +import org.junit.Test; +import org.mitre.synthea.engine.Module; +import org.mitre.synthea.engine.State; +import org.mitre.synthea.export.FhirR4; +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; + + /** + * Class setup - load the mapping file containing all tests. + */ + @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 = FhirR4.getContext().newJsonParser(); + 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, 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, null); + + assertEquals("2022-02-22", i.getRecordedElement().getValueAsString()); + } + + @Test + public void testSetValues_getField_diff_applicability() { + Procedure p1 = new Procedure(); + Date startDate = new Date(0); + Date endDate = new Date(1000000); + p1.setPerformed(new Period().setStart(startDate).setEnd(endDate)); + + Procedure p2 = new Procedure(); + p2.setPerformed(new DateTimeType(new Date(0))); + + Bundle b = new Bundle(); + b.addEntry().setResource(p1); + b.addEntry().setResource(p2); + + Map action = getActionByName("testSetValues_getField_diff_applicability"); + + Actions.applyAction(b, action, null, null); + + Extension e1 = p1.getExtensionByUrl("http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-recorded"); + assertNotNull(e1); + String d1 = ((DateTimeType) e1.getValue()).getValueAsString(); + assertEquals(0, ZonedDateTime.parse(d1).toInstant().getEpochSecond()); + + Extension e2 = p2.getExtensionByUrl("http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-recorded"); + assertNotNull(e2); + String d2 = ((DateTimeType) e2.getValue()).getValueAsString(); + assertEquals(0, ZonedDateTime.parse(d2).toInstant().getEpochSecond()); + } + + @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, 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, null); + + // NOTE: this expected value may change if we ever add randomness to the date -> dateTime + // transform + assertEquals("1999-09-29T00:00:00Z", + ((DateTimeType) date.getExtension().get(0).getValue()).getValueAsString()); + } + + @Test + public void testSetValues_object() { + Patient p = new Patient(); + p.addName().addGiven("Mel").setFamily("Maroon"); + + Bundle b = new Bundle(); + b.addEntry().setResource(p); + + Map action = getActionByName("testSetValues_object"); + + Actions.applyAction(b, action, null, null); + + /* + + - name: testSetValues_object + set_values: + - applicability: Patient + fields: + - location: Patient.maritalStatus.coding + value: + system: http://snomedct.io + code: "36629006" + display: "Legally married (finding)" + + */ + + Coding c = p.getMaritalStatus().getCodingFirstRep(); + + assertEquals("http://snomedct.io", c.getSystem()); + assertEquals("36629006", c.getCode()); + assertEquals("Legally married (finding)", c.getDisplay()); + } + + @Test + public void testKeepResources() throws Exception { + Bundle b = loadFixtureBundle("sample_complete_patient.json"); + + + Map action = getActionByName("testKeepResources"); + + Actions.applyAction(b, action, null, 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, null); + + countProvenance = b.getEntry().stream() + .filter(bec -> bec.getResource().getResourceType() == ResourceType.Provenance).count(); + + assertEquals(0, countProvenance); + } + + @Test + public void testDeleteResourcesCascade() throws Exception { + Bundle b = loadFixtureBundle("sample_complete_patient.json"); + + System.out.println(b.getEntry().size()); + + Map action = getActionByName("testDeleteResourcesCascade"); + + // action deletes Patient resource, everything should reference back to Patient + + Actions.applyAction(b, action, null, null); + + System.out.println(b.getEntry().size()); + b.getEntry().forEach(e -> System.out.println(e.getResource().getResourceType())); + } + + @Test + public void testDateFilter() throws Exception { + Bundle b = loadFixtureBundle("sample_complete_patient.json"); + + System.out.println(b.getEntry().size()); + Map action = getActionByName("testDateFilter"); + + Actions.applyAction(b, action, null, null); + + System.out.println(b.getEntry().size()); + + } + + @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, 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 testShiftDates() throws Exception { + Patient p = new Patient(); + p.addName().addGiven("Terry").setFamily("Teal"); + DateType date = new DateType(); + date.fromStringValue("1999-09-29"); + p.setBirthDateElement(date); + + Bundle b = new Bundle(); + b.addEntry().setResource(p); + + Observation o = new Observation(); + Period period = new Period(); + period.setStartElement(new DateTimeType("1999-10-05T10:24:01-05:00")); + period.setEndElement(new DateTimeType("1999-10-06T10:24:01-05:00")); + o.setEffective(period); + o.setIssuedElement(new InstantType("1999-10-06T10:24:01-05:00")); + o.setValue(new TimeType("10:24:01")); + + b.addEntry().setResource(o); + + Map action = getActionByName("testShiftDates"); + Actions.applyAction(b, action, null, null); + + assertEquals("1998-09-29", p.getBirthDateElement().getValueAsString()); + assertEquals("1998-10-05T10:24:01-05:00", period.getStartElement().getValueAsString()); + assertEquals("1998-10-06T10:24:01-05:00", period.getEndElement().getValueAsString()); + } + + @Test + public void testExec() throws Exception { + Map action = getActionByName("testExecuteScript"); + + 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); + + Bundle updatedBundle = Actions.applyAction(b, action, null, new FlexporterJavascriptContext()); + + /* + function apply(bundle) { + bundle['entry'][0]['resource']['meta'] = {profile: ['http://example.com/dummy-profile']} + } + + function apply2(resource, bundle) { + if (resource.resourceType == 'Patient') { + resource.birthDate = '2022-02-22'; + } + } + + */ + + Patient outPatient = (Patient) updatedBundle.getEntryFirstRep().getResource(); + + assertEquals("http://example.com/dummy-profile", outPatient.getMeta().getProfile().get(0).getValueAsString()); + + assertEquals("2022-02-22", outPatient.getBirthDateElement().getValueAsString()); + } + + @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); + + + List procedures = b.getEntry().stream() + .filter(bec -> bec.getResource().getResourceType() == ResourceType.Procedure) + .map(bec -> (Procedure) bec.getResource()) + .collect(Collectors.toList()); + + Map action = getActionByName("testCreateResources_createBasedOn"); + + Actions.applyAction(b, action, null, null); + + // there should now be one ServiceRequest per Procedure + + // get a map of id --> servicerequest, for easy lookups + Map serviceRequests = b.getEntry().stream() + .filter(bec -> bec.getResource().getResourceType() == ResourceType.ServiceRequest) + .map(bec -> (ServiceRequest) bec.getResource()) + .collect(Collectors.toMap(ServiceRequest::getId, Function.identity())); + + assertEquals(procedures.size(), serviceRequests.size()); + + String patientId = b.getEntryFirstRep().getResource().getId(); + + // iterate over the procedures so we can find the servicerequest for each + for (Procedure proc : procedures) { + + // "ServiceRequest/".length == 15 + String basedOn = proc.getBasedOnFirstRep().getReference().substring(15); + + ServiceRequest sr = serviceRequests.remove(basedOn); + assertNotNull(sr); + assertEquals("plan", sr.getIntent().toCode()); + assertEquals(patientId, sr.getSubject().getReference()); + assertEquals(proc.getEncounter().getReference(), sr.getEncounter().getReference()); + assertTrue(proc.getCode().equalsDeep(sr.getCode())); + } + + // we removed each SR as we checked it, to ensure there are none left + assertEquals(0, serviceRequests.size()); + + } + + @Test + public void testCreateResources_createBasedOnState() throws Exception { + Patient p = new Patient(); + p.setId("mypatient"); + + Bundle b = new Bundle(); + b.setType(BundleType.COLLECTION); + b.addEntry().setResource(p); + + Person person = new Person(0L); + person.history = new LinkedList(); + Module m = Module.getModuleByPath("sinusitis"); + + // this is cheating but the alternative is to pick a seed that goes through this path + // which is flaky + for (String stateName : List.of("Initial", "Potential_Onset", "Bacterial_Infection_Starts", + "Doctor_Visit", "Penicillin_Allergy_Check", "Prescribe_Alternative_Antibiotic")) { + State s = m.getState(stateName).clone(); + + s.entered = 120_000L; + s.exited = 120_000L; + + person.history.add(0, s); + } + person.attributes.put(m.name, person.history); + + + Map action = getActionByName("testCreateResources_createBasedOnState"); + + Actions.applyAction(b, action, person, null); + + + + List entries = b.getEntry(); + assertEquals(2, entries.size()); + /* + - name: testCreateResources_createBasedOnState + create_resource: + - resourceType: MedicationRequest + based_on: + module: Sinusitis + state: Prescribe_Alternative_Antibiotic + profiles: + - http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medicationnotrequested + fields: + - location: MedicationRequest.doNotPerform + value: "true" + - location: MedicationRequest.status + value: completed + - location: MedicationRequest.intent + value: order + # - location: MedicationRequest.encounter.reference + # value: $getField([Procedure.encounter.reference]) + - location: MedicationRequest.subject.reference + value: $findRef([Patient]) + # - location: MedicationRequest.medicationCodeableConcept + # value: $getField([Procedure.code]) + - location: MedicationRequest.authoredOn + value: $getField([State.entered]) + */ + + Resource newResource = entries.get(1).getResource(); + + assertEquals("MedicationRequest", newResource.getResourceType().toString()); + + MedicationRequest mr = (MedicationRequest) newResource; + + assertEquals(true, mr.getDoNotPerform()); + assertEquals("COMPLETED", mr.getStatus().toString()); + assertEquals("ORDER", mr.getIntent().toString()); + assertEquals("Patient/mypatient", mr.getSubject().getReference()); + + // note: the date conversion loses the millis part + // so this will only work if the value % 1000 == 0 + assertEquals(120_000L, mr.getAuthoredOn().toInstant().toEpochMilli()); + } + + + @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, null); + + 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..30d163d2da --- /dev/null +++ b/src/test/java/org/mitre/synthea/export/flexporter/CustomFHIRPathResourceGeneratorR4Test.java @@ -0,0 +1,193 @@ +package org.mitre.synthea.export.flexporter; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; + +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; +import org.mitre.synthea.export.FhirR4; + + +public class CustomFHIRPathResourceGeneratorR4Test { + + @SuppressWarnings("unused") + private static void logPatientJson(Patient p) { + String patientJson = FhirR4.getContext().newJsonParser().setPrettyPrint(true) + .encodeResourceToString(p); + + System.out.println(patientJson); + } + + private Patient createPatient(Map fhirPathMapping) { + CustomFHIRPathResourceGeneratorR4 fhirPathGenerator = + new CustomFHIRPathResourceGeneratorR4<>(); + fhirPathGenerator.setMapping(fhirPathMapping); + return fhirPathGenerator.generateResource(Patient.class); + } + + private void updatePatient(Patient p, Map fhirPathMapping) { + CustomFHIRPathResourceGeneratorR4 fhirPathGenerator = + new CustomFHIRPathResourceGeneratorR4<>(); + 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()); + } + + @Test + public void testSingleFieldSetter() { + Patient p = new Patient(); + CustomFHIRPathResourceGeneratorR4.setField(p, "name.given", "TestName"); + assertEquals("TestName", p.getNameFirstRep().getGivenAsSingleString()); + } +} 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..785eec0bf2 --- /dev/null +++ b/src/test/java/org/mitre/synthea/export/flexporter/FhirPathUtilsTest.java @@ -0,0 +1,124 @@ +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 java.util.Map; + +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")); + } + + @Test + public void testVariables() { + Patient p1 = new Patient(); + p1.addName().addGiven("Jeff").setFamily("Goldblum"); + Bundle b1 = new Bundle(); + b1.addEntry().setResource(p1); + + Patient p2 = new Patient(); + p2.addName().addGiven("Jamie Lee").setFamily("Curtis"); + Bundle b2 = new Bundle(); + b2.addEntry().setResource(p2); + + String fhirpath = "Patient.name.family in %jurassicNames"; + + Map variables = Map.of("jurassicNames", List.of("Neill", "Dern", "Goldblum")); + + assertTrue(FhirPathUtils.appliesToBundle(b1, fhirpath, variables)); + assertFalse(FhirPathUtils.appliesToBundle(b2, fhirpath, variables)); + } +} diff --git a/src/test/java/org/mitre/synthea/export/flexporter/FieldWrapperTest.java b/src/test/java/org/mitre/synthea/export/flexporter/FieldWrapperTest.java new file mode 100644 index 0000000000..d547f71473 --- /dev/null +++ b/src/test/java/org/mitre/synthea/export/flexporter/FieldWrapperTest.java @@ -0,0 +1,77 @@ +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.time.LocalDateTime; + +import org.hl7.fhir.instance.model.api.IBase; +import org.hl7.fhir.r4.model.DateTimeType; +import org.hl7.fhir.r4.model.DateType; +import org.hl7.fhir.r4.model.Goal; +import org.hl7.fhir.r4.model.Observation; +import org.hl7.fhir.r4.model.Procedure; +import org.hl7.fhir.r4.model.Reference; +import org.junit.Test; +import org.mitre.synthea.export.flexporter.FieldWrapper.DateFieldWrapper; +import org.mitre.synthea.export.flexporter.FieldWrapper.ReferenceFieldWrapper; + + +public class FieldWrapperTest { + @Test + public void testGetReference() { + ReferenceFieldWrapper rfw = new ReferenceFieldWrapper(Observation.class, "subject"); + + Observation obs = new Observation(); + obs.setSubject(new Reference().setReference("Patient/1")); + + assertEquals("Patient/1", rfw.getReference(obs)); + } + + @Test + public void testGetNestedField() { + DateFieldWrapper dfw = new DateFieldWrapper(Goal.class, "target.due"); + + Goal goal = new Goal(); + goal.addTarget().setDue(new DateType("2023-08-01")); + + IBase result = dfw.getSingle(goal); + + assertTrue(result instanceof DateType); + assertEquals("2023-08-01", ((DateType)result).getValueAsString()); + + LocalDateTime jan12023 = LocalDateTime.of(2023, 1, 1, 0, 0); + LocalDateTime dec312023 = LocalDateTime.of(2023, 12, 31, 0, 0); + LocalDateTime jan11999 = LocalDateTime.of(1999, 1, 1, 0, 0); + LocalDateTime dec312021 = LocalDateTime.of(2021, 12, 31, 0, 0); + + assertTrue(dfw.valueInRange(goal, jan12023, dec312023)); + assertFalse(dfw.valueInRange(goal, jan11999, dec312021)); + } + + + @Test + public void testGetNestedFieldChoiceType() { + DateFieldWrapper dfw = new DateFieldWrapper(Procedure.class, "performed"); + + Procedure p = new Procedure(); + p.setPerformed(new DateTimeType("2023-08-11T13:51:00")); + + IBase result = dfw.getSingle(p); + assertTrue(result instanceof DateTimeType); + assertEquals("2023-08-11T13:51:00", ((DateTimeType)result).getValueAsString()); + } + + @Test + public void testSetNestedFieldChoiceType() { + DateFieldWrapper dfw = new DateFieldWrapper(Procedure.class, "performed"); + + Procedure p = new Procedure(); + dfw.set(p, new DateTimeType("2002-08-11T13:51:00")); + + IBase result = dfw.getSingle(p); + assertTrue(result instanceof DateTimeType); + assertEquals("2002-08-11T13:51:00", ((DateTimeType)result).getValueAsString()); + } +} diff --git a/src/test/java/org/mitre/synthea/export/flexporter/FlexporterJavaScriptContextTest.java b/src/test/java/org/mitre/synthea/export/flexporter/FlexporterJavaScriptContextTest.java new file mode 100644 index 0000000000..6e912f2d9b --- /dev/null +++ b/src/test/java/org/mitre/synthea/export/flexporter/FlexporterJavaScriptContextTest.java @@ -0,0 +1,63 @@ +package org.mitre.synthea.export.flexporter; + +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertTrue; + +import ca.uhn.fhir.parser.IParser; + +import org.hl7.fhir.r4.model.Bundle; +import org.hl7.fhir.r4.model.DateType; +import org.hl7.fhir.r4.model.DomainResource; +import org.hl7.fhir.r4.model.Patient; +import org.junit.Test; +import org.mitre.synthea.export.FhirR4; + +public class FlexporterJavaScriptContextTest { + + @Test + public void testJavascriptContext() { + FlexporterJavascriptContext context = new FlexporterJavascriptContext(); + + context.loadFunction("function applySomeProfile(resource) {\n" + + " resource['meta'] = {profile: [\"http://example.com/random-profile\"]}\n" + + "}"); + + context.loadFunction("function giveEveryResourceSomeText(bundle) {\n" + + " bundle.entry.forEach(e => e.resource.text = {\n" + + " \"status\": \"generated\",\n" + + " \"div\": \"
javascript was here
\"\n" + + " });\n" + + "}"); + + Patient p = new Patient(); + p.addName().addGiven("Alex").setFamily("Aquamarine"); + DateType date = new DateType(); + date.fromStringValue("1999-09-29"); + p.setBirthDateElement(date); + + Bundle b = new Bundle(); + b.addEntry().setResource(p); + + IParser parser = FhirR4.getContext().newJsonParser(); + + String bundleJson = parser.encodeResourceToString(b); + context.loadBundle(bundleJson); + + context.applyFunctionToBundle("giveEveryResourceSomeText"); + context.applyFunctionToResources("applySomeProfile", "Patient"); + + String outBundleJson = context.getBundle(); + + Bundle outBundle = parser.parseResource(Bundle.class, outBundleJson); + + outBundle.getEntry().forEach(entry -> { + DomainResource resource = (DomainResource) entry.getResource(); + assertEquals("http://example.com/random-profile", resource.getMeta().getProfile().get(0).getValueAsString()); + + assertTrue(resource.getText().getDivAsString().contains("javascript was here")); + // check here is "contains" instead of simple equality + // because HAPI seems to add the xmlns to the text, which is probably consistent, + // but this is the real point of the test + }); + } +} diff --git a/src/test/java/org/mitre/synthea/helpers/RandomCodeGeneratorTest.java b/src/test/java/org/mitre/synthea/helpers/RandomCodeGeneratorTest.java index ce6ecae964..ec7b635527 100644 --- a/src/test/java/org/mitre/synthea/helpers/RandomCodeGeneratorTest.java +++ b/src/test/java/org/mitre/synthea/helpers/RandomCodeGeneratorTest.java @@ -1,7 +1,10 @@ package org.mitre.synthea.helpers; +import static org.junit.Assert.assertThrows; import static org.mitre.synthea.TestHelper.SNOMED_URI; +import ca.uhn.fhir.parser.DataFormatException; + import java.io.IOException; import java.io.InputStream; import java.nio.charset.StandardCharsets; @@ -57,7 +60,7 @@ public void throwsWhenNoExpansion() throws IOException { try { RandomCodeGenerator.getCode(VALUE_SET_URI, SEED, this.code); } catch (RuntimeException e) { - Assert.assertEquals("ValueSet does not contain expansion", e.getMessage()); + Assert.assertEquals("ValueSet does not contain compose or expansion", e.getMessage()); return; } Assert.fail("Should have thrown a no expansion exception"); @@ -107,14 +110,10 @@ public void throwsWhenMissingCodeElements() throws IOException { public void throwsWhenInvalidResponse() throws IOException { prepareServer("noExpansion.ValueSet.json", true); - try { - RandomCodeGenerator.getCode(VALUE_SET_URI, SEED, this.code); - } catch (RuntimeException e) { - Assert.assertEquals("JsonProcessingException while parsing valueSet response", - e.getMessage()); - return; - } - Assert.fail("Should have thrown a JsonProcessingException exception"); + assertThrows( + DataFormatException.class, + () -> RandomCodeGenerator.getCode(VALUE_SET_URI, SEED, this.code) + ); } diff --git a/src/test/resources/flexporter/mcode.yml b/src/test/resources/flexporter/mcode.yml new file mode 100644 index 0000000000..c33962e412 --- /dev/null +++ b/src/test/resources/flexporter/mcode.yml @@ -0,0 +1,84 @@ +--- +# name is just a friendly name for this mapping +name: mCODE Flexporter Test + +# applicability determines whether this mapping applies to a given file. +# for now the assumption is 1 file = 1 synthea patient bundle. +applicability: Condition.code.coding.where($this.code in %primaryCancerConditionCodes) +# for real mCODE: +# In FHIR terms, these are patients who have a Condition where +# Condition.code is a member of the value set [PrimaryOrUncertainBehaviorCancerDisorderVS] +# and +# Condition.verificationStatus is confirmed. +# -- https://build.fhir.org/ig/HL7/fhir-mCODE-ig/conformance-patients.html + +variables: + primaryCancerConditionCodes: + - '188151006' # Malignant neoplasm of central part of female breast (disorder) + - '254837009' # Malignant neoplasm of breast (disorder) (B) + - '93761005' # Primary malignant neoplasm of colon (C) + - '109838007' # Overlapping malignant neoplasm of colon (C) + - '363406005' # Malignant tumor of colon (C) + - '94260004' # Secondary malignant neoplasm of colon (C) -- note this is a "secondary" code but is intended to be a primary cancer + - '254637007' # Non-small cell lung cancer (disorder) (L) + - '254632001' # Small cell carcinoma of lung (disorder) (L) + - '424132000' # Non-small cell carcinoma of lung, TNM stage 1 (disorder) (L) + - '425048006' # Non-small cell carcinoma of lung, TNM stage 2 (disorder) (L) + - '422968005' # Non-small cell carcinoma of lung, TNM stage 3 (disorder) (L) + - '423121009' # Non-small cell carcinoma of lung, TNM stage 4 (disorder) (L) + - '67811000119102' # Primary small cell malignant neoplasm of lung, TNM stage 1 (disorder) (L) + - '67821000119109' # Primary small cell malignant neoplasm of lung, TNM stage 2 (disorder) (L) + - '67831000119107' # Primary small cell malignant neoplasm of lung, TNM stage 3 (disorder) (L) + - '67841000119103' # Primary small cell malignant neoplasm of lung, TNM stage 4 (disorder) (L) + + +# reminder - the fhir_mapper for Synthea->mCODE 1.0 is here: +# https://github.com/standardhealth/fhir-mapper/blob/mcode1/src/mapping/mappers/SyntheaToV10.js + +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/mcode/StructureDefinition/mcode-cancer-patient + applicability: Patient + + - profile: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-stage-group + applicability: Observation.code.coding.where($this.code = '21908-9') + + - profile: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-primary-tumor-category + applicability: Observation.code.coding.where($this.code = '21905-5') + + - profile: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-regional-nodes-category + applicability: Observation.code.coding.where($this.code = '21906-3') + + - profile: http://hl7.org/fhir/us/mcode/StructureDefinition/mcode-tnm-clinical-distant-metastases-category + applicability: Observation.code.coding.where($this.code = '21907-1') + + + - name: Create TNM References + set_values: + # TODO: make applicability optionally a list + # because sometimes it will be easier/cleaner to define 2 separate fhirpaths than make 1 complex one or duplicate an action here + - applicability: Observation.code.coding.where($this.code = '21908-9') + fields: + - location: Observation.hasMember.where(display='Tumor Category').reference + value: $findRef([Observation.code.coding.where($this.code = '21905-5')]) + - location: Observation.hasMember.where(display='Nodes Category').reference + value: $findRef([Observation.code.coding.where($this.code = '21906-3')]) + - location: Observation.hasMember.where(display='Metastases Category').reference + value: $findRef([Observation.code.coding.where($this.code = '21907-1')]) + + + - name: Set Primary Cancer Focus + set_values: + - applicability: Observation.code.coding.where($this.code = '21905-5') # Primary Tumor Category + fields: + - location: Observation.focus.reference + value: $findRef([Condition.code.coding.where($this.code = '254837009')]) + diff --git a/src/test/resources/flexporter/qicore_minimal.yaml b/src/test/resources/flexporter/qicore_minimal.yaml new file mode 100644 index 0000000000..822469e153 --- /dev/null +++ b/src/test/resources/flexporter/qicore_minimal.yaml @@ -0,0 +1,69 @@ +--- +# name is just a friendly name for this mapping +name: QI Core Minimal + +# 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-encounter-diagnosis + 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: Set Missing Values + 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 + + - applicability: Procedure.performed.ofType(Period) + fields: + - location: Procedure.extension.where(url='http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-recorded').valueDateTime + value: $getField([Procedure.performed.start]) + - applicability: Procedure.performed.ofType(dateTime) + fields: + - location: Procedure.extension.where(url='http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-recorded').valueDateTime + value: $getField([Procedure.performed]) + + + 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" + }, { + "type": { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "DL", + "display": "Driver's License" + } ], + "text": "Driver's License" + }, + "system": "urn:oid:2.16.840.1.113883.4.3.25", + "value": "S99966502" + }, { + "type": { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/v2-0203", + "code": "PPN", + "display": "Passport Number" + } ], + "text": "Passport Number" + }, + "system": "http://standardhealthrecord.org/fhir/StructureDefinition/passportNumber", + "value": "X89909962X" + } ], + "name": [ { + "use": "official", + "family": "Gerlach374", + "given": [ "Lindsay928" ], + "prefix": [ "Mr." ] + } ], + "telecom": [ { + "system": "phone", + "value": "555-450-5873", + "use": "home" + } ], + "gender": "male", + "birthDate": "1950-10-24", + "address": [ { + "extension": [ { + "url": "http://hl7.org/fhir/StructureDefinition/geolocation", + "extension": [ { + "url": "latitude", + "valueDecimal": 42.167344139459686 + }, { + "url": "longitude", + "valueDecimal": -71.07262371813607 + } ] + } ], + "line": [ "690 Raynor Overpass" ], + "city": "Randolph", + "state": "MA", + "country": "US" + } ], + "maritalStatus": { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/v3-MaritalStatus", + "code": "M", + "display": "M" + } ], + "text": "M" + }, + "multipleBirthBoolean": false, + "communication": [ { + "language": { + "coding": [ { + "system": "urn:ietf:bcp:47", + "code": "en-US", + "display": "English" + } ], + "text": "English" + } + } ] + }, + "request": { + "method": "POST", + "url": "Patient" + } + }, { + "fullUrl": "urn:uuid:3699e7e7-8b1b-4a68-8011-e7a166598566", + "resource": { + "resourceType": "Encounter", + "id": "3699e7e7-8b1b-4a68-8011-e7a166598566", + "meta": { + "profile": [ "http://hl7.org/fhir/us/core/StructureDefinition/us-core-encounter", "http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-encounter" ] + }, + "identifier": [ { + "use": "official", + "system": "https://github.com/synthetichealth/synthea", + "value": "3699e7e7-8b1b-4a68-8011-e7a166598566" + } ], + "status": "finished", + "class": { + "system": "http://terminology.hl7.org/CodeSystem/v3-ActCode", + "code": "AMB" + }, + "type": [ { + "coding": [ { + "system": "http://snomed.info/sct", + "code": "162673000", + "display": "General examination of patient (procedure)" + } ], + "text": "General examination of patient (procedure)" + } ], + "subject": { + "reference": "urn:uuid:d5582579-7193-4866-5560-a01e723b6552", + "display": "Mr. Lindsay928 Gerlach374" + }, + "participant": [ { + "type": [ { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/v3-ParticipationType", + "code": "PPRF", + "display": "primary performer" + } ], + "text": "primary performer" + } ], + "period": { + "start": "1979-01-02T11:44:52-05:00", + "end": "1979-01-02T11:59:52-05:00" + }, + "individual": { + "reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999962229", + "display": "Dr. Alphonso102 Nienow652" + } + } ], + "period": { + "start": "1979-01-02T11:44:52-05:00", + "end": "1979-01-02T11:59:52-05:00" + }, + "location": [ { + "location": { + "reference": "Location?identifier=https://github.com/synthetichealth/synthea|cb6521ac-69d9-3b02-b34a-15e5d2ed50ea", + "display": "PCP74147" + } + } ], + "serviceProvider": { + "reference": "Organization?identifier=https://github.com/synthetichealth/synthea|dd406540-fa97-3a90-858e-0a0ea61cf07b", + "display": "PCP74147" + } + }, + "request": { + "method": "POST", + "url": "Encounter" + } + }, { + "fullUrl": "urn:uuid:9a01d04d-86de-75e6-5c07-a4ba74966e68", + "resource": { + "resourceType": "Condition", + "id": "9a01d04d-86de-75e6-5c07-a4ba74966e68", + "meta": { + "profile": [ "http://hl7.org/fhir/us/core/StructureDefinition/us-core-condition" ] + }, + "clinicalStatus": { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/condition-clinical", + "code": "active" + } ] + }, + "verificationStatus": { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/condition-ver-status", + "code": "confirmed" + } ] + }, + "category": [ { + "coding": [ { + "system": "http://terminology.hl7.org/CodeSystem/condition-category", + "code": "encounter-diagnosis", + "display": "Encounter Diagnosis" + } ] + } ], + "code": { + "coding": [ { + "system": "http://snomed.info/sct", + "code": "15777000", + "display": "Prediabetes" + } ], + "text": "Prediabetes" + }, + "subject": { + "reference": "urn:uuid:d5582579-7193-4866-5560-a01e723b6552" + }, + "encounter": { + "reference": "urn:uuid:3699e7e7-8b1b-4a68-8011-e7a166598566" + }, + "onsetDateTime": "1979-01-02T11:44:52-05:00", + "recordedDate": "1979-01-02T11:44:52-05:00" + }, + "request": { + "method": "POST", + "url": "Condition" + } + }, { + "fullUrl": "urn:uuid:585cb148-8912-c5f6-d96e-e3d5105e6c03", + "resource": { + "resourceType": "CareTeam", + "id": "585cb148-8912-c5f6-d96e-e3d5105e6c03", + "meta": { + "profile": [ "http://hl7.org/fhir/us/core/StructureDefinition/us-core-careteam" ] + }, + "status": "active", + "subject": { + "reference": "urn:uuid:d5582579-7193-4866-5560-a01e723b6552" + }, + "encounter": { + "reference": "urn:uuid:3699e7e7-8b1b-4a68-8011-e7a166598566" + }, + "period": { + "start": "1979-01-02T11:44:52-05:00" + }, + "participant": [ { + "role": [ { + "coding": [ { + "system": "http://snomed.info/sct", + "code": "116154003", + "display": "Patient" + } ], + "text": "Patient" + } ], + "member": { + "reference": "urn:uuid:d5582579-7193-4866-5560-a01e723b6552", + "display": "Mr. Lindsay928 Gerlach374" + } + }, { + "role": [ { + "coding": [ { + "system": "http://snomed.info/sct", + "code": "223366009", + "display": "Healthcare professional (occupation)" + } ], + "text": "Healthcare professional (occupation)" + } ], + "member": { + "reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999962229", + "display": "Dr. Alphonso102 Nienow652" + } + }, { + "role": [ { + "coding": [ { + "system": "http://snomed.info/sct", + "code": "224891009", + "display": "Healthcare services (qualifier value)" + } ], + "text": "Healthcare services (qualifier value)" + } ], + "member": { + "reference": "Organization?identifier=https://github.com/synthetichealth/synthea|dd406540-fa97-3a90-858e-0a0ea61cf07b", + "display": "PCP74147" + } + } ], + "reasonCode": [ { + "coding": [ { + "system": "http://snomed.info/sct", + "code": "15777000", + "display": "Prediabetes" + } ], + "text": "Prediabetes" + } ], + "managingOrganization": [ { + "reference": "Organization?identifier=https://github.com/synthetichealth/synthea|dd406540-fa97-3a90-858e-0a0ea61cf07b", + "display": "PCP74147" + } ] + }, + "request": { + "method": "POST", + "url": "CareTeam" + } + }, { + "fullUrl": "urn:uuid:50a0789d-acf1-9448-58f3-5edce8b59e73", + "resource": { + "resourceType": "CarePlan", + "id": "50a0789d-acf1-9448-58f3-5edce8b59e73", + "meta": { + "profile": [ "http://hl7.org/fhir/us/core/StructureDefinition/us-core-careplan" ] + }, + "text": { + "status": "generated", + "div": "
Care Plan for Diabetes self management plan.
Activities:
  • Diabetes self management plan
  • Diabetes self management plan

Care plan is meant to treat Prediabetes.
" + }, + "status": "active", + "intent": "order", + "category": [ { + "coding": [ { + "system": "http://hl7.org/fhir/us/core/CodeSystem/careplan-category", + "code": "assess-plan" + } ] + }, { + "coding": [ { + "system": "http://snomed.info/sct", + "code": "698360004", + "display": "Diabetes self management plan" + } ], + "text": "Diabetes self management plan" + } ], + "subject": { + "reference": "urn:uuid:d5582579-7193-4866-5560-a01e723b6552" + }, + "encounter": { + "reference": "urn:uuid:3699e7e7-8b1b-4a68-8011-e7a166598566" + }, + "period": { + "start": "1979-01-02T11:44:52-05:00" + }, + "careTeam": [ { + "reference": "urn:uuid:585cb148-8912-c5f6-d96e-e3d5105e6c03" + } ], + "addresses": [ { + "reference": "urn:uuid:9a01d04d-86de-75e6-5c07-a4ba74966e68" + } ], + "activity": [ { + "detail": { + "code": { + "coding": [ { + "system": "http://snomed.info/sct", + "code": "160670007", + "display": "Diabetic diet" + } ], + "text": "Diabetic diet" + }, + "status": "in-progress", + "location": { + "display": "PCP74147" + } + } + }, { + "detail": { + "code": { + "coding": [ { + "system": "http://snomed.info/sct", + "code": "229065009", + "display": "Exercise therapy" + } ], + "text": "Exercise therapy" + }, + "status": "in-progress", + "location": { + "display": "PCP74147" + } + } + } ] + }, + "request": { + "method": "POST", + "url": "CarePlan" + } + }, { + "fullUrl": "urn:uuid:d96f0eb1-e968-03d9-fd4c-d38d5192c590", + "resource": { + "resourceType": "DiagnosticReport", + "id": "d96f0eb1-e968-03d9-fd4c-d38d5192c590", + "meta": { + "profile": [ "http://hl7.org/fhir/us/core/StructureDefinition/us-core-diagnosticreport-note" ] + }, + "status": "final", + "category": [ { + "coding": [ { + "system": "http://loinc.org", + "code": "34117-2", + "display": "History and physical note" + }, { + "system": "http://loinc.org", + "code": "51847-2", + "display": "Evaluation+Plan note" + } ] + } ], + "code": { + "coding": [ { + "system": "http://loinc.org", + "code": "34117-2", + "display": "History and physical note" + }, { + "system": "http://loinc.org", + "code": "51847-2", + "display": "Evaluation+Plan note" + } ] + }, + "subject": { + "reference": "urn:uuid:d5582579-7193-4866-5560-a01e723b6552" + }, + "encounter": { + "reference": "urn:uuid:3699e7e7-8b1b-4a68-8011-e7a166598566" + }, + "effectiveDateTime": "1979-01-02T11:44:52-05:00", + "issued": "1979-01-02T11:44:52.558-05:00", + "performer": [ { + "reference": "Practitioner?identifier=http://hl7.org/fhir/sid/us-npi|9999962229", + "display": "Dr. Alphonso102 Nienow652" + } ], + "presentedForm": [ { + "contentType": "text/plain; charset=utf-8", + "data": 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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..fce2713676 --- /dev/null +++ b/src/test/resources/flexporter/test_mapping.yaml @@ -0,0 +1,203 @@ +--- +# 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 + + + + - 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_getField_diff_applicability + set_values: + - applicability: Procedure.performed.ofType(Period) + fields: + - location: Procedure.extension.where(url='http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-recorded').valueDateTime + value: $getField([Procedure.performed.start]) + - applicability: Procedure.performed.ofType(dateTime) + fields: + - location: Procedure.extension.where(url='http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-recorded').valueDateTime + value: $getField([Procedure.performed]) + + - 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: testSetValues_object + set_values: + - applicability: Patient + fields: + - location: Patient.maritalStatus.coding + value: + system: http://snomedct.io + code: "36629006" + display: "Legally married (finding)" + + + + - 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: + resource: Procedure + fields: + - location: ServiceRequest.intent + value: plan + - location: ServiceRequest.encounter.reference + value: $getField([Procedure.encounter.reference]) + - location: ServiceRequest.subject.reference + value: $findRef([Patient]) + - location: ServiceRequest.code + value: $getField([Procedure.code]) + + # this works if the VS is loaded but otherwise tries to make a network lookup + # so disable for now + # - location: ServiceRequest.code.coding + # value: $randomCode([http://hl7.org/fhir/us/mcode/ValueSet/mcode-laterality-vs]) + + # TODO: is "writeback" the best term here? + writeback: + - location: Procedure.basedOn.reference + value: $setRef([ServiceRequest]) + + - name: testCreateResources_createBasedOnState + create_resource: + - resourceType: MedicationRequest + based_on: + module: Sinusitis + state: Prescribe_Alternative_Antibiotic + profiles: + - http://hl7.org/fhir/us/qicore/StructureDefinition/qicore-medicationnotrequested + fields: + - location: MedicationRequest.doNotPerform + value: "true" + - location: MedicationRequest.status + value: completed + - location: MedicationRequest.intent + value: order + # - location: MedicationRequest.encounter.reference + # value: $getField([Procedure.encounter.reference]) + - location: MedicationRequest.subject.reference + value: $findRef([Patient]) + # - location: MedicationRequest.medicationCodeableConcept + # value: $getField([Procedure.code]) + - location: MedicationRequest.authoredOn + value: $getField([State.entered]) + + - 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]) + + - name: testExecuteScript + execute_script: + - apply_to: bundle + function_name: apply + function: | + function apply(bundle) { + bundle['entry'][0]['resource']['meta'] = {profile: ['http://example.com/dummy-profile']} + } + - apply_to: resource + function_name: apply2 + resource_type: Patient + function: | + function apply2(resource, bundle) { + resource.birthDate = '2022-02-22'; + } + + - name: testShiftDates + shift_dates: P-1Y + # P[n]Y[n]M[n]DT[n]H[n]M[n]S + + - name: testDateFilter + min_date: !!str "2000-01-01T00:00:00" + max_date: !!str "2000-12-31T23:59:59" + + - name: testKeepResources + keep_resources: + - Patient + - Encounter + - Condition + + - name: testDeleteResources + delete_resources: + - Provenance + + - name: testDeleteResourcesCascade + delete_resources: + - Patient \ No newline at end of file