Examples with ConceptDefinitionComponent org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent used on opensource projects

Example 61 with ConceptDefinitionComponent

use of org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method generateCodeSystemContent.

private boolean generateCodeSystemContent(XhtmlNode x, CodeSystem cs, boolean hasExtensions, Map<ConceptMap, String> mymaps, List<String> langs) throws FHIRFormatError, DefinitionException, IOException {
    XhtmlNode p = x.para();
    if (cs.getContent() == CodeSystemContentMode.COMPLETE)
        p.tx("This code system " + cs.getUrl() + " defines the following codes:");
    else if (cs.getContent() == CodeSystemContentMode.EXAMPLE)
        p.tx("This code system " + cs.getUrl() + " defines many codes, of which the following are some examples:");
    else if (cs.getContent() == CodeSystemContentMode.FRAGMENT)
        p.tx("This code system " + cs.getUrl() + " defines many codes, of which the following are a subset:");
    else if (cs.getContent() == CodeSystemContentMode.NOTPRESENT) {
        p.tx("This code system " + cs.getUrl() + " defines many codes, but they are not represented here");
        return false;
    }
    XhtmlNode t = x.table("codes");
    boolean commentS = false;
    boolean deprecated = false;
    boolean display = false;
    boolean hierarchy = false;
    for (ConceptDefinitionComponent c : cs.getConcept()) {
        commentS = commentS || conceptsHaveComments(c);
        deprecated = deprecated || conceptsHaveDeprecated(cs, c);
        display = display || conceptsHaveDisplay(c);
        hierarchy = hierarchy || c.hasConcept();
        scanLangs(c, langs);
    }
    addMapHeaders(addTableHeaderRowStandard(t, hierarchy, display, true, commentS, deprecated), mymaps);
    for (ConceptDefinitionComponent c : cs.getConcept()) {
        hasExtensions = addDefineRowToTable(t, c, 0, hierarchy, display, commentS, deprecated, mymaps, cs.getUrl(), cs) || hasExtensions;
    }
    if (langs.size() > 0) {
        Collections.sort(langs);
        x.para().b().tx("Additional Language Displays");
        t = x.table("codes");
        XhtmlNode tr = t.tr();
        tr.td().b().tx("Code");
        for (String lang : langs) tr.td().b().addText(describeLang(lang));
        for (ConceptDefinitionComponent c : cs.getConcept()) {
            addLanguageRow(c, t, langs);
        }
    }
    return hasExtensions;
}

Example 62 with ConceptDefinitionComponent

use of org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent in project org.hl7.fhir.core by hapifhir.

the class BaseWorkerContext method validateOnServer.

private ValidationResult validateOnServer(ValueSet vs, Parameters pin) throws FHIRException {
    if (vs != null)
        pin.addParameter().setName("valueSet").setResource(vs);
    for (ParametersParameterComponent pp : pin.getParameter()) if (pp.getName().equals("profile"))
        throw new Error("Can only specify profile in the context");
    if (expParameters == null)
        throw new Error("No ExpansionProfile provided");
    pin.addParameter().setName("profile").setResource(expParameters);
    txLog.clearLastId();
    Parameters pOut;
    if (vs == null)
        pOut = txClient.validateCS(pin);
    else
        pOut = txClient.validateVS(pin);
    boolean ok = false;
    String message = "No Message returned";
    String display = null;
    TerminologyServiceErrorClass err = TerminologyServiceErrorClass.UNKNOWN;
    for (ParametersParameterComponent p : pOut.getParameter()) {
        if (p.getName().equals("result"))
            ok = ((BooleanType) p.getValue()).getValue().booleanValue();
        else if (p.getName().equals("message"))
            message = ((StringType) p.getValue()).getValue();
        else if (p.getName().equals("display"))
            display = ((StringType) p.getValue()).getValue();
        else if (p.getName().equals("cause")) {
            try {
                IssueType it = IssueType.fromCode(((StringType) p.getValue()).getValue());
                if (it == IssueType.UNKNOWN)
                    err = TerminologyServiceErrorClass.UNKNOWN;
                else if (it == IssueType.NOTSUPPORTED)
                    err = TerminologyServiceErrorClass.VALUESET_UNSUPPORTED;
            } catch (FHIRException e) {
            }
        }
    }
    if (!ok)
        return new ValidationResult(IssueSeverity.ERROR, message, err).setTxLink(txLog.getLastId()).setTxLink(txLog.getLastId());
    else if (message != null && !message.equals("No Message returned"))
        return new ValidationResult(IssueSeverity.WARNING, message, new ConceptDefinitionComponent().setDisplay(display)).setTxLink(txLog.getLastId()).setTxLink(txLog.getLastId());
    else if (display != null)
        return new ValidationResult(new ConceptDefinitionComponent().setDisplay(display)).setTxLink(txLog.getLastId()).setTxLink(txLog.getLastId());
    else
        return new ValidationResult(new ConceptDefinitionComponent()).setTxLink(txLog.getLastId()).setTxLink(txLog.getLastId());
}

Example 63 with ConceptDefinitionComponent

use of org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent in project org.hl7.fhir.core by hapifhir.

the class NarrativeGenerator method generateCodeSystemContent.

private boolean generateCodeSystemContent(XhtmlNode x, CodeSystem cs, boolean hasExtensions, List<UsedConceptMap> maps, String lang) throws FHIRFormatError, DefinitionException, IOException {
    XhtmlNode p = x.para();
    if (cs.getContent() == CodeSystemContentMode.COMPLETE)
        p.tx(context.translator().translateAndFormat("xhtml-gen-cs", lang, "This code system %s defines the following codes", cs.getUrl()) + ":");
    else if (cs.getContent() == CodeSystemContentMode.EXAMPLE)
        p.tx(context.translator().translateAndFormat("xhtml-gen-cs", lang, "This code system %s defines many codes, of which the following are some examples", cs.getUrl()) + ":");
    else if (cs.getContent() == CodeSystemContentMode.FRAGMENT)
        p.tx(context.translator().translateAndFormat("xhtml-gen-cs", lang, "This code system %s defines many codes, of which the following are a subset", cs.getUrl()) + ":");
    else if (cs.getContent() == CodeSystemContentMode.NOTPRESENT) {
        p.tx(context.translator().translateAndFormat("xhtml-gen-cs", lang, "This code system %s defines many codes, but they are not represented here", cs.getUrl()));
        return false;
    }
    XhtmlNode t = x.table("codes");
    boolean commentS = false;
    boolean deprecated = false;
    boolean display = false;
    boolean hierarchy = false;
    boolean version = false;
    for (ConceptDefinitionComponent c : cs.getConcept()) {
        commentS = commentS || conceptsHaveComments(c);
        deprecated = deprecated || conceptsHaveDeprecated(cs, c);
        display = display || conceptsHaveDisplay(c);
        version = version || conceptsHaveVersion(c);
        hierarchy = hierarchy || c.hasConcept();
    }
    addMapHeaders(addTableHeaderRowStandard(t, hierarchy, display, true, commentS, version, deprecated, lang), maps);
    for (ConceptDefinitionComponent c : cs.getConcept()) {
        hasExtensions = addDefineRowToTable(t, c, 0, hierarchy, display, commentS, version, deprecated, maps, cs.getUrl(), cs, lang) || hasExtensions;
    }
    // }
    return hasExtensions;
}

Example 64 with ConceptDefinitionComponent

use of org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent 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 version, boolean deprecated, List<UsedConceptMap> maps, String system, CodeSystem cs, String lang) throws FHIRFormatError, DefinitionException, IOException {
    boolean hasExtensions = false;
    XhtmlNode tr = t.tr();
    XhtmlNode td = tr.td();
    if (hasHierarchy) {
        td.addText(Integer.toString(i + 1));
        td = tr.td();
        String s = Utilities.padLeft("", '\u00A0', i * 2);
        td.addText(s);
    }
    td.attribute("style", "white-space:nowrap").addText(c.getCode());
    XhtmlNode a;
    if (c.hasCodeElement()) {
        td.an(cs.getId() + "-" + Utilities.nmtokenize(c.getCode()));
    }
    if (hasDisplay) {
        td = tr.td();
        if (c.hasDisplayElement()) {
            if (lang == null) {
                td.addText(c.getDisplay());
            } else if (lang.equals("*")) {
                boolean sl = false;
                for (ConceptDefinitionDesignationComponent cd : c.getDesignation()) if (cd.getUse().is("http://terminology.hl7.org/CodeSystem/designation-usage", "display") && cd.hasLanguage() && !c.getDisplay().equalsIgnoreCase(cd.getValue()))
                    sl = true;
                td.addText((sl ? cs.getLanguage("en") + ": " : "") + c.getDisplay());
                for (ConceptDefinitionDesignationComponent cd : c.getDesignation()) {
                    if (cd.getUse().is("http://terminology.hl7.org/CodeSystem/designation-usage", "display") && cd.hasLanguage() && !c.getDisplay().equalsIgnoreCase(cd.getValue())) {
                        td.br();
                        td.addText(cd.getLanguage() + ": " + cd.getValue());
                    }
                }
            } else if (lang.equals(cs.getLanguage()) || (lang.equals("en") && !cs.hasLanguage())) {
                td.addText(c.getDisplay());
            } else {
                for (ConceptDefinitionDesignationComponent cd : c.getDesignation()) {
                    if (cd.getUse().is("http://terminology.hl7.org/CodeSystem/designation-usage", "display") && cd.hasLanguage() && cd.getLanguage().equals(lang)) {
                        td.addText(cd.getValue());
                    }
                }
            }
        }
    }
    td = tr.td();
    if (c != null && c.hasDefinitionElement()) {
        if (lang == null) {
            if (hasMarkdownInDefinitions(cs))
                addMarkdown(td, c.getDefinition());
            else
                td.addText(c.getDefinition());
        } else if (lang.equals("*")) {
            boolean sl = false;
            for (ConceptDefinitionDesignationComponent cd : c.getDesignation()) if (cd.getUse().is("http://terminology.hl7.org/CodeSystem/designation-usage", "definition") && cd.hasLanguage() && !c.getDefinition().equalsIgnoreCase(cd.getValue()))
                sl = true;
            td.addText((sl ? cs.getLanguage("en") + ": " : "") + c.getDefinition());
            for (ConceptDefinitionDesignationComponent cd : c.getDesignation()) {
                if (cd.getUse().is("http://terminology.hl7.org/CodeSystem/designation-usage", "definition") && cd.hasLanguage() && !c.getDefinition().equalsIgnoreCase(cd.getValue())) {
                    td.br();
                    td.addText(cd.getLanguage() + ": " + cd.getValue());
                }
            }
        } else if (lang.equals(cs.getLanguage()) || (lang.equals("en") && !cs.hasLanguage())) {
            td.addText(c.getDefinition());
        } else {
            for (ConceptDefinitionDesignationComponent cd : c.getDesignation()) {
                if (cd.getUse().is("http://terminology.hl7.org/CodeSystem/designation-usage", "definition") && cd.hasLanguage() && cd.getLanguage().equals(lang)) {
                    td.addText(cd.getValue());
                }
            }
        }
    }
    if (deprecated) {
        td = tr.td();
        Boolean b = CodeSystemUtilities.isDeprecated(cs, c);
        if (b != null && b) {
            smartAddText(td, context.translator().translate("xhtml-gen-cs", "Deprecated", lang));
            hasExtensions = true;
            if (ToolingExtensions.hasExtension(c, ToolingExtensions.EXT_REPLACED_BY)) {
                Coding cc = (Coding) ToolingExtensions.getExtension(c, ToolingExtensions.EXT_REPLACED_BY).getValue();
                td.tx(" (replaced by ");
                String url = getCodingReference(cc, system);
                if (url != null) {
                    td.ah(url).addText(cc.getCode());
                    td.tx(": " + cc.getDisplay() + ")");
                } else
                    td.addText(cc.getCode() + " '" + cc.getDisplay() + "' in " + cc.getSystem() + ")");
            }
        }
    }
    if (comment) {
        td = tr.td();
        Extension ext = c.getExtensionByUrl(ToolingExtensions.EXT_CS_COMMENT);
        if (ext != null) {
            hasExtensions = true;
            String bc = ext.hasValue() ? ext.getValue().primitiveValue() : null;
            Map<String, String> translations = ToolingExtensions.getLanguageTranslations(ext.getValue());
            if (lang == null) {
                if (bc != null)
                    td.addText(bc);
            } else if (lang.equals("*")) {
                boolean sl = false;
                for (String l : translations.keySet()) if (bc == null || !bc.equalsIgnoreCase(translations.get(l)))
                    sl = true;
                if (bc != null) {
                    td.addText((sl ? cs.getLanguage("en") + ": " : "") + bc);
                }
                for (String l : translations.keySet()) {
                    if (bc == null || !bc.equalsIgnoreCase(translations.get(l))) {
                        if (!td.getChildNodes().isEmpty())
                            td.br();
                        td.addText(l + ": " + translations.get(l));
                    }
                }
            } else if (lang.equals(cs.getLanguage()) || (lang.equals("en") && !cs.hasLanguage())) {
                if (bc != null)
                    td.addText(bc);
            } else {
                if (bc != null)
                    translations.put(cs.getLanguage("en"), bc);
                for (String l : translations.keySet()) {
                    if (l.equals(lang)) {
                        td.addText(translations.get(l));
                    }
                }
            }
        }
    }
    if (version) {
        td = tr.td();
        if (c.hasUserData("cs.version.notes"))
            td.addText(c.getUserString("cs.version.notes"));
    }
    for (UsedConceptMap m : maps) {
        td = tr.td();
        List<TargetElementComponentWrapper> mappings = findMappingsForCode(c.getCode(), m.getMap());
        boolean first = true;
        for (TargetElementComponentWrapper mapping : mappings) {
            if (!first)
                td.br();
            first = false;
            XhtmlNode span = td.span(null, mapping.comp.hasEquivalence() ? mapping.comp.getEquivalence().toCode() : "");
            span.addText(getCharForEquivalence(mapping.comp));
            a = td.ah(prefix + m.getLink() + "#" + makeAnchor(mapping.group.getTarget(), mapping.comp.getCode()));
            a.addText(mapping.comp.getCode());
            if (!Utilities.noString(mapping.comp.getComment()))
                td.i().tx("(" + mapping.comp.getComment() + ")");
        }
    }
    for (String e : CodeSystemUtilities.getOtherChildren(cs, c)) {
        tr = t.tr();
        td = tr.td();
        String s = Utilities.padLeft("", '.', i * 2);
        td.addText(s);
        a = td.ah("#" + Utilities.nmtokenize(e));
        a.addText(c.getCode());
    }
    for (ConceptDefinitionComponent cc : c.getConcept()) {
        hasExtensions = addDefineRowToTable(t, cc, i + 1, hasHierarchy, hasDisplay, comment, version, deprecated, maps, system, cs, lang) || hasExtensions;
    }
    return hasExtensions;
}

Example 65 with ConceptDefinitionComponent

use of org.hl7.fhir.r5.model.CodeSystem.ConceptDefinitionComponent in project org.hl7.fhir.core by hapifhir.

the class ValueSetCheckerSimple method validateCode.

private ValidationResult validateCode(Coding code, CodeSystem cs) {
    ConceptDefinitionComponent cc = cs.hasUserData("tx.cs.special") ? ((SpecialCodeSystem) cs.getUserData("tx.cs.special")).findConcept(code) : findCodeInConcept(cs.getConcept(), code.getCode());
    if (cc == null) {
        if (cs.getContent() == CodeSystemContentMode.FRAGMENT) {
            return new ValidationResult(IssueSeverity.WARNING, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_FRAGMENT, gen(code), cs.getUrl()));
        } else {
            return new ValidationResult(IssueSeverity.ERROR, context.formatMessage(I18nConstants.UNKNOWN_CODE__IN_, gen(code), cs.getUrl()));
        }
    }
    if (code.getDisplay() == null) {
        return new ValidationResult(code.getSystem(), cc);
    }
    CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
    if (cc.hasDisplay()) {
        b.append(cc.getDisplay());
        if (code.getDisplay().equalsIgnoreCase(cc.getDisplay())) {
            return new ValidationResult(code.getSystem(), cc);
        }
    }
    for (ConceptDefinitionDesignationComponent ds : cc.getDesignation()) {
        b.append(ds.getValue());
        if (code.getDisplay().equalsIgnoreCase(ds.getValue())) {
            return new ValidationResult(code.getSystem(), cc);
        }
    }
    // also check to see if the value set has another display
    ConceptReferenceComponent vs = findValueSetRef(code.getSystem(), code.getCode());
    if (vs != null && (vs.hasDisplay() || vs.hasDesignation())) {
        if (vs.hasDisplay()) {
            b.append(vs.getDisplay());
            if (code.getDisplay().equalsIgnoreCase(vs.getDisplay())) {
                return new ValidationResult(code.getSystem(), cc);
            }
        }
        for (ConceptReferenceDesignationComponent ds : vs.getDesignation()) {
            b.append(ds.getValue());
            if (code.getDisplay().equalsIgnoreCase(ds.getValue())) {
                return new ValidationResult(code.getSystem(), cc);
            }
        }
    }
    return new ValidationResult(IssueSeverity.WARNING, context.formatMessage(I18nConstants.DISPLAY_NAME_FOR__SHOULD_BE_ONE_OF__INSTEAD_OF_, code.getSystem(), code.getCode(), b.toString(), code.getDisplay()), code.getSystem(), cc);
}