Examples with XmlParser org.hl7.fhir.r4b.formats.XmlParser used on opensource projects

Example 36 with XmlParser

use of org.hl7.fhir.r4b.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class IEEE11073Convertor method generateLoincMdcMap.

private static ConceptMap generateLoincMdcMap(CodeSystem mdc, String dst, String src) throws IOException, FHIRException {
    ConceptMap cm = new ConceptMap();
    cm.setId("loinc-mdc");
    cm.setUrl("http:/???/fhir/ConceptMap/loinc-mdc");
    cm.setVersion("[todo]");
    cm.setName("LoincMdcCrossMap");
    cm.setTitle("Cross Map between LOINC and MDC");
    cm.setStatus(PublicationStatus.DRAFT);
    cm.setExperimental(true);
    cm.setDateElement(new DateTimeType());
    cm.setPublisher("HL7, Inc");
    ContactDetail cd = cm.addContact();
    cd.setName("LOINC + IEEE");
    ContactPoint cp = cd.addTelecom();
    cp.setSystem(ContactPointSystem.URL);
    cp.setValue("http://loinc.org");
    cm.setDescription("A Cross Map between the LOINC and MDC Code systems");
    cm.setPurpose("To implementers map between medical device codes and LOINC codes");
    cm.setCopyright("This content LOINC \u00ae is copyright \u00a9 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at http://loinc.org/terms-of-use");
    cm.setSource(new UriType("http://loinc.org/vs"));
    cm.setTarget(new UriType(MDC_ALL_VALUES));
    ConceptMapGroupComponent g = cm.addGroup();
    g.setSource("urn:iso:std:iso:11073:10101");
    g.setTarget("http://loinc.org");
    CSVReader csv = new CSVReader(new FileInputStream(src));
    csv.readHeaders();
    while (csv.line()) {
        SourceElementComponent e = g.addElement();
        e.setCode(csv.cell("IEEE_CF_CODE10"));
        e.setDisplay(csv.cell("IEEE_DESCRIPTION"));
        TargetElementComponent t = e.addTarget();
        t.setEquivalence(ConceptMapEquivalence.EQUIVALENT);
        t.setCode(csv.cell("LOINC_NUM"));
        t.setDisplay(csv.cell("LOINC_LONG_COMMON_NAME"));
    }
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dst, "conceptmap-" + cm.getId() + ".xml")), cm);
    System.out.println("Done");
    return cm;
}

Example 37 with XmlParser

use of org.hl7.fhir.r4b.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class IEEE11073Convertor method generateMDC.

public static CodeSystem generateMDC(String src, String dst, UcumService ucum) throws IOException, FHIRException {
    CSVReader csv = new CSVReader(new FileInputStream(src));
    csv.readHeaders();
    CodeSystem cs = new CodeSystem();
    Map<String, String> ucumIssues = new HashMap<String, String>();
    int errorCount = 0;
    cs.setId("MDC");
    cs.setUrl("urn:iso:std:iso:11073:10101");
    cs.setVersion("[todo]");
    cs.setName("11073:10101 codes for the FHIR community");
    cs.setStatus(PublicationStatus.ACTIVE);
    cs.setExperimental(false);
    cs.setDateElement(new DateTimeType());
    cs.setPublisher("HL7 (FHIR Project)");
    ContactDetail cd = cs.addContact();
    ContactPoint cp = cd.addTelecom();
    cp.setSystem(ContactPointSystem.URL);
    cp.setValue("http://ieee?");
    cs.setDescription("1073 Codes for the FHIR community (generated from the Rosetta data");
    Identifier i = new Identifier();
    cs.setIdentifier(i);
    i.setSystem("urn:ietf:rfc:3986");
    i.setValue("urn:oid:2.16.840.1.113883.6.24");
    cs.setCaseSensitive(false);
    cs.setContent(CodeSystemContentMode.COMPLETE);
    cs.addProperty().setCode("ucum").setDescription("UCUM units associated with Concept").setType(PropertyType.STRING);
    cs.addProperty().setCode("unit").setDescription("MDC units associated with Concept").setType(PropertyType.STRING);
    cs.addProperty().setCode("refid").setDescription("MDC Reference Id for Concept").setType(PropertyType.CODE);
    Set<String> codes = new HashSet<String>();
    while (csv.line()) {
        if (csv.has("CF_CODE10")) {
            String code = csv.cell("CF_CODE10");
            if (codes.contains(code))
                System.out.println("Duplicate Code " + code);
            else {
                codes.add(code);
                ConceptDefinitionComponent c = cs.addConcept();
                c.setCode(code);
                c.setDisplay(csv.cell("Common Term"));
                c.setDefinition(csv.cell("Term Description"));
                String vd = csv.cell("Vendor_Description");
                if (!c.hasDefinition())
                    c.setDefinition(vd);
                if (!c.hasDisplay())
                    c.setDisplay(vd);
                String refid = csv.cell("REFID");
                c.addProperty().setCode("refid").setValue(new CodeType().setValue(refid));
                if (csv.has("Synonym"))
                    c.addDesignation().setValue(csv.cell("Synonym")).setUse(new Coding().setSystem("http://hl7.org/fhir/designation-use").setCode("synonym"));
                if (csv.has("Acronym"))
                    c.addDesignation().setValue(csv.cell("Acronym")).setUse(new Coding().setSystem("http://hl7.org/fhir/designation-use").setDisplay("acronym"));
                if (csv.has("Systematic Name")) {
                    String sysName = csv.cell("Systematic Name");
                    if (!c.hasDefinition())
                        c.setDefinition(sysName);
                    c.addDesignation().setValue(sysName).setUse(new Coding().setSystem("http://hl7.org/fhir/designation-use").setCode("structured-name"));
                }
                if (csv.has("UOM_MDC"))
                    c.addProperty().setCode("unit").setValue(new StringType().setValue(csv.cell("UOM_MDC")));
                if (csv.has("UOM_UCUM")) {
                    CommaSeparatedStringBuilder ul = new CommaSeparatedStringBuilder();
                    for (String u : csv.cell("UOM_UCUM").split(" ")) {
                        String msg = ucum.validate(u);
                        if (msg != null) {
                            errorCount++;
                            ucumIssues.put(u, msg);
                        } else
                            ul.append(u);
                    }
                    if (ul.length() > 0)
                        c.addProperty().setCode("ucum").setValue(new StringType().setValue(ul.toString()));
                }
            }
        }
    }
    csv.close();
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dst, "codesystem-" + cs.getId() + ".xml")), cs);
    System.out.println(errorCount + "UCUM errors");
    for (String u : sorted(ucumIssues.keySet())) System.out.println("Invalid UCUM code: " + u + " because " + ucumIssues.get(u));
    return cs;
}

Example 38 with XmlParser

use of org.hl7.fhir.r4b.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class ISO21090Importer method generateValueSet.

private void generateValueSet(EnumValueSet evs) throws Exception {
    ValueSet bvs = ctxt.fetchResource(ValueSet.class, evs.getTemplate());
    if (bvs == null)
        throw new Exception("Did not find template value set " + evs.getTemplate());
    ValueSet vs = bvs.copy();
    vs.getCompose().getInclude().clear();
    vs.getIdentifier().clear();
    vs.setName("ISO 20190 " + evs.getName() + " Enumeration");
    vs.setId(evs.getName());
    vs.setUrl("http://hl7.org/fhir/iso21090/ValueSet/" + vs.getId());
    vs.setDate(new Date());
    vs.setExperimental(false);
    ConceptSetComponent inc = vs.getCompose().addInclude().setSystem(evs.getSystem());
    for (String code : evs.getCodes()) {
        inc.addConcept().setCode(code);
    }
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "iso21090\\ValueSet-" + evs.getName() + ".xml")), vs);
}

Example 39 with XmlParser

use of org.hl7.fhir.r4b.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class ISO21090Importer method generateType.

private void generateType(DataType dt) throws Exception {
    StructureDefinition sd = new StructureDefinition();
    sd.setId(dt.getName());
    sd.setUrl("http://hl7.org/fhir/iso21090/StructureDefinition/" + sd.getId());
    sd.setName(dt.getName() + " data type");
    sd.setStatus(PublicationStatus.ACTIVE);
    sd.setExperimental(false);
    sd.setPublisher("HL7 / ISO");
    sd.setDate(new Date());
    sd.setDescription(dt.getDoco());
    sd.setKind(StructureDefinitionKind.LOGICAL);
    sd.setAbstract(Utilities.existsInList(dt.getName(), "HXIT", "QTY"));
    sd.setType("Element");
    if (dt.getParent() == null)
        sd.setBaseDefinition("http://hl7.org/fhir/StructureDefinition/Element");
    else
        sd.setBaseDefinition("http://hl7.org/fhir/iso21090/StructureDefinition/" + dt.getParent());
    sd.setDerivation(TypeDerivationRule.SPECIALIZATION);
    ElementDefinition ed = sd.getDifferential().addElement();
    ed.setPath(dt.getName());
    produceProperties(sd.getDifferential().getElement(), dt.getName(), dt.getProperties(), true, false);
    produceProperties(sd.getDifferential().getElement(), dt.getName(), dt.getProperties(), false, false);
    ed = sd.getSnapshot().addElement();
    ed.setPath(dt.getName());
    if (dt.getParent() != null)
        addParentProperties(sd.getSnapshot().getElement(), dt.getName(), dt.getParent(), true, true);
    produceProperties(sd.getSnapshot().getElement(), dt.getName(), dt.getProperties(), true, true);
    if (dt.getParent() != null)
        addParentProperties(sd.getSnapshot().getElement(), dt.getName(), dt.getParent(), false, true);
    produceProperties(sd.getSnapshot().getElement(), dt.getName(), dt.getProperties(), false, true);
    ed.getBase().setPath(ed.getPath()).setMin(ed.getMin()).setMax(ed.getMax());
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path("[tmp]", "iso21090\\StructureDefinition-" + dt.getName() + ".xml")), sd);
}

Example 40 with XmlParser

use of org.hl7.fhir.r4b.formats.XmlParser in project org.hl7.fhir.core by hapifhir.

the class UTGCaseSensitivePopulator method scanFolders.

private void scanFolders(File folder, Bundle bundle) throws FileNotFoundException, IOException {
    Calendar today = Calendar.getInstance();
    Date dt = today.getTime();
    today.set(Calendar.HOUR_OF_DAY, 0);
    Date d = today.getTime();
    System.out.println("Scan " + folder.getAbsolutePath());
    for (File f : folder.listFiles()) {
        if (f.isDirectory() && !f.getName().equals("retired")) {
            scanFolders(f, bundle);
        } else if (f.getName().endsWith(".xml")) {
            processFile(f, bundle, new XmlParser(), d, dt);
        } else if (f.getName().endsWith(".json")) {
            processFile(f, bundle, new JsonParser(), d, dt);
        }
    }
}