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

Example 11 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.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).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 12 with TargetElementComponent

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

the class MappingSheetParser method readConceptMap.

private void readConceptMap(ConceptMap cm) throws FHIRException {
    for (ConceptMapGroupComponent g : cm.getGroup()) {
        for (SourceElementComponent e : g.getElement()) {
            if (e.hasId() && e.getTarget().size() == 1 && e.hasExtension(ToolingExtensions.EXT_MAPPING_TYPE)) {
                TargetElementComponent t = e.getTargetFirstRep();
                MappingRow row = new MappingRow();
                row.sequence = e.getId();
                row.identifier = e.getCode();
                row.name = e.getExtensionString(ToolingExtensions.EXT_MAPPING_NAME);
                row.dataType = e.getExtensionString(ToolingExtensions.EXT_MAPPING_TYPE);
                row.cardinality = e.getExtensionString(ToolingExtensions.EXT_MAPPING_CARD);
                if (e.getTargetFirstRep().getEquivalence() == ConceptMapEquivalence.UNMATCHED) {
                    row.attribute = "N/A";
                } else {
                    OtherElementComponent dep = getDependency(t, "http://hl7.org/fhirpath");
                    if (dep != null)
                        row.condition = dep.getValue();
                    row.attribute = t.getCode();
                    row.type = t.getExtensionString(ToolingExtensions.EXT_MAPPING_TGTTYPE);
                    row.minMax = t.getExtensionString(ToolingExtensions.EXT_MAPPING_TGTCARD);
                    row.dtMapping = t.getExtensionString("http://hl7.org/fhir/StructureDefinition/ConceptMap-type-mapping");
                    row.vocabMapping = t.getExtensionString("http://hl7.org/fhir/StructureDefinition/ConceptMap-vocab-mapping");
                    if (t.getProduct().size() > 0) {
                        row.derived = t.getProductFirstRep().getProperty();
                        row.derivedMapping = t.getProductFirstRep().getValue();
                    }
                }
                row.comments = t.getComment();
                rows.add(row);
            }
        }
    }
}

Example 13 with TargetElementComponent

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

the class StructureMapUtilities method parseConceptMap.

private void parseConceptMap(StructureMap result, FHIRLexer lexer) throws FHIRLexerException {
    lexer.token("conceptmap");
    ConceptMap map = new ConceptMap();
    String id = lexer.readConstant("map id");
    if (id.startsWith("#")) {
        throw lexer.error("Concept Map identifier must start with #");
    }
    map.setId(id);
    // todo: how to add this to the text format
    map.setStatus(PublicationStatus.DRAFT);
    result.getContained().add(map);
    lexer.token("{");
    // lexer.token("source");
    // map.setSource(new UriType(lexer.readConstant("source")));
    // lexer.token("target");
    // map.setSource(new UriType(lexer.readConstant("target")));
    Map<String, String> prefixes = new HashMap<String, String>();
    while (lexer.hasToken("prefix")) {
        lexer.token("prefix");
        String n = lexer.take();
        lexer.token("=");
        String v = lexer.readConstant("prefix url");
        prefixes.put(n, v);
    }
    while (lexer.hasToken("unmapped")) {
        lexer.token("unmapped");
        lexer.token("for");
        String n = readPrefix(prefixes, lexer);
        ConceptMapGroupComponent g = getGroup(map, n, null);
        lexer.token("=");
        String v = lexer.take();
        if (v.equals("provided")) {
            g.getUnmapped().setMode(ConceptMapGroupUnmappedMode.PROVIDED);
        } else {
            throw lexer.error("Only unmapped mode PROVIDED is supported at this time");
        }
    }
    while (!lexer.hasToken("}")) {
        String srcs = readPrefix(prefixes, lexer);
        lexer.token(":");
        String sc = lexer.getCurrent().startsWith("\"") ? lexer.readConstant("code") : lexer.take();
        ConceptMapEquivalence eq = readEquivalence(lexer);
        String tgts = (eq != ConceptMapEquivalence.UNMATCHED) ? readPrefix(prefixes, lexer) : "";
        ConceptMapGroupComponent g = getGroup(map, srcs, tgts);
        SourceElementComponent e = g.addElement();
        e.setCode(sc);
        if (e.getCode().startsWith("\"")) {
            e.setCode(lexer.processConstant(e.getCode()));
        }
        TargetElementComponent tgt = e.addTarget();
        tgt.setEquivalence(eq);
        if (tgt.getEquivalence() != ConceptMapEquivalence.UNMATCHED) {
            lexer.token(":");
            tgt.setCode(lexer.take());
            if (tgt.getCode().startsWith("\"")) {
                tgt.setCode(lexer.processConstant(tgt.getCode()));
            }
        }
        tgt.setComment(lexer.getFirstComment());
    }
    lexer.token("}");
}

Example 14 with TargetElementComponent

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

the class ConceptMapSpreadsheetGenerator method renderGroup.

private void renderGroup(ConceptMapGroupComponent grp, int i) {
    Sheet sheet = makeSheet("Mapping Table " + Integer.toString(i));
    addHeaders(sheet, "Source", "Display", "Relationship", "Target", "Display");
    addRow(sheet, grp.getSource(), "", "", grp.getTarget(), "");
    for (SourceElementComponent s : grp.getElement()) {
        for (TargetElementComponent t : s.getTarget()) {
            addRow(sheet, s.getCode(), s.getDisplay(), t.getEquivalenceElement().asStringValue(), t.getCode(), t.getDisplay());
        }
    }
}

Example 15 with TargetElementComponent

use of org.hl7.fhir.r5.model.ConceptMap.TargetElementComponent 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;
}