Examples with ZipGenerator org.hl7.fhir.utilities.ZipGenerator used on opensource projects

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Example 1 with ZipGenerator

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

the class Publisher method minify.

private void minify(String srcFile, String dstFile) throws Exception {
    CloseProtectedZipInputStream source = new CloseProtectedZipInputStream(new FileInputStream(srcFile));
    ZipGenerator dest = new ZipGenerator(dstFile);
    ZipEntry entry = null;
    while ((entry = source.getNextEntry()) != null) {
        String name = entry.getName();
        if (name.endsWith(".xsd"))
            dest.addStream(entry.getName(), stripXsd(source), false);
        else if (name.endsWith(".json") && !name.endsWith(".schema.json"))
            dest.addStream(entry.getName(), stripJson(source), false);
        else if (name.endsWith(".xml"))
            dest.addStream(entry.getName(), stripXml(source), false);
        else
            dest.addStream(entry.getName(), source, false);
    }
    source.actualClose();
    dest.close();
}
Also used : ZipEntry(java.util.zip.ZipEntry) ZipGenerator(org.hl7.fhir.utilities.ZipGenerator) CSFileInputStream(org.hl7.fhir.utilities.CSFileInputStream) FileInputStream(java.io.FileInputStream) CloseProtectedZipInputStream(org.hl7.fhir.utilities.CloseProtectedZipInputStream)

Example 2 with ZipGenerator

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

the class Publisher method produceArchive.

private void produceArchive() throws Exception {
    String target = page.getFolders().archiveDir + "v" + page.getVersion() + ".zip";
    File tf = new CSFile(target);
    if (tf.exists())
        tf.delete();
    ZipGenerator zip = new ZipGenerator(target);
    int c = 0;
    String[] files = new CSFile(page.getFolders().dstDir).list();
    for (String f : files) {
        File fn = new CSFile(page.getFolders().dstDir + f);
        if (!fn.isDirectory()) {
            if (f.endsWith(".html")) {
                String src = TextFile.fileToString(fn.getAbsolutePath());
                String srcn = src.replace("<!-- achive note -->", "This is an old version of FHIR retained for archive purposes. Do not use for anything else");
                if (!srcn.equals(src))
                    c++;
                srcn = srcn.replace("<body>", "<body><div class=\"watermark\"/>").replace("<body class=\"book\">", "<body class=\"book\"><div class=\"watermark\"/>");
                zip.addFileSource(f, srcn, false);
            // Utilities.stringToFile(srcn, target+File.separator+f);
            } else if (f.endsWith(".css")) {
                String src = TextFile.fileToString(fn.getAbsolutePath());
                src = src.replace("#fff", "lightcyan");
                zip.addFileSource(f, src, false);
            // Utilities.stringToFile(srcn, target+File.separator+f);
            } else
                zip.addFileName(f, fn.getAbsolutePath(), false);
        } else if (!fn.getAbsolutePath().endsWith("v2") && !fn.getAbsolutePath().endsWith("v3")) {
        // used to put stuff in sub-directories. clean them out if they
        // still exist
        // Utilities.clearDirectory(fn.getAbsolutePath());
        // fn.delete();
        }
    }
    if (c < 3)
        // so
        throw new Exception("header note replacement in archive failed");
    // check
    // the
    // syntax
    // of
    // the
    // string
    // constant
    // above
    zip.close();
}
Also used : CSFile(org.hl7.fhir.utilities.CSFile) IniFile(org.hl7.fhir.utilities.IniFile) File(java.io.File) CSFile(org.hl7.fhir.utilities.CSFile) TextFile(org.hl7.fhir.utilities.TextFile) ZipGenerator(org.hl7.fhir.utilities.ZipGenerator) ContactPoint(org.hl7.fhir.r5.model.ContactPoint) TransformerException(javax.xml.transform.TransformerException) IOException(java.io.IOException) FHIRException(org.hl7.fhir.exceptions.FHIRException) FileNotFoundException(java.io.FileNotFoundException) UnsupportedEncodingException(java.io.UnsupportedEncodingException)

Example 3 with ZipGenerator

use of org.hl7.fhir.utilities.ZipGenerator in project org.hl7.fhir.core by hapifhir.

the class ArgonautConverter method saveResource.

private void saveResource(Resource resource, String extraType) throws Exception {
    if (!WANT_SAVE)
        return;
    DomainResource dr = null;
    if (resource instanceof DomainResource) {
        dr = (DomainResource) resource;
        if (!dr.hasText()) {
            NarrativeGenerator generator = new NarrativeGenerator("", "", context);
            generator.generate(dr);
        }
    }
    XmlParser xparser = new XmlParser();
    xparser.setOutputStyle(OutputStyle.PRETTY);
    JsonParser jparser = new JsonParser();
    jparser.setOutputStyle(OutputStyle.PRETTY);
    ByteArrayOutputStream ba = new ByteArrayOutputStream();
    xparser.compose(ba, resource);
    ba.close();
    byte[] srcX = ba.toByteArray();
    ba = new ByteArrayOutputStream();
    jparser.compose(ba, resource);
    ba.close();
    byte[] srcJ = ba.toByteArray();
    String rn = resource.getResourceType().toString();
    if (extraType != null)
        rn = rn + extraType;
    zipX.addBytes(resource.getId() + ".xml", srcX, false);
    zipJ.addBytes(resource.getId() + ".json", srcJ, false);
    if (!zipsX.containsKey(rn)) {
        zipsX.put(rn, new ZipGenerator(Utilities.path(destFolder, "xml/type", rn + ".xml.zip")));
        zipsJ.put(rn, new ZipGenerator(Utilities.path(destFolder, "json/type", rn + ".json.zip")));
        stats.put(rn, new Stats());
    }
    zipsJ.get(rn).addBytes(resource.getId() + ".json", srcJ, false);
    zipsX.get(rn).addBytes(resource.getId() + ".xml", srcX, false);
    Stats ss = stats.get(rn);
    ss.setInstances(ss.getInstances() + 1);
    String profile = resource.getUserString("profile");
    validate(srcX, profile, resource, ss);
}
Also used : NarrativeGenerator(org.hl7.fhir.dstu3.utils.NarrativeGenerator) XmlParser(org.hl7.fhir.dstu3.formats.XmlParser) ByteArrayOutputStream(java.io.ByteArrayOutputStream) ZipGenerator(org.hl7.fhir.utilities.ZipGenerator) JsonParser(org.hl7.fhir.dstu3.formats.JsonParser)

Example 4 with ZipGenerator

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

the class Publisher method produceSpec.

private void produceSpec() throws Exception {
    for (ImplementationGuideDefn ig : page.getDefinitions().getSortedIgs()) {
        for (LogicalModel lm : ig.getLogicalModels()) {
            page.log(" ...logical model " + lm.getId(), LogMessageType.Process);
            produceLogicalModel(lm, ig);
        }
    }
    for (StructureDefinition ed : page.getWorkerContext().getExtensionDefinitions()) {
        String filename = "extension-" + (ed.getUrl().startsWith("http://fhir-registry.smarthealthit.org/StructureDefinition/") ? ed.getUrl().substring(59).toLowerCase() : ed.getUrl().substring(40).toLowerCase());
        ed.setUserData("filename", filename);
        ImplementationGuideDefn ig = page.getDefinitions().getIgs().get(ed.getUserString(ToolResourceUtilities.NAME_RES_IG));
        if (ig == null) {
            ig = page.getDefinitions().getIgs().get("core");
        }
        ed.setUserData("path", (ig.isCore() ? "" : ig.getCode() + File.separator) + filename + ".html");
    }
    page.updateDiffEngineDefinitions();
    loadValueSets2();
    page.log(" ...extensions", LogMessageType.Process);
    for (StructureDefinition ae : page.getWorkerContext().getExtensionDefinitions()) produceExtensionDefinition(ae);
    checkAllOk();
    page.log(" ...resource identities", LogMessageType.Process);
    for (String rname : page.getDefinitions().getBaseResources().keySet()) {
        ResourceDefn r = page.getDefinitions().getBaseResources().get(rname);
        produceResource1(r, r.isAbstract());
    }
    for (String rname : page.getDefinitions().sortedResourceNames()) {
        if (!rname.equals("ValueSet") && !rname.equals("CodeSystem") && wantBuild(rname)) {
            ResourceDefn r = page.getDefinitions().getResources().get(rname);
            produceResource1(r, false);
        }
    }
    if (buildFlags.get("all")) {
        page.log(" ...base profiles", LogMessageType.Process);
        produceBaseProfile();
    }
    for (String rname : page.getDefinitions().getBaseResources().keySet()) {
        ResourceDefn r = page.getDefinitions().getBaseResources().get(rname);
        page.log(" ...resource " + r.getName(), LogMessageType.Process);
        produceResource2(r, !rname.equals("Parameters"), rname.equals("Resource") ? "Meta" : null, false);
    }
    for (String rname : page.getDefinitions().sortedResourceNames()) {
        if (!rname.equals("ValueSet") && !rname.equals("CodeSystem") && wantBuild(rname)) {
            ResourceDefn r = page.getDefinitions().getResources().get(rname);
            page.log(" ...resource " + r.getName(), LogMessageType.Process);
            produceResource2(r, false, null, false);
        }
    }
    for (Compartment c : page.getDefinitions().getCompartments()) {
        if (buildFlags.get("all")) {
            page.log(" ...compartment " + c.getName(), LogMessageType.Process);
            produceCompartment(c);
        }
    }
    Regenerator regen = new Regenerator(page.getFolders().srcDir, page.getDefinitions(), page.getWorkerContext());
    regen.generate();
    Bundle searchParamsFeed = new Bundle();
    searchParamsFeed.setId("searchParams");
    searchParamsFeed.setType(BundleType.COLLECTION);
    searchParamsFeed.setMeta(new Meta().setLastUpdated(page.getResourceBundle().getMeta().getLastUpdated()));
    Set<String> uris = new HashSet<String>();
    for (ResourceDefn rd : page.getDefinitions().getBaseResources().values()) addSearchParams(uris, searchParamsFeed, rd);
    for (String n : page.getDefinitions().sortedResourceNames()) {
        ResourceDefn rd = page.getDefinitions().getResources().get(n);
        addSearchParams(uris, searchParamsFeed, rd);
    }
    for (Profile cp : page.getDefinitions().getPackList()) {
        addSearchParams(uris, searchParamsFeed, cp);
    }
    checkBundleURLs(searchParamsFeed);
    for (String n : page.getIni().getPropertyNames("pages")) {
        if (buildFlags.get("all") || buildFlags.get("page-" + n.toLowerCase())) {
            page.log(" ...page " + n, LogMessageType.Process);
            producePage(n, page.getIni().getStringProperty("pages", n));
        }
    }
    for (ImplementationGuideDefn ig : page.getDefinitions().getSortedIgs()) {
        for (String n : ig.getPageList()) {
            page.log(" ...ig page " + n, LogMessageType.Process);
            produceIgPage(n, ig);
        }
        for (ImplementationGuideDefinitionPageComponent page : ig.getSpecialPages()) {
            produceIgPage(ig, page);
        }
        for (Profile p : ig.getProfiles()) {
            if (!p.getOperations().isEmpty()) {
                produceIgOperations(ig, p);
            }
        }
    }
    if (page.getIni().getPropertyNames("ig-pages") != null) {
        for (String n : page.getIni().getPropertyNames("ig-pages")) {
            page.log(" ...page " + n, LogMessageType.Process);
            for (ImplementationGuideDefn ig : page.getDefinitions().getSortedIgs()) {
                if (!ig.isCore())
                    produceIgPage(n, ig, page.getIni().getStringProperty("ig-pages", n));
            }
        }
    }
    for (String n : page.getDefinitions().getDictionaries().keySet()) {
        if (buildFlags.get("all")) {
            // || buildFlags.get("dict-" + n.toLowerCase())) {
            page.log(" ...dictionary " + n, LogMessageType.Process);
            produceDictionary(page.getDefinitions().getDictionaries().get(n));
        }
    }
    int i = 0;
    for (String n : page.getIni().getPropertyNames("sid")) {
        page.log(" ...sid " + n, LogMessageType.Process);
        produceSid(i, n, page.getIni().getStringProperty("sid", n));
        i++;
    }
    if (buildFlags.get("all")) {
        page.log(" ...check Fragments", LogMessageType.Process);
        checkFragments();
        for (Profile p : page.getDefinitions().getPackList()) {
            // if (!n.startsWith("http://")) {
            page.log(" ...Profile " + p.getId(), LogMessageType.Process);
            produceConformancePackage(null, p, null);
        // }
        }
        produceUml();
        page.getVsValidator().checkDuplicates(page.getValidationErrors());
        if (buildFlags.get("all")) {
            // if (page.getToc().containsKey("1.1"))
            // throw new Exception("Duplicate DOC Entry "+"1.1");
            page.getToc().put("1.1", new TocEntry("1.1", "Table Of Contents", "toc.html", false));
            page.log(" ...page toc.html", LogMessageType.Process);
            producePage("toc.html", null);
        }
        checkAllOk();
        page.log(" ...collections ", LogMessageType.Process);
        com.google.gson.JsonObject diff = new com.google.gson.JsonObject();
        page.getDiffEngine().getDiffAsJson(diff);
        Gson gson = new GsonBuilder().setPrettyPrinting().create();
        String json = gson.toJson(diff);
        TextFile.stringToFile(json, Utilities.path(page.getFolders().dstDir, "fhir.diff.json"));
        DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
        DocumentBuilder builder = dbf.newDocumentBuilder();
        Document doc = builder.newDocument();
        Element element = doc.createElement("difference");
        doc.appendChild(element);
        page.getDiffEngine().getDiffAsXml(doc, element);
        prettyPrint(doc, Utilities.path(page.getFolders().dstDir, "fhir.diff.xml"));
        checkBundleURLs(page.getResourceBundle());
        checkStructureDefinitions(page.getResourceBundle());
        page.getResourceBundle().getEntry().sort(new ProfileBundleSorter());
        FileOutputStream s = new FileOutputStream(page.getFolders().dstDir + "profiles-resources.xml");
        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, page.getResourceBundle());
        s.close();
        s = new FileOutputStream(page.getFolders().dstDir + "profiles-resources.json");
        new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, page.getResourceBundle());
        s.close();
        checkBundleURLs(page.getTypeBundle());
        checkStructureDefinitions(page.getTypeBundle());
        page.getTypeBundle().getEntry().sort(new ProfileBundleSorter());
        s = new FileOutputStream(page.getFolders().dstDir + "profiles-types.xml");
        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, page.getTypeBundle());
        s.close();
        s = new FileOutputStream(page.getFolders().dstDir + "profiles-types.json");
        new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, page.getTypeBundle());
        s.close();
        Bundle extensionsFeed = new Bundle();
        extensionsFeed.setId("extensions");
        extensionsFeed.setType(BundleType.COLLECTION);
        extensionsFeed.setMeta(new Meta().setLastUpdated(page.getResourceBundle().getMeta().getLastUpdated()));
        Set<String> urls = new HashSet<String>();
        for (StructureDefinition ed : page.getWorkerContext().getExtensionDefinitions()) {
            if (!urls.contains(ed.getUrl())) {
                urls.add(ed.getUrl());
                extensionsFeed.getEntry().add(new BundleEntryComponent().setResource(ed).setFullUrl("http://hl7.org/fhir/" + ed.fhirType() + "/" + ed.getId()));
            }
        }
        checkBundleURLs(extensionsFeed);
        checkStructureDefinitions(extensionsFeed);
        s = new FileOutputStream(page.getFolders().dstDir + "extension-definitions.xml");
        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, extensionsFeed);
        s.close();
        s = new FileOutputStream(page.getFolders().dstDir + "extension-definitions.json");
        new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, extensionsFeed);
        s.close();
        Utilities.copyFile(page.getFolders().dstDir + "extension-definitions.xml", page.getFolders().dstDir + "examples" + File.separator + "extension-definitions.xml");
        s = new FileOutputStream(page.getFolders().dstDir + "search-parameters.xml");
        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, searchParamsFeed);
        s.close();
        s = new FileOutputStream(page.getFolders().dstDir + "search-parameters.json");
        new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, searchParamsFeed);
        s.close();
        Utilities.copyFile(page.getFolders().dstDir + "search-parameters.xml", page.getFolders().dstDir + "examples" + File.separator + "search-parameters.xml");
        for (ResourceDefn rd : page.getDefinitions().getResources().values()) addOtherProfiles(profileBundle, rd);
        for (Profile cp : page.getDefinitions().getPackList()) {
            addOtherProfiles(profileBundle, cp);
        }
        checkBundleURLs(profileBundle);
        checkStructureDefinitions(profileBundle);
        s = new FileOutputStream(page.getFolders().dstDir + "profiles-others.xml");
        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, profileBundle);
        s.close();
        s = new FileOutputStream(page.getFolders().dstDir + "profiles-others.json");
        new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, profileBundle);
        s.close();
        Utilities.copyFile(page.getFolders().dstDir + "profiles-others.xml", page.getFolders().dstDir + "examples" + File.separator + "profiles-others.xml");
        // todo-bundle - should this be checked?
        // int ec = 0;
        // for (Resource e : valueSetsFeed.getItem()) {
        // ValueSet vs = (ValueSet) e;
        // if (!vs.getUrl().equals(e.getId())) {
        // ec++;
        // page.log("Valueset id mismatch: atom entry has '"+e.getId()+"', but value set is '"+vs.getUrl()+"'", LogMessageType.Error);
        // }
        // }
        // if (ec > 0)
        // throw new Exception("Cannot continue due to value set mis-identification");
        checkBundleURLs(dataElements);
        s = new FileOutputStream(page.getFolders().dstDir + "dataelements.xml");
        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, dataElements);
        s.close();
        Utilities.copyFile(page.getFolders().dstDir + "dataelements.xml", page.getFolders().dstDir + "examples" + File.separator + "dataelements.xml");
        s = new FileOutputStream(page.getFolders().dstDir + "dataelements.json");
        new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, dataElements);
        s.close();
        checkBundleURLs(valueSetsFeed);
        s = new FileOutputStream(page.getFolders().dstDir + "valuesets.xml");
        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, valueSetsFeed);
        s.close();
        Utilities.copyFile(page.getFolders().dstDir + "valuesets.xml", page.getFolders().dstDir + "examples" + File.separator + "valuesets.xml");
        s = new FileOutputStream(page.getFolders().dstDir + "valuesets.json");
        new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, valueSetsFeed);
        s.close();
        checkBundleURLs(conceptMapsFeed);
        s = new FileOutputStream(page.getFolders().dstDir + "conceptmaps.xml");
        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, conceptMapsFeed);
        s.close();
        Utilities.copyFile(page.getFolders().dstDir + "conceptmaps.xml", page.getFolders().dstDir + "examples" + File.separator + "conceptmaps.xml");
        s = new FileOutputStream(page.getFolders().dstDir + "conceptmaps.json");
        new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, conceptMapsFeed);
        s.close();
        checkBundleURLs(externals);
        s = new FileOutputStream(page.getFolders().dstDir + "external-resources.xml");
        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, externals);
        s.close();
        Utilities.copyFile(page.getFolders().dstDir + "external-resources.xml", page.getFolders().dstDir + "examples" + File.separator + "external-resources.xml");
        s = new FileOutputStream(page.getFolders().dstDir + "external-resources.json");
        new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, externals);
        s.close();
        ImplementationGuide expIg = new ImplementationGuide();
        expIg.addFhirVersion(page.getVersion());
        expIg.setPackageId(pidRoot() + ".expansions");
        expIg.setVersion(page.getVersion().toCode());
        expIg.setLicense(ImplementationGuide.SPDXLicense.CC01_0);
        expIg.setTitle("FHIR " + page.getVersion().getDisplay() + " package : Expansions");
        expIg.setDescription("Expansions for the " + page.getVersion().getDisplay() + " version of the FHIR standard");
        NPMPackageGenerator npm = new NPMPackageGenerator(Utilities.path(page.getFolders().dstDir, pidRoot() + ".expansions.tgz"), "http://hl7.org/fhir", "http://hl7.org/fhir", PackageType.CORE, expIg, page.getGenDate().getTime(), true);
        Bundle expansionFeed = new Bundle();
        Set<String> urlset = new HashSet<>();
        expansionFeed.setId("valueset-expansions");
        expansionFeed.setType(BundleType.COLLECTION);
        expansionFeed.setMeta(new Meta().setLastUpdated(page.getGenDate().getTime()));
        expansionFeed.getFormatCommentsPre().add("This collection contains expansions for all the value sets that are used on an element of type \r\n" + "'code', to help with code generation (saves the code generator having to figure out how to \r\n" + "do the expansions or find a terminology server that supports the same version of the value sets");
        for (ValueSet vs : page.getValueSets().getList()) {
            if (!urlset.contains(vs.getUrl())) {
                urlset.add(vs.getUrl());
                if (vs.getUserData(ToolResourceUtilities.NAME_VS_USE_MARKER) != null) {
                    ValueSet evs = null;
                    if (vs.hasUserData("expansion"))
                        evs = (ValueSet) vs.getUserData("expansion");
                    else {
                        ValueSetExpansionOutcome vse = page.getWorkerContext().expandVS(vs, true, false);
                        if (vse.getValueset() != null) {
                            evs = vse.getValueset();
                            vs.setUserData("expansion", evs);
                        }
                    }
                    if (evs != null) {
                        ValueSet vsc = vs.copy();
                        vsc.setText(null);
                        vsc.setExpansion(evs.getExpansion());
                        expansionFeed.addEntry().setFullUrl("http://hl7.org/fhir/" + vsc.fhirType() + "/" + vsc.getId()).setResource(vsc);
                        npm.addFile(Category.RESOURCE, "ValueSet-" + vsc.getId() + ".json", new JsonParser().composeBytes(vsc));
                    }
                }
            }
        }
        npm.finish();
        if (!isCIBuild) {
            String id = pidRoot() + ".expansions";
            new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).addPackageToCache(id, "current", new FileInputStream(Utilities.path(page.getFolders().dstDir, id + ".tgz")), Utilities.path(page.getFolders().dstDir, id + ".tgz"));
        }
        s = new FileOutputStream(page.getFolders().dstDir + "expansions.xml");
        new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(s, expansionFeed);
        s.close();
        s = new FileOutputStream(page.getFolders().dstDir + "expansions.json");
        new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(s, expansionFeed);
        s.close();
        produceComparisons();
        produceSpecMap();
        processRDF();
        page.log("....version maps", LogMessageType.Process);
        ZipGenerator zip = new ZipGenerator(page.getFolders().dstDir + "r3r4maps.zip");
        zip.addFiles(Utilities.path(page.getFolders().rootDir, "implementations", "r3maps", "R3toR4", ""), "r3/", null, null);
        zip.addFiles(Utilities.path(page.getFolders().rootDir, "implementations", "r3maps", "R4toR3", ""), "r4/", null, null);
        zip.close();
        page.log("....definitions", LogMessageType.Process);
        zip = new ZipGenerator(page.getFolders().dstDir + "definitions.xml.zip");
        zip.addFileName("version.info", page.getFolders().dstDir + "version.info", false);
        zip.addFileName("profiles-types.xml", page.getFolders().dstDir + "profiles-types.xml", false);
        zip.addFileName("profiles-resources.xml", page.getFolders().dstDir + "profiles-resources.xml", false);
        zip.addFileName("profiles-others.xml", page.getFolders().dstDir + "profiles-others.xml", false);
        zip.addFileName("extension-definitions.xml", page.getFolders().dstDir + "extension-definitions.xml", false);
        zip.addFileName("search-parameters.xml", page.getFolders().dstDir + "search-parameters.xml", false);
        zip.addFileName("valuesets.xml", page.getFolders().dstDir + "valuesets.xml", false);
        zip.addFileName("conceptmaps.xml", page.getFolders().dstDir + "conceptmaps.xml", false);
        zip.addFileName("dataelements.xml", page.getFolders().dstDir + "dataelements.xml", false);
        zip.addFileName("fhir-all-xsd.zip", page.getFolders().dstDir + "fhir-all-xsd.zip", false);
        zip.close();
        zip = new ZipGenerator(page.getFolders().dstDir + "definitions.json.zip");
        zip.addFileName("version.info", page.getFolders().dstDir + "version.info", false);
        zip.addFileName("profiles-types.json", page.getFolders().dstDir + "profiles-types.json", false);
        zip.addFileName("profiles-resources.json", page.getFolders().dstDir + "profiles-resources.json", false);
        zip.addFileName("profiles-others.json", page.getFolders().dstDir + "profiles-others.json", false);
        zip.addFileName("extension-definitions.json", page.getFolders().dstDir + "extension-definitions.json", false);
        zip.addFileName("search-parameters.json", page.getFolders().dstDir + "search-parameters.json", false);
        zip.addFileName("valuesets.json", page.getFolders().dstDir + "valuesets.json", false);
        zip.addFileName("conceptmaps.json", page.getFolders().dstDir + "conceptmaps.json", false);
        zip.addFileName("dataelements.json", page.getFolders().dstDir + "dataelements.json", false);
        zip.addFileName("fhir.schema.json.zip", page.getFolders().dstDir + "fhir.schema.json.zip", false);
        zip.close();
        zip = new ZipGenerator(page.getFolders().dstDir + "definitions.xlsx.zip");
        for (String rn : page.getDefinitions().sortedResourceNames()) {
            zip.addFileName(rn.toLowerCase() + ".xlsx", page.getFolders().dstDir + rn.toLowerCase() + ".xlsx", false);
        }
        zip.close();
        // this is the actual package used by the validator.
        zip = new ZipGenerator(page.getFolders().dstDir + "validator.pack");
        // conformance resources
        zip.addFileName("profiles-types.json", page.getFolders().dstDir + "profiles-types.json", false);
        zip.addFileName("profiles-resources.json", page.getFolders().dstDir + "profiles-resources.json", false);
        zip.addFileName("profiles-others.json", page.getFolders().dstDir + "profiles-others.json", false);
        zip.addFileName("extension-definitions.json", page.getFolders().dstDir + "extension-definitions.json", false);
        zip.addFileName("valuesets.json", page.getFolders().dstDir + "valuesets.json", false);
        zip.addFileName("conceptmaps.json", page.getFolders().dstDir + "conceptmaps.json", false);
        // native schema
        zip.addFileName("fhir-all-xsd.zip", page.getFolders().dstDir + "fhir-all-xsd.zip", false);
        zip.addFileName("fhir.schema.json.zip", page.getFolders().dstDir + "fhir.schema.json.zip", false);
        zip.addFileName("fhir.shex", page.getFolders().dstDir + "fhir.shex", false);
        zip.close();
        page.log("....dstu3 format (xml)", LogMessageType.Process);
        DSTU3ValidationConvertor dstu3 = new DSTU3ValidationConvertor();
        dstu3.convert(page.getFolders().dstDir + "profiles-types.xml", page.getFolders().tmpDir + "profiles-types-r3.xml");
        dstu3.convert(page.getFolders().dstDir + "profiles-resources.xml", page.getFolders().tmpDir + "profiles-resources-r3.xml");
        dstu3.convert(page.getFolders().dstDir + "profiles-others.xml", page.getFolders().tmpDir + "profiles-others-r3.xml");
        dstu3.convert(page.getFolders().dstDir + "extension-definitions.xml", page.getFolders().tmpDir + "extension-definitions-r3.xml");
        dstu3.convert(page.getFolders().dstDir + "search-parameters.xml", page.getFolders().tmpDir + "search-parameters-r3.xml");
        dstu3.convert(page.getFolders().dstDir + "valuesets.xml", page.getFolders().tmpDir + "valuesets-r3.xml");
        dstu3.convert(page.getFolders().dstDir + "conceptmaps.xml", page.getFolders().tmpDir + "conceptmaps-r3.xml");
        dstu3.convert(page.getFolders().dstDir + "dataelements.xml", page.getFolders().tmpDir + "dataelements-r3.xml");
        zip = new ZipGenerator(page.getFolders().dstDir + "definitions-r3.xml.zip");
        zip.addFileName("profiles-types.xml", page.getFolders().tmpDir + "profiles-types-r3.xml", false);
        zip.addFileName("profiles-resources.xml", page.getFolders().tmpDir + "profiles-resources-r3.xml", false);
        zip.addFileName("profiles-others.xml", page.getFolders().tmpDir + "profiles-others-r3.xml", false);
        zip.addFileName("extension-definitions.xml", page.getFolders().tmpDir + "extension-definitions-r3.xml", false);
        zip.addFileName("search-parameters.xml", page.getFolders().tmpDir + "search-parameters-r3.xml", false);
        zip.addFileName("valuesets.xml", page.getFolders().tmpDir + "valuesets-r3.xml", false);
        zip.addFileName("conceptmaps.xml", page.getFolders().tmpDir + "conceptmaps-r3.xml", false);
        zip.addFileName("dataelements.xml", page.getFolders().tmpDir + "dataelements-r3.xml", false);
        zip.close();
        page.log("....dstu3 format (json)", LogMessageType.Process);
        dstu3.convertJ(page.getFolders().dstDir + "profiles-types.xml", page.getFolders().tmpDir + "profiles-types-r3.json");
        dstu3.convertJ(page.getFolders().dstDir + "profiles-resources.xml", page.getFolders().tmpDir + "profiles-resources-r3.json");
        dstu3.convertJ(page.getFolders().dstDir + "profiles-others.xml", page.getFolders().tmpDir + "profiles-others-r3.json");
        dstu3.convertJ(page.getFolders().dstDir + "extension-definitions.xml", page.getFolders().tmpDir + "extension-definitions-r3.json");
        dstu3.convertJ(page.getFolders().dstDir + "search-parameters.xml", page.getFolders().tmpDir + "search-parameters-r3.json");
        dstu3.convertJ(page.getFolders().dstDir + "valuesets.xml", page.getFolders().tmpDir + "valuesets-r3.json");
        dstu3.convertJ(page.getFolders().dstDir + "conceptmaps.xml", page.getFolders().tmpDir + "conceptmaps-r3.json");
        dstu3.convertJ(page.getFolders().dstDir + "dataelements.xml", page.getFolders().tmpDir + "dataelements-r3.json");
        zip = new ZipGenerator(page.getFolders().dstDir + "definitions-r3.json.zip");
        zip.addFileName("profiles-types.json", page.getFolders().tmpDir + "profiles-types-r3.json", false);
        zip.addFileName("profiles-resources.json", page.getFolders().tmpDir + "profiles-resources-r3.json", false);
        zip.addFileName("profiles-others.json", page.getFolders().tmpDir + "profiles-others-r3.json", false);
        zip.addFileName("extension-definitions.json", page.getFolders().tmpDir + "extension-definitions-r3.json", false);
        zip.addFileName("search-parameters.json", page.getFolders().tmpDir + "search-parameters-r3.json", false);
        zip.addFileName("valuesets.json", page.getFolders().tmpDir + "valuesets-r3.json", false);
        zip.addFileName("conceptmaps.json", page.getFolders().tmpDir + "conceptmaps-r3.json", false);
        zip.addFileName("dataelements.json", page.getFolders().tmpDir + "dataelements-r3.json", false);
        zip.close();
        System.gc();
        page.log("....r4 in r5 format", LogMessageType.Process);
        zip = new ZipGenerator(page.getFolders().dstDir + "definitions-r2asr3.xml.zip");
        page.getDiffEngine().saveR4AsR5(zip, FhirFormat.XML);
        zip.close();
        zip = new ZipGenerator(page.getFolders().dstDir + "definitions-r2asr3.json.zip");
        page.getDiffEngine().saveR4AsR5(zip, FhirFormat.JSON);
        zip.close();
        zip = new ZipGenerator(page.getFolders().dstDir + "all-valuesets.zip");
        zip.addFileName("valuesets.xml", page.getFolders().dstDir + "valuesets.xml", false);
        zip.addFileName("valuesets.json", page.getFolders().dstDir + "valuesets.json", false);
        zip.addFileName("conceptmaps.xml", page.getFolders().dstDir + "conceptmaps.xml", false);
        zip.addFileName("conceptmaps.json", page.getFolders().dstDir + "conceptmaps.json", false);
        zip.close();
        page.log("....IG Builder Resources", LogMessageType.Process);
        zip = new ZipGenerator(page.getFolders().tmpDir + "ig-template.zip");
        zip.addFolder(Utilities.path(page.getFolders().rootDir, "tools", "ig"), "", false, null);
        zip.close();
        zip = new ZipGenerator(page.getFolders().dstDir + "igpack.zip");
        zip.addFileName("fhir.css", page.getFolders().dstDir + "fhir.css", false);
        zip.addFileName("spec.internals", page.getFolders().dstDir + "spec.internals", false);
        zip.addFileName("profiles-types.xml", page.getFolders().dstDir + "profiles-types.xml", false);
        zip.addFileName("profiles-resources.xml", page.getFolders().dstDir + "profiles-resources.xml", false);
        zip.addFileName("profiles-others.xml", page.getFolders().dstDir + "profiles-others.xml", false);
        zip.addFileName("extension-definitions.xml", page.getFolders().dstDir + "extension-definitions.xml", false);
        zip.addFileName("search-parameters.xml", page.getFolders().dstDir + "search-parameters.xml", false);
        zip.addFileName("valuesets.xml", page.getFolders().dstDir + "valuesets.xml", false);
        zip.addFileName("conceptmaps.xml", page.getFolders().dstDir + "conceptmaps.xml", false);
        zip.addFileName("dataelements.xml", page.getFolders().dstDir + "dataelements.xml", false);
        zip.addFileName("version.info", page.getFolders().dstDir + "version.info", false);
        zip.addFileName("mappingSpaces.details", page.getFolders().srcDir + "mappingSpaces.xml", false);
        zip.addFileName("redirect.asp.template", page.getFolders().srcDir + "redirect.asp", false);
        zip.addFileName("redirect.cgi.template", page.getFolders().srcDir + "redirect.cgi", false);
        zip.addFileName("redirect.php.template", page.getFolders().srcDir + "redirect.php", false);
        zip.addFileName("ig-template.zip", Utilities.path(page.getFolders().tmpDir, "ig-template.zip"), false);
        zip.addFiles(Utilities.path(page.getFolders().rootDir, "publish", ""), "", ".png", null);
        zip.addFiles(Utilities.path(page.getFolders().rootDir, "publish", ""), "", ".gif", null);
        zip.close();
        page.log("....IG Builder (2)", LogMessageType.Process);
        SpecNPMPackageGenerator self = new SpecNPMPackageGenerator();
        self.generate(page.getFolders().dstDir, page.getBaseURL(), false, page.getGenDate().getTime(), pidRoot());
        if (!isCIBuild) {
            new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION).addPackageToCache(pidRoot() + ".core", "current", new FileInputStream(Utilities.path(page.getFolders().dstDir, pidRoot() + ".core.tgz")), Utilities.path(page.getFolders().dstDir, pidRoot() + ".core.tgz"));
        }
        page.log(" ...zips", LogMessageType.Process);
        zip = new ZipGenerator(page.getFolders().dstDir + "examples.zip");
        zip.addFiles(page.getFolders().dstDir + "examples" + File.separator, "", null, "expansions.xml");
        zip.close();
        zip = new ZipGenerator(page.getFolders().dstDir + "examples-json.zip");
        gson = new GsonBuilder().setPrettyPrinting().create();
        File f = new CSFile(page.getFolders().dstDir);
        File[] files = f.listFiles();
        String[] noExt = new String[] { ".schema.json", ".canonical.json", ".diff.json", "expansions.json", "package.json", "choice-elements.json", "backbone-elements.json" };
        for (int fi = 0; fi < files.length; fi++) {
            if (files[fi].isFile() && (files[fi].getName().endsWith(".json"))) {
                boolean ok = true;
                for (String n : noExt) {
                    ok = ok && !files[fi].getName().endsWith(n);
                }
                if (ok) {
                    JsonObject jr = JSONUtil.parse(TextFile.fileToString(files[fi]));
                    if (!jr.has("url")) {
                        JsonObject meta = JSONUtil.forceObject(jr, "meta");
                        JsonArray labels = JSONUtil.forceArray(meta, "tag");
                        JsonObject label = JSONUtil.addObj(labels);
                        label.addProperty("system", "http://terminology.hl7.org/CodeSystem/v3-ActReason");
                        label.addProperty("code", "HTEST");
                        label.addProperty("display", "test health data");
                    }
                    String jrs = gson.toJson(jr);
                    zip.addBytes(files[fi].getName(), jrs.getBytes(Charsets.UTF_8), true);
                }
            }
        }
        zip.close();
        NDJsonWriter ndjson = new NDJsonWriter(page.getFolders().dstDir + "examples-ndjson.zip", page.getFolders().tmpDir);
        ndjson.addFilesFiltered(page.getFolders().dstDir, ".json", new String[] { ".schema.json", ".canonical.json", ".diff.json", "expansions.json", "package.json" });
        ndjson.close();
        zip = new ZipGenerator(page.getFolders().dstDir + "examples-ttl.zip");
        zip.addFilesFiltered(page.getFolders().dstDir, "", ".ttl", new String[0]);
        zip.close();
        page.log("Check HTML Links", LogMessageType.Process);
        page.getHTMLChecker().produce();
        checkAllOk();
    } else
        page.log("Partial Build - terminating now", LogMessageType.Error);
}
Also used : Meta(org.hl7.fhir.r5.model.Meta) JsonObject(com.google.gson.JsonObject) DocumentBuilderFactory(javax.xml.parsers.DocumentBuilderFactory) ImplementationGuide(org.hl7.fhir.r5.model.ImplementationGuide) NDJsonWriter(org.hl7.fhir.utilities.NDJsonWriter) Compartment(org.hl7.fhir.definitions.model.Compartment) Element(org.w3c.dom.Element) JsonObject(com.google.gson.JsonObject) Gson(com.google.gson.Gson) CSFile(org.hl7.fhir.utilities.CSFile) Document(org.w3c.dom.Document) XhtmlDocument(org.hl7.fhir.utilities.xhtml.XhtmlDocument) ResourceDefn(org.hl7.fhir.definitions.model.ResourceDefn) Profile(org.hl7.fhir.definitions.model.Profile) DSTU3ValidationConvertor(org.hl7.fhir.tools.converters.DSTU3ValidationConvertor) LogicalModel(org.hl7.fhir.definitions.model.LogicalModel) StructureDefinition(org.hl7.fhir.r5.model.StructureDefinition) ValueSet(org.hl7.fhir.r5.model.ValueSet) HashSet(java.util.HashSet) JsonParser(org.hl7.fhir.r5.formats.JsonParser) XmlParser(org.hl7.fhir.r5.formats.XmlParser) FilesystemPackageCacheManager(org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager) GsonBuilder(com.google.gson.GsonBuilder) SpecNPMPackageGenerator(org.hl7.fhir.tools.converters.SpecNPMPackageGenerator) Bundle(org.hl7.fhir.r5.model.Bundle) NPMPackageGenerator(org.hl7.fhir.r5.utils.NPMPackageGenerator) SpecNPMPackageGenerator(org.hl7.fhir.tools.converters.SpecNPMPackageGenerator) ImplementationGuideDefn(org.hl7.fhir.definitions.model.ImplementationGuideDefn) ContactPoint(org.hl7.fhir.r5.model.ContactPoint) CSFileInputStream(org.hl7.fhir.utilities.CSFileInputStream) FileInputStream(java.io.FileInputStream) JsonArray(com.google.gson.JsonArray) BundleEntryComponent(org.hl7.fhir.r5.model.Bundle.BundleEntryComponent) Regenerator(org.hl7.fhir.definitions.parsers.Regenerator) DocumentBuilder(javax.xml.parsers.DocumentBuilder) FileOutputStream(java.io.FileOutputStream) ValueSetExpansionOutcome(org.hl7.fhir.r5.terminologies.ValueSetExpander.ValueSetExpansionOutcome) ImplementationGuideDefinitionPageComponent(org.hl7.fhir.r5.model.ImplementationGuide.ImplementationGuideDefinitionPageComponent) ZipGenerator(org.hl7.fhir.utilities.ZipGenerator) IniFile(org.hl7.fhir.utilities.IniFile) File(java.io.File) CSFile(org.hl7.fhir.utilities.CSFile) TextFile(org.hl7.fhir.utilities.TextFile)

Example 5 with ZipGenerator

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

the class Publisher method processRDF.

private void processRDF() throws Exception, FileNotFoundException {
    // first, process the RIM file
    String rim = TextFile.fileToString(Utilities.path(page.getFolders().rootDir, "tools", "tx", "v3", "rim.ttl"));
    ByteArrayOutputStream tmp = new ByteArrayOutputStream();
    FhirTurtleGenerator ttl = new FhirTurtleGenerator(tmp, page.getDefinitions(), page.getWorkerContext(), page.getValidationErrors());
    ttl.executeV3(page.getValueSets(), page.getCodeSystems());
    rim = rim + tmp.toString();
    TextFile.stringToFile(rim, Utilities.path(page.getFolders().dstDir, "rim.ttl"));
    ttl = new FhirTurtleGenerator(new FileOutputStream(Utilities.path(page.getFolders().dstDir, "fhir.ttl")), page.getDefinitions(), page.getWorkerContext(), page.getValidationErrors());
    ttl.executeMain();
    W5TurtleGenerator w5 = new W5TurtleGenerator(new FileOutputStream(Utilities.path(page.getFolders().dstDir, "w5.ttl")), page.getDefinitions(), page.getWorkerContext(), page.getValidationErrors());
    w5.executeMain();
    RDFValidator val = new RDFValidator();
    val.validate(Utilities.path(page.getFolders().dstDir, "fhir.ttl"));
    val.validate(Utilities.path(page.getFolders().dstDir, "rim.ttl"));
    val.validate(Utilities.path(page.getFolders().dstDir, "w5.ttl"));
    ZipGenerator zip = new ZipGenerator(Utilities.path(page.getFolders().dstDir, "fhir.rdf.ttl.zip"));
    zip.addFileName("fhir.ttl", Utilities.path(page.getFolders().dstDir, "fhir.ttl"), false);
    zip.addFileName("rim.ttl", Utilities.path(page.getFolders().dstDir, "rim.ttl"), false);
    zip.addFileName("w5.ttl", Utilities.path(page.getFolders().dstDir, "w5.ttl"), false);
    zip.close();
    // now that the RDF is generated, run any sparql rules that have been defined
    Element test = loadDom(new FileInputStream(Utilities.path(page.getFolders().srcDir, "sparql-rules.xml")), false).getDocumentElement();
    test = XMLUtil.getFirstChild(test);
    while (test != null) {
        if (test.getNodeName().equals("assertion")) {
            String sparql = test.getTextContent();
            page.getValidationErrors().addAll(val.assertion(sparql, test.getAttribute("id"), test.getAttribute("rowtype"), test.getAttribute("message"), test.getAttribute("description"), IssueSeverity.fromCode(test.getAttribute("level"))));
        }
        test = XMLUtil.getNextSibling(test);
    }
    checkAllOk();
}
Also used : FileOutputStream(java.io.FileOutputStream) Element(org.w3c.dom.Element) RDFValidator(org.hl7.fhir.rdf.RDFValidator) ByteArrayOutputStream(java.io.ByteArrayOutputStream) W5TurtleGenerator(org.hl7.fhir.definitions.generators.specification.W5TurtleGenerator) FhirTurtleGenerator(org.hl7.fhir.definitions.generators.specification.FhirTurtleGenerator) ZipGenerator(org.hl7.fhir.utilities.ZipGenerator) CSFileInputStream(org.hl7.fhir.utilities.CSFileInputStream) FileInputStream(java.io.FileInputStream)

Aggregations

ZipGenerator (org.hl7.fhir.utilities.ZipGenerator)7 File (java.io.File)4 FileInputStream (java.io.FileInputStream)4 ByteArrayOutputStream (java.io.ByteArrayOutputStream)3 CSFile (org.hl7.fhir.utilities.CSFile)3 CSFileInputStream (org.hl7.fhir.utilities.CSFileInputStream)3 IniFile (org.hl7.fhir.utilities.IniFile)3 TextFile (org.hl7.fhir.utilities.TextFile)3 Element (org.w3c.dom.Element)3 FileOutputStream (java.io.FileOutputStream)2 IOException (java.io.IOException)2 JsonParser (org.hl7.fhir.r5.formats.JsonParser)2 XmlParser (org.hl7.fhir.r5.formats.XmlParser)2 ContactPoint (org.hl7.fhir.r5.model.ContactPoint)2 Gson (com.google.gson.Gson)1 GsonBuilder (com.google.gson.GsonBuilder)1 JsonArray (com.google.gson.JsonArray)1 JsonObject (com.google.gson.JsonObject)1 FileNotFoundException (java.io.FileNotFoundException)1 UnsupportedEncodingException (java.io.UnsupportedEncodingException)1
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