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Merge pull request #1219 from synthetichealth/flexporter
Flexporter
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,18 @@ | ||
| #!/usr/bin/env sh | ||
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| ############################################################################## | ||
| ## | ||
| ## Flexporter launcher for UN*X | ||
| ## | ||
| ############################################################################## | ||
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| ARGS= | ||
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| for arg in "$@" | ||
| do | ||
| ARGS=$ARGS\'$arg\', | ||
| # Trailing comma ok, don't need to remove it | ||
| done | ||
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| ./gradlew flexporter -Params="[$ARGS]" | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,222 @@ | ||
| import ca.uhn.fhir.parser.DataFormatException; | ||
| import ca.uhn.fhir.parser.IParser; | ||
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| import com.fasterxml.jackson.core.type.TypeReference; | ||
| import com.fasterxml.jackson.databind.ObjectMapper; | ||
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| 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; | ||
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| 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; | ||
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| /** | ||
| * 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 { | ||
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| /** | ||
| * 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<String> argsQ = new ArrayDeque<String>(Arrays.asList(args)); | ||
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| File igDirectory = null; | ||
| File sourceFile = null; | ||
| File mappingFile = null; | ||
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| while (!argsQ.isEmpty()) { | ||
| String currArg = argsQ.poll(); | ||
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| if (currArg.equals("-ig")) { | ||
| String value = argsQ.poll(); | ||
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| if (value == null) { | ||
| throw new FileNotFoundException("No implementation guide directory provided"); | ||
| } | ||
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| igDirectory = new File(value); | ||
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| 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)); | ||
| } | ||
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| } else if (currArg.equals("-fm")) { | ||
| String value = argsQ.poll(); | ||
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| if (value == null) { | ||
| throw new FileNotFoundException("No mapping file provided"); | ||
| } | ||
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| mappingFile = new File(value); | ||
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| if (!mappingFile.exists()) { | ||
| throw new FileNotFoundException( | ||
| String.format("Specified mapping file (%s) does not exist", value)); | ||
| } | ||
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| } else if (currArg.equals("-s")) { | ||
| String value = argsQ.poll(); | ||
| sourceFile = new File(value); | ||
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| if (value == null) { | ||
| throw new FileNotFoundException("No Synthea source FHIR provided"); | ||
| } | ||
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| if (!sourceFile.exists()) { | ||
| throw new FileNotFoundException( | ||
| String.format("Specified Synthea source FHIR (%s) does not exist", value)); | ||
| } | ||
| } | ||
| } | ||
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| if (mappingFile == null || sourceFile == null) { | ||
| usage(); | ||
| System.exit(1); | ||
| } | ||
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| convertFhir(mappingFile, igDirectory, sourceFile); | ||
| } | ||
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| private static Bundle convertFhir(Bundle bundle, Mapping mapping) { | ||
| if (FhirPathUtils.appliesToBundle(bundle, mapping.applicability, mapping.variables)) { | ||
| bundle = Actions.applyMapping(bundle, mapping, null, new FlexporterJavascriptContext()); | ||
| } | ||
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| return bundle; | ||
| } | ||
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| private static void convertFhir(File mappingFile, File igDirectory, File sourceFhir) | ||
| throws IOException { | ||
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| Mapping mapping = Mapping.parseMapping(mappingFile); | ||
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| if (igDirectory != null) { | ||
| loadIG(igDirectory); | ||
| } | ||
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| IParser parser = FhirR4.getContext().newJsonParser().setPrettyPrint(true); | ||
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| handleFile(sourceFhir, mapping, parser); | ||
| } | ||
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| 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); | ||
| } | ||
| } | ||
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| } else { | ||
| String fhirJson = new String(Files.readAllBytes(sourceFhir.toPath())); | ||
| Bundle bundle = parser.parseResource(Bundle.class, fhirJson); | ||
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| 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)); | ||
| } | ||
| } | ||
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| bundle = convertFhir(bundle, mapping); | ||
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| String bundleJson = parser.encodeResourceToString(bundle); | ||
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| new File("./output/flexporter/").mkdirs(); | ||
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| String outFileName = "" + System.currentTimeMillis() + "_" + sourceFhir.getName(); | ||
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| File outFile = | ||
| new File("./output/flexporter/" + outFileName); | ||
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| Files.write(outFile.toPath(), bundleJson.getBytes(Charset.defaultCharset()), | ||
| StandardOpenOption.CREATE_NEW); | ||
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| System.out.println("Wrote " + outFile); | ||
| } | ||
| } | ||
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| static void loadIG(File igDirectory) throws IOException { | ||
| File[] artifacts = igDirectory.listFiles(); | ||
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| for (File artifact : artifacts) { | ||
| if (artifact.isFile() && FilenameUtils.getExtension(artifact.toString()).equals("json")) { | ||
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| IParser parser = FhirR4.getContext().newJsonParser(); | ||
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| String fhirJson = new String(Files.readAllBytes(artifact.toPath())); | ||
| IBaseResource resource = null; | ||
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| 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(); | ||
| } | ||
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| 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(); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| private static boolean isDirEmpty(final Path directory) throws IOException { | ||
| try (DirectoryStream<Path> dirStream = Files.newDirectoryStream(directory)) { | ||
| return !dirStream.iterator().hasNext(); | ||
| } | ||
| } | ||
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| private static void usage() { | ||
| System.out.println("Usage: run_flexporter -fm MAPPING_FILE -s SOURCE_FHIR [-ig IG_FOLDER]"); | ||
| } | ||
| } |
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