Examples with Value org.hl7.fhir.utilities.graphql.Value used on opensource projects

Example 61 with Value

use of org.hl7.fhir.utilities.graphql.Value 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 62 with Value

use of org.hl7.fhir.utilities.graphql.Value 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 63 with Value

use of org.hl7.fhir.utilities.graphql.Value in project kindling by HL7.

the class OldSpreadsheetParser method checkW5.

private String checkW5(String value, String path) throws Exception {
    if (Utilities.noString(value))
        return null;
    if (!definitions.getW5s().containsKey(value)) {
        if (!value.contains(".")) {
            throw new Exception("Unknown w5 value " + value + " at " + path);
        } else {
            String[] vs = value.split("\\.");
            if (vs.length != 2)
                throw new Exception("improper w5 value " + value + " at " + path);
            if (!definitions.getW5s().containsKey(vs[0]))
                throw new Exception("Unknown w5 value " + value + " at " + path);
            W5Entry w5 = definitions.getW5s().get(vs[0]);
            if (!w5.getSubClasses().contains(vs[1]))
                throw new Exception("Unknown w5 value " + value + " at " + path);
        }
    }
    return value;
}

Example 64 with Value

use of org.hl7.fhir.utilities.graphql.Value in project kindling by HL7.

the class OldSpreadsheetParser method parseConformancePackage.

public void parseConformancePackage(Profile ap, Definitions definitions, String folder, String usage, List<ValidationMessage> issues, WorkGroup wg) throws Exception {
    try {
        isProfile = true;
        this.folder = folder;
        checkMappings(ap);
        Sheet sheet = loadSheet("Bindings");
        if (sheet != null)
            readBindings(sheet);
        sheet = loadSheet("Metadata");
        for (int row = 0; row < sheet.rows.size(); row++) {
            String n = sheet.getColumn(row, "Name");
            String v = sheet.getColumn(row, "Value");
            if (n != null && v != null) {
                if (ap.getMetadata().containsKey(n))
                    ap.getMetadata().get(n).add(v);
                else {
                    ArrayList<String> vl = new ArrayList<String>();
                    vl.add(v);
                    ap.getMetadata().put(n, vl);
                }
            }
        }
        if (!Utilities.noString(ap.metadata("category")))
            usage = ap.metadata("category");
        if (ap.hasMetadata("name"))
            ap.setTitle(ap.metadata("name"));
        if (ap.hasMetadata("introduction"))
            ap.setIntroduction(Utilities.path(folder, ap.metadata("introduction")));
        if (ap.hasMetadata("notes"))
            ap.setNotes(Utilities.path(folder, ap.metadata("notes")));
        if (!ap.hasMetadata("id"))
            throw new Exception("Error parsing " + ap.getId() + "/" + ap.getTitle() + " no 'id' found in metadata");
        if (!ap.metadata("id").matches(FormatUtilities.ID_REGEX))
            throw new Exception("Error parsing " + ap.getId() + "/" + ap.getTitle() + " 'id' is not a valid id");
        if (wg == null)
            wg = workgroups.get(ap.metadata("workgroup"));
        if (wg == null)
            wg = committee;
        if (wg == null)
            throw new Exception("Error parsing " + ap.getId() + "/" + ap.getTitle() + " : no workgroup value in the metadata");
        if (!ap.metadata("id").equals(ap.metadata("id").toLowerCase()))
            throw new Exception("Error parsing " + ap.getId() + "/" + ap.getTitle() + " 'id' must be all lowercase");
        this.profileExtensionBase = ap.metadata("extension.uri");
        if (ig == null || ig.isCore()) {
            if (!profileExtensionBase.startsWith("http://hl7.org/fhir/StructureDefinition/") && !profileExtensionBase.startsWith("http://fhir-registry.smarthealthit.org/StructureDefinition/"))
                throw new Exception("Core extensions must have a url starting with http://hl7.org/fhir/StructureDefinition/ for " + ap.getId());
        } else {
            if (!profileExtensionBase.startsWith("http://hl7.org/fhir/StructureDefinition/" + ig.getCode() + "-"))
                throw new Exception("Core extensions must have a url starting with http://hl7.org/fhir/StructureDefinition/" + ig.getCode() + "- for " + ap.getId());
        }
        Map<String, Invariant> invariants = null;
        sheet = loadSheet("Extensions-Inv");
        if (sheet != null) {
            invariants = readInvariants(sheet, "", "Extensions-Inv");
        }
        sheet = loadSheet("Extensions");
        if (sheet != null) {
            int row = 0;
            while (row < sheet.rows.size()) {
                if (sheet.getColumn(row, "Code").startsWith("!"))
                    row++;
                else
                    row = processExtension(null, sheet, row, definitions, ap.metadata("extension.uri"), ap, issues, invariants, wg);
            }
        }
        List<String> namedSheets = new ArrayList<String>();
        if (ap.getMetadata().containsKey("published.structure")) {
            for (String n : ap.getMetadata().get("published.structure")) {
                if (!Utilities.noString(n)) {
                    if (ig != null && !ig.isCore() && !n.toLowerCase().startsWith(ig.getCode() + "-"))
                        throw new Exception("Error: published structure names must start with the implementation guide code (" + ig.getCode() + "-)");
                    String fmm = ap.metadata("fmm-" + n);
                    if (Utilities.noString(fmm))
                        fmm = ap.metadata("fmm");
                    if (Utilities.noString(fmm))
                        // default fmm value
                        fmm = "1";
                    ap.getProfiles().add(parseProfileSheet(definitions, ap, n, namedSheets, true, usage, issues, wg, fmm));
                }
            }
        }
        int i = 0;
        while (i < namedSheets.size()) {
            String fmm = ap.metadata("fmm-" + namedSheets.get(i));
            if (Utilities.noString(fmm))
                fmm = ap.metadata("fmm");
            if (Utilities.noString(fmm))
                // default fmm value
                fmm = "1";
            ap.getProfiles().add(parseProfileSheet(definitions, ap, namedSheets.get(i), namedSheets, false, usage, issues, wg, fmm));
            i++;
        }
        if (namedSheets.isEmpty() && xls.getSheets().containsKey("Search"))
            readSearchParams(ap, xls.getSheets().get("Search"), this.profileExtensionBase);
        if (xls.getSheets().containsKey("Operations"))
            readOperations(ap.getOperations(), loadSheet("Operations"));
    } catch (Exception e) {
        throw new Exception("exception parsing pack " + ap.getSource() + ": " + e.getMessage(), e);
    }
}

Example 65 with Value

use of org.hl7.fhir.utilities.graphql.Value in project kindling by HL7.

the class SpreadSheetReloader method parseBinding.

private void parseBinding(OperationDefinitionParameterComponent param, String value, XSSFSheet bindings) {
    if (Utilities.noString(value)) {
        param.setBinding(null);
    } else {
        XSSFRow cols = bindings.getRow(0);
        XSSFRow row = lookupRow(bindings, cols, CN_BINDING_NAME, value);
        if (row == null) {
            throw new FHIRException("Unable to find binding " + value + " in " + xlsx);
        }
        OperationDefinitionParameterBindingComponent bs = param.getBinding();
        bs.removeExtension(BuildExtensions.EXT_NAME);
        readExt(bs, row, cols, CN_BINDING_NAME, BuildExtensions.EXT_BINDING_NAME, ExtensionType.String);
        readExt(bs, row, cols, CN_DEFINITION, BuildExtensions.EXT_DEFINITION, ExtensionType.String);
        bs.setStrength(BindingStrength.fromCode(getValue(row, cols, CN_STRENGTH)));
        bs.setValueSet(getValue(row, cols, CN_VALUE_SET));
        readExt(bs, row, cols, CN_OID, BuildExtensions.EXT_VS_OID, ExtensionType.String);
        readExt(bs, row, cols, CN_URI, BuildExtensions.EXT_URI, ExtensionType.String);
        readExt(bs, row, cols, CN_WEBSITE_EMAIL, BuildExtensions.EXT_WEBSITE, ExtensionType.Uri);
        readExt(bs, row, cols, CN_V2, BuildExtensions.EXT_V2_MAP, ExtensionType.String);
        readExt(bs, row, cols, CN_V3, BuildExtensions.EXT_V3_MAP, ExtensionType.String);
        readExt(bs, row, cols, CN_COPYRIGHT, BuildExtensions.EXT_COPYRIGHT, ExtensionType.String);
        readExt(bs, row, cols, CN_COMMITTEE_NOTES, BuildExtensions.EXT_COMMITTEE_NOTES, ExtensionType.Markdown);
    }
}