Examples with BindingSpecification org.hl7.fhir.definitions.model.BindingSpecification used on opensource projects

Example 6 with BindingSpecification

use of org.hl7.fhir.definitions.model.BindingSpecification 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 7 with BindingSpecification

use of org.hl7.fhir.definitions.model.BindingSpecification 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");
}

Example 8 with BindingSpecification

use of org.hl7.fhir.definitions.model.BindingSpecification in project kindling by HL7.

the class ResourceParser method parseBinding.

public BindingSpecification parseBinding(ElementDefinitionBindingComponent binding) throws IOException {
    BindingSpecification bs = new BindingSpecification("core", binding.getExtensionString("http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName"), "true".equals(binding.getExtensionString("http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding")));
    bs.setStrength(binding.getStrength());
    bs.setBindingMethod(BindingMethod.ValueSet);
    bs.setDescription(binding.getDescription());
    bs.setReference(binding.getValueSet());
    if (bs.hasReference()) {
        bs.setValueSet(loadValueSet(bs.getReference(), false));
    }
    if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) {
        bs.setMaxReference(binding.getExtensionString("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"));
        bs.setMaxValueSet(loadValueSet(bs.getMaxReference(), false));
    }
    if (binding.hasExtension(BuildExtensions.EXT_V2_MAP)) {
        bs.setV2Map(binding.getExtensionString(BuildExtensions.EXT_V2_MAP));
    }
    if (binding.hasExtension(BuildExtensions.EXT_V3_MAP)) {
        bs.setV3Map(binding.getExtensionString(BuildExtensions.EXT_V3_MAP));
    }
    if (binding.hasExtension(BuildExtensions.EXT_DEFINITION)) {
        bs.setDefinition(binding.getExtensionString(BuildExtensions.EXT_DEFINITION));
    }
    if (binding.hasExtension(BuildExtensions.EXT_URI)) {
        bs.setUri(binding.getExtensionString(BuildExtensions.EXT_URI));
    }
    if (binding.hasExtension(BuildExtensions.EXT_WEBSITE)) {
        bs.setWebSite(binding.getExtensionString(BuildExtensions.EXT_WEBSITE));
    }
    if (binding.hasExtension(BuildExtensions.EXT_EMAIL)) {
        bs.setEmail(binding.getExtensionString(BuildExtensions.EXT_EMAIL));
    }
    if (binding.hasExtension(BuildExtensions.EXT_COPYRIGHT)) {
        bs.setCopyright(binding.getExtensionString(BuildExtensions.EXT_COPYRIGHT));
    }
    if (binding.hasExtension(BuildExtensions.EXT_CS_OID)) {
        bs.setCsOid(binding.getExtensionString(BuildExtensions.EXT_CS_OID));
    }
    if (binding.hasExtension(BuildExtensions.EXT_VS_OID)) {
        bs.setVsOid(binding.getExtensionString(BuildExtensions.EXT_VS_OID));
    }
    if (binding.hasExtension(BuildExtensions.EXT_STATUS)) {
        bs.setStatus(PublicationStatus.fromCode(binding.getExtensionString(BuildExtensions.EXT_STATUS)));
    }
    return bs;
}

Example 9 with BindingSpecification

use of org.hl7.fhir.definitions.model.BindingSpecification in project kindling by HL7.

the class ResourceParser method parseBinding.

private BindingSpecification parseBinding(OperationDefinitionParameterBindingComponent binding) throws IOException {
    BindingSpecification bs = new BindingSpecification("core", binding.getExtensionString(BuildExtensions.EXT_BINDING_NAME), "true".equals(binding.getExtensionString("http://hl7.org/fhir/StructureDefinition/elementdefinition-isCommonBinding")));
    bs.setStrength(binding.getStrength());
    bs.setBindingMethod(BindingMethod.ValueSet);
    bs.setReference(binding.getValueSet());
    if (bs.hasReference()) {
        bs.setValueSet(loadValueSet(bs.getReference(), false));
    }
    if (binding.hasExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet")) {
        bs.setMaxReference(binding.getExtensionString("http://hl7.org/fhir/StructureDefinition/elementdefinition-maxValueSet"));
        bs.setMaxValueSet(loadValueSet(bs.getMaxReference(), false));
    }
    if (binding.hasExtension(BuildExtensions.EXT_V2_MAP)) {
        bs.setV2Map(binding.getExtensionString(BuildExtensions.EXT_V2_MAP));
    }
    if (binding.hasExtension(BuildExtensions.EXT_V3_MAP)) {
        bs.setV3Map(binding.getExtensionString(BuildExtensions.EXT_V3_MAP));
    }
    if (binding.hasExtension(BuildExtensions.EXT_DEFINITION)) {
        bs.setDefinition(binding.getExtensionString(BuildExtensions.EXT_DEFINITION));
    }
    if (binding.hasExtension(BuildExtensions.EXT_URI)) {
        bs.setUri(binding.getExtensionString(BuildExtensions.EXT_URI));
    }
    if (binding.hasExtension(BuildExtensions.EXT_WEBSITE)) {
        bs.setWebSite(binding.getExtensionString(BuildExtensions.EXT_WEBSITE));
    }
    if (binding.hasExtension(BuildExtensions.EXT_EMAIL)) {
        bs.setEmail(binding.getExtensionString(BuildExtensions.EXT_EMAIL));
    }
    if (binding.hasExtension(BuildExtensions.EXT_COPYRIGHT)) {
        bs.setCopyright(binding.getExtensionString(BuildExtensions.EXT_COPYRIGHT));
    }
    if (binding.hasExtension(BuildExtensions.EXT_CS_OID)) {
        bs.setCsOid(binding.getExtensionString(BuildExtensions.EXT_CS_OID));
    }
    if (binding.hasExtension(BuildExtensions.EXT_VS_OID)) {
        bs.setVsOid(binding.getExtensionString(BuildExtensions.EXT_VS_OID));
    }
    if (binding.hasExtension(BuildExtensions.EXT_STATUS)) {
        bs.setStatus(PublicationStatus.fromCode(binding.getExtensionString(BuildExtensions.EXT_STATUS)));
    }
    return bs;
}

Example 10 with BindingSpecification

use of org.hl7.fhir.definitions.model.BindingSpecification in project kindling by HL7.

the class TerminologyNotesGenerator method scan.

private void scan(ElementDefn e, String path) throws Exception {
    if (e.hasBinding()) {
        BindingSpecification cd = e.getBinding();
        if (!txusages.containsKey(cd)) {
            txusages.put(cd, new ArrayList<CDUsage>());
            c++;
            txusages.get(cd).add(new CDUsage(String.valueOf(c), null));
        }
        txusages.get(cd).add(new CDUsage(path, e));
    }
    for (ElementDefn c : e.getElements()) {
        scan(c, path + "." + c.getName());
    }
}