Examples with ValidationMessage org.hl7.fhir.utilities.validation.ValidationMessage used on opensource projects

Example 1 with ValidationMessage

use of org.hl7.fhir.utilities.validation.ValidationMessage in project kindling by HL7.

the class Publisher method checkFragment.

public void checkFragment(Fragment f) {
    try {
        // System.out.println("    "+f.page+"/"+f.id);
        String xml = f.getXml();
        DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
        factory.setNamespaceAware(true);
        DocumentBuilder builder = factory.newDocumentBuilder();
        InputSource is = new InputSource(new StringReader(xml));
        Document doc = builder.parse(is);
        org.w3c.dom.Element base = doc.getDocumentElement();
        String type = base.getAttribute("fragment");
        if (!page.getDefinitions().hasPrimitiveType(type)) {
            if (f.isJson()) {
                org.hl7.fhir.r5.elementmodel.JsonParser p = new org.hl7.fhir.r5.elementmodel.JsonParser(page.getWorkerContext());
                p.setupValidation(ValidationPolicy.QUICK, null);
                p.parse(base.getTextContent(), type);
            } else {
                org.hl7.fhir.r5.elementmodel.XmlParser p = new org.hl7.fhir.r5.elementmodel.XmlParser(page.getWorkerContext());
                p.setupValidation(ValidationPolicy.QUICK, null);
                p.parse(XMLUtil.getFirstChild(base), type);
            }
        }
    } catch (Exception e) {
        page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.STRUCTURE, f.getPage(), "Fragment Error in page " + f.getPage() + (f.id != null ? "#" + f.id : "") + ": " + e.getMessage(), IssueSeverity.ERROR));
    }
}

Example 2 with ValidationMessage

use of org.hl7.fhir.utilities.validation.ValidationMessage in project kindling by HL7.

the class Publisher method checkBundleURLs.

/**
 * This is not true of bundles generally, but it is true of all the
 * conformance bundles produced by the spec:
 *
 * all entries must have a fullUrl, and it must equal http://hl7.org/fhir/[type]/[id]
 *
 * @param bnd - the bundle to check
 */
private void checkBundleURLs(Bundle bnd) {
    int i = 0;
    for (BundleEntryComponent e : bnd.getEntry()) {
        i++;
        if (!e.getResource().hasUserData("external.url")) {
            if (!e.hasFullUrl())
                page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "Bundle " + bnd.getId(), "no Full URL on entry " + Integer.toString(i), IssueSeverity.ERROR));
            else if (!e.getFullUrl().endsWith("/" + e.getResource().getResourceType().toString() + "/" + e.getResource().getId()) && e.getResource().getResourceType() != ResourceType.CodeSystem)
                page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "Bundle " + bnd.getId(), "URL doesn't match resource and id on entry " + Integer.toString(i) + " : " + e.getFullUrl() + " should end with /" + e.getResource().getResourceType().toString() + "/" + e.getResource().getId(), IssueSeverity.ERROR));
            else if (!e.getFullUrl().equals("http://hl7.org/fhir/" + e.getResource().getResourceType().toString() + "/" + e.getResource().getId()) && e.getResource().getResourceType() != ResourceType.CodeSystem)
                page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "Bundle " + bnd.getId(), "URL is non-FHIR " + Integer.toString(i) + " : " + e.getFullUrl() + " should start with http://hl7.org/fhir/ for HL7-defined artifacts", IssueSeverity.WARNING));
            if (e.getResource() instanceof CanonicalResource) {
                CanonicalResource m = (CanonicalResource) e.getResource();
                String url = m.getUrl();
                if (url != null && url.startsWith("http://hl7.org/fhir") && !SIDUtilities.isKnownSID(url)) {
                    if (!page.getVersion().toCode().equals(m.getVersion()))
                        page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "Bundle " + bnd.getId(), "definitions in FHIR space should have the correct version (url = " + url + ", version = " + m.getVersion() + ")", IssueSeverity.ERROR));
                }
            }
        }
    }
}

Example 3 with ValidationMessage

use of org.hl7.fhir.utilities.validation.ValidationMessage in project kindling by HL7.

the class Publisher method execute.

/**
 * Entry point to the publisher. This classes Java Main() calls this function
 * to actually produce the specification
 *
 * @param folder
 * @throws IOException
 */
public void execute(String folder) throws IOException {
    tester = new PublisherTestSuites();
    page.log("Publish FHIR in folder " + folder + " @ " + Config.DATE_FORMAT().format(page.getGenDate().getTime()), LogMessageType.Process);
    if (web)
        page.log("Build final copy for HL7 web site", LogMessageType.Process);
    else
        page.log("Build local copy", LogMessageType.Process);
    if (outputdir != null) {
        page.log("Create output in " + outputdir, LogMessageType.Process);
    }
    page.log("Detected Java version: " + System.getProperty("java.version") + " from " + System.getProperty("java.home") + " on " + System.getProperty("os.arch"), LogMessageType.Process);
    try {
        tester.initialTests();
        page.setFolders(new FolderManager(folder, outputdir));
        if (!initialize(folder))
            throw new Exception("Unable to publish as preconditions aren't met");
        cache = new IniFile(page.getFolders().rootDir + "temp" + File.separator + "build.cache");
        loadSuppressedMessages(page.getFolders().rootDir);
        boolean doAny = false;
        for (String n : dates.keySet()) {
            Long d = cache.getLongProperty("dates", n);
            boolean b = d == null || (dates.get(n) > d);
            cache.setLongProperty("dates", n, dates.get(n).longValue(), null);
            buildFlags.put(n.toLowerCase(), b);
            doAny = doAny || b;
        }
        cache.save();
        if (noPartialBuild || !doAny || !(new File(page.getFolders().dstDir + "qa.html").exists()))
            // nothing - build all
            buildFlags.put("all", true);
        if (singlePage != null) {
            for (String n : buildFlags.keySet()) buildFlags.put(n, false);
            buildFlags.put("page-" + singlePage.toLowerCase(), true);
        } else if (singleResource != null) {
            for (String n : buildFlags.keySet()) buildFlags.put(n, false);
            buildFlags.put(singleResource.toLowerCase(), true);
        }
        if (!buildFlags.get("all")) {
            if (!noSound) {
                AudioUtilities.tone(1000, 10);
                AudioUtilities.tone(1400, 10);
                AudioUtilities.tone(1800, 10);
                AudioUtilities.tone(1000, 10);
                AudioUtilities.tone(1400, 10);
                AudioUtilities.tone(1800, 10);
            }
            page.log("Partial Build (if you want a full build, just run the build again)", LogMessageType.Process);
            CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
            for (String n : buildFlags.keySet()) if (buildFlags.get(n))
                b.append(n);
            page.log("  Build: " + b.toString(), LogMessageType.Process);
        } else {
            if (!noSound)
                AudioUtilities.tone(1200, 30);
            page.log("Full Build", LogMessageType.Process);
        }
        if (isGenerate && page.getBuildId() == null)
            page.setBuildId(getGitBuildId());
        page.log("Version " + page.getVersion() + "-" + page.getBuildId(), LogMessageType.Hint);
        Utilities.createDirectory(page.getFolders().dstDir);
        Utilities.deleteTempFiles();
        page.getBreadCrumbManager().parse(page.getFolders().srcDir + "hierarchy.xml");
        page.loadSnomed();
        page.loadLoinc();
        page.loadUcum();
        buildFeedsAndMaps();
        prsr.setExternals(externals);
        prsr.parse(page.getGenDate(), page.getValidationErrors());
        for (String n : page.getDefinitions().sortedResourceNames()) if (!page.getBreadCrumbManager().knowsResource(n))
            page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "hierarchy.xml", "Resource not found: " + n, IssueSeverity.ERROR));
        for (String n : prsr.getErrors()) page.getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.INVALID, -1, -1, "source spreadsheets", n, IssueSeverity.ERROR));
        if (web) {
            page.log("Clear Directory", LogMessageType.Process);
            Utilities.clearDirectory(page.getFolders().dstDir);
        }
        if (web || (isGenerate && buildFlags.get("all"))) {
            Utilities.createDirectory(page.getFolders().dstDir + "html");
            Utilities.createDirectory(page.getFolders().dstDir + "examples");
        }
        for (ImplementationGuideDefn ig : page.getDefinitions().getSortedIgs()) if (!ig.isCore())
            Utilities.createDirectory(page.getFolders().dstDir + ig.getCode());
        if (buildFlags.get("all")) {
            copyStaticContent();
        }
        page.makeRenderingContext();
        loadValueSets1();
        prsr.getRegistry().commit();
        generateSCMaps();
        validate();
        processProfiles();
        checkAllOk();
        if (isGenerate) {
            produceSpecification();
            checkAllOk();
        }
        if (doValidate)
            validationProcess();
        page.saveSnomed();
        page.getWorkerContext().saveCache();
        processWarnings(false);
        if (isGenerate && buildFlags.get("all"))
            produceQA();
        if (!buildFlags.get("all")) {
            page.log("This was a Partial Build", LogMessageType.Process);
            CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
            for (String n : buildFlags.keySet()) if (buildFlags.get(n))
                b.append(n);
            page.log("  Build: " + b.toString(), LogMessageType.Process);
        } else
            page.log("This was a Full Build", LogMessageType.Process);
        if (!noSound) {
            AudioUtilities.tone(800, 10);
            AudioUtilities.tone(1000, 10);
            AudioUtilities.tone(1200, 10);
            AudioUtilities.tone(1000, 10);
            AudioUtilities.tone(800, 10);
        }
        page.log("Finished publishing FHIR @ " + Config.DATE_FORMAT().format(Calendar.getInstance().getTime()), LogMessageType.Process);
    } catch (Exception e) {
        if (!(e instanceof NullPointerException)) {
            // because NullPointerException is unexpected...
            try {
                processWarnings(e instanceof EValidationFailed);
            } catch (Exception e2) {
                page.log("  ERROR: Unable to process warnings: " + e2.getMessage(), LogMessageType.Error);
                e2.printStackTrace();
            }
        }
        if (buildFlags.containsKey("all") && !buildFlags.get("all")) {
            page.log("This was a Partial Build", LogMessageType.Process);
            CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
            for (String n : buildFlags.keySet()) if (buildFlags.get(n))
                b.append(n);
            page.log("  Build: " + b.toString(), LogMessageType.Process);
        } else
            page.log("This was a Full Build", LogMessageType.Process);
        if (!noSound) {
            AudioUtilities.tone(800, 20);
            AudioUtilities.tone(1000, 20);
            AudioUtilities.tone(1200, 20);
        }
        try {
            Thread.sleep(50);
        } catch (InterruptedException e1) {
        }
        if (!noSound) {
            AudioUtilities.tone(800, 20);
            AudioUtilities.tone(1000, 20);
            AudioUtilities.tone(1200, 20);
        }
        try {
            Thread.sleep(50);
        } catch (InterruptedException e1) {
        }
        if (!noSound) {
            AudioUtilities.tone(800, 20);
            AudioUtilities.tone(1000, 20);
            AudioUtilities.tone(1200, 20);
        }
        page.log("FHIR build failure @ " + Config.DATE_FORMAT().format(Calendar.getInstance().getTime()), LogMessageType.Process);
        System.out.println("Error: " + e.getMessage());
        e.printStackTrace();
        TextFile.stringToFile(StringUtils.defaultString(e.getMessage()), Utilities.path(folder, "publish", "simple-error.txt"));
        System.exit(1);
    }
}

Example 4 with ValidationMessage

use of org.hl7.fhir.utilities.validation.ValidationMessage in project kindling by HL7.

the class Publisher method processWarnings.

private void processWarnings(boolean showOnlyErrors) throws Exception {
    String xslt = Utilities.path(page.getFolders().rootDir, "implementations", "xmltools", "OwnerResources.xslt");
    OutputStreamWriter s = new OutputStreamWriter(new FileOutputStream(page.getFolders().dstDir + "warnings.xml"), "UTF-8");
    s.write("<warnings>");
    for (WorkGroup wg : page.getDefinitions().getWorkgroups().values()) {
        s.write("<wg code=\"" + wg.getCode() + "\" name=\"" + wg.getName() + "\" url=\"" + wg.getUrl() + "\"/>\r\n");
    }
    for (PageInformation pn : page.getDefinitions().getPageInfo().values()) {
        s.write("<page name=\"" + pn.getName() + "\" wg=\"" + pn.getWgCode() + "\" fmm=\"" + pn.getFmm() + "\"/>\r\n");
    }
    try {
        s.write(new String(XsltUtilities.saxonTransform(page.getFolders().dstDir + "profiles-resources.xml", xslt)));
        s.write(new String(XsltUtilities.saxonTransform(page.getFolders().dstDir + "profiles-types.xml", xslt)));
        s.write(new String(XsltUtilities.saxonTransform(page.getFolders().dstDir + "profiles-others.xml", xslt)));
    } catch (Exception e) {
        for (ValidationMessage err : page.getValidationErrors()) {
            if (!page.getSuppressedMessages().contains(err.getDisplay()))
                System.out.println(err.summary());
        }
        System.out.println("WARNING: Unable to create warnings file - one or more profiles-* files unavailable or invalid");
        System.out.println("To determine the cause of the build failure, look in the log prior to the warning and information messages immediately above");
    }
    for (ValidationMessage e : page.getValidationErrors()) {
        if (!page.getSuppressedMessages().contains(e.getDisplay()))
            s.write(e.toXML());
    }
    s.write("</warnings>");
    s.flush();
    s.close();
    String xslt2 = Utilities.path(page.getFolders().rootDir, "implementations", "xmltools", "CategorizeWarnings.xslt");
    FileOutputStream s2 = new FileOutputStream(page.getFolders().dstDir + "work-group-warnings.xml");
    try {
        s2.write(XsltUtilities.saxonTransform(page.getFolders().dstDir + "warnings.xml", xslt2).getBytes("UTF8"));
    } catch (Exception e) {
    // nothing - do not want to know.
    }
    s2.flush();
    s2.close();
    String xslt3 = Utilities.path(page.getFolders().rootDir, "implementations", "xmltools", "RenderWarnings.xslt");
    try {
        String hw = XsltUtilities.saxonTransform(page.getFolders().dstDir + "work-group-warnings.xml", xslt3);
        if (!showOnlyErrors)
            page.log(hw, LogMessageType.Process);
    } catch (Exception e) {
    // nothing - do not want to know.
    }
    int i = 0;
    int w = 0;
    int ee = 0;
    for (ValidationMessage e : page.getValidationErrors()) {
        if (e.getLevel() == IssueSeverity.ERROR || e.getLevel() == IssueSeverity.FATAL) {
            ee++;
            page.log(e.summary(), LogMessageType.Hint);
        } else if (e.getLevel() == IssueSeverity.WARNING) {
            w++;
        } else if (e.getLevel() == IssueSeverity.INFORMATION) {
            i++;
        }
    }
    page.getQa().setCounts(ee, w, i);
}

Example 5 with ValidationMessage

use of org.hl7.fhir.utilities.validation.ValidationMessage in project kindling by HL7.

the class PageProcessor method resolveBinding.

public BindingResolution resolveBinding(StructureDefinition profile, String ref, String description, String path) throws FHIRException {
    BindingResolution br = new BindingResolution();
    if (ref.contains("|"))
        ref = ref.substring(0, ref.indexOf("|"));
    if (ref.startsWith("http://terminology.hl7.org/ValueSet/v3-") || ref.startsWith("http://terminology.hl7.org/ValueSet/v2-")) {
        ValueSet vs = workerContext.fetchResource(ValueSet.class, ref);
        if (vs == null) {
            br.url = "v3/" + ref.substring(39) + "/vs.html";
            br.display = ref.substring(39);
        } else {
            br.url = vs.getUserString("path");
            br.display = vs.present();
        }
    } else if (definitions.getValuesets().has(ref)) {
        ValueSet vs = definitions.getValuesets().get(ref);
        br.url = vs.getUserString("path");
        br.display = vs.present();
    } else if (ref.startsWith("ValueSet/")) {
        ValueSet vs = definitions.getValuesets().get(ref.substring(8));
        if (vs == null) {
            br.url = ref.substring(9) + ".html";
            br.display = ref.substring(9);
        } else {
            br.url = vs.getUserString("path");
            br.display = vs.present();
        }
    } else if (ref.startsWith("http://hl7.org/fhir/ValueSet/")) {
        ValueSet vs = definitions.getValuesets().get(ref);
        if (vs == null)
            vs = definitions.getExtraValuesets().get(ref);
        if (vs != null) {
            br.url = vs.getUserString("path");
            if (Utilities.noString(br.url))
                br.url = ref.substring(23) + ".html";
            br.display = vs.present();
        } else if (ref.substring(23).equals("use-context")) {
            // special case because this happens before the value set is created
            br.url = "valueset-" + ref.substring(23) + ".html";
            br.display = "Context of Use ValueSet";
        } else if (ref.startsWith("http://terminology.hl7.org/ValueSet/v3-")) {
            br.url = "v3/" + ref.substring(26) + "/index.html";
            br.display = ref.substring(26);
        } else if (ref.startsWith("http://terminology.hl7.org/ValueSet/v2-")) {
            br.url = "v2/" + ref.substring(26) + "/index.html";
            br.display = ref.substring(26);
        } else if (ref.startsWith("#")) {
            br.url = null;
            br.display = ref;
        } else {
            br.url = ref;
            br.display = "????";
            getValidationErrors().add(new ValidationMessage(Source.Publisher, IssueType.NOTFOUND, -1, -1, path, "Unresolved Value set " + ref, IssueSeverity.WARNING));
        }
    } else {
        br.url = ref;
        if (ref.equals("http://tools.ietf.org/html/bcp47"))
            br.display = "IETF BCP-47";
        else if (ref.equals("http://www.rfc-editor.org/bcp/bcp13.txt"))
            br.display = "IETF BCP-13";
        else if (ref.equals("http://www.ncbi.nlm.nih.gov/nuccore?db=nuccore"))
            br.display = "NucCore";
        else if (ref.equals("https://rtmms.nist.gov/rtmms/index.htm#!rosetta"))
            br.display = "Rosetta";
        else if (ref.equals("http://www.iso.org/iso/country_codes.htm"))
            br.display = "ISO Country Codes";
        else if (ref.equals("http://www.ncbi.nlm.nih.gov/clinvar/variation"))
            br.display = "ClinVar";
        else if (!Utilities.noString(description))
            br.display = description;
        else
            br.display = "????";
    }
    return br;
}