Examples with CodeListToValueSetParser org.hl7.fhir.definitions.parsers.CodeListToValueSetParser used on opensource projects

Example 1 with CodeListToValueSetParser

use of org.hl7.fhir.definitions.parsers.CodeListToValueSetParser 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 2 with CodeListToValueSetParser

use of org.hl7.fhir.definitions.parsers.CodeListToValueSetParser in project kindling by HL7.

the class BindingsParser method processLine.

private void processLine(List<BindingSpecification> results, Sheet sheet, int row) throws Exception {
    BindingSpecification cd = new BindingSpecification("core", sheet.getColumn(row, "Binding Name"), true);
    if (!cd.getName().startsWith("!")) {
        if (Character.isLowerCase(cd.getName().charAt(0)))
            throw new Exception("binding name " + cd.getName() + " is illegal - must start with a capital letter");
        cd.setDefinition(Utilities.appendPeriod(sheet.getColumn(row, "Definition")));
        cd.setBindingMethod(readBinding(sheet.getColumn(row, "Binding"), cd.getName() + " in " + filename));
        boolean utg = "y".equals(sheet.getColumn(row, "UTG"));
        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) {
            cd.setValueSet(new ValueSet());
            cd.getValueSet().setId(ref.substring(1));
            cd.getValueSet().setUrl("http://hl7.org/fhir/ValueSet/" + ref.substring(1));
            cd.getValueSet().setVersion(version);
            if (!Utilities.noString(sheet.getColumn(row, "Committee"))) {
                cd.getValueSet().addExtension().setUrl(ToolingExtensions.EXT_WORKGROUP).setValue(new CodeType(sheet.getColumn(row, "Committee").toLowerCase()));
            }
            cd.getValueSet().setUserData("filename", "valueset-" + cd.getValueSet().getId());
            cd.getValueSet().setUserData("path", "valueset-" + cd.getValueSet().getId() + ".html");
            cd.getValueSet().setName(cd.getName());
            cd.getValueSet().setTitle(cd.getName());
            cd.getValueSet().setDateElement(new DateTimeType(genDate));
            cd.getValueSet().setStatus(PublicationStatus.DRAFT);
            cd.getValueSet().setDescription(sheet.getColumn(row, "Description"));
            if (!cd.getValueSet().hasDescription())
                cd.getValueSet().setDescription(cd.getDefinition());
            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");
            new CodeListToValueSetParser(cs, ref.substring(1), cd.getValueSet(), version, codeSystems, maps, packageInfo).execute(sheet.getColumn(row, "v2"), sheet.getColumn(row, "v3"), utg);
        } 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, sheet.getColumn(row, "Committee").toLowerCase()));
            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, sheet.getColumn(row, "Committee").toLowerCase()));
        } else if (cd.getBinding() == BindingMethod.Special) {
            cd.setValueSet(new ValueSet());
            cd.getValueSet().setId(ref.substring(1));
            cd.getValueSet().setUrl("http://hl7.org/fhir/ValueSet/" + ref.substring(1));
            cd.getValueSet().setVersion(version);
            cd.getValueSet().setName(cd.getName());
        // do nothing more: this will get filled out once all the resources are loaded
        }
        // do this anyway in the short term
        cd.setReference(sheet.getColumn(row, "Reference"));
        if (cd.getValueSet() != null) {
            touchVS(cd.getValueSet());
            ValueSetUtilities.markStatus(cd.getValueSet(), Utilities.noString(sheet.getColumn(row, "Committee")) ? "vocab" : sheet.getColumn(row, "Committee").toLowerCase(), null, null, Utilities.noString(sheet.getColumn(row, "FMM")) ? null : sheet.getColumn(row, "FMM"), null, Utilities.noString(sheet.getColumn(row, "Normative-Version")) ? null : sheet.getColumn(row, "Normative-Version"));
        }
        if (cd.getMaxValueSet() != null) {
            touchVS(cd.getMaxValueSet());
            ValueSetUtilities.markStatus(cd.getMaxValueSet(), Utilities.noString(sheet.getColumn(row, "Committee")) ? "vocab" : sheet.getColumn(row, "Committee").toLowerCase(), null, null, Utilities.noString(sheet.getColumn(row, "FMM")) ? null : sheet.getColumn(row, "FMM"), null, Utilities.noString(sheet.getColumn(row, "Max-Normative-Version")) ? null : sheet.getColumn(row, "Max-Normative-Version"));
        }
        cd.setDescription(sheet.getColumn(row, "Description"));
        cd.setSource(filename);
        cd.setUri(sheet.getColumn(row, "Uri"));
        cd.setStrength(readBindingStrength(sheet.getColumn(row, "Conformance")));
        String oid = sheet.getColumn(row, "Oid");
        if (!Utilities.noString(oid))
            // no cs oid in this case
            cd.setVsOid(oid);
        cd.setWebSite(sheet.getColumn(row, "Website"));
        cd.setStatus(PublicationStatus.fromCode(sheet.getColumn(row, "Status")));
        cd.setEmail(sheet.getColumn(row, "Email"));
        cd.setV2Map(sheet.getColumn(row, "v2"));
        cd.setV3Map(sheet.getColumn(row, "v3"));
        if (cd.getBinding() == BindingMethod.Unbound) {
            cd.setStrength(BindingStrength.EXAMPLE);
        }
        results.add(cd);
    }
}