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Example 26 with org.hl7.fhir.r5.utils.validation

use of org.hl7.fhir.r5.utils.validation in project kindling by HL7.

the class DefinitionsUsageTracker method usage.

private void usage(org.hl7.fhir.r5.elementmodel.Element instance, ElementDefn definition, String path) throws Exception {
    definition.setCoveredByExample(true);
    for (Element c : instance.getChildren()) {
        String p = c.getProperty().getDefinition().getPath();
        ElementDefn ed = definitions.getElementByPath(p.split("\\."), "example usage", true);
        if (ed != null)
            usage(c, ed, path + "." + c.getName());
    // else if (!c.getName().equals("extension"))
    // System.out.println("error finding "+c.getName()+" at "+path);
    }
}
Also used : Element(org.hl7.fhir.r5.elementmodel.Element) ElementDefn(org.hl7.fhir.definitions.model.ElementDefn)

Example 27 with org.hl7.fhir.r5.utils.validation

use of org.hl7.fhir.r5.utils.validation in project kindling by HL7.

the class ExampleInspector method fetch.

@Override
public Element fetch(IResourceValidator validator, Object appContext, String url) throws IOException, FHIRException {
    String[] parts = url.split("\\/");
    if (parts.length == 2 && definitions.hasResource(parts[0])) {
        ResourceDefn r = definitions.getResourceByName(parts[0]);
        for (Example e : r.getExamples()) {
            if (e.getElement() == null && e.hasXml()) {
                e.setElement(new org.hl7.fhir.r5.elementmodel.XmlParser(context).parse(e.getXml()));
                if (e.getElement().getProperty().getStructure().getBaseDefinition().contains("MetadataResource")) {
                    String urle = e.getElement().getChildValue("url");
                    String v = e.getElement().getChildValue("url");
                    if (urle != null && urle.startsWith("http://hl7.org/fhir") && !version.toCode().equals(v)) {
                        e.getElement().setChildValue("version", version.toCode());
                    }
                }
            }
            if (e.getElement() != null) {
                if (e.getElement().fhirType().equals("Bundle")) {
                    for (Base b : e.getElement().listChildrenByName("entry")) {
                        if (b.getChildByName("resource").hasValues()) {
                            Element res = (Element) b.getChildByName("resource").getValues().get(0);
                            if (res.fhirType().equals(parts[0]) && parts[1].equals(res.getChildValue("id"))) {
                                return res;
                            }
                        }
                    }
                } else if (e.getElement().fhirType().equals(parts[0]) && e.getId().equals(parts[1])) {
                    return e.getElement();
                }
            }
        }
        try {
            if (parts[0].equals("StructureDefinition"))
                return new ObjectConverter(context).convert(context.fetchResourceWithException(StructureDefinition.class, "http://hl7.org/fhir/" + parts[0] + "/" + parts[1]));
            if (parts[0].equals("OperationDefinition"))
                return new ObjectConverter(context).convert(context.fetchResourceWithException(OperationDefinition.class, "http://hl7.org/fhir/" + parts[0] + "/" + parts[1]));
            if (parts[0].equals("SearchParameter"))
                return new ObjectConverter(context).convert(context.fetchResourceWithException(SearchParameter.class, "http://hl7.org/fhir/" + parts[0] + "/" + parts[1]));
            if (parts[0].equals("ValueSet"))
                return new ObjectConverter(context).convert(context.fetchResourceWithException(ValueSet.class, "http://hl7.org/fhir/" + parts[0] + "/" + parts[1]));
            if (parts[0].equals("CodeSystem"))
                return new ObjectConverter(context).convert(context.fetchResourceWithException(CodeSystem.class, "http://hl7.org/fhir/" + parts[0] + "/" + parts[1]));
        } catch (Exception e) {
            return null;
        }
        return null;
    } else
        return null;
}
Also used : XmlParser(org.hl7.fhir.r5.formats.XmlParser) ObjectConverter(org.hl7.fhir.r5.elementmodel.ObjectConverter) Example(org.hl7.fhir.definitions.model.Example) Element(org.hl7.fhir.r5.elementmodel.Element) ResourceDefn(org.hl7.fhir.definitions.model.ResourceDefn) Base(org.hl7.fhir.r5.model.Base) URISyntaxException(java.net.URISyntaxException) FileNotFoundException(java.io.FileNotFoundException) SAXException(org.xml.sax.SAXException) NotImplementedException(org.apache.commons.lang3.NotImplementedException) DefinitionException(org.hl7.fhir.exceptions.DefinitionException) PathEngineException(org.hl7.fhir.exceptions.PathEngineException) ValidationException(org.everit.json.schema.ValidationException) MalformedURLException(java.net.MalformedURLException) JsonSyntaxException(com.google.gson.JsonSyntaxException) IOException(java.io.IOException) ParserConfigurationException(javax.xml.parsers.ParserConfigurationException) FHIRException(org.hl7.fhir.exceptions.FHIRException)

Example 28 with org.hl7.fhir.r5.utils.validation

use of org.hl7.fhir.r5.utils.validation in project kindling by HL7.

the class SpecNPMPackageGenerator method makeResourceList5.

private List<ResourceEntry> makeResourceList5(Map<String, byte[]> files, String version, List<ResourceEntry> res) throws FHIRFormatError, IOException {
    for (String k : files.keySet()) {
        if (k.endsWith(".xml")) {
            Bundle b = (Bundle) new org.hl7.fhir.r5.formats.XmlParser().parse(files.get(k));
            for (org.hl7.fhir.r5.model.Bundle.BundleEntryComponent be : b.getEntry()) {
                if (be.hasResource()) {
                    ResourceEntry e = new ResourceEntry();
                    e.type = be.getResource().fhirType();
                    e.id = be.getResource().getId();
                    e.json = new org.hl7.fhir.r5.formats.JsonParser().composeBytes(be.getResource());
                    e.xml = new org.hl7.fhir.r5.formats.XmlParser().composeBytes(be.getResource());
                    e.conf = true;
                    if (be.getResource() instanceof org.hl7.fhir.r5.model.CanonicalResource)
                        e.canonical = ((org.hl7.fhir.r5.model.CanonicalResource) be.getResource()).getUrl();
                    res.add(e);
                }
            }
        }
    }
    return null;
}
Also used : XmlParser(org.hl7.fhir.r5.formats.XmlParser) Bundle(org.hl7.fhir.r5.model.Bundle) JsonParser(org.hl7.fhir.r5.formats.JsonParser)

Example 29 with org.hl7.fhir.r5.utils.validation

use of org.hl7.fhir.r5.utils.validation in project kindling by HL7.

the class DSTU3ValidationConvertor method convert.

public void convert(String bundleSource, String bundleTarget) throws Exception {
    System.out.println("Convert " + bundleSource);
    try {
        source = (Bundle) new XmlParser().parse(new FileInputStream(bundleSource));
        org.hl7.fhir.dstu3.model.Bundle target = Bundle30_50.convertBundle(source);
        new org.hl7.fhir.dstu3.formats.XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(bundleTarget), target);
    } catch (Exception e) {
        throw new Exception(e);
    }
}
Also used : XmlParser(org.hl7.fhir.r5.formats.XmlParser) FileOutputStream(java.io.FileOutputStream) FileInputStream(java.io.FileInputStream)

Example 30 with org.hl7.fhir.r5.utils.validation

use of org.hl7.fhir.r5.utils.validation in project kindling by HL7.

the class SourceParser method loadCompositeType.

private String loadCompositeType(String n, Map<String, org.hl7.fhir.definitions.model.TypeDefn> map, String fmm, boolean isAbstract) throws Exception {
    TypeParser tp = new TypeParser(version.toString());
    List<TypeRef> ts = tp.parse(n, false, null, context, true);
    definitions.getKnownTypes().addAll(ts);
    StandardsStatus status = loadStatus(n);
    String nv = loadNormativeVersion(n);
    try {
        TypeRef t = ts.get(0);
        File csv = new CSFile(dtDir + t.getName().toLowerCase() + ".xml");
        if (csv.exists()) {
            OldSpreadsheetParser p = new OldSpreadsheetParser("core", new CSFileInputStream(csv), csv.getName(), csv.getAbsolutePath(), definitions, srcDir, logger, registry, version, context, genDate, isAbstract, page, true, ini, wg("fhir"), definitions.getProfileIds(), fpUsages, page.getConceptMaps(), exceptionIfExcelNotNormalised, page.packageInfo(), page.getRc());
            org.hl7.fhir.definitions.model.TypeDefn el = p.parseCompositeType();
            el.setFmmLevel(fmm);
            el.setStandardsStatus(status);
            el.setNormativeVersion(nv);
            map.put(t.getName(), el);
            genTypeProfile(el);
            errors.addAll(p.getErrors());
            return el.getName();
        } else {
            String p = ini.getStringProperty("types", n);
            csv = new CSFile(dtDir + p.toLowerCase() + ".xml");
            if (!csv.exists())
                throw new Exception("unable to find a definition for " + n + " in " + p);
            XLSXmlParser xls = new XLSXmlParser(new CSFileInputStream(csv), csv.getAbsolutePath());
            new XLSXmlNormaliser(csv.getAbsolutePath(), exceptionIfExcelNotNormalised).go();
            Sheet sheet = xls.getSheets().get("Restrictions");
            boolean found = false;
            for (int i = 0; i < sheet.rows.size(); i++) {
                if (sheet.getColumn(i, "Name").equals(n)) {
                    found = true;
                    Invariant inv = new Invariant();
                    inv.setId(n);
                    inv.setEnglish(sheet.getColumn(i, "Rules"));
                    inv.setOcl(sheet.getColumn(i, "OCL"));
                    inv.setXpath(sheet.getColumn(i, "XPath"));
                    inv.setExpression(sheet.getColumn(i, "Expression"));
                    inv.setExplanation(sheet.getColumn(i, "Explanation"));
                    inv.setTurtle(sheet.getColumn(i, "RDF"));
                    ProfiledType pt = new ProfiledType();
                    pt.setDefinition(sheet.getColumn(i, "Definition"));
                    pt.setDescription(sheet.getColumn(i, "Rules"));
                    String structure = sheet.getColumn(i, "Structure");
                    if (!Utilities.noString(structure)) {
                        String[] parts = structure.split("\\;");
                        for (String pp : parts) {
                            String[] words = pp.split("\\=");
                            pt.getRules().put(words[0], words[1]);
                        }
                    }
                    pt.setName(n);
                    pt.setBaseType(p);
                    pt.setInvariant(inv);
                    definitions.getConstraints().put(n, pt);
                }
            }
            if (!found)
                throw new Exception("Unable to find definition for " + n);
            return n;
        }
    } catch (Exception e) {
        throw new Exception("Unable to load " + n + ": " + e.getMessage(), e);
    }
}
Also used : Invariant(org.hl7.fhir.definitions.model.Invariant) ProfiledType(org.hl7.fhir.definitions.model.ProfiledType) TypeRef(org.hl7.fhir.definitions.model.TypeRef) XLSXmlParser(org.hl7.fhir.utilities.xls.XLSXmlParser) XLSXmlNormaliser(org.hl7.fhir.utilities.xls.XLSXmlNormaliser) CSFile(org.hl7.fhir.utilities.CSFile) IOException(java.io.IOException) FHIRException(org.hl7.fhir.exceptions.FHIRException) FileNotFoundException(java.io.FileNotFoundException) SAXException(org.xml.sax.SAXException) ParserConfigurationException(javax.xml.parsers.ParserConfigurationException) OldSpreadsheetParser(org.hl7.fhir.definitions.parsers.spreadsheets.OldSpreadsheetParser) TypeDefn(org.hl7.fhir.definitions.model.TypeDefn) StandardsStatus(org.hl7.fhir.utilities.StandardsStatus) IniFile(org.hl7.fhir.utilities.IniFile) File(java.io.File) CSFile(org.hl7.fhir.utilities.CSFile) TextFile(org.hl7.fhir.utilities.TextFile) Sheet(org.hl7.fhir.utilities.xls.XLSXmlParser.Sheet) CSFileInputStream(org.hl7.fhir.utilities.CSFileInputStream)

Aggregations

Test (org.junit.jupiter.api.Test)427 Turtle (org.hl7.fhir.dstu3.utils.formats.Turtle)334 Test (org.junit.Test)241 FHIRException (org.hl7.fhir.exceptions.FHIRException)104 ArrayList (java.util.ArrayList)101 IOException (java.io.IOException)78 MockHttpServletResponse (org.springframework.mock.web.MockHttpServletResponse)70 Date (java.util.Date)65 List (java.util.List)64 IBaseResource (org.hl7.fhir.instance.model.api.IBaseResource)61 FileOutputStream (java.io.FileOutputStream)59 CodeableReference (org.hl7.fhir.r5.model.CodeableReference)58 File (java.io.File)57 InputStream (java.io.InputStream)51 ParameterizedTest (org.junit.jupiter.params.ParameterizedTest)50 IBundleProvider (ca.uhn.fhir.rest.api.server.IBundleProvider)48 Bundle (org.hl7.fhir.dstu3.model.Bundle)48 MethodSource (org.junit.jupiter.params.provider.MethodSource)46 Arrays (java.util.Arrays)45 Collectors (java.util.stream.Collectors)45