Code in client program just like CCDTransformerTest giving ClassCast error about cda2fhir HOT 7 OPEN

This worked for me:
ContinuityOfCareDocument cda = (ContinuityOfCareDocument) CDAUtil.loadAs(in, ConsolPackage.eINSTANCE.getContinuityOfCareDocument());

from cda2fhir.

Here is the class:

private static File dataFile = null;

public static void main(String[] argv) {
    System.out.println("CCD-2-Json-client starts.");
    System.out.println("Checking input arguments...");
    if (argv.length != 1) {
        System.err.println("Usage: java CCD-2-Json-client datafile");
        System.exit(1);
    }
    //try {
    	//File stylesheetFile = new File(argv[0]);
    	dataFile = new File(argv[0]);
    //} catch (IOException ioe) {
        // I/O error
    //    ioe.printStackTrace();
    //    System.out.println("One or more files not found...terminating.");
    //    System.exit(1);
    //}
    CCD2JsonClient ccd2json = new CCD2JsonClient();
    	
    // run examples
    
    ccd2json.execute();
    System.out.println("CCD-2-Json-client DONE!.");
}

// default, no-arg constructor

public CCD2JsonClient() {}
    
private void execute()
{
    // Load MDHT CDA packages. Otherwise ContinuityOfCareDocument and similar documents will not be recognised.
    // This has to be called before loading the document; otherwise will have no effect.
    CDAUtil.loadPackages();
    
    try {
	    System.out.println(" runReferenceCCDInstance....");
	    runReferenceCCDInstance( dataFile );
	    System.out.println(" runReferenceCCDInstanceWithoutDAF....");
	    runReferenceCCDInstanceWithoutDAF( dataFile );
	    System.out.println(" runReferenceCCDInstanceWithoutDAFAndNarrative....");
		runReferenceCCDInstanceWithoutDAFAndNarrative( dataFile );
    } catch( Exception e ) {
	    System.err.println(" Exception translating dataFile with stylesheet: " );
	    e.printStackTrace();
	    System.err.println(" program terminates. " );
	    System.exit(1);
    }
}


// with DAF profile in meta.profile
//public void runReferenceCCDInstance( File styleSheet, File dataFile ) throws Exception {
public void runReferenceCCDInstance( File dataFile ) throws Exception {
    //FileInputStream fis = new FileInputStream("src/test/resources/C-CDA_R2-1_CCD.xml");
    FileInputStream fis = new FileInputStream( dataFile );

    ClinicalDocument cda = CDAUtil.load(fis);
    ICDATransformer ccdTransformer = new CCDTransformerImpl(IdGeneratorEnum.COUNTER);
    Config.setGenerateDafProfileMetadata(true);
    Config.setGenerateNarrative(true);
    Bundle bundle = ccdTransformer.transformDocument(cda);
    if(bundle != null) 
    	FHIRUtil.printJSON(bundle, "output/output01.json");
}

// without DAF profile in meta.profile
//public void runReferenceCCDInstanceWithoutDAF( File styleSheet, File dataFile ) throws Exception {
public void runReferenceCCDInstanceWithoutDAF( File dataFile ) throws Exception {
    //FileInputStream fis = new FileInputStream("src/test/resources/C-CDA_R2-1_CCD.xml");
    FileInputStream fis = new FileInputStream( dataFile );

    ClinicalDocument cda = CDAUtil.load(fis);
    ICDATransformer ccdTransformer = new CCDTransformerImpl(IdGeneratorEnum.COUNTER);
    Config.setGenerateDafProfileMetadata(false);
    Config.setGenerateNarrative(true);
    Bundle bundle = ccdTransformer.transformDocument(cda);
    if(bundle != null)
        FHIRUtil.printJSON(bundle, "output/output01-wo-daf.json");
}

// C-CDA_R2-1_CCD.xml - without DAF profile in meta.profile and without narrative generated in resources
//public void runReferenceCCDInstanceWithoutDAFAndNarrative( File styleSheet, File dataFile ) throws Exception {
public void runReferenceCCDInstanceWithoutDAFAndNarrative( File dataFile ) throws Exception {
    //FileInputStream fis = new FileInputStream("src/test/resources/C-CDA_R2-1_CCD.xml");
    FileInputStream fis = new FileInputStream( dataFile );

    ClinicalDocument cda = CDAUtil.load(fis);
    ICDATransformer ccdTransformer = new CCDTransformerImpl(IdGeneratorEnum.COUNTER);
    Config.setGenerateDafProfileMetadata(false);
    Config.setGenerateNarrative(false);
    Bundle bundle = ccdTransformer.transformDocument(cda);
    if(bundle != null)
        FHIRUtil.printJSON(bundle, "output/output01-wo-daf-narrative.json");
}

}


from cda2fhir.

Here is the log:

Run of CCD2JsonClient:

C:\dl\mihin\0projects\ccda-to-fhir 15:12:56.65

runccd2jsonclient
[INFO] Scanning for projects...
[WARNING]
[WARNING] Some problems were encountered while building the effective model for org.mihin:ccdr-to-fhir:jar:0.0.1-SNAPSHOT
[WARNING] 'dependencies.dependency.(groupId:artifactId:type:classifier)' must be unique: org.openehealth.ipf.oht.mdht:ipf-oht-mdht-uml-hl7-vocab:jar -> duplicate declaration of version 1.2.0.201212201425 @ line 149, column 15
[WARNING] 'dependencies.dependency.systemPath' for org.hl7.fhir:validator:jar should not point at files within the project directory, ${project.basedir}/lib/org.hl7.fhir.validator.jar will be unresolvable by dependent projects @ line 227, column 25
[WARNING] 'dependencies.dependency.systemPath' for tr.com.srdc.cda2fhir:cda2fhir:jar should not point at files within the project directory, ${project.basedir}/lib/cda2fhir-0.2.jar will be unresolvable by dependent projects @ line 242, column 25
[WARNING] 'build.plugins.plugin.version' for org.apache.maven.plugins:maven-jar-plugin is missing. @ line 279, column 11
[WARNING]
[WARNING] It is highly recommended to fix these problems because they threaten the stability of your build.
[WARNING]
[WARNING] For this reason, future Maven versions might no longer support building such malformed projects.
[WARNING]
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building CCDR to FHIR conversion project 0.0.1-SNAPSHOT
[INFO] ------------------------------------------------------------------------
[INFO]
[INFO] >>> exec-maven-plugin:1.2.1:java (default-cli) > validate @ ccdr-to-fhir >>>
[INFO]
[INFO] <<< exec-maven-plugin:1.2.1:java (default-cli) < validate @ ccdr-to-fhir <<<
[INFO]
[INFO]
[INFO] --- exec-maven-plugin:1.2.1:java (default-cli) @ ccdr-to-fhir ---
log4j:WARN No appenders could be found for logger (org.mihin.ccda2fhir.clients.CCD2JsonClient).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
runReferenceCCDInstance....
15:13:07.783 [org.mihin.ccda2fhir.clients.CCD2JsonClient.main()] INFO c.u.f.u.VersionUtil - HAPI FHIR version is: 2.0
15:13:07.790 [org.mihin.ccda2fhir.clients.CCD2JsonClient.main()] INFO c.u.f.c.FhirContext - Creating new FHIR context for FHIR version [DSTU2]
15:13:07.796 [org.mihin.ccda2fhir.clients.CCD2JsonClient.main()] INFO t.c.s.c.c.Config - System file encoding is: windows-1252
15:13:07.800 [org.mihin.ccda2fhir.clients.CCD2JsonClient.main()] ERROR t.c.s.c.t.CCDTransformerImpl - ClinicalDocument could not be cast to ContinuityOfCareDocument. Returning null
java.lang.ClassCastException: org.openhealthtools.mdht.uml.cda.impl.ClinicalDocumentImpl cannot be cast to org.openhealthtools.mdht.uml.cda.consol.ContinuityOfCareDocument
at tr.com.srdc.cda2fhir.transform.CCDTransformerImpl.transformDocument(CCDTransformerImpl.java:150)
at org.mihin.ccda2fhir.clients.CCD2JsonClient.runReferenceCCDInstance(CCD2JsonClient.java:121)
at org.mihin.ccda2fhir.clients.CCD2JsonClient.execute(CCD2JsonClient.java:93)
at org.mihin.ccda2fhir.clients.CCD2JsonClient.main(CCD2JsonClient.java:60)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:297)
at java.lang.Thread.run(Thread.java:748)
runReferenceCCDInstanceWithoutDAF....
15:13:07.901 [org.mihin.ccda2fhir.clients.CCD2JsonClient.main()] ERROR t.c.s.c.t.CCDTransformerImpl - ClinicalDocument could not be cast to ContinuityOfCareDocument. Returning null
java.lang.ClassCastException: org.openhealthtools.mdht.uml.cda.impl.ClinicalDocumentImpl cannot be cast to org.openhealthtools.mdht.uml.cda.consol.ContinuityOfCareDocument
at tr.com.srdc.cda2fhir.transform.CCDTransformerImpl.transformDocument(CCDTransformerImpl.java:150)
at org.mihin.ccda2fhir.clients.CCD2JsonClient.runReferenceCCDInstanceWithoutDAF(CCD2JsonClient.java:136)
at org.mihin.ccda2fhir.clients.CCD2JsonClient.execute(CCD2JsonClient.java:95)
at org.mihin.ccda2fhir.clients.CCD2JsonClient.main(CCD2JsonClient.java:60)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:297)
at java.lang.Thread.run(Thread.java:748)
runReferenceCCDInstanceWithoutDAFAndNarrative....
15:13:08.003 [org.mihin.ccda2fhir.clients.CCD2JsonClient.main()] ERROR t.c.s.c.t.CCDTransformerImpl - ClinicalDocument could not be cast to ContinuityOfCareDocument. Returning null
java.lang.ClassCastException: org.openhealthtools.mdht.uml.cda.impl.ClinicalDocumentImpl cannot be cast to org.openhealthtools.mdht.uml.cda.consol.ContinuityOfCareDocument
at tr.com.srdc.cda2fhir.transform.CCDTransformerImpl.transformDocument(CCDTransformerImpl.java:150)
at org.mihin.ccda2fhir.clients.CCD2JsonClient.runReferenceCCDInstanceWithoutDAFAndNarrative(CCD2JsonClient.java:151)
at org.mihin.ccda2fhir.clients.CCD2JsonClient.execute(CCD2JsonClient.java:97)
at org.mihin.ccda2fhir.clients.CCD2JsonClient.main(CCD2JsonClient.java:60)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:297)
at java.lang.Thread.run(Thread.java:748)
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 2.328 s
[INFO] Finished at: 2018-02-23T15:13:08-05:00
[INFO] Final Memory: 19M/369M
[INFO] ------------------------------------------------------------------------

C:\dl\mihin\0projects\ccda-to-fhir 15:13:08.19

from cda2fhir.

P.S. I'm using the file from your test/resources dir, "C-CDA_R2-1_CCD.xml" as a test file (after renaming it).
maven is v3.5.2, Java 1.8.0_161 (64-bit).
my command to run the client class:
mvn exec:java -Dexec.mainClass="org.mihin.ccda2fhir.clients.CCD2JsonClient" -Dexec.args="input/inputCCD01.xml"

from cda2fhir.

Hi,

Nothing seems wrong in your code, and I can actually run it successfully when I copy your class directly in the cda2fhir project itself. You can test it.

I can only reproduce the error when I comment the following line, which is a must for loading CDA definitions from the mdht library:

CDAUtil.loadPackages();

I suspect that the required libraries, especially mdht is found in your classpath while you are trying to run via mvn exec. Can you make sure of this and test again?

from cda2fhir.

from cda2fhir.

This worked to get the bundle with bare minimum resources. It still misses all the references like e.g. medication section has only the coding and the text part but is missing all the references to medication statement, substance etc. Similarly for the other sections.

I face this particular issue only when running this as a spring boot WEB project. When run as a regular spring boot application, this issue does not occuer. I assume it is not loading certain packages when run as a web project.

Any leads would be appreciated.

from cda2fhir.