Examples with ValueSet org.hl7.fhir.r4.model.ValueSet used on opensource projects

Example 31 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project kindling by HL7.

the class ValueSetGenerator method loadOperationOutcomeValueSet.

public void loadOperationOutcomeValueSet(BindingSpecification cd) throws Exception {
    ValueSet vs = new ValueSet();
    cd.setValueSet(vs);
    cd.setBindingMethod(BindingMethod.ValueSet);
    vs.setId("operation-outcome");
    vs.setUrl("http://hl7.org/fhir/ValueSet/" + vs.getId());
    vs.setName("OperationOutcomeCodes");
    vs.setTitle("Operation Outcome Codes");
    vs.setPublisher("HL7 (FHIR Project)");
    vs.setVersion(version);
    vs.setUserData("filename", "valueset-" + vs.getId());
    if (!vs.hasExtension(ToolingExtensions.EXT_WORKGROUP)) {
        vs.addExtension().setUrl(ToolingExtensions.EXT_WORKGROUP).setValue(new CodeType("fhir"));
    } else {
        String ec = ToolingExtensions.readStringExtension(vs, ToolingExtensions.EXT_WORKGROUP);
        if (!ec.equals("fhir"))
            System.out.println("ValueSet " + vs.getUrl() + " WG mismatch 11: is " + ec + ", want to set to " + "fhir");
    }
    vs.setUserData("path", "valueset-" + vs.getId() + ".html");
    ContactDetail c = vs.addContact();
    c.addTelecom().setSystem(ContactPointSystem.URL).setValue("http://hl7.org/fhir");
    c.addTelecom().setSystem(ContactPointSystem.EMAIL).setValue("fhir@lists.hl7.org");
    vs.setDescription("Operation Outcome codes used by FHIR test servers (see Implementation file translations.xml)");
    vs.setStatus(PublicationStatus.DRAFT);
    if (!vs.hasCompose())
        vs.setCompose(new ValueSetComposeComponent());
    vs.getCompose().addInclude().setSystem("http://terminology.hl7.org/CodeSystem/operation-outcome");
    CodeSystem cs = new CodeSystem();
    cs.setHierarchyMeaning(CodeSystemHierarchyMeaning.ISA);
    Set<String> codes = translator.listTranslations("ecode");
    for (String s : sorted(codes)) {
        Map<String, String> langs = translator.translations(s);
        ConceptDefinitionComponent cv = cs.addConcept();
        cv.setCode(s);
        cv.setDisplay(langs.get("en"));
        for (String lang : langs.keySet()) {
            if (!lang.equals("en")) {
                String value = langs.get(lang);
                ConceptDefinitionDesignationComponent dc = cv.addDesignation();
                dc.setLanguage(lang);
                dc.setValue(value);
                dc.getUse().setSystem("http://terminology.hl7.org/CodeSystem/designation-usage").setCode("display");
            }
        }
    }
    CodeSystemConvertor.populate(cs, vs);
    cs.setUrl("http://terminology.hl7.org/CodeSystem/operation-outcome");
    cs.setVersion(version);
    cs.setCaseSensitive(true);
    cs.setContent(CodeSystemContentMode.COMPLETE);
    definitions.getCodeSystems().see(cs, packageInfo);
}

Example 32 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project kindling by HL7.

the class BindingsParser method loadValueSet.

private ValueSet loadValueSet(String ref, String committee) throws Exception {
    String folder = new File(filename).getParent();
    String srcName;
    IParser p;
    if (new File(Utilities.path(folder, ref + ".xml")).exists()) {
        p = new XmlParser();
        srcName = Utilities.path(folder, ref + ".xml");
    } else if (new File(Utilities.path(folder, ref + ".json")).exists()) {
        p = new JsonParser();
        srcName = Utilities.path(folder, ref + ".json");
    } else
        throw new Exception("Unable to find source for " + ref + " in " + filename + " (" + Utilities.path(folder, ref + ".xml/json)"));
    FileInputStream input = new FileInputStream(srcName);
    try {
        ValueSet result = ValueSetUtilities.makeShareable((ValueSet) p.parse(input));
        result.setId(ref.substring(9));
        if (!result.hasExperimental())
            result.setExperimental(false);
        // if (!result.hasUrl())
        result.setUrl("http://hl7.org/fhir/ValueSet/" + ref.substring(9));
        if (!result.hasVersion() || result.getUrl().startsWith("http://hl7.org/fhir"))
            result.setVersion(version);
        if (!Utilities.noString(committee)) {
            if (!result.hasExtension(ToolingExtensions.EXT_WORKGROUP)) {
                result.addExtension().setUrl(ToolingExtensions.EXT_WORKGROUP).setValue(new CodeType(committee));
            } else {
                String ec = ToolingExtensions.readStringExtension(result, ToolingExtensions.EXT_WORKGROUP);
                if (!ec.equals(committee))
                    System.out.println("ValueSet " + result.getUrl() + " WG mismatch 1: is " + ec + ", want to set to " + committee);
            }
        }
        result.setUserData("filename", "valueset-" + ref.substring(9));
        result.setUserData("path", "valueset-" + ref.substring(9) + ".html");
        new CodeSystemConvertor(codeSystems).convert(p, result, srcName, packageInfo);
        return result;
    } finally {
        IOUtils.closeQuietly(input);
    }
}

Example 33 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project kindling by HL7.

the class OldSpreadsheetParser method readBindings.

// Adds bindings to global definition.bindings. Returns list of
// newly found bindings in the sheet.
private void readBindings(Sheet sheet) throws Exception {
    for (int row = 0; row < sheet.rows.size(); row++) {
        String bindingName = sheet.getColumn(row, "Binding Name");
    }
    ValueSetGenerator vsGen = new ValueSetGenerator(definitions, version.toCode(), genDate, context.translator(), packageInfo);
    for (int row = 0; row < sheet.rows.size(); row++) {
        String bindingName = sheet.getColumn(row, "Binding Name");
        // Ignore bindings whose name start with "!"
        if (Utilities.noString(bindingName) || bindingName.startsWith("!"))
            continue;
        // if (Character.isLowerCase(bindingName.charAt(0)))
        // throw new Exception("binding name "+bindingName+" is illegal - must start with a capital letter");
        BindingSpecification cd = new BindingSpecification(usageContext, bindingName, false);
        if (definitions != null)
            definitions.getAllBindings().add(cd);
        cd.setDefinition(Utilities.appendPeriod(sheet.getColumn(row, "Definition")));
        cd.setBindingMethod(BindingsParser.readBinding(sheet.getColumn(row, "Binding"), cd.getName() + " in " + folder));
        String ref = sheet.getColumn(row, "Reference");
        if (!cd.getBinding().equals(BindingMethod.Unbound) && Utilities.noString(ref))
            throw new Exception("binding " + cd.getName() + " is missing a reference");
        if (cd.getBinding() == BindingMethod.CodeList) {
            if (ref.startsWith("#valueset-"))
                throw new Exception("don't start code list references with #valueset-");
            cd.setValueSet(ValueSetUtilities.makeShareable(new ValueSet()));
            valuesets.add(cd.getValueSet());
            cd.getValueSet().setVersion(version.toCode());
            cd.getValueSet().setId(igSuffix(ig) + ref.substring(1));
            cd.getValueSet().setUrl("http://hl7.org/fhir/ValueSet/" + igSuffix(ig) + ref.substring(1));
            cd.getValueSet().setUserData("filename", "valueset-" + cd.getValueSet().getId());
            if (!cd.getValueSet().hasExtension(ToolingExtensions.EXT_WORKGROUP)) {
                cd.getValueSet().addExtension().setUrl(ToolingExtensions.EXT_WORKGROUP).setValue(new CodeType(committee.getCode()));
            } else {
                String ec = ToolingExtensions.readStringExtension(cd.getValueSet(), ToolingExtensions.EXT_WORKGROUP);
                if (!ec.equals(committee))
                    System.out.println("ValueSet " + cd.getValueSet().getUrl() + " WG mismatch 3: is " + ec + ", want to set to " + committee.getCode());
            }
            if (ig != null) {
                cd.getValueSet().setUserDataINN(ToolResourceUtilities.NAME_RES_IG, ig);
                cd.getValueSet().setUserData("path", "valueset-" + cd.getValueSet().getId() + ".html");
            } else
                cd.getValueSet().setUserData("path", "valueset-" + cd.getValueSet().getId() + ".html");
            if (!cd.getValueSet().getUserData("path").equals(cd.getValueSet().getUserData("filename") + ".html"))
                throw new Exception("Mis-identified value set");
            if (!ref.startsWith("#"))
                throw new Exception("Error parsing binding " + cd.getName() + ": code list reference '" + ref + "' must started with '#'");
            Sheet cs = xls.getSheets().get(ref.substring(1));
            if (cs == null)
                throw new Exception("Error parsing binding " + cd.getName() + ": code list reference '" + ref + "' not resolved");
            vsGen.updateHeader(cd, cd.getValueSet());
            new CodeListToValueSetParser(cs, ref.substring(1), cd.getValueSet(), version.toCode(), codeSystems, maps, packageInfo).execute(sheet.getColumn(row, "v2"), checkV3Mapping(sheet.getColumn(row, "v3")), getIsUtg(bindingName));
        } else if (cd.getBinding() == BindingMethod.ValueSet) {
            if (ref.startsWith("http:"))
                // will sort this out later
                cd.setReference(sheet.getColumn(row, "Reference"));
            else
                cd.setValueSet(loadValueSet(ref));
        } else if (cd.getBinding() == BindingMethod.Special) {
            if ("#operation-outcome".equals(sheet.getColumn(row, "Reference")))
                new ValueSetGenerator(definitions, version.toCode(), genDate, context.translator(), packageInfo).loadOperationOutcomeValueSet(cd);
            else
                throw new Exception("Special bindings are only allowed in bindings.xml");
        }
        // do this anyway in the short term
        cd.setReference(sheet.getColumn(row, "Reference"));
        if (cd.getValueSet() != null) {
            ValueSet vs = cd.getValueSet();
            ValueSetUtilities.makeShareable(vs);
            vs.setUserData("filename", "valueset-" + vs.getId());
            if (!vs.hasExtension(ToolingExtensions.EXT_WORKGROUP)) {
                vs.addExtension().setUrl(ToolingExtensions.EXT_WORKGROUP).setValue(new CodeType(committee.getCode()));
            } else {
                String ec = ToolingExtensions.readStringExtension(vs, ToolingExtensions.EXT_WORKGROUP);
                if (!ec.equals(committee.getCode()))
                    System.out.println("ValueSet " + vs.getUrl() + " WG mismatch 4: is " + ec + ", want to set to " + committee.getCode());
            }
            if (ig != null) {
                vs.setUserDataINN(ToolResourceUtilities.NAME_RES_IG, ig);
                vs.setUserData("path", ig.getCode() + "/valueset-" + vs.getId() + ".html");
            } else
                vs.setUserData("path", "valueset-" + vs.getId() + ".html");
            if (!ValueSetUtilities.hasOID(vs))
                ValueSetUtilities.setOID(vs, "urn:oid:" + BindingSpecification.DEFAULT_OID_VS + registry.idForUri(vs.getUrl()));
            if (vs.getUserData("cs") != null) {
                if (!CodeSystemUtilities.hasOID((CodeSystem) vs.getUserData("cs")))
                    CodeSystemUtilities.setOID((CodeSystem) vs.getUserData("cs"), "urn:oid:" + BindingSpecification.DEFAULT_OID_CS + registry.idForUri(((CodeSystem) vs.getUserData("cs")).getUrl()));
            }
            if (definitions != null)
                definitions.getBoundValueSets().put(vs.getUrl(), vs);
            else
                ig.getValueSets().add(vs);
        } else if (cd.getReference() != null && cd.getReference().startsWith("http:")) {
            if (definitions != null)
                definitions.getUnresolvedBindings().add(cd);
            else
                ig.getUnresolvedBindings().add(cd);
        }
        cd.setDescription(sheet.getColumn(row, "Description"));
        if (!Utilities.noString(sheet.getColumn(row, "Example")))
            throw new Exception("The 'Example' column is no longer supported");
        if (!Utilities.noString(sheet.getColumn(row, "Extensible")))
            throw new Exception("The 'Extensible' column is no longer supported");
        cd.setStrength(BindingsParser.readBindingStrength(sheet.getColumn(row, "Conformance")));
        if (cd.getBinding() == BindingMethod.Unbound) {
            cd.setStrength(BindingStrength.EXAMPLE);
        }
        cd.setSource(name);
        cd.setUri(sheet.getColumn(row, "Uri"));
        String oid = sheet.getColumn(row, "Oid");
        if (!Utilities.noString(oid))
            // no cs oid in this case
            cd.setVsOid(oid);
        cd.setStatus(PublicationStatus.fromCode(sheet.getColumn(row, "Status")));
        cd.setWebSite(sheet.getColumn(row, "Website"));
        cd.setEmail(sheet.getColumn(row, "Email"));
        cd.setCopyright(sheet.getColumn(row, "Copyright"));
        cd.setV2Map(sheet.getColumn(row, "v2"));
        cd.setV3Map(checkV3Mapping(sheet.getColumn(row, "v3")));
        String max = sheet.getColumn(row, "Max");
        if (!Utilities.noString(max))
            if (max.startsWith("http:")) {
                // will sort this out later
                cd.setMaxReference(max);
            } else
                cd.setMaxValueSet(loadValueSet(max));
        bindings.put(cd.getName(), cd);
        if (cd.getValueSet() != null) {
            ValueSet vs = cd.getValueSet();
            vsGen.updateHeader(cd, cd.getValueSet());
        }
    }
}

Example 34 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project kindling by HL7.

the class SourceParser method loadValueSet.

private void loadValueSet(String n) throws FileNotFoundException, Exception {
    XmlParser xml = new XmlParser();
    ValueSet vs = (ValueSet) xml.parse(new CSFileInputStream(srcDir + ini.getStringProperty("valuesets", n).replace('\\', File.separatorChar)));
    new CodeSystemConvertor(definitions.getCodeSystems()).convert(xml, vs, srcDir + ini.getStringProperty("valuesets", n).replace('\\', File.separatorChar), page.packageInfo());
    vs.setId(FormatUtilities.makeId(n));
    vs.setUrl("http://hl7.org/fhir/ValueSet/" + vs.getId());
    if (!vs.hasVersion() || vs.getUrl().startsWith("http://hl7.org/fhir"))
        vs.setVersion(version.toCode());
    vs.setUserData("path", "valueset-" + vs.getId() + ".html");
    vs.setUserData("filename", "valueset-" + vs.getId());
    definitions.getExtraValuesets().put(n, vs);
    definitions.getExtraValuesets().put(vs.getUrl(), vs);
}

Example 35 with ValueSet

use of org.hl7.fhir.r4.model.ValueSet in project kindling by HL7.

the class SourceParser method loadGlobalBindings.

private void loadGlobalBindings() throws Exception {
    logger.log("Load Common Bindings", LogMessageType.Process);
    BindingsParser parser = new BindingsParser(new CSFileInputStream(new CSFile(termDir + "bindings.xml")), termDir + "bindings.xml", srcDir, registry, version.toCode(), definitions.getCodeSystems(), page.getConceptMaps(), genDate, exceptionIfExcelNotNormalised, page.packageInfo());
    List<BindingSpecification> cds = parser.parse();
    for (BindingSpecification cd : cds) {
        definitions.getAllBindings().add(cd);
        definitions.getCommonBindings().put(cd.getName(), cd);
        if (cd.getValueSet() != null) {
            vsGen.updateHeader(cd, cd.getValueSet());
            definitions.getBoundValueSets().put(cd.getValueSet().getUrl(), cd.getValueSet());
        } else if (cd.getReference() != null && cd.getReference().startsWith("http:")) {
            definitions.getUnresolvedBindings().add(cd);
        }
        if (cd.getMaxValueSet() != null) {
            vsGen.updateHeader(cd, cd.getMaxValueSet());
            definitions.getBoundValueSets().put(cd.getMaxValueSet().getUrl(), cd.getMaxValueSet());
        }
    }
    if (!page.getDefinitions().getBoundValueSets().containsKey("http://hl7.org/fhir/ValueSet/data-absent-reason"))
        throw new Exception("d-a-r not found");
}