Examples with Package org.hl7.fhir.utilities.graphql.Package used on opensource projects

Example 31 with Package

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

the class FilesystemPackageCacheManager method loadPackageFromFile.

private NpmPackage loadPackageFromFile(String id, String folder) throws IOException {
    File f = new File(Utilities.path(folder, id));
    if (!f.exists()) {
        throw new FHIRException("Package '" + id + "  not found in folder " + folder);
    }
    if (!f.isDirectory()) {
        throw new FHIRException("File for '" + id + "  found in folder " + folder + ", not a folder");
    }
    File fp = new File(Utilities.path(folder, id, "package", "package.json"));
    if (!fp.exists()) {
        throw new FHIRException("Package '" + id + "  found in folder " + folder + ", but does not contain a package.json file in /package");
    }
    return NpmPackage.fromFolder(f.getAbsolutePath());
}

Example 32 with Package

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

the class FilesystemPackageCacheManager method addPackageToCache.

/**
 * Add an already fetched package to the cache
 */
@Override
public NpmPackage addPackageToCache(String id, String version, InputStream packageTgzInputStream, String sourceDesc) throws IOException {
    checkValidVersionString(version, id);
    if (progress) {
        log("Installing " + id + "#" + (version == null ? "?" : version) + " to the package cache");
        log("  Fetching:");
    }
    NpmPackage npm = NpmPackage.fromPackage(packageTgzInputStream, sourceDesc, true);
    if (progress) {
        log("");
        logn("  Installing: ");
    }
    if (!suppressErrors && npm.name() == null || id == null || !id.equalsIgnoreCase(npm.name())) {
        if (!id.equals("hl7.fhir.r5.core") && !id.equals("hl7.fhir.us.immds")) {
            // temporary work around
            throw new IOException("Attempt to import a mis-identified package. Expected " + id + ", got " + npm.name());
        }
    }
    if (version == null)
        version = npm.version();
    String v = version;
    return new CacheLock(id + "#" + version).doWithLock(() -> {
        NpmPackage pck = null;
        String packRoot = Utilities.path(cacheFolder, id + "#" + v);
        try {
            // ok, now we have a lock on it... check if something created it while we were waiting
            if (!new File(packRoot).exists() || Utilities.existsInList(v, "current", "dev")) {
                Utilities.createDirectory(packRoot);
                try {
                    Utilities.clearDirectory(packRoot);
                } catch (Throwable t) {
                    log("Unable to clear directory: " + packRoot + ": " + t.getMessage() + " - this may cause problems later");
                }
                int i = 0;
                int c = 0;
                int size = 0;
                for (Entry<String, NpmPackageFolder> e : npm.getFolders().entrySet()) {
                    String dir = e.getKey().equals("package") ? Utilities.path(packRoot, "package") : Utilities.path(packRoot, "package", e.getKey());
                    if (!(new File(dir).exists()))
                        Utilities.createDirectory(dir);
                    for (Entry<String, byte[]> fe : e.getValue().getContent().entrySet()) {
                        String fn = Utilities.path(dir, Utilities.cleanFileName(fe.getKey()));
                        byte[] cnt = fe.getValue();
                        TextFile.bytesToFile(cnt, fn);
                        size = size + cnt.length;
                        i++;
                        if (progress && i % 50 == 0) {
                            c++;
                            logn(".");
                            if (c == 120) {
                                log("");
                                logn("  ");
                                c = 2;
                            }
                        }
                    }
                }
                IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
                ini.setTimeStampFormat("yyyyMMddhhmmss");
                ini.setTimestampProperty("packages", id + "#" + v, Timestamp.from(Instant.now()), null);
                ini.setIntegerProperty("package-sizes", id + "#" + v, size, null);
                ini.save();
                if (progress)
                    log(" done.");
            }
            pck = loadPackageInfo(packRoot);
            if (!id.equals(JSONUtil.str(npm.getNpm(), "name")) || !v.equals(JSONUtil.str(npm.getNpm(), "version"))) {
                if (!id.equals(JSONUtil.str(npm.getNpm(), "name"))) {
                    npm.getNpm().addProperty("original-name", JSONUtil.str(npm.getNpm(), "name"));
                    npm.getNpm().remove("name");
                    npm.getNpm().addProperty("name", id);
                }
                if (!v.equals(JSONUtil.str(npm.getNpm(), "version"))) {
                    npm.getNpm().addProperty("original-version", JSONUtil.str(npm.getNpm(), "version"));
                    npm.getNpm().remove("version");
                    npm.getNpm().addProperty("version", v);
                }
                TextFile.stringToFile(new GsonBuilder().setPrettyPrinting().create().toJson(npm.getNpm()), Utilities.path(cacheFolder, id + "#" + v, "package", "package.json"), false);
            }
        } catch (Exception e) {
            try {
                // don't leave a half extracted package behind
                log("Clean up package " + packRoot + " because installation failed: " + e.getMessage());
                e.printStackTrace();
                Utilities.clearDirectory(packRoot);
                new File(packRoot).delete();
            } catch (Exception ei) {
            // nothing
            }
            throw e;
        }
        return pck;
    });
}

Example 33 with Package

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

the class NpmPackage method fromFolder.

public static NpmPackage fromFolder(String folder, PackageType defType, String... exemptions) throws IOException {
    NpmPackage res = new NpmPackage();
    res.loadFiles(folder, new File(folder), exemptions);
    if (!res.folders.containsKey("package")) {
        res.folders.put("package", res.new NpmPackageFolder("package"));
    }
    if (!res.folders.get("package").hasFile("package.json") && defType != null) {
        TextFile.stringToFile("{ \"type\" : \"" + defType.getCode() + "\"}", Utilities.path(res.folders.get("package").folder.getAbsolutePath(), "package.json"));
    }
    res.npm = (JsonObject) new com.google.gson.JsonParser().parse(new String(res.folders.get("package").fetchFile("package.json")));
    return res;
}

Example 34 with Package

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

the class NpmPackage method unPack.

public void unPack(String dir, boolean withAppend) throws IOException {
    for (NpmPackageFolder folder : folders.values()) {
        String dn = folder.getName();
        if (!dn.equals("package") && (dn.startsWith("package/") || dn.startsWith("package\\"))) {
            dn = dn.substring(8);
        }
        if (dn.equals("$root")) {
            dn = dir;
        } else {
            dn = Utilities.path(dir, dn);
        }
        Utilities.createDirectory(dn);
        for (String s : folder.listFiles()) {
            String fn = Utilities.path(dn, s);
            File f = new File(fn);
            if (withAppend && f.getName().startsWith("_append.")) {
                String appendFn = Utilities.path(dn, s.substring(8));
                if (new File(appendFn).exists())
                    TextFile.appendBytesToFile(folder.fetchFile(s), appendFn);
                else
                    TextFile.bytesToFile(folder.fetchFile(s), appendFn);
            } else
                TextFile.bytesToFile(folder.fetchFile(s), fn);
        }
    // if (path != null)
    // FileUtils.copyDirectory(new File(path), new File(dir));
    }
}

Example 35 with Package

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

the class NpmPackage method readStream.

public void readStream(InputStream tgz, String desc, boolean progress) throws IOException {
    GzipCompressorInputStream gzipIn;
    try {
        gzipIn = new GzipCompressorInputStream(tgz);
    } catch (Exception e) {
        throw new IOException("Error reading " + (desc == null ? "package" : desc) + ": " + e.getMessage(), e);
    }
    try (TarArchiveInputStream tarIn = new TarArchiveInputStream(gzipIn)) {
        TarArchiveEntry entry;
        int i = 0;
        int c = 12;
        while ((entry = (TarArchiveEntry) tarIn.getNextEntry()) != null) {
            i++;
            String n = entry.getName();
            if (entry.isDirectory()) {
                String dir = n.substring(0, n.length() - 1);
                if (dir.startsWith("package/")) {
                    dir = dir.substring(8);
                }
                folders.put(dir, new NpmPackageFolder(dir));
            } else {
                int count;
                byte[] data = new byte[BUFFER_SIZE];
                ByteArrayOutputStream fos = new ByteArrayOutputStream();
                try (BufferedOutputStream dest = new BufferedOutputStream(fos, BUFFER_SIZE)) {
                    while ((count = tarIn.read(data, 0, BUFFER_SIZE)) != -1) {
                        dest.write(data, 0, count);
                    }
                }
                fos.close();
                loadFile(n, fos.toByteArray());
            }
            if (progress && i % 50 == 0) {
                c++;
                System.out.print(".");
                if (c == 120) {
                    System.out.println("");
                    System.out.print("  ");
                    c = 2;
                }
            }
        }
    }
    try {
        npm = JsonTrackingParser.parseJson(folders.get("package").fetchFile("package.json"));
    } catch (Exception e) {
        throw new IOException("Error parsing " + (desc == null ? "" : desc + "#") + "package/package.json: " + e.getMessage(), e);
    }
    checkIndexed(desc);
}