Examples with TargetElementComponent org.hl7.fhir.r4.model.ConceptMap.TargetElementComponent used on opensource projects

Example 1 with TargetElementComponent

use of org.hl7.fhir.r4.model.ConceptMap.TargetElementComponent in project bunsen by cerner.

the class ConceptMaps method expandMappingsIterator.

private static Iterator<Mapping> expandMappingsIterator(ConceptMap map) {
    List<Mapping> mappings = new ArrayList<>();
    for (ConceptMapGroupComponent group : map.getGroup()) {
        for (SourceElementComponent element : group.getElement()) {
            for (TargetElementComponent target : element.getTarget()) {
                Mapping mapping = new Mapping();
                mapping.setConceptMapUri(map.getUrl());
                mapping.setConceptMapVersion(map.getVersion());
                try {
                    String sourceValue = map.getSource() instanceof UriType ? map.getSourceUriType().getValue() : map.getSourceReference().getReference();
                    mapping.setSourceValueSet(sourceValue);
                    String targetValue = map.getTarget() instanceof UriType ? map.getTargetUriType().getValue() : map.getTargetReference().getReference();
                    mapping.setTargetValueSet(targetValue);
                } catch (FHIRException fhirException) {
                    // an exception.
                    throw new RuntimeException(fhirException);
                }
                mapping.setSourceSystem(group.getSource());
                mapping.setSourceValue(element.getCode());
                mapping.setTargetSystem(group.getTarget());
                mapping.setTargetValue(target.getCode());
                if (target.getEquivalence() != null) {
                    mapping.setEquivalence(target.getEquivalence().toCode());
                }
                mappings.add(mapping);
            }
        }
    }
    return mappings.iterator();
}

Example 2 with TargetElementComponent

use of org.hl7.fhir.r4.model.ConceptMap.TargetElementComponent 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 3 with TargetElementComponent

use of org.hl7.fhir.r4.model.ConceptMap.TargetElementComponent 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;
}

Example 4 with TargetElementComponent

use of org.hl7.fhir.r4.model.ConceptMap.TargetElementComponent in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method addExpansionRowToTable.

private void addExpansionRowToTable(XhtmlNode t, ValueSetExpansionContainsComponent c, int i, boolean doSystem, Map<ConceptMap, String> mymaps) {
    XhtmlNode tr = t.addTag("tr");
    XhtmlNode td = tr.addTag("td");
    String tgt = makeAnchor(c.getSystem(), c.getCode());
    td.addTag("a").setAttribute("name", tgt).addText(" ");
    String s = Utilities.padLeft("", '.', i * 2);
    td.addText(s);
    Resource e = context.fetchCodeSystem(c.getSystem());
    if (e == null)
        td.addText(c.getCode());
    else {
        XhtmlNode a = td.addTag("a");
        a.addText(c.getCode());
        a.setAttribute("href", prefix + getCsRef(e) + "#" + Utilities.nmtokenize(c.getCode()));
    }
    if (doSystem) {
        td = tr.addTag("td");
        td.addText(c.getSystem());
    }
    td = tr.addTag("td");
    if (c.hasDisplayElement())
        td.addText(c.getDisplay());
    for (ConceptMap m : mymaps.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.getEquivalence().toString());
            span.addText(getCharForEquivalence(mapping));
            XhtmlNode a = td.addTag("a");
            a.setAttribute("href", prefix + mymaps.get(m) + "#" + mapping.getCode());
            a.addText(mapping.getCode());
            if (!Utilities.noString(mapping.getComments()))
                td.addTag("i").addText("(" + mapping.getComments() + ")");
        }
    }
    for (ValueSetExpansionContainsComponent cc : c.getContains()) {
        addExpansionRowToTable(t, cc, i + 1, doSystem, mymaps);
    }
}

Example 5 with TargetElementComponent

use of org.hl7.fhir.r4.model.ConceptMap.TargetElementComponent in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method generate.

public void generate(ConceptMap cm) {
    XhtmlNode x = new XhtmlNode(NodeType.Element, "div");
    x.addTag("h2").addText(cm.getName() + " (" + cm.getUrl() + ")");
    XhtmlNode p = x.addTag("p");
    p.addText("Mapping from ");
    AddVsRef(((Reference) cm.getSource()).getReference(), p);
    p.addText(" to ");
    AddVsRef(((Reference) cm.getTarget()).getReference(), p);
    p = x.addTag("p");
    if (cm.getExperimental())
        p.addText(Utilities.capitalize(cm.getStatus().toString()) + " (not intended for production usage). ");
    else
        p.addText(Utilities.capitalize(cm.getStatus().toString()) + ". ");
    p.addText("Published on " + cm.getDateElement().toHumanDisplay() + " by " + cm.getPublisher());
    if (!cm.getContact().isEmpty()) {
        p.addText(" (");
        boolean firsti = true;
        for (ConceptMapContactComponent ci : cm.getContact()) {
            if (firsti)
                firsti = false;
            else
                p.addText(", ");
            if (ci.hasName())
                p.addText(ci.getName() + ": ");
            boolean first = true;
            for (ContactPoint c : ci.getTelecom()) {
                if (first)
                    first = false;
                else
                    p.addText(", ");
                addTelecom(p, c);
            }
            p.addText("; ");
        }
        p.addText(")");
    }
    p.addText(". ");
    p.addText(cm.getCopyright());
    if (!Utilities.noString(cm.getDescription()))
        x.addTag("p").addText(cm.getDescription());
    x.addTag("br");
    if (!cm.getElement().isEmpty()) {
        SourceElementComponent cc = cm.getElement().get(0);
        String src = cc.getSystem();
        boolean comments = false;
        boolean ok = cc.getTarget().size() == 1;
        Map<String, HashSet<String>> sources = new HashMap<String, HashSet<String>>();
        sources.put("code", new HashSet<String>());
        Map<String, HashSet<String>> targets = new HashMap<String, HashSet<String>>();
        targets.put("code", new HashSet<String>());
        if (ok) {
            String dst = cc.getTarget().get(0).getSystem();
            for (SourceElementComponent ccl : cm.getElement()) {
                ok = ok && src.equals(ccl.getSystem()) && ccl.getTarget().size() == 1 && dst.equals(ccl.getTarget().get(0).getSystem()) && ccl.getTarget().get(0).getDependsOn().isEmpty() && ccl.getTarget().get(0).getProduct().isEmpty();
                if (ccl.hasSystem())
                    sources.get("code").add(ccl.getSystem());
                for (TargetElementComponent ccm : ccl.getTarget()) {
                    comments = comments || !Utilities.noString(ccm.getComments());
                    for (OtherElementComponent d : ccm.getDependsOn()) {
                        if (!sources.containsKey(d.getElement()))
                            sources.put(d.getElement(), new HashSet<String>());
                        sources.get(d.getElement()).add(d.getSystem());
                    }
                    if (ccm.hasSystem())
                        targets.get("code").add(ccm.getSystem());
                    for (OtherElementComponent d : ccm.getProduct()) {
                        if (!targets.containsKey(d.getElement()))
                            targets.put(d.getElement(), new HashSet<String>());
                        targets.get(d.getElement()).add(d.getSystem());
                    }
                }
            }
        }
        String display;
        if (ok) {
            // simple
            XhtmlNode tbl = x.addTag("table").setAttribute("class", "grid");
            XhtmlNode tr = tbl.addTag("tr");
            tr.addTag("td").addTag("b").addText("Source Code");
            tr.addTag("td").addTag("b").addText("Equivalence");
            tr.addTag("td").addTag("b").addText("Destination Code");
            if (comments)
                tr.addTag("td").addTag("b").addText("Comments");
            for (SourceElementComponent ccl : cm.getElement()) {
                tr = tbl.addTag("tr");
                XhtmlNode td = tr.addTag("td");
                td.addText(ccl.getCode());
                display = getDisplayForConcept(ccl.getSystem(), ccl.getCode());
                if (display != null)
                    td.addText(" (" + display + ")");
                TargetElementComponent ccm = ccl.getTarget().get(0);
                tr.addTag("td").addText(!ccm.hasEquivalence() ? "" : ccm.getEquivalence().toCode());
                td = tr.addTag("td");
                td.addText(ccm.getCode());
                display = getDisplayForConcept(ccm.getSystem(), ccm.getCode());
                if (display != null)
                    td.addText(" (" + display + ")");
                if (comments)
                    tr.addTag("td").addText(ccm.getComments());
            }
        } else {
            XhtmlNode tbl = x.addTag("table").setAttribute("class", "grid");
            XhtmlNode tr = tbl.addTag("tr");
            XhtmlNode td;
            tr.addTag("td").setAttribute("colspan", Integer.toString(sources.size())).addTag("b").addText("Source Concept");
            tr.addTag("td").addTag("b").addText("Equivalence");
            tr.addTag("td").setAttribute("colspan", Integer.toString(targets.size())).addTag("b").addText("Destination Concept");
            if (comments)
                tr.addTag("td").addTag("b").addText("Comments");
            tr = tbl.addTag("tr");
            if (sources.get("code").size() == 1)
                tr.addTag("td").addTag("b").addText("Code " + sources.get("code").toString() + "");
            else
                tr.addTag("td").addTag("b").addText("Code");
            for (String s : sources.keySet()) {
                if (!s.equals("code")) {
                    if (sources.get(s).size() == 1)
                        tr.addTag("td").addTag("b").addText(getDescForConcept(s) + " " + sources.get(s).toString());
                    else
                        tr.addTag("td").addTag("b").addText(getDescForConcept(s));
                }
            }
            tr.addTag("td");
            if (targets.get("code").size() == 1)
                tr.addTag("td").addTag("b").addText("Code " + targets.get("code").toString());
            else
                tr.addTag("td").addTag("b").addText("Code");
            for (String s : targets.keySet()) {
                if (!s.equals("code")) {
                    if (targets.get(s).size() == 1)
                        tr.addTag("td").addTag("b").addText(getDescForConcept(s) + " " + targets.get(s).toString() + "");
                    else
                        tr.addTag("td").addTag("b").addText(getDescForConcept(s));
                }
            }
            if (comments)
                tr.addTag("td");
            for (SourceElementComponent ccl : cm.getElement()) {
                tr = tbl.addTag("tr");
                td = tr.addTag("td");
                if (sources.get("code").size() == 1)
                    td.addText(ccl.getCode());
                else
                    td.addText(ccl.getSystem() + " / " + ccl.getCode());
                display = getDisplayForConcept(ccl.getSystem(), ccl.getCode());
                if (display != null)
                    td.addText(" (" + display + ")");
                TargetElementComponent ccm = ccl.getTarget().get(0);
                for (String s : sources.keySet()) {
                    if (!s.equals("code")) {
                        td = tr.addTag("td");
                        td.addText(getCode(ccm.getDependsOn(), s, sources.get(s).size() != 1));
                        display = getDisplay(ccm.getDependsOn(), s);
                        if (display != null)
                            td.addText(" (" + display + ")");
                    }
                }
                tr.addTag("td").addText(ccm.getEquivalence().toString());
                td = tr.addTag("td");
                if (targets.get("code").size() == 1)
                    td.addText(ccm.getCode());
                else
                    td.addText(ccm.getSystem() + " / " + ccm.getCode());
                display = getDisplayForConcept(ccm.getSystem(), ccm.getCode());
                if (display != null)
                    td.addText(" (" + display + ")");
                for (String s : targets.keySet()) {
                    if (!s.equals("code")) {
                        td = tr.addTag("td");
                        td.addText(getCode(ccm.getProduct(), s, targets.get(s).size() != 1));
                        display = getDisplay(ccm.getProduct(), s);
                        if (display != null)
                            td.addText(" (" + display + ")");
                    }
                }
                if (comments)
                    tr.addTag("td").addText(ccm.getComments());
            }
        }
    }
    inject(cm, x, NarrativeStatus.GENERATED);
}