Examples with ConceptMap org.hl7.fhir.r4b.model.ConceptMap used on opensource projects

Example 56 with ConceptMap

use of org.hl7.fhir.r4b.model.ConceptMap in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method addExpansionRowToTable.

private void addExpansionRowToTable(XhtmlNode t, ValueSetExpansionContainsComponent c, int i, boolean doSystem, boolean doDefinition, Map<ConceptMap, String> mymaps, CodeSystem allCS, List<String> langs) {
    XhtmlNode tr = t.tr();
    XhtmlNode td = tr.td();
    String tgt = makeAnchor(c.getSystem(), c.getCode());
    td.an(tgt);
    String s = Utilities.padLeft("", '\u00A0', i * 2);
    td.addText(s);
    addCodeToTable(c.getAbstract(), c.getSystem(), c.getCode(), c.getDisplay(), td);
    if (doSystem) {
        td = tr.td();
        td.addText(c.getSystem());
    }
    td = tr.td();
    if (c.hasDisplayElement())
        td.addText(c.getDisplay());
    if (doDefinition) {
        CodeSystem cs = allCS;
        if (cs == null)
            cs = context.fetchCodeSystem(c.getSystem());
        td = tr.td();
        if (cs != null)
            td.addText(CodeSystemUtilities.getCodeDefinition(cs, c.getCode()));
    }
    for (ConceptMap m : mymaps.keySet()) {
        td = tr.td();
        List<TargetElementComponentWrapper> mappings = findMappingsForCode(c.getCode(), m);
        boolean first = true;
        for (TargetElementComponentWrapper mapping : mappings) {
            if (!first)
                td.br();
            first = false;
            XhtmlNode span = td.span(null, mapping.comp.getEquivalence().toString());
            span.addText(getCharForEquivalence(mapping.comp));
            XhtmlNode a = td.ah(prefix + mymaps.get(m) + "#" + mapping.comp.getCode());
            a.addText(mapping.comp.getCode());
            if (!Utilities.noString(mapping.comp.getComment()))
                td.i().tx("(" + mapping.comp.getComment() + ")");
        }
    }
    for (Extension ext : c.getExtension()) {
        if (ToolingExtensions.EXT_TRANSLATION.equals(ext.getUrl())) {
            String lang = ToolingExtensions.readStringExtension(ext, "lang");
            if (!Utilities.noString(lang) && !langs.contains(lang))
                langs.add(lang);
        }
    }
    for (ValueSetExpansionContainsComponent cc : c.getContains()) {
        addExpansionRowToTable(t, cc, i + 1, doSystem, doDefinition, mymaps, allCS, langs);
    }
}

Example 57 with ConceptMap

use of org.hl7.fhir.r4b.model.ConceptMap in project org.hl7.fhir.core by hapifhir.

the class RdfParser method composeConceptMapOtherElementComponent.

protected void composeConceptMapOtherElementComponent(Complex parent, String parentType, String name, ConceptMap.OtherElementComponent element, int index) {
    if (element == null)
        return;
    Complex t;
    if (Utilities.noString(parentType))
        t = parent;
    else {
        t = parent.predicate("fhir:" + parentType + '.' + name);
    }
    composeBackboneElement(t, "dependsOn", name, element, index);
    if (element.hasPropertyElement())
        composeUri(t, "ConceptMap", "property", element.getPropertyElement(), -1);
    if (element.hasSystemElement())
        composeCanonical(t, "ConceptMap", "system", element.getSystemElement(), -1);
    if (element.hasValueElement())
        composeString(t, "ConceptMap", "value", element.getValueElement(), -1);
    if (element.hasDisplayElement())
        composeString(t, "ConceptMap", "display", element.getDisplayElement(), -1);
}

Example 58 with ConceptMap

use of org.hl7.fhir.r4b.model.ConceptMap in project org.hl7.fhir.core by hapifhir.

the class ConceptMapEngineTest method codingTranslate.

@Test
@DisplayName("Coding is translated according to ConceptMap")
void codingTranslate() throws IOException {
    final ConceptMap.SourceElementComponent sourceElementComponent = getSourceElementComponent();
    final ConceptMapEngine conceptMapEngine = getConceptMapEngine(Arrays.asList(sourceElementComponent));
    Coding coding = new Coding(null, SOURCE_CODE_STRING, "Body Weight");
    Coding actual = conceptMapEngine.translate(coding, CONCEPT_MAP_URL);
    assertEquals(TARGET_CODE_STRING, actual.getCode());
}

Example 59 with ConceptMap

use of org.hl7.fhir.r4b.model.ConceptMap in project org.hl7.fhir.core by hapifhir.

the class ConceptMapEngineTest method getConceptMapEngine.

@Nonnull
private ConceptMapEngine getConceptMapEngine(Collection<ConceptMap.SourceElementComponent> elements) throws IOException {
    ConceptMap conceptMap = getConceptMap(elements);
    SimpleWorkerContext simpleWorkerContext = mock(SimpleWorkerContext.class);
    when(simpleWorkerContext.fetchResource(ConceptMap.class, CONCEPT_MAP_URL)).thenReturn(conceptMap);
    return new ConceptMapEngine(simpleWorkerContext);
}

Example 60 with ConceptMap

use of org.hl7.fhir.r4b.model.ConceptMap in project org.hl7.fhir.core by hapifhir.

the class ConceptMapRenderer method render.

public boolean render(XhtmlNode x, ConceptMap cm) throws FHIRFormatError, DefinitionException, IOException {
    x.h2().addText(cm.getName() + " (" + cm.getUrl() + ")");
    XhtmlNode p = x.para();
    p.tx("Mapping from ");
    if (cm.hasSource())
        AddVsRef(cm.getSource().primitiveValue(), p);
    else
        p.tx("(not specified)");
    p.tx(" to ");
    if (cm.hasTarget())
        AddVsRef(cm.getTarget().primitiveValue(), p);
    else
        p.tx("(not specified)");
    p = x.para();
    if (cm.getExperimental())
        p.addText(Utilities.capitalize(cm.getStatus().toString()) + " (not intended for production usage). ");
    else
        p.addText(Utilities.capitalize(cm.getStatus().toString()) + ". ");
    p.tx("Published on " + (cm.hasDate() ? cm.getDateElement().toHumanDisplay() : "?ngen-10?") + " by " + cm.getPublisher());
    if (!cm.getContact().isEmpty()) {
        p.tx(" (");
        boolean firsti = true;
        for (ContactDetail ci : cm.getContact()) {
            if (firsti)
                firsti = false;
            else
                p.tx(", ");
            if (ci.hasName())
                p.addText(ci.getName() + ": ");
            boolean first = true;
            for (ContactPoint c : ci.getTelecom()) {
                if (first)
                    first = false;
                else
                    p.tx(", ");
                addTelecom(p, c);
            }
        }
        p.tx(")");
    }
    p.tx(". ");
    p.addText(cm.getCopyright());
    if (!Utilities.noString(cm.getDescription()))
        addMarkdown(x, cm.getDescription());
    x.br();
    CodeSystem cs = getContext().getWorker().fetchCodeSystem("http://hl7.org/fhir/concept-map-relationship");
    if (cs == null)
        cs = getContext().getWorker().fetchCodeSystem("http://hl7.org/fhir/concept-map-equivalence");
    String eqpath = cs == null ? null : cs.getUserString("path");
    for (ConceptMapGroupComponent grp : cm.getGroup()) {
        String src = grp.getSource();
        boolean comment = false;
        boolean ok = true;
        Map<String, HashSet<String>> sources = new HashMap<String, HashSet<String>>();
        Map<String, HashSet<String>> targets = new HashMap<String, HashSet<String>>();
        sources.put("code", new HashSet<String>());
        targets.put("code", new HashSet<String>());
        SourceElementComponent cc = grp.getElement().get(0);
        String dst = grp.getTarget();
        sources.get("code").add(grp.getSource());
        targets.get("code").add(grp.getTarget());
        for (SourceElementComponent ccl : grp.getElement()) {
            ok = ok && ccl.getTarget().size() == 1 && ccl.getTarget().get(0).getDependsOn().isEmpty() && ccl.getTarget().get(0).getProduct().isEmpty();
            for (TargetElementComponent ccm : ccl.getTarget()) {
                comment = comment || !Utilities.noString(ccm.getComment());
                for (OtherElementComponent d : ccm.getDependsOn()) {
                    if (!sources.containsKey(d.getProperty()))
                        sources.put(d.getProperty(), new HashSet<String>());
                    sources.get(d.getProperty()).add(d.getSystem());
                }
                for (OtherElementComponent d : ccm.getProduct()) {
                    if (!targets.containsKey(d.getProperty()))
                        targets.put(d.getProperty(), new HashSet<String>());
                    targets.get(d.getProperty()).add(d.getSystem());
                }
            }
        }
        String display;
        if (ok) {
            // simple
            XhtmlNode tbl = x.table("grid");
            XhtmlNode tr = tbl.tr();
            tr.td().b().tx("Source Code");
            tr.td().b().tx("Relationship");
            tr.td().b().tx("Destination Code");
            if (comment)
                tr.td().b().tx("Comment");
            for (SourceElementComponent ccl : grp.getElement()) {
                tr = tbl.tr();
                XhtmlNode td = tr.td();
                td.addText(ccl.getCode());
                display = getDisplayForConcept(systemFromCanonical(grp.getSource()), versionFromCanonical(grp.getSource()), ccl.getCode());
                if (display != null && !isSameCodeAndDisplay(ccl.getCode(), display))
                    td.tx(" (" + display + ")");
                TargetElementComponent ccm = ccl.getTarget().get(0);
                if (!ccm.hasEquivalence())
                    tr.td().tx(":" + "(" + ConceptMapEquivalence.NULL.toCode() + ")");
                else {
                    String code = ccm.getEquivalenceElement().primitiveValue();
                    tr.td().ah(eqpath + "#" + code).tx(presentEquivalenceCode(code));
                }
                td = tr.td();
                td.addText(ccm.getCode());
                display = getDisplayForConcept(systemFromCanonical(grp.getTarget()), versionFromCanonical(grp.getTarget()), ccm.getCode());
                if (display != null && !isSameCodeAndDisplay(ccm.getCode(), display))
                    td.tx(" (" + display + ")");
                if (comment)
                    tr.td().addText(ccm.getComment());
                addUnmapped(tbl, grp);
            }
        } else {
            boolean hasRelationships = false;
            for (int si = 0; si < grp.getElement().size(); si++) {
                SourceElementComponent ccl = grp.getElement().get(si);
                for (int ti = 0; ti < ccl.getTarget().size(); ti++) {
                    TargetElementComponent ccm = ccl.getTarget().get(ti);
                    if (ccm.hasEquivalence()) {
                        hasRelationships = true;
                    }
                }
            }
            XhtmlNode tbl = x.table("grid");
            XhtmlNode tr = tbl.tr();
            XhtmlNode td;
            tr.td().colspan(Integer.toString(1 + sources.size())).b().tx("Source Concept Details");
            if (hasRelationships) {
                tr.td().b().tx("Relationship");
            }
            tr.td().colspan(Integer.toString(1 + targets.size())).b().tx("Destination Concept Details");
            if (comment) {
                tr.td().b().tx("Comment");
            }
            tr = tbl.tr();
            if (sources.get("code").size() == 1) {
                String url = sources.get("code").iterator().next();
                renderCSDetailsLink(tr, url, true);
            } else
                tr.td().b().tx("Code");
            for (String s : sources.keySet()) {
                if (!s.equals("code")) {
                    if (sources.get(s).size() == 1) {
                        String url = sources.get(s).iterator().next();
                        renderCSDetailsLink(tr, url, false);
                    } else
                        tr.td().b().addText(getDescForConcept(s));
                }
            }
            if (hasRelationships) {
                tr.td();
            }
            if (targets.get("code").size() == 1) {
                String url = targets.get("code").iterator().next();
                renderCSDetailsLink(tr, url, true);
            } else
                tr.td().b().tx("Code");
            for (String s : targets.keySet()) {
                if (!s.equals("code")) {
                    if (targets.get(s).size() == 1) {
                        String url = targets.get(s).iterator().next();
                        renderCSDetailsLink(tr, url, false);
                    } else
                        tr.td().b().addText(getDescForConcept(s));
                }
            }
            if (comment)
                tr.td();
            for (int si = 0; si < grp.getElement().size(); si++) {
                SourceElementComponent ccl = grp.getElement().get(si);
                boolean slast = si == grp.getElement().size() - 1;
                boolean first = true;
                if (false) {
                    tr = tbl.tr();
                    td = tr.td().style("border-right-width: 0px");
                    if (!first)
                        td.style("border-top-style: none");
                    else
                        td.style("border-bottom-style: none");
                    if (sources.get("code").size() == 1)
                        td.addText(ccl.getCode());
                    else
                        td.addText(grp.getSource() + " / " + ccl.getCode());
                    display = getDisplayForConcept(systemFromCanonical(grp.getSource()), versionFromCanonical(grp.getSource()), ccl.getCode());
                    tr.td().style("border-left-width: 0px").tx(display == null ? "" : display);
                    tr.td().colspan("4").style("background-color: #efefef").tx("(not mapped)");
                } else {
                    for (int ti = 0; ti < ccl.getTarget().size(); ti++) {
                        TargetElementComponent ccm = ccl.getTarget().get(ti);
                        boolean last = ti == ccl.getTarget().size() - 1;
                        tr = tbl.tr();
                        td = tr.td().style("border-right-width: 0px");
                        if (!first && !last)
                            td.style("border-top-style: none; border-bottom-style: none");
                        else if (!first)
                            td.style("border-top-style: none");
                        else if (!last)
                            td.style("border-bottom-style: none");
                        if (first) {
                            if (sources.get("code").size() == 1)
                                td.addText(ccl.getCode());
                            else
                                td.addText(grp.getSource() + " / " + ccl.getCode());
                            display = ccl.hasDisplay() ? ccl.getDisplay() : getDisplayForConcept(systemFromCanonical(grp.getSource()), versionFromCanonical(grp.getSource()), ccl.getCode());
                            td = tr.td();
                            if (!last)
                                td.style("border-left-width: 0px; border-bottom-style: none");
                            else
                                td.style("border-left-width: 0px");
                            td.tx(display == null ? "" : display);
                        } else {
                            // for display
                            td = tr.td();
                            if (!last)
                                td.style("border-left-width: 0px; border-top-style: none; border-bottom-style: none");
                            else
                                td.style("border-top-style: none; border-left-width: 0px");
                        }
                        for (String s : sources.keySet()) {
                            if (!s.equals("code")) {
                                td = tr.td();
                                if (first) {
                                    td.addText(getValue(ccm.getDependsOn(), s, sources.get(s).size() != 1));
                                    display = getDisplay(ccm.getDependsOn(), s);
                                    if (display != null)
                                        td.tx(" (" + display + ")");
                                }
                            }
                        }
                        first = false;
                        if (hasRelationships) {
                            if (!ccm.hasEquivalence())
                                tr.td();
                            else {
                                String code = ccm.getEquivalenceElement().toString();
                                tr.td().ah(eqpath + "#" + code).tx(presentEquivalenceCode(code));
                            }
                        }
                        td = tr.td().style("border-right-width: 0px");
                        if (targets.get("code").size() == 1)
                            td.addText(ccm.getCode());
                        else
                            td.addText(grp.getTarget() + " / " + ccm.getCode());
                        display = ccm.hasDisplay() ? ccm.getDisplay() : getDisplayForConcept(systemFromCanonical(grp.getTarget()), versionFromCanonical(grp.getTarget()), ccm.getCode());
                        tr.td().style("border-left-width: 0px").tx(display == null ? "" : display);
                        for (String s : targets.keySet()) {
                            if (!s.equals("code")) {
                                td = tr.td();
                                td.addText(getValue(ccm.getProduct(), s, targets.get(s).size() != 1));
                                display = getDisplay(ccm.getProduct(), s);
                                if (display != null)
                                    td.tx(" (" + display + ")");
                            }
                        }
                        if (comment)
                            tr.td().addText(ccm.getComment());
                    }
                }
                addUnmapped(tbl, grp);
            }
        }
    }
    return true;
}