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bartolli/v1.java

Last active July 7, 2024 19:47
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  1. bartolli revised this gist Jul 7, 2024. 1 changed file with 22 additions and 3 deletions.
    25 changes: 22 additions & 3 deletions v1.java
    View file
    Original file line number Diff line number Diff line change
    @@ -22,33 +22,49 @@ public FhirConverter() {

    // Method to convert JSON to XML
    public String convertJsonToXml(String json) {
    // Create a JSON parser
    IParser jsonParser = ctx.newJsonParser().setPrettyPrint(true);
    // Parse JSON to a FHIR resource
    IBaseResource resource = jsonParser.parseResource(json);
    // Create an XML parser
    IParser xmlParser = ctx.newXmlParser().setPrettyPrint(true);
    // Encode the FHIR resource to XML
    return xmlParser.encodeResourceToString(resource);
    }

    // Method to convert XML to JSON
    public String convertXmlToJson(String xml) {
    // Create an XML parser
    IParser xmlParser = ctx.newXmlParser().setPrettyPrint(true);
    // Parse XML to a FHIR resource
    IBaseResource resource = xmlParser.parseResource(xml);
    // Create a JSON parser
    IParser jsonParser = ctx.newJsonParser().setPrettyPrint(true);
    // Encode the FHIR resource to JSON
    return jsonParser.encodeResourceToString(resource);
    }

    // Method to convert JSON to RDF (Turtle)
    public String convertJsonToTurtle(String json) {
    // Create a JSON parser
    IParser jsonParser = ctx.newJsonParser();
    // Parse JSON to a FHIR resource
    IBaseResource resource = jsonParser.parseResource(json);
    IParser rdfParser = ctx.newRDFParser();
    // Create an RDF parser (Turtle format)
    IParser rdfParser = ctx.newRDFParser(); // This returns an instance of RDFParser
    // Encode the FHIR resource to RDF (Turtle format)
    return rdfParser.encodeResourceToString(resource);
    }

    // Method to convert RDF (Turtle) to JSON
    public String convertTurtleToJson(String turtle) {
    IParser rdfParser = ctx.newRDFParser();
    // Create an RDF parser (Turtle format)
    IParser rdfParser = ctx.newRDFParser(); // This returns an instance of RDFParser
    // Parse RDF (Turtle format) to a FHIR resource
    IBaseResource resource = rdfParser.parseResource(turtle);
    // Create a JSON parser
    IParser jsonParser = ctx.newJsonParser().setPrettyPrint(true);
    // Encode the FHIR resource to JSON
    return jsonParser.encodeResourceToString(resource);
    }

    @@ -66,9 +82,11 @@ public static void main(String[] args) {
    try {
    FhirConverter converter = new FhirConverter();

    // Read the input file content
    String inputContent = new String(Files.readAllBytes(Paths.get(inputFile)));
    String outputContent = null;

    // Perform the conversion based on the specified format
    switch (format) {
    case "xml-to-json":
    outputContent = converter.convertXmlToJson(inputContent);
    @@ -87,7 +105,8 @@ public static void main(String[] args) {
    System.exit(1);
    }

    Files.write(Paths.get(outputFile), outputContent.getBytes());
    // Write the output content to the specified file
    Files.write(Paths.get(outputFile), (outputContent != null ? outputContent.getBytes() : "Error during conversion. Output content is null.".getBytes()));
    System.out.println("Conversion successful! Output written to " + outputFile);

    } catch (IOException e) {
  2. bartolli revised this gist Jul 7, 2024. 1 changed file with 17 additions and 0 deletions.
    17 changes: 17 additions & 0 deletions v2_build_error.log
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    Original file line number Diff line number Diff line change
    @@ -0,0 +1,17 @@
    (base) Projects/java/fhir-converter ❯ java -Dlogback.configurationFile=file:logback.xml -jar target/fhir-converter-1.0-SNAPSHOT-jar-with-dependencies.jar /Users/bartolli/Projects/fhirtordf/Darrick836_Wunsch504_cb6aca68-e6a3-ee70-5876-9f255c3eac48.json output.ttl json-to-turtle
    [main] INFO com.example.FhirConverter - Starting FHIR Converter
    [main] INFO ca.uhn.fhir.util.VersionUtil - HAPI FHIR version 7.2.1 - Rev 547c9320f1
    [main] INFO ca.uhn.fhir.context.FhirContext - Creating new FHIR context for FHIR version [R4]
    [main] INFO com.example.FhirConverter - FhirConverter initialized
    [main] INFO ca.uhn.fhir.util.XmlUtil - Unable to determine StAX implementation: java.xml/META-INF/MANIFEST.MF not found
    [main] INFO ca.uhn.fhir.context.support.DefaultProfileValidationSupport - Loading structure definitions from classpath: /org/hl7/fhir/r4/model/profile/profiles-resources.xml
    [main] INFO ca.uhn.fhir.context.support.DefaultProfileValidationSupport - Loading structure definitions from classpath: /org/hl7/fhir/r4/model/profile/profiles-types.xml
    [main] INFO ca.uhn.fhir.context.support.DefaultProfileValidationSupport - Loading structure definitions from classpath: /org/hl7/fhir/r4/model/profile/profiles-others.xml
    [main] INFO ca.uhn.fhir.context.support.DefaultProfileValidationSupport - Loading structure definitions from classpath: /org/hl7/fhir/r4/model/extension/extension-definitions.xml
    Exception in thread "main" java.lang.UnsupportedOperationException: HAPI-0269:
    at org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext.generateSnapshot(HapiWorkerContext.java:297)
    at org.hl7.fhir.r4.elementmodel.ParserBase.getDefinition(ParserBase.java:145)
    at org.hl7.fhir.r4.elementmodel.JsonParser.parse(JsonParser.java:132)
    at org.hl7.fhir.r4.elementmodel.JsonParser.parse(JsonParser.java:113)
    at com.example.FhirConverter.convertJsonToTurtle(FhirConverter.java:96)
    at com.example.FhirConverter.main(FhirConverter.java:159)
  3. bartolli revised this gist Jul 7, 2024. 2 changed files with 182 additions and 0 deletions.
    0 gistfile1.txt → v1.java
    View file
    File renamed without changes.
    182 changes: 182 additions & 0 deletions v2.java
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    Original file line number Diff line number Diff line change
    @@ -0,0 +1,182 @@
    package com.example;

    import ca.uhn.fhir.context.FhirContext;
    import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
    // import ca.uhn.fhir.context.support.IValidationSupport;
    import ca.uhn.fhir.context.support.ValidationSupportContext;
    import ca.uhn.fhir.parser.IParser;
    import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
    import org.hl7.fhir.exceptions.FHIRException;
    import org.hl7.fhir.common.hapi.validation.support.SnapshotGeneratingValidationSupport;
    import org.hl7.fhir.instance.model.api.IBaseResource;
    import org.hl7.fhir.r4.model.StructureDefinition;
    import org.hl7.fhir.r4.elementmodel.Element;
    import org.hl7.fhir.r4.elementmodel.JsonParser;
    import org.hl7.fhir.r4.elementmodel.TurtleParser;
    import org.hl7.fhir.r4.context.SimpleWorkerContext;
    import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
    import org.hl7.fhir.r4.utils.formats.Turtle;
    import org.slf4j.LoggerFactory;
    // import org.hl7.fhir.utilities.npm.NpmPackage;
    // import org.hl7.fhir.r4.context.IWorkerContext;

    // import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome; // Import for ValueSetExpander
    // import org.hl7.fhir.instance.model.api.IBaseResource;

    import java.io.ByteArrayInputStream;
    import java.io.ByteArrayOutputStream;
    import java.io.FileNotFoundException;
    import java.io.IOException;
    import java.nio.charset.StandardCharsets;
    import java.nio.file.Files;
    import java.nio.file.Path;
    import java.nio.file.Paths;

    import org.slf4j.Logger;
    // import org.slf4j.LoggerFactory;

    public class FhirConverter {
    private static final Logger logger = LoggerFactory.getLogger(FhirConverter.class);

    private FhirContext ctx;
    private ValidationSupportChain validationSupportChain;
    private HapiWorkerContext workerContext;

    public FhirConverter() throws IOException {
    this.ctx = FhirContext.forR4();
    DefaultProfileValidationSupport defaultValidationSupport = new DefaultProfileValidationSupport(ctx);
    SnapshotGeneratingValidationSupport snapshotGenerator = new SnapshotGeneratingValidationSupport(ctx);
    this.validationSupportChain = new ValidationSupportChain(defaultValidationSupport, snapshotGenerator);

    this.workerContext = new HapiWorkerContext(ctx, validationSupportChain);
    logger.info("FhirConverter initialized");
    }

    private void loadLocalResource(SimpleWorkerContext swc, String filePath) throws IOException {
    Path path = Paths.get(filePath);
    String xmlContent = Files.readString(path);
    IParser xmlParser = ctx.newXmlParser();
    IBaseResource resource = xmlParser.parseResource(xmlContent);

    if (resource instanceof StructureDefinition) {
    StructureDefinition sd = (StructureDefinition) resource;
    swc.cacheResource(sd); // Using cacheResource instead of loadResource
    } else {
    logger.error("Resource at " + filePath + " is not a StructureDefinition");
    throw new IllegalArgumentException("Resource at " + filePath + " is not a StructureDefinition");
    }
    }


    public String convertJsonToTurtle(String json) {
    logger.debug("Starting JSON to Turtle conversion");

    try {
    IParser parser = ctx.newJsonParser();
    IBaseResource resource = parser.parseResource(json);

    if (resource instanceof StructureDefinition) {
    StructureDefinition sd = (StructureDefinition) resource;
    logger.debug("Processing StructureDefinition");

    if (!sd.hasSnapshot()) {
    logger.debug("Generating snapshot for StructureDefinition");
    String definitionsPath = "/Users/bartolli/Projects/java/fhir-converter/src/main/resources/org/hl7/fhir/r4/model/profile"; // Update this path!!!

    SimpleWorkerContext swc = new SimpleWorkerContext();
    loadLocalResource(swc, definitionsPath + "/profiles-resources.xml");
    loadLocalResource(swc, definitionsPath + "/profiles-types.xml");
    loadLocalResource(swc, definitionsPath + "/profiles-others.xml");
    validationSupportChain.generateSnapshot(new ValidationSupportContext(validationSupportChain), sd, sd.getUrl(), null, sd.getName());
    json = parser.encodeResourceToString(sd);
    }
    }

    JsonParser jsonParser = new JsonParser(workerContext);
    Element element = jsonParser.parse(new ByteArrayInputStream(json.getBytes(StandardCharsets.UTF_8)));

    ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
    TurtleParser turtleParser = new TurtleParser(workerContext);
    Turtle turtle = new Turtle();

    turtleParser.compose(element, turtle, null); // base can be null or your base URI
    turtle.commit(outputStream, false); // Write the composed Turtle to the output stream

    logger.info("Conversion completed successfully");
    return outputStream.toString(StandardCharsets.UTF_8);

    } catch (FileNotFoundException e) {
    logger.error("File not found while initializing SimpleWorkerContext or loading resources", e);
    } catch (IOException e) {
    logger.error("IO exception while initializing SimpleWorkerContext, loading resources, or parsing", e);
    } catch (FHIRException e) {
    logger.error("FHIR exception while initializing SimpleWorkerContext, loading resources, or serializing", e);
    }
    return null; // Return null if any exceptions are caught
    }



    // Existing methods for XML and JSON conversion
    public String convertJsonToXml(String json) {
    IParser jsonParser = ctx.newJsonParser();
    IBaseResource resource = jsonParser.parseResource(json);
    IParser xmlParser = ctx.newXmlParser().setPrettyPrint(true);
    return xmlParser.encodeResourceToString(resource);
    }

    public String convertXmlToJson(String xml) {
    IParser xmlParser = ctx.newXmlParser();
    IBaseResource resource = xmlParser.parseResource(xml);
    IParser jsonParser = ctx.newJsonParser().setPrettyPrint(true);
    return jsonParser.encodeResourceToString(resource);
    }

    public static void main(String[] args) {
    logger.info("Starting FHIR Converter");
    if (args.length != 3) {
    logger.error("Usage: java -jar fhir-converter.jar <inputFile> <outputFile> <format>");
    System.exit(1);
    }

    String inputFile = args[0];
    String outputFile = args[1];
    String format = args[2];

    try {
    FhirConverter converter = new FhirConverter();
    String inputContent = new String(Files.readAllBytes(Paths.get(inputFile)));
    String outputContent = null;

    switch (format) {
    case "xml-to-json":
    outputContent = converter.convertXmlToJson(inputContent);
    break;
    case "json-to-xml":
    outputContent = converter.convertJsonToXml(inputContent);
    break;
    case "json-to-turtle":
    outputContent = converter.convertJsonToTurtle(inputContent);
    break;
    case "turtle-to-json":
    // Implement turtle to json conversion if required
    System.err.println("Turtle to JSON conversion not implemented.");
    break;
    default:
    logger.error("Unknown format: " + format);
    System.exit(1);
    }

    if (outputContent != null) {
    Files.write(Paths.get(outputFile), outputContent.getBytes(StandardCharsets.UTF_8));
    logger.info("Conversion successful! Output written to " + outputFile);
    } else {
    logger.error("Conversion failed: output content is null");
    System.exit(1);
    }
    } catch (IOException e) {
    logger.error("Error during conversion", e);
    System.exit(1);
    }
    }
    }
  4. bartolli created this gist Jul 7, 2024.
    98 changes: 98 additions & 0 deletions gistfile1.txt
    View file
    Original file line number Diff line number Diff line change
    @@ -0,0 +1,98 @@
    package com.example;

    import ca.uhn.fhir.context.FhirContext;
    import ca.uhn.fhir.parser.IParser;
    import org.apache.jena.query.ARQ;
    import org.hl7.fhir.instance.model.api.IBaseResource;

    import java.io.IOException;
    import java.nio.file.Files;
    import java.nio.file.Paths;

    public class FhirConverter {

    private FhirContext ctx;

    public FhirConverter() {
    // Initialize FHIR context for R4
    this.ctx = FhirContext.forR4();
    // Initialize ARQ context
    ARQ.init();
    }

    // Method to convert JSON to XML
    public String convertJsonToXml(String json) {
    IParser jsonParser = ctx.newJsonParser().setPrettyPrint(true);
    IBaseResource resource = jsonParser.parseResource(json);
    IParser xmlParser = ctx.newXmlParser().setPrettyPrint(true);
    return xmlParser.encodeResourceToString(resource);
    }

    // Method to convert XML to JSON
    public String convertXmlToJson(String xml) {
    IParser xmlParser = ctx.newXmlParser().setPrettyPrint(true);
    IBaseResource resource = xmlParser.parseResource(xml);
    IParser jsonParser = ctx.newJsonParser().setPrettyPrint(true);
    return jsonParser.encodeResourceToString(resource);
    }

    // Method to convert JSON to RDF (Turtle)
    public String convertJsonToTurtle(String json) {
    IParser jsonParser = ctx.newJsonParser();
    IBaseResource resource = jsonParser.parseResource(json);
    IParser rdfParser = ctx.newRDFParser();
    return rdfParser.encodeResourceToString(resource);
    }

    // Method to convert RDF (Turtle) to JSON
    public String convertTurtleToJson(String turtle) {
    IParser rdfParser = ctx.newRDFParser();
    IBaseResource resource = rdfParser.parseResource(turtle);
    IParser jsonParser = ctx.newJsonParser().setPrettyPrint(true);
    return jsonParser.encodeResourceToString(resource);
    }

    public static void main(String[] args) {
    if (args.length != 3) {
    System.err.println("Usage: java -jar fhir-converter.jar <inputFile> <outputFile> <format>");
    System.err.println("<format>: xml-to-json, json-to-xml, json-to-turtle, turtle-to-json");
    System.exit(1);
    }

    String inputFile = args[0];
    String outputFile = args[1];
    String format = args[2];

    try {
    FhirConverter converter = new FhirConverter();

    String inputContent = new String(Files.readAllBytes(Paths.get(inputFile)));
    String outputContent = null;

    switch (format) {
    case "xml-to-json":
    outputContent = converter.convertXmlToJson(inputContent);
    break;
    case "json-to-xml":
    outputContent = converter.convertJsonToXml(inputContent);
    break;
    case "json-to-turtle":
    outputContent = converter.convertJsonToTurtle(inputContent);
    break;
    case "turtle-to-json":
    outputContent = converter.convertTurtleToJson(inputContent);
    break;
    default:
    System.err.println("Unknown format: " + format);
    System.exit(1);
    }

    Files.write(Paths.get(outputFile), outputContent.getBytes());
    System.out.println("Conversion successful! Output written to " + outputFile);

    } catch (IOException e) {
    e.printStackTrace();
    System.exit(1);
    }
    }
    }