Examples with FINAL org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL used on opensource projects

Example 6 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL 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 7 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project kindling by HL7.

the class Publisher method copyImage.

private void copyImage(String folder, String n) throws IOException {
    if (n.contains("*")) {
        final String filter = n.replace("?", ".?").replace("*", ".*?");
        File[] files = new File(folder).listFiles(new FilenameFilter() {

            @Override
            public boolean accept(File dir, String name) {
                return name.matches(filter);
            }
        });
        for (File f : files) {
            Utilities.copyFile(f, new CSFile(page.getFolders().dstDir + f.getName()));
            page.getHTMLChecker().registerFile(f.getName(), "Support File", HTMLLinkChecker.determineType(n), true);
        }
    } else {
        Utilities.copyFile(new CSFile(Utilities.path(folder, n)), new CSFile(page.getFolders().dstDir + (n.contains("/") ? n.substring(n.lastIndexOf("/") + 1) : n)));
        page.getHTMLChecker().registerFile(n, "Support File", HTMLLinkChecker.determineType(n), true);
    }
}

Example 8 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project kindling by HL7.

the class PageProcessor method asText.

private String asText(List<CodeType> list) {
    StringBuilder b = new StringBuilder();
    boolean first = true;
    for (CodeType rn : list) {
        if (first) {
            first = false;
            b.append("<br/>(");
        } else
            b.append(", ");
        final String value = rn.getValue();
        if ("Any".equals(value))
            b.append("Any");
        else
            b.append("<a href=\"").append(value.toLowerCase()).append(".html\">").append(value).append("</a>");
    }
    if (!first)
        b.append(")");
    return b.toString();
}

Example 9 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project kindling by HL7.

the class Publisher method copyIgImage.

private void copyIgImage(ImplementationGuideDefn ig, String path) throws IOException {
    File file = new File(Utilities.path(page.getFolders().rootDir, ig.getSource(), "..", path));
    String prefix = ig.isCore() ? "" : ig.getCode() + File.separator;
    if (path.contains("*")) {
        final String filter = file.getName().replace("?", ".?").replace("*", ".*?");
        File[] files = new File(file.getParent()).listFiles(new FilenameFilter() {

            @Override
            public boolean accept(File dir, String name) {
                return name.matches(filter);
            }
        });
        for (File f : files) {
            Utilities.copyFile(f, new CSFile(Utilities.path(page.getFolders().dstDir, prefix + f.getName())));
            page.getHTMLChecker().registerFile(prefix + f.getName(), "Support File", HTMLLinkChecker.determineType(f.getName()), true);
        }
    } else {
        Utilities.copyFile(file, new CSFile(Utilities.path(page.getFolders().dstDir, prefix + file.getName())));
        page.getHTMLChecker().registerFile(prefix + file.getName(), "Support File", HTMLLinkChecker.determineType(file.getName()), true);
    }
}

Example 10 with FINAL

use of org.hl7.fhir.r4.model.Observation.ObservationStatus.FINAL in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7DocumentReferenceFHIRConversionTest method doc_ref_doc_status_test.

@ParameterizedTest
@ValueSource(strings = { "MDM^T02", "MDM^T06" })
void doc_ref_doc_status_test(String segment) {
    String documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + "TXA|1||TEXT|||20180117144200|201801180346||<PHYSID1>||||||||PA||AV|||<PHYSID2>||\n" + "OBX|1|ST|100||This is content|||||||X\n";
    DocumentReference report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
    DocumentReference.ReferredDocumentStatus docStatus = report.getDocStatus();
    // TXA.17
    assertThat(docStatus.toCode()).isEqualTo("preliminary");
    assertThat(docStatus.getDefinition()).contains("This is a preliminary composition or document (also known as initial or interim).");
    assertThat(docStatus.getSystem()).isEqualTo("http://hl7.org/fhir/composition-status");
    // Check OBX.11 as fallback
    documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1|||555|||20170825010500|||||||||||||002|||||F||||||||\n" + "TXA|1||TEXT|||20180117144200|201801180346||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + "OBX|1|SN|||||||||F";
    report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
    docStatus = report.getDocStatus();
    // OBX.11
    assertThat(docStatus.toCode()).isEqualTo("final");
    assertThat(docStatus.getDefinition()).contains("This version of the composition is complete and verified by an appropriate person and no further work is planned.");
    assertThat(docStatus.getSystem()).isEqualTo("http://hl7.org/fhir/composition-status");
    // Check a value that is not mapped results is no docStatus
    documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS\n" + "OBR|1|||555|||20170825010500|||||||||||||002|||||F\n" + "TXA|1||TEXT|||20180117144200|201801180346||<PHYSID1>||||||||||AV|||<PHYSID2>\n" + "OBX|1|SN|||||||||X";
    report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
    // OBX-11 'X' is not mapped
    assertThat(report.getDocStatus()).isNull();
}