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

Example 36 with Operation

use of org.hl7.fhir.utilities.graphql.Operation 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 37 with Operation

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

the class OldSpreadsheetParser method readOperations.

private void readOperations(List<Operation> oplist, Sheet sheet) throws Exception {
    Map<String, Operation> ops = new HashMap<String, Operation>();
    Map<String, OperationParameter> params = new HashMap<String, OperationParameter>();
    if (sheet != null) {
        for (int row = 0; row < sheet.rows.size(); row++) {
            String name = sheet.getColumn(row, "Name");
            String use = sheet.getColumn(row, "Use");
            String doco = sheet.getColumn(row, "Documentation");
            String type = sheet.getColumn(row, "Type");
            List<OperationExample> examples = loadOperationExamples(sheet.getColumn(row, "Example.Request"), sheet.getColumn(row, "Example.Response"));
            List<OperationExample> examples2 = loadOperationExamples(sheet.getColumn(row, "Example2.Request"), sheet.getColumn(row, "Example2.Response"));
            if (name != null && !name.equals("") && !name.startsWith("!")) {
                if (!name.contains(".")) {
                    if (!type.equals("operation"))
                        throw new Exception("Invalid type on operation " + type + " at " + getLocation(row));
                    if (!name.toLowerCase().equals(name))
                        throw new Exception("Invalid name on operation " + name + " - must be all lower case (use dashes) at " + getLocation(row));
                    params.clear();
                    boolean system = false;
                    boolean istype = false;
                    boolean instance = false;
                    for (String c : use.split("\\|")) {
                        c = c.trim();
                        if ("system".equalsIgnoreCase(c))
                            system = true;
                        else if ("resource".equalsIgnoreCase(c))
                            istype = true;
                        else if ("instance".equalsIgnoreCase(c))
                            instance = true;
                        else
                            throw new Exception("unknown operation use code " + c + " at " + getLocation(row));
                    }
                    Operation op = new Operation(name, system, istype, instance, sheet.getColumn(row, "Type"), sheet.getColumn(row, "Title"), doco, sheet.getColumn(row, "Footer"), examples, parseBoolean(sheet.getColumn(row, "Idempotent"), row, false));
                    op.setStandardsStatus(StandardsStatus.fromCode(sheet.getColumn(row, "Standards-Status")));
                    op.setNormativeVersion(sheet.getColumn(row, "Normative-Version"));
                    op.setFooter2(sheet.getColumn(row, "Footer2"));
                    op.setFmm(sheet.getColumn(row, "fmm"));
                    op.getExamples2().addAll(examples2);
                    oplist.add(op);
                    ops.put(name, op);
                } else {
                    String context = name.substring(0, name.lastIndexOf('.'));
                    String pname = name.substring(name.lastIndexOf('.') + 1);
                    Operation operation;
                    List<OperationParameter> plist;
                    if (context.contains(".")) {
                        String opname = name.substring(0, name.indexOf('.'));
                        // inside of a tuple
                        if (!Utilities.noString(use))
                            throw new Exception("Tuple parameters: use must be blank at " + getLocation(row));
                        operation = ops.get(opname);
                        if (operation == null)
                            throw new Exception("Unknown Operation '" + opname + "' at " + getLocation(row));
                        OperationParameter param = params.get(context);
                        if (param == null)
                            throw new Exception("Tuple parameter '" + context + "' not found at " + getLocation(row));
                        if (!param.getFhirType().equals("Tuple"))
                            throw new Exception("Tuple parameter '" + context + "' type must be Tuple at " + getLocation(row));
                        plist = param.getParts();
                    } else {
                        if (!use.equals("in") && !use.equals("out"))
                            throw new Exception("Only allowed use is 'in' or 'out' at " + getLocation(row));
                        operation = ops.get(context);
                        if (operation == null)
                            throw new Exception("Unknown Operation '" + context + "' at " + getLocation(row));
                        plist = operation.getParameters();
                    }
                    String profile = sheet.getColumn(row, "Profile");
                    String min = sheet.getColumn(row, "Min");
                    String max = sheet.getColumn(row, "Max");
                    OperationParameter p = new OperationParameter(pname, use, doco, Integer.parseInt(min), max, type, sheet.getColumn(row, "Search Type"), profile);
                    String bs = sheet.getColumn(row, "Binding");
                    if (!Utilities.noString(bs))
                        p.setBs(bindings.get(bs));
                    plist.add(p);
                    params.put(name, p);
                }
            }
        }
    }
}

Example 38 with Operation

use of org.hl7.fhir.utilities.graphql.Operation 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 39 with Operation

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

the class Regenerator method generateOperation.

private void generateOperation(String root, ResourceDefn r, Operation op) throws IOException {
    OperationDefinition opd = op.getResource().copy();
    opd.setId(r.getName() + "-" + op.getName());
    opd.setUrl("http://hl7.org/fhir/build/OperationDefinition/" + opd.getId());
    if (!Utilities.noString(op.getFooter())) {
        opd.addExtension(BuildExtensions.EXT_FOOTER, new MarkdownType(op.getFooter()));
    }
    if (!Utilities.noString(op.getFooter2())) {
        opd.addExtension(BuildExtensions.EXT_FOOTER2, new MarkdownType(op.getFooter2()));
    }
    for (OperationExample opex : op.getExamples()) {
        Extension ex = new Extension(BuildExtensions.EXT_OP_EXAMPLE);
        if (!Utilities.noString(opex.getContent())) {
            ex.addExtension(BuildExtensions.EXT_OP_EXAMPLE_CONTENT, new StringType(opex.getContent()));
        }
        if (!Utilities.noString(opex.getComment())) {
            ex.addExtension(BuildExtensions.EXT_OP_EXAMPLE_COMMENT, new StringType(opex.getComment()));
        }
        ex.addExtension(BuildExtensions.EXT_OP_EXAMPLE_RESPONSE, new BooleanType(opex.isResponse()));
        ex.addExtension(BuildExtensions.EXT_OP_EXAMPLE_LIST, new IntegerType(1));
        opd.addExtension(ex);
    }
    for (OperationExample opex : op.getExamples2()) {
        Extension ex = new Extension(BuildExtensions.EXT_OP_EXAMPLE);
        if (!Utilities.noString(opex.getContent())) {
            ex.addExtension(BuildExtensions.EXT_OP_EXAMPLE_CONTENT, new StringType(opex.getContent()));
        }
        if (!Utilities.noString(opex.getComment())) {
            ex.addExtension(BuildExtensions.EXT_OP_EXAMPLE_COMMENT, new StringType(opex.getComment()));
        }
        ex.addExtension(BuildExtensions.EXT_OP_EXAMPLE_RESPONSE, new BooleanType(opex.isResponse()));
        ex.addExtension(BuildExtensions.EXT_OP_EXAMPLE_LIST, new IntegerType(2));
        opd.addExtension(ex);
    }
    File fn = new File(Utilities.path(root, opd.fhirType().toLowerCase() + "-" + opd.getId() + ".gen.xml"));
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(fn), opd);
    fn.setLastModified(r.getTimestamp());
}

Example 40 with Operation

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

the class ProfileGenerator method produceOpParam.

private void produceOpParam(String path, List<OperationDefinitionParameterComponent> opd, OperationParameter p, OperationParameterUse defUse) throws Exception {
    OperationDefinitionParameterComponent pp = new OperationDefinitionParameterComponent();
    pp.setName(p.getName());
    if (path.contains("."))
        pp.setUse(defUse);
    else if (p.getUse().equals("in"))
        pp.setUse(OperationParameterUse.IN);
    else if (p.getUse().equals("out"))
        pp.setUse(OperationParameterUse.OUT);
    else
        // but this is validated elsewhere
        throw new Exception("Unable to determine parameter use: " + p.getUse() + " at " + path + "." + p.getName());
    pp.setDocumentation(preProcessMarkdown(p.getDoc(), "Operation Parameter Doco"));
    pp.setMin(p.getMin());
    pp.setMax(p.getMax());
    if (p.getBs() != null) {
        if (p.getBs().hasMax())
            throw new Error("Max binding not handled yet");
        pp.setBinding(new OperationDefinitionParameterBindingComponent().setStrength(p.getBs().getStrength()).setValueSet(buildValueSetReference(p.getBs())));
        if (!Utilities.noString(p.getBinding().getName())) {
            pp.getBinding().addExtension("http://hl7.org/fhir/StructureDefinition/elementdefinition-bindingName", new StringType(p.getBinding().getName()));
        }
    }
    if (!Utilities.noString(p.getProfile())) {
        pp.addTargetProfile(p.getProfile());
    }
    opd.add(pp);
    if (p.getFhirType().equals("Tuple")) {
        for (OperationParameter part : p.getParts()) {
            produceOpParam(path + "." + p.getName(), pp.getPart(), part, pp.getUse());
        }
    } else {
        List<TypeRef> trs = new TypeParser(version.toCode()).parse(p.getFhirType(), false, null, null, false);
        if (trs.size() > 1) {
            if (p.getSearchType() != null)
                pp.setSearchType(SearchParamType.fromCode(p.getSearchType()));
            pp.setType(Enumerations.FHIRAllTypes.fromCode("Element"));
            for (TypeRef tr : trs) {
                pp.addExtension(ToolingExtensions.EXT_ALLOWED_TYPE, new UriType(tr.getName()));
                if (tr.getParams().size() > 0)
                    throw new Error("Multiple types for an operation parameter, where one is a reference, is not supported by the build tools");
            }
        } else {
            TypeRef tr = trs.get(0);
            if (definitions.getConstraints().containsKey(tr.getName())) {
                ProfiledType pt = definitions.getConstraints().get(tr.getName());
                pp.setType(Enumerations.FHIRAllTypes.fromCode(pt.getBaseType().equals("*") ? "Type" : pt.getBaseType()));
                pp.addTargetProfile("http://hl7.org/fhir/StructureDefinition/" + pt.getName());
            } else {
                if (p.getSearchType() != null)
                    pp.setSearchType(SearchParamType.fromCode(p.getSearchType()));
                pp.setType(Enumerations.FHIRAllTypes.fromCode(tr.getName().equals("*") ? "Type" : tr.getName()));
                if (tr.getParams().size() == 1 && !tr.getParams().get(0).equals("Any"))
                    pp.addTargetProfile("http://hl7.org/fhir/StructureDefinition/" + tr.getParams().get(0));
            }
        }
    }
}