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

Example 16 with TargetElementComponent

use of org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent 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 17 with TargetElementComponent

use of org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent 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 18 with TargetElementComponent

use of org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent 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 && 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 && 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.getAppInfo(), 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).getComp().getTarget().size() == 0)
                message = "Concept map " + su + " found no translation for " + src.getCode();
            else {
                for (TargetElementComponent tgt : list.get(0).getComp().getTarget()) {
                    if (tgt.getRelationship() == null || EnumSet.of(ConceptMapRelationship.RELATEDTO, ConceptMapRelationship.EQUIVALENT, ConceptMapRelationship.SOURCEISNARROWERTHANTARGET).contains(tgt.getRelationship())) {
                        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).getGroup().getTarget());
                        }
                    }
                }
                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 19 with TargetElementComponent

use of org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent in project pathling by aehrc.

the class ConceptMapBuilder method build.

@Nonnull
public ConceptMap build() {
    final Map<Pair<VersionedSystem, VersionedSystem>, List<ConceptMapEntry>> mappingsBySystem = entries.stream().collect(Collectors.groupingBy(ConceptMapBuilder::getVersionedSystems));
    final ConceptMap result = new ConceptMap();
    result.setStatus(PublicationStatus.ACTIVE);
    mappingsBySystem.forEach((srcAndTarget, systemMappings) -> {
        final ConceptMapGroupComponent group = result.addGroup();
        group.setSource(srcAndTarget.getLeft().getSystem());
        group.setSourceVersion(srcAndTarget.getLeft().getVersion());
        group.setTarget(srcAndTarget.getRight().getSystem());
        group.setTargetVersion(srcAndTarget.getRight().getVersion());
        systemMappings.forEach(m -> {
            final SourceElementComponent sourceElement = group.addElement();
            sourceElement.setCode(m.getSource().getCode());
            final TargetElementComponent targetElement = sourceElement.addTarget();
            targetElement.setCode(m.getTarget().getCode());
            targetElement.setEquivalence(m.getEquivalence());
        });
    });
    return result;
}

Example 20 with TargetElementComponent

use of org.hl7.fhir.r5.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();
}