Examples with ConceptMap org.hl7.fhir.r5.model.ConceptMap used on opensource projects

Example 21 with ConceptMap

use of org.hl7.fhir.r5.model.ConceptMap in project org.hl7.fhir.core by hapifhir.

the class PackageMaintainer method check.

private void check(String ver) throws IOException {
    System.out.println("Check " + ver);
    List<String> allIds = listResources(Utilities.path(PATH, "hl7.fhir." + ver + ".examples", "package"));
    List<String> coreIds = listResources(Utilities.path(PATH, "hl7.fhir." + ver + ".core", "package"));
    for (String s : coreIds) {
        if (!allIds.contains(s)) {
            System.out.println("Core contains " + s + " but allIds doesn't");
        }
    }
    for (String s : allIds) {
        if (!coreIds.contains(s)) {
            String c = s.substring(0, s.indexOf("-"));
            if (Utilities.existsInList(c, "CodeSystem", "ValueSet", "ConceptMap", "StructureDefinition", "StructureMap", "NamingSystem", "SearchParameter", "OperationDefinition", "CapabilityStatement", "Conformance"))
                System.out.println("Examples contains " + s + " but core doesn't");
        }
    }
    strip(new File(Utilities.path(PATH, "hl7.fhir." + ver + ".core", "package")));
    strip(new File(Utilities.path(PATH, "hl7.fhir." + ver + ".expansions", "package")));
    if (!ver.equals("r2b"))
        strip(new File(Utilities.path(PATH, "hl7.fhir." + ver + ".elements", "package")));
}

Example 22 with ConceptMap

use of org.hl7.fhir.r5.model.ConceptMap 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 23 with ConceptMap

use of org.hl7.fhir.r5.model.ConceptMap in project org.hl7.fhir.core by hapifhir.

the class ExamplesPackageBuilder method process.

private void process(String source) throws FHIRFormatError, FileNotFoundException, IOException {
    Set<String> set = new HashSet<>();
    for (File f : new File(source).listFiles()) {
        if (f.getName().endsWith(".json")) {
            JsonObject obj = JsonTrackingParser.parseJson(new FileInputStream(f));
            if (obj.has("resourceType") && obj.has("id")) {
                String type = obj.get("resourceType").getAsString();
                String id = obj.get("id").getAsString();
                byte[] content = TextFile.fileToBytes(f);
                if (type.equals("ConceptMap")) {
                    System.out.println("convert " + f.getName());
                    content = r5ToR4B(content);
                    TextFile.bytesToFile(content, f);
                }
            // TextFile.bytesToFile(content, Utilities.path(dest2, type+"-"+id+".json"));
            // if (!set.contains(type+"/"+id)) {
            // set.add(type+"/"+id);
            // pck.addFile(Category.RESOURCE, type+"-"+id+".json", content);
            // }
            }
        }
    }
// pck.finish();
// 
}

Example 24 with ConceptMap

use of org.hl7.fhir.r5.model.ConceptMap in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method addMapHeaders.

private void addMapHeaders(XhtmlNode tr, Map<ConceptMap, String> mymaps) {
    for (ConceptMap m : mymaps.keySet()) {
        XhtmlNode td = tr.addTag("td");
        XhtmlNode b = td.addTag("b");
        XhtmlNode a = b.addTag("a");
        a.setAttribute("href", prefix + mymaps.get(m));
        a.addText(m.hasDescription() ? m.getDescription() : m.getName());
    }
}

Example 25 with ConceptMap

use of org.hl7.fhir.r5.model.ConceptMap in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method addDefineRowToTable.

private boolean addDefineRowToTable(XhtmlNode t, ConceptDefinitionComponent c, int i, boolean hasHierarchy, boolean hasDisplay, boolean comment, boolean deprecated, Map<ConceptMap, String> maps, String system) {
    boolean hasExtensions = false;
    XhtmlNode tr = t.addTag("tr");
    XhtmlNode td = tr.addTag("td");
    if (hasHierarchy) {
        td.addText(Integer.toString(i + 1));
        td = tr.addTag("td");
        String s = Utilities.padLeft("", '\u00A0', i * 2);
        td.addText(s);
    }
    td.addText(c.getCode());
    XhtmlNode a;
    if (c.hasCodeElement()) {
        a = td.addTag("a");
        a.setAttribute("name", Utilities.nmtokenize(c.getCode()));
        a.addText(" ");
    }
    if (hasDisplay) {
        td = tr.addTag("td");
        if (c.hasDisplayElement())
            td.addText(c.getDisplay());
    }
    td = tr.addTag("td");
    if (c != null)
        smartAddText(td, c.getDefinition());
    if (deprecated) {
        td = tr.addTag("td");
        Boolean b = ToolingExtensions.getDeprecated(c);
        if (b != null && b) {
            smartAddText(td, "Deprecated");
            hasExtensions = true;
            if (ToolingExtensions.hasExtension(c, ToolingExtensions.EXT_REPLACED_BY)) {
                Coding cc = (Coding) ToolingExtensions.getExtension(c, ToolingExtensions.EXT_REPLACED_BY).getValue();
                td.addText(" (replaced by ");
                String url = getCodingReference(cc, system);
                if (url != null) {
                    td.addTag("a").setAttribute("href", url).addText(cc.getCode());
                    td.addText(": " + cc.getDisplay() + ")");
                } else
                    td.addText(cc.getCode() + " '" + cc.getDisplay() + "' in " + cc.getSystem() + ")");
            }
        }
    }
    if (comment) {
        td = tr.addTag("td");
        String s = ToolingExtensions.getComment(c);
        if (s != null) {
            smartAddText(td, s);
            hasExtensions = true;
        }
    }
    for (ConceptMap m : maps.keySet()) {
        td = tr.addTag("td");
        List<TargetElementComponent> mappings = findMappingsForCode(c.getCode(), m);
        boolean first = true;
        for (TargetElementComponent mapping : mappings) {
            if (!first)
                td.addTag("br");
            first = false;
            XhtmlNode span = td.addTag("span");
            span.setAttribute("title", mapping.hasEquivalence() ? mapping.getEquivalence().toCode() : "");
            span.addText(getCharForEquivalence(mapping));
            a = td.addTag("a");
            a.setAttribute("href", prefix + maps.get(m) + "#" + makeAnchor(mapping.getCodeSystem(), mapping.getCode()));
            a.addText(mapping.getCode());
            if (!Utilities.noString(mapping.getComments()))
                td.addTag("i").addText("(" + mapping.getComments() + ")");
        }
    }
    for (CodeType e : ToolingExtensions.getSubsumes(c)) {
        hasExtensions = true;
        tr = t.addTag("tr");
        td = tr.addTag("td");
        String s = Utilities.padLeft("", '.', i * 2);
        td.addText(s);
        a = td.addTag("a");
        a.setAttribute("href", "#" + Utilities.nmtokenize(e.getValue()));
        a.addText(c.getCode());
    }
    for (ConceptDefinitionComponent cc : c.getConcept()) {
        hasExtensions = addDefineRowToTable(t, cc, i + 1, hasHierarchy, hasDisplay, comment, deprecated, maps, system) || hasExtensions;
    }
    return hasExtensions;
}