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initial public commit of 'flexible exporter' aka flexporter
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| Original file line number | Diff line number | Diff line change |
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| @@ -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 |
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| @@ -0,0 +1,147 @@ | ||
| import java.io.File; | ||
| import java.io.FileNotFoundException; | ||
| import java.io.IOException; | ||
| import java.nio.file.DirectoryStream; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.nio.file.StandardOpenOption; | ||
| import java.util.Arrays; | ||
| import java.util.LinkedList; | ||
| import java.util.Queue; | ||
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| import org.hl7.fhir.r4.model.Bundle; | ||
| import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; | ||
| import org.hl7.fhir.r4.model.Resource; | ||
| import org.mitre.synthea.export.flexporter.Actions; | ||
| import org.mitre.synthea.export.flexporter.FhirPathUtils; | ||
| import org.mitre.synthea.export.flexporter.Mapping; | ||
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| import ca.uhn.fhir.parser.IParser; | ||
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| public class RunFlexporter { | ||
| public static void main(String[] args) throws Exception { | ||
| Queue<String> argsQ = new LinkedList<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("-m")) { | ||
| 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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| public static void convertFhir(File mappingFile, File igDirectory, File sourceFhir) | ||
| throws IOException { | ||
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| Mapping mapping = Mapping.parseMapping(mappingFile); | ||
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| IParser parser = FhirPathUtils.FHIR_CTX.newJsonParser().setPrettyPrint(true); | ||
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| if (sourceFhir.isDirectory()) { | ||
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| // TODO | ||
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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 is modified in-place | ||
| convertFhir(bundle, mapping); | ||
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| String bundleJson = parser.encodeResourceToString(bundle); | ||
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| File outFile = | ||
| new File("./output/" + System.currentTimeMillis() + "_" + sourceFhir.getName()); | ||
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| Files.write(outFile.toPath(), bundleJson.getBytes(), StandardOpenOption.CREATE_NEW); | ||
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| System.out.println("Wrote " + outFile); | ||
| } | ||
| } | ||
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| public static Bundle convertFhir(Bundle bundle, Mapping mapping) { | ||
| Actions.applyMapping(bundle, mapping, null); | ||
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| return bundle; | ||
| } | ||
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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 -m MAPPING_FILE -s SOURCE_FHIR [-i IG_FOLDER]"); | ||
| } | ||
| } |
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