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

Example 66 with ConceptMap

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

the class NarrativeGenerator method generateExpansion.

private boolean generateExpansion(XhtmlNode x, ValueSet vs, ValueSet src, boolean header) throws FHIRFormatError, DefinitionException, IOException {
    boolean hasExtensions = false;
    List<String> langs = new ArrayList<String>();
    Map<ConceptMap, String> mymaps = new HashMap<ConceptMap, String>();
    if (header) {
        XhtmlNode h = x.addTag(getHeader());
        h.tx("Value Set Contents");
        if (IsNotFixedExpansion(vs))
            addMarkdown(x, vs.getDescription());
        if (vs.hasCopyright())
            generateCopyright(x, vs);
    }
    if (ToolingExtensions.hasExtension(vs.getExpansion(), "http://hl7.org/fhir/StructureDefinition/valueset-toocostly"))
        x.para().setAttribute("style", "border: maroon 1px solid; background-color: #FFCCCC; font-weight: bold; padding: 8px").addText(vs.getExpansion().getContains().isEmpty() ? tooCostlyNoteEmpty : tooCostlyNoteNotEmpty);
    else {
        Integer count = countMembership(vs);
        if (count == null)
            x.para().tx("This value set does not contain a fixed number of concepts");
        else
            x.para().tx("This value set contains " + count.toString() + " concepts");
    }
    generateVersionNotice(x, vs.getExpansion());
    CodeSystem allCS = null;
    // checkDoSystem(vs, src);
    boolean doSystem = true;
    boolean doDefinition = checkDoDefinition(vs.getExpansion().getContains());
    if (doSystem && allFromOneSystem(vs)) {
        doSystem = false;
        XhtmlNode p = x.para();
        p.tx("All codes from system ");
        allCS = context.fetchCodeSystem(vs.getExpansion().getContains().get(0).getSystem());
        String ref = null;
        if (allCS != null)
            ref = getCsRef(allCS);
        if (ref == null)
            p.code(vs.getExpansion().getContains().get(0).getSystem());
        else
            p.ah(prefix + ref).code(vs.getExpansion().getContains().get(0).getSystem());
    }
    XhtmlNode t = x.table("codes");
    XhtmlNode tr = t.tr();
    tr.td().b().tx("Code");
    if (doSystem)
        tr.td().b().tx("System");
    tr.td().b().tx("Display");
    if (doDefinition)
        tr.td().b().tx("Definition");
    addMapHeaders(tr, mymaps);
    for (ValueSetExpansionContainsComponent c : vs.getExpansion().getContains()) {
        addExpansionRowToTable(t, c, 0, doSystem, doDefinition, mymaps, allCS, langs);
    }
    if (langs.size() > 0) {
        Collections.sort(langs);
        x.para().b().tx("Additional Language Displays");
        t = x.table("codes");
        tr = t.tr();
        tr.td().b().tx("Code");
        for (String lang : langs) tr.td().b().addText(describeLang(lang));
        for (ValueSetExpansionContainsComponent c : vs.getExpansion().getContains()) {
            addLanguageRow(c, t, langs);
        }
    }
    return hasExtensions;
}

Example 67 with ConceptMap

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

the class NarrativeGenerator method generate.

public boolean generate(ResourceContext rcontext, ConceptMap cm) throws FHIRFormatError, DefinitionException, IOException {
    XhtmlNode x = new XhtmlNode(NodeType.Element, "div");
    x.h2().addText(cm.getName() + " (" + cm.getUrl() + ")");
    XhtmlNode p = x.para();
    if (cm.hasSource() || cm.hasTarget())
        p.tx("Mapping from ");
    if (!cm.hasSource())
        p.tx("(unspecified)");
    else
        AddVsRef(rcontext, cm.getSource() instanceof Reference ? ((Reference) cm.getSource()).getReference() : ((UriType) cm.getSource()).asStringValue(), p);
    p.tx(" to ");
    if (!cm.hasTarget())
        p.tx("(unspecified)");
    else
        AddVsRef(rcontext, cm.getTarget() instanceof Reference ? ((Reference) cm.getTarget()).getReference() : ((UriType) cm.getTarget()).asStringValue(), p);
    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() : "??") + " 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();
    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("Equivalence");
            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(grp.getSource(), ccl.getCode());
                if (display != null)
                    td.tx(" (" + display + ")");
                TargetElementComponent ccm = ccl.getTarget().get(0);
                tr.td().addText(!ccm.hasEquivalence() ? "" : ccm.getEquivalence().toCode());
                td = tr.td();
                td.addText(ccm.getCode());
                display = getDisplayForConcept(grp.getTarget(), ccm.getCode());
                if (display != null)
                    td.tx(" (" + display + ")");
                if (comment)
                    tr.td().addText(ccm.getComment());
            }
        } else {
            XhtmlNode tbl = x.table("grid");
            XhtmlNode tr = tbl.tr();
            XhtmlNode td;
            tr.td().colspan(Integer.toString(sources.size())).b().tx("Source Concept");
            tr.td().b().tx("Equivalence");
            tr.td().colspan(Integer.toString(targets.size())).b().tx("Destination Concept");
            if (comment)
                tr.td().b().tx("Comment");
            tr = tbl.tr();
            if (sources.get("code").size() == 1)
                tr.td().b().tx("Code " + sources.get("code").toString() + "");
            else
                tr.td().b().tx("Code");
            for (String s : sources.keySet()) {
                if (!s.equals("code")) {
                    if (sources.get(s).size() == 1)
                        tr.td().b().addText(getDescForConcept(s) + " " + sources.get(s).toString());
                    else
                        tr.td().b().addText(getDescForConcept(s));
                }
            }
            tr.td();
            if (targets.get("code").size() == 1)
                tr.td().b().tx("Code " + targets.get("code").toString());
            else
                tr.td().b().tx("Code");
            for (String s : targets.keySet()) {
                if (!s.equals("code")) {
                    if (targets.get(s).size() == 1)
                        tr.td().b().addText(getDescForConcept(s) + " " + targets.get(s).toString() + "");
                    else
                        tr.td().b().addText(getDescForConcept(s));
                }
            }
            if (comment)
                tr.td();
            for (SourceElementComponent ccl : grp.getElement()) {
                tr = tbl.tr();
                td = tr.td();
                if (sources.get("code").size() == 1)
                    td.addText(ccl.getCode());
                else
                    td.addText(grp.getSource() + " / " + ccl.getCode());
                display = getDisplayForConcept(grp.getSource(), ccl.getCode());
                if (display != null)
                    td.tx(" (" + display + ")");
                TargetElementComponent ccm = ccl.getTarget().get(0);
                for (String s : sources.keySet()) {
                    if (!s.equals("code")) {
                        td = tr.td();
                        td.addText(getCode(ccm.getDependsOn(), s, sources.get(s).size() != 1));
                        display = getDisplay(ccm.getDependsOn(), s);
                        if (display != null)
                            td.tx(" (" + display + ")");
                    }
                }
                if (!ccm.hasEquivalence())
                    tr.td().tx(":" + "(" + ConceptMapEquivalence.EQUIVALENT.toCode() + ")");
                else
                    tr.td().tx(":" + ccm.getEquivalence().toCode());
                td = tr.td();
                if (targets.get("code").size() == 1)
                    td.addText(ccm.getCode());
                else
                    td.addText(grp.getTarget() + " / " + ccm.getCode());
                display = getDisplayForConcept(grp.getTarget(), ccm.getCode());
                if (display != null)
                    td.tx(" (" + display + ")");
                for (String s : targets.keySet()) {
                    if (!s.equals("code")) {
                        td = tr.td();
                        td.addText(getCode(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());
            }
        }
    }
    inject(cm, x, NarrativeStatus.GENERATED);
    return true;
}

Example 68 with ConceptMap

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

the class TurtleTests method test_conceptmap_example.

@Test
public void test_conceptmap_example() throws FileNotFoundException, IOException, Exception {
    System.out.println("conceptmap-example.ttl");
    new Turtle().parse(TextFile.fileToString("C:\\work\\org.hl7.fhir\\build\\publish\\conceptmap-example.ttl"));
}

Example 69 with ConceptMap

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

the class StructureMapUtilities method translate.

public Base translate(TransformContext context, StructureMap map, Base source, String conceptMapUrl, String fieldToReturn) throws FHIRException {
    Coding src = new Coding();
    if (source.isPrimitive()) {
        src.setCode(source.primitiveValue());
    } else if ("Coding".equals(source.fhirType())) {
        Base[] b = source.getProperty("system".hashCode(), "system", true);
        if (b.length == 1)
            src.setSystem(b[0].primitiveValue());
        b = source.getProperty("code".hashCode(), "code", true);
        if (b.length == 1)
            src.setCode(b[0].primitiveValue());
    } else if ("CE".equals(source.fhirType())) {
        Base[] b = source.getProperty("codeSystem".hashCode(), "codeSystem", true);
        if (b.length == 1)
            src.setSystem(b[0].primitiveValue());
        b = source.getProperty("code".hashCode(), "code", true);
        if (b.length == 1)
            src.setCode(b[0].primitiveValue());
    } else
        throw new FHIRException("Unable to translate source " + source.fhirType());
    String su = conceptMapUrl;
    if (conceptMapUrl.equals("http://hl7.org/fhir/ConceptMap/special-oid2uri")) {
        String uri = worker.oid2Uri(src.getCode());
        if (uri == null)
            uri = "urn:oid:" + src.getCode();
        if ("uri".equals(fieldToReturn))
            return new UriType(uri);
        else
            throw new FHIRException("Error in return code");
    } else {
        ConceptMap cmap = null;
        if (conceptMapUrl.startsWith("#")) {
            for (Resource r : map.getContained()) {
                if (r instanceof ConceptMap && ((ConceptMap) r).getId().equals(conceptMapUrl.substring(1))) {
                    cmap = (ConceptMap) r;
                    su = map.getUrl() + "#" + conceptMapUrl;
                }
            }
            if (cmap == null)
                throw new FHIRException("Unable to translate - cannot find map " + conceptMapUrl);
        } else {
            if (conceptMapUrl.contains("#")) {
                String[] p = conceptMapUrl.split("\\#");
                StructureMap mapU = worker.fetchResource(StructureMap.class, p[0]);
                for (Resource r : mapU.getContained()) {
                    if (r instanceof ConceptMap && ((ConceptMap) r).getId().equals(p[1])) {
                        cmap = (ConceptMap) r;
                        su = conceptMapUrl;
                    }
                }
            }
            if (cmap == null)
                cmap = worker.fetchResource(ConceptMap.class, conceptMapUrl);
        }
        Coding outcome = null;
        boolean done = false;
        String message = null;
        if (cmap == null) {
            if (services == null)
                message = "No map found for " + conceptMapUrl;
            else {
                outcome = services.translate(context.appInfo, src, conceptMapUrl);
                done = true;
            }
        } else {
            List<SourceElementComponentWrapper> list = new ArrayList<SourceElementComponentWrapper>();
            for (ConceptMapGroupComponent g : cmap.getGroup()) {
                for (SourceElementComponent e : g.getElement()) {
                    if (!src.hasSystem() && src.getCode().equals(e.getCode()))
                        list.add(new SourceElementComponentWrapper(g, e));
                    else if (src.hasSystem() && src.getSystem().equals(g.getSource()) && src.getCode().equals(e.getCode()))
                        list.add(new SourceElementComponentWrapper(g, e));
                }
            }
            if (list.size() == 0)
                done = true;
            else if (list.get(0).comp.getTarget().size() == 0)
                message = "Concept map " + su + " found no translation for " + src.getCode();
            else {
                for (TargetElementComponent tgt : list.get(0).comp.getTarget()) {
                    if (tgt.getEquivalence() == null || EnumSet.of(ConceptMapEquivalence.EQUAL, ConceptMapEquivalence.RELATEDTO, ConceptMapEquivalence.EQUIVALENT, ConceptMapEquivalence.WIDER).contains(tgt.getEquivalence())) {
                        if (done) {
                            message = "Concept map " + su + " found multiple matches for " + src.getCode();
                            done = false;
                        } else {
                            done = true;
                            outcome = new Coding().setCode(tgt.getCode()).setSystem(list.get(0).group.getTarget());
                        }
                    } else if (tgt.getEquivalence() == ConceptMapEquivalence.UNMATCHED) {
                        done = true;
                    }
                }
                if (!done)
                    message = "Concept map " + su + " found no usable translation for " + src.getCode();
            }
        }
        if (!done)
            throw new FHIRException(message);
        if (outcome == null)
            return null;
        if ("code".equals(fieldToReturn))
            return new CodeType(outcome.getCode());
        else
            return outcome;
    }
}

Example 70 with ConceptMap

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

the class ValueSetRenderer method findReleventMaps.

private List<UsedConceptMap> findReleventMaps(ValueSet vs) throws FHIRException {
    List<UsedConceptMap> res = new ArrayList<UsedConceptMap>();
    for (CanonicalResource md : getContext().getWorker().allConformanceResources()) {
        if (md instanceof ConceptMap) {
            ConceptMap cm = (ConceptMap) md;
            if (isSource(vs, cm.getSource())) {
                ConceptMapRenderInstructions re = findByTarget(cm.getTarget());
                if (re != null) {
                    ValueSet vst = cm.hasTarget() ? getContext().getWorker().fetchResource(ValueSet.class, cm.hasTargetCanonicalType() ? cm.getTargetCanonicalType().getValue() : cm.getTargetUriType().asStringValue()) : null;
                    res.add(new UsedConceptMap(re, vst == null ? cm.getUserString("path") : vst.getUserString("path"), cm));
                }
            }
        }
    }
    return res;
// Map<ConceptMap, String> mymaps = new HashMap<ConceptMap, String>();
// for (ConceptMap a : context.getWorker().findMapsForSource(vs.getUrl())) {
// String url = "";
// ValueSet vsr = context.getWorker().fetchResource(ValueSet.class, ((Reference) a.getTarget()).getReference());
// if (vsr != null)
// url = (String) vsr.getUserData("filename");
// mymaps.put(a, url);
// }
// Map<ConceptMap, String> mymaps = new HashMap<ConceptMap, String>();
// for (ConceptMap a : context.getWorker().findMapsForSource(cs.getValueSet())) {
// String url = "";
// ValueSet vsr = context.getWorker().fetchResource(ValueSet.class, ((Reference) a.getTarget()).getReference());
// if (vsr != null)
// url = (String) vsr.getUserData("filename");
// mymaps.put(a, url);
// }
// also, look in the contained resources for a concept map
// for (Resource r : cs.getContained()) {
// if (r instanceof ConceptMap) {
// ConceptMap cm = (ConceptMap) r;
// if (((Reference) cm.getSource()).getReference().equals(cs.getValueSet())) {
// String url = "";
// ValueSet vsr = context.getWorker().fetchResource(ValueSet.class, ((Reference) cm.getTarget()).getReference());
// if (vsr != null)
// url = (String) vsr.getUserData("filename");
// mymaps.put(cm, url);
// }
// }
// }
}