mirror of
https://github.com/hapifhir/org.hl7.fhir.core.git
synced 2025-02-09 06:14:45 +00:00
load dependency Packages, and load content from URL correctly
This commit is contained in:
Grahame Grieve
parent
13da3db00d
commit
52b80cf71c
@ -118,4 +118,11 @@ public class VersionUtilities {
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return v1.substring(0, 3).equals(v2.substring(0, 3));
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}
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public static boolean isCorePackage(String s) {
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if (s.contains("#")) {
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s = s.substring(0, s.indexOf("#"));
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}
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return Utilities.existsInList(s, "hl7.fhir.core","hl7.fhir.r2.core", "hl7.fhir.r2b.core", "hl7.fhir.r3.core", "hl7.fhir.r4.core");
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}
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}
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@ -62,486 +62,497 @@ import com.google.gson.JsonElement;
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import com.google.gson.JsonObject;
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/**
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* info and loader for a package
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*
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* Packages may exist on disk in the cache, or purely in memory when they are loaded on the fly
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*
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* Packages are contained in subfolders (see the package spec). The FHIR resources will be in "package"
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*
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* @author Grahame Grieve
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*
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*/
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public class NpmPackage {
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* info and loader for a package
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*
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* Packages may exist on disk in the cache, or purely in memory when they are loaded on the fly
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*
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* Packages are contained in subfolders (see the package spec). The FHIR resources will be in "package"
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*
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* @author Grahame Grieve
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*
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*/
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public class NpmPackage {
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private String path;
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private List<String> folders = new ArrayList<String>();
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private Map<String, byte[]> content = new HashMap<String, byte[]>();
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private JsonObject npm;
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private IniFile cache;
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private Map<String, List<String>> types = new HashMap<>();
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private Map<String, String> urls = new HashMap<>();
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private String path;
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private List<String> folders = new ArrayList<String>();
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private Map<String, byte[]> content = new HashMap<String, byte[]>();
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private JsonObject npm;
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private IniFile cache;
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private Map<String, List<String>> types = new HashMap<>();
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private Map<String, String> urls = new HashMap<>();
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public NpmPackage(JsonObject npm, Map<String, byte[]> content, List<String> folders) {
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this.path = null;
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this.content = content;
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this.npm = npm;
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this.folders = folders;
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}
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public NpmPackage(String path) throws IOException {
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this.path = path;
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if (path != null) {
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for (String f : sorted(new File(path).list())) {
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if (new File(Utilities.path(path, f)).isDirectory()) {
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folders.add(f);
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}
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}
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npm = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.fileToString(Utilities.path(path, "package", "package.json")));
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File ji = new File(Utilities.path(path, "package", ".index.json"));
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if (ji.exists()) {
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readIndexFile((JsonObject) new com.google.gson.JsonParser().parse(TextFile.fileToString(ji)));
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}
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cache = new IniFile(Utilities.path(path, "cache.ini"));
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}
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}
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private void readIndexFile(JsonObject index) throws IOException {
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for (JsonElement e : index.getAsJsonArray("files")) {
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JsonObject file = (JsonObject) e;
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String type = file.get("resourceType").getAsString();
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String name = file.get("filename").getAsString();
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String url = file.has("url") ? file.get("url").getAsString() : null;
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String version = file.has("version") ? file.get("version").getAsString() : null;
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if (!types.containsKey(type))
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types.put(type, new ArrayList<>());
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types.get(type).add(name);
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if (version != null)
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url = url + "|" + version;
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urls.put(url, name);
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}
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}
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public NpmPackage(JsonObject npm, Map<String, byte[]> content, List<String> folders) {
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this.path = null;
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this.content = content;
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this.npm = npm;
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this.folders = folders;
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}
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private List<String> sorted(String[] keys) {
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List<String> names = new ArrayList<String>();
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for (String s : keys)
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names.add(s);
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Collections.sort(names);
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return names;
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}
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private static final int BUFFER_SIZE = 1024;
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public static NpmPackage fromPackage(InputStream tgz) throws IOException {
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return fromPackage(tgz, false);
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}
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public static NpmPackage fromPackage(InputStream tgz, boolean progress) throws IOException {
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NpmPackage res = new NpmPackage(null);
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boolean hasIndex = false;
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GzipCompressorInputStream gzipIn = new GzipCompressorInputStream(tgz);
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try (TarArchiveInputStream tarIn = new TarArchiveInputStream(gzipIn)) {
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TarArchiveEntry entry;
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int i = 0;
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int c = 12;
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while ((entry = (TarArchiveEntry) tarIn.getNextEntry()) != null) {
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i++;
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if (entry.isDirectory()) {
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res.folders.add(entry.getName());
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} else {
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hasIndex = hasIndex || "package/.index.json".equals(entry.getName());
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int count;
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byte data[] = new byte[BUFFER_SIZE];
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ByteArrayOutputStream fos = new ByteArrayOutputStream();
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try (BufferedOutputStream dest = new BufferedOutputStream(fos, BUFFER_SIZE)) {
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while ((count = tarIn.read(data, 0, BUFFER_SIZE)) != -1) {
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dest.write(data, 0, count);
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}
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}
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fos.close();
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res.content.put(entry.getName(), fos.toByteArray());
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}
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i++;
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if (progress && i % 50 == 0) {
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c++;
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System.out.print(".");
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if (c == 120) {
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System.out.println("");
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System.out.print(" ");
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c = 2;
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}
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}
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public NpmPackage(String path) throws IOException {
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this.path = path;
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if (path != null) {
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for (String f : sorted(new File(path).list())) {
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if (new File(Utilities.path(path, f)).isDirectory()) {
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folders.add(f);
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}
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}
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if (!hasIndex) {
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NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();
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indexer.start();
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for (String n : res.getContent().keySet()) {
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if (n.startsWith("package/")) {
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indexer.seeFile(n.substring(8), res.content.get(n));
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}
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}
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res.content.put("package/.index.json", indexer.build().getBytes(Charsets.UTF_8));
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npm = (JsonObject) new com.google.gson.JsonParser().parse(TextFile.fileToString(Utilities.path(path, "package", "package.json")));
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File ji = new File(Utilities.path(path, "package", ".index.json"));
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if (ji.exists()) {
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readIndexFile((JsonObject) new com.google.gson.JsonParser().parse(TextFile.fileToString(ji)));
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}
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res.npm = JsonTrackingParser.parseJson(res.content.get("package/package.json"));
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res.readIndexFile((JsonObject) new com.google.gson.JsonParser().parse(new String(res.content.get("package/.index.json"))));
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return res;
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}
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public static NpmPackage fromZip(InputStream stream, boolean dropRootFolder) throws IOException {
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NpmPackage res = new NpmPackage(null);
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ZipInputStream zip = new ZipInputStream(stream);
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ZipEntry ze;
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while ((ze = zip.getNextEntry()) != null) {
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int size;
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byte[] buffer = new byte[2048];
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ByteArrayOutputStream bytes = new ByteArrayOutputStream();
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BufferedOutputStream bos = new BufferedOutputStream(bytes, buffer.length);
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while ((size = zip.read(buffer, 0, buffer.length)) != -1) {
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bos.write(buffer, 0, size);
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}
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bos.flush();
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bos.close();
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if (bytes.size() > 0)
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if (dropRootFolder)
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res.content.put(ze.getName().substring(ze.getName().indexOf("/")+1), bytes.toByteArray());
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else
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res.content.put(ze.getName(), bytes.toByteArray());
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zip.closeEntry();
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}
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zip.close();
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res.npm = (JsonObject) new com.google.gson.JsonParser().parse(new String(res.content.get("package/package.json")));
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if (res.content.containsKey("package/.index.json"))
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res.readIndexFile((JsonObject) new com.google.gson.JsonParser().parse(new String(res.content.get("package/.index.json"))));
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return res;
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}
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/**
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* Accessing the contents of the package - get a list of files in a subfolder of the package
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*
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* @param folder
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* @return
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* @throws IOException
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*/
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public List<String> list(String folder) throws IOException {
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List<String> res = new ArrayList<String>();
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if (path != null) {
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File f = new File(Utilities.path(path, folder));
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if (f.exists() && f.isDirectory())
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for (String s : f.list())
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res.add(s);
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} else {
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for (String s : content.keySet()) {
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if (s.startsWith(folder+"/") && !s.substring(folder.length()+2).contains("/"))
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res.add(s.substring(folder.length()+1));
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}
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}
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return res;
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}
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public List<String> listResources(String... types) throws IOException {
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List<String> res = new ArrayList<String>();
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if (this.types.size() > 0) {
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for (String s : types) {
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if (this.types.containsKey(s))
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res.addAll(this.types.get(s));
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}
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} else {
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List<String> files = list("package");
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for (String s : files) {
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String[] n = s.split("\\-");
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if (Utilities.existsInList(n[0], types))
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res.add(s);
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}
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}
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return res;
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}
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/**
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* Copies all the files in the package folder [folder] to the nominated dest,
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* and returns a list of all the file names copied
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*
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* @param folder
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* @return
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* @throws IOException
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*/
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public List<String> copyTo(String folder, String dest) throws IOException {
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List<String> res = new ArrayList<String>();
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if (path != null) {
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copyToDest(Utilities.path(path, folder), Utilities.path(path, folder), dest, res);
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} else {
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for (Entry<String, byte[]> e : content.entrySet()) {
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if (e.getKey().startsWith(folder+"/")) {
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String s = e.getKey().substring(folder.length()+1);
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res.add(s);
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String dst = Utilities.path(dest, s);
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String dstDir = Utilities.getDirectoryForFile(dst);
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Utilities.createDirectory(dstDir);
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TextFile.bytesToFile(e.getValue(), dst);
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}
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}
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}
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return res;
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}
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private void copyToDest(String base, String folder, String dest, List<String> res) throws IOException {
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for (File f : new File(folder).listFiles()) {
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if (f.isDirectory()) {
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copyToDest(base, f.getAbsolutePath(), Utilities.path(dest, f.getName()), res);
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} else {
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String dst = Utilities.path(dest, f.getName());
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FileUtils.copyFile(f, new File(dst), true);
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res.add(f.getAbsolutePath().substring(base.length()+1));
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}
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}
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}
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/**
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* get a stream that contains the contents of one of the files in a folder
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*
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* @param folder
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* @param file
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* @return
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* @throws IOException
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*/
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public InputStream load(String folder, String file) throws IOException {
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if (content.containsKey(folder+"/"+file))
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return new ByteArrayInputStream(content.get(folder+"/"+file));
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else {
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File f = new File(Utilities.path(path, folder, file));
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if (f.exists())
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return new FileInputStream(f);
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throw new IOException("Unable to find the file "+folder+"/"+file+" in the package "+name());
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}
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}
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/**
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* Handle to the package json file
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*
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* @return
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*/
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public JsonObject getNpm() {
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return npm;
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}
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/**
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* convenience method for getting the package name
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* @return
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*/
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public String name() {
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return npm.get("name").getAsString();
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}
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public String date() {
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return npm.has("date") ? npm.get("date").getAsString() : null;
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}
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public String canonical() {
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return npm.has("canonical") ? npm.get("canonical").getAsString() : null;
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}
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/**
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* convenience method for getting the package version
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* @return
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*/
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public String version() {
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return npm.get("version").getAsString();
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}
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/**
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* convenience method for getting the package fhir version
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* @return
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*/
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public String fhirVersion() {
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if ("hl7.fhir.core".equals(npm.get("name").getAsString()))
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return npm.get("version").getAsString();
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else if (npm.get("name").getAsString().startsWith("hl7.fhir.r2.") || npm.get("name").getAsString().startsWith("hl7.fhir.r2b.") || npm.get("name").getAsString().startsWith("hl7.fhir.r3.") || npm.get("name").getAsString().startsWith("hl7.fhir.r4.") || npm.get("name").getAsString().startsWith("hl7.fhir.r5."))
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return npm.get("version").getAsString();
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else {
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JsonObject dep = npm.getAsJsonObject("dependencies");
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if (dep == null)
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throw new FHIRException("no dependencies found in the Package definition");
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for (Entry<String, JsonElement> e : dep.entrySet()) {
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if (Utilities.existsInList(e.getKey(), "hl7.fhir.r2.core", "hl7.fhir.r2b.core", "hl7.fhir.r3.core", "hl7.fhir.r4.core"))
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return e.getValue().getAsString();
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if (Utilities.existsInList(e.getKey(), "hl7.fhir.core")) // while all packages are updated
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return e.getValue().getAsString();
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}
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if (npm.has("fhirVersions")) {
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return npm.getAsJsonArray("fhirVersions").get(0).getAsString();
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}
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// legacy simplifier support:
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if (dep.has("simplifier.core.r4"))
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return "4.0";
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if (dep.has("simplifier.core.r3"))
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return "3.0";
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if (dep.has("simplifier.core.r2"))
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return "2.0";
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throw new FHIRException("no core dependency or FHIR Version found in the Package definition");
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}
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}
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public String summary() {
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if (path != null)
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return path;
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else
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return "memory";
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}
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public boolean isType(PackageType template) {
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return template.getCode().equals(type());
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}
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public String type() {
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return npm.get("type").getAsString();
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}
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public String description() {
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return npm.has("description") ? npm.get("description").getAsString() : null;
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}
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public String getPath() {
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return path;
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}
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public IniFile getCache() {
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return cache;
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}
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/**
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* only for use by the package manager itself
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*
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* @param path
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*/
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public void setPath(String path) {
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this.path = path;
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}
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public String getWebLocation() {
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if (npm.has("url"))
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return npm.get("url").getAsString();
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else
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return npm.get("canonical").getAsString();
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}
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public boolean hasFile(String folder, String name) throws IOException {
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String file = folder+"/"+name;
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return content.containsKey(file);
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}
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public InputStream loadResource(String type, String id) throws IOException {
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String file = type+"-"+id+".json";
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if (content.containsKey("package/"+file))
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return new ByteArrayInputStream(content.get("package/"+file));
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else {
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File f = new File(Utilities.path(path, "package", file));
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if (f.exists())
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return new FileInputStream(f);
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else
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return null;
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}
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}
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/** special case when playing around inside the package **/
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public Map<String, byte[]> getContent() {
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return content;
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}
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public static NpmPackage fromFolder(String folder, String... exemptions) throws IOException {
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return fromFolder(folder, null, exemptions);
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}
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public static NpmPackage fromFolder(String folder, PackageType defType, String... exemptions) throws IOException {
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NpmPackage res = new NpmPackage(null);
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loadFiles(res, folder, new File(folder), exemptions);
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if (!res.content.containsKey("package/package.json") && defType != null)
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res.content.put("package/package.json", TextFile.stringToBytes("{ \"type\" : \""+defType.getCode()+"\"}", false));
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res.npm = (JsonObject) new com.google.gson.JsonParser().parse(new String(res.content.get("package/package.json")));
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return res;
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}
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private static void loadFiles(NpmPackage res, String base, File folder, String... exemptions) throws FileNotFoundException, IOException {
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for (File f : folder.listFiles()) {
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if (!f.getName().equals(".git") || !Utilities.existsInList(f.getName(), exemptions)) {
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if (f.isDirectory())
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loadFiles(res, base, f);
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else {
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String name = f.getAbsolutePath().substring(base.length()+1).replace("\\", "/");
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byte[] cnt = TextFile.fileToBytes(f);
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res.content.put(name, cnt);
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}
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}
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}
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}
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||||
|
||||
public void unPack(String dir) throws IOException {
|
||||
for (String s : content.keySet()) {
|
||||
String fn = Utilities.path(dir, s);
|
||||
String dn = Utilities.getDirectoryForFile(fn);
|
||||
Utilities.createDirectory(dn);
|
||||
TextFile.bytesToFile(content.get(s), fn);
|
||||
}
|
||||
if (path != null)
|
||||
FileUtils.copyDirectory(new File(path), new File(dir));
|
||||
}
|
||||
|
||||
public void save(OutputStream stream) throws IOException {
|
||||
TarArchiveOutputStream tar;
|
||||
ByteArrayOutputStream OutputStream;
|
||||
BufferedOutputStream bufferedOutputStream;
|
||||
GzipCompressorOutputStream gzipOutputStream;
|
||||
|
||||
OutputStream = new ByteArrayOutputStream();
|
||||
bufferedOutputStream = new BufferedOutputStream(OutputStream);
|
||||
gzipOutputStream = new GzipCompressorOutputStream(bufferedOutputStream);
|
||||
tar = new TarArchiveOutputStream(gzipOutputStream);
|
||||
|
||||
NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();
|
||||
indexer.start();
|
||||
|
||||
for (String s : content.keySet()) {
|
||||
byte[] b = content.get(s);
|
||||
if (s.startsWith("package/")) {
|
||||
indexer.seeFile(tail(s), b);
|
||||
}
|
||||
if (!s.endsWith(".index.json") && !s.equals("package/package.json")) {
|
||||
TarArchiveEntry entry = new TarArchiveEntry(s);
|
||||
entry.setSize(b.length);
|
||||
tar.putArchiveEntry(entry);
|
||||
tar.write(b);
|
||||
tar.closeArchiveEntry();
|
||||
}
|
||||
}
|
||||
byte[] cnt = new GsonBuilder().setPrettyPrinting().create().toJson(npm).getBytes(Charset.forName("UTF-8"));
|
||||
TarArchiveEntry entry = new TarArchiveEntry("package/package.json");
|
||||
entry.setSize(cnt.length);
|
||||
tar.putArchiveEntry(entry);
|
||||
tar.write(cnt);
|
||||
tar.closeArchiveEntry();
|
||||
|
||||
cnt = indexer.build().getBytes(Charset.forName("UTF-8"));
|
||||
entry = new TarArchiveEntry("package/.index.json");
|
||||
entry.setSize(cnt.length);
|
||||
tar.putArchiveEntry(entry);
|
||||
tar.write(cnt);
|
||||
tar.closeArchiveEntry();
|
||||
|
||||
tar.finish();
|
||||
tar.close();
|
||||
gzipOutputStream.close();
|
||||
bufferedOutputStream.close();
|
||||
OutputStream.close();
|
||||
byte[] b = OutputStream.toByteArray();
|
||||
stream.write(b);
|
||||
}
|
||||
|
||||
private String tail(String s) {
|
||||
return s.substring(s.lastIndexOf("/")+1);
|
||||
cache = new IniFile(Utilities.path(path, "cache.ini"));
|
||||
}
|
||||
}
|
||||
|
||||
private void readIndexFile(JsonObject index) throws IOException {
|
||||
for (JsonElement e : index.getAsJsonArray("files")) {
|
||||
JsonObject file = (JsonObject) e;
|
||||
String type = file.get("resourceType").getAsString();
|
||||
String name = file.get("filename").getAsString();
|
||||
String url = file.has("url") ? file.get("url").getAsString() : null;
|
||||
String version = file.has("version") ? file.get("version").getAsString() : null;
|
||||
if (!types.containsKey(type))
|
||||
types.put(type, new ArrayList<>());
|
||||
types.get(type).add(name);
|
||||
if (version != null)
|
||||
url = url + "|" + version;
|
||||
urls.put(url, name);
|
||||
}
|
||||
}
|
||||
|
||||
private List<String> sorted(String[] keys) {
|
||||
List<String> names = new ArrayList<String>();
|
||||
for (String s : keys)
|
||||
names.add(s);
|
||||
Collections.sort(names);
|
||||
return names;
|
||||
}
|
||||
|
||||
private static final int BUFFER_SIZE = 1024;
|
||||
|
||||
public static NpmPackage fromPackage(InputStream tgz) throws IOException {
|
||||
return fromPackage(tgz, false);
|
||||
}
|
||||
|
||||
public static NpmPackage fromPackage(InputStream tgz, boolean progress) throws IOException {
|
||||
NpmPackage res = new NpmPackage(null);
|
||||
boolean hasIndex = false;
|
||||
GzipCompressorInputStream gzipIn = new GzipCompressorInputStream(tgz);
|
||||
try (TarArchiveInputStream tarIn = new TarArchiveInputStream(gzipIn)) {
|
||||
TarArchiveEntry entry;
|
||||
|
||||
int i = 0;
|
||||
int c = 12;
|
||||
while ((entry = (TarArchiveEntry) tarIn.getNextEntry()) != null) {
|
||||
i++;
|
||||
if (entry.isDirectory()) {
|
||||
res.folders.add(entry.getName());
|
||||
} else {
|
||||
hasIndex = hasIndex || "package/.index.json".equals(entry.getName());
|
||||
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();
|
||||
res.content.put(entry.getName(), fos.toByteArray());
|
||||
}
|
||||
i++;
|
||||
if (progress && i % 50 == 0) {
|
||||
c++;
|
||||
System.out.print(".");
|
||||
if (c == 120) {
|
||||
System.out.println("");
|
||||
System.out.print(" ");
|
||||
c = 2;
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
if (!hasIndex) {
|
||||
NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();
|
||||
indexer.start();
|
||||
for (String n : res.getContent().keySet()) {
|
||||
if (n.startsWith("package/")) {
|
||||
indexer.seeFile(n.substring(8), res.content.get(n));
|
||||
}
|
||||
}
|
||||
res.content.put("package/.index.json", indexer.build().getBytes(Charsets.UTF_8));
|
||||
}
|
||||
res.npm = JsonTrackingParser.parseJson(res.content.get("package/package.json"));
|
||||
res.readIndexFile((JsonObject) new com.google.gson.JsonParser().parse(new String(res.content.get("package/.index.json"))));
|
||||
return res;
|
||||
}
|
||||
|
||||
|
||||
public static NpmPackage fromZip(InputStream stream, boolean dropRootFolder) throws IOException {
|
||||
NpmPackage res = new NpmPackage(null);
|
||||
ZipInputStream zip = new ZipInputStream(stream);
|
||||
ZipEntry ze;
|
||||
while ((ze = zip.getNextEntry()) != null) {
|
||||
int size;
|
||||
byte[] buffer = new byte[2048];
|
||||
|
||||
ByteArrayOutputStream bytes = new ByteArrayOutputStream();
|
||||
BufferedOutputStream bos = new BufferedOutputStream(bytes, buffer.length);
|
||||
|
||||
while ((size = zip.read(buffer, 0, buffer.length)) != -1) {
|
||||
bos.write(buffer, 0, size);
|
||||
}
|
||||
bos.flush();
|
||||
bos.close();
|
||||
if (bytes.size() > 0)
|
||||
if (dropRootFolder)
|
||||
res.content.put(ze.getName().substring(ze.getName().indexOf("/")+1), bytes.toByteArray());
|
||||
else
|
||||
res.content.put(ze.getName(), bytes.toByteArray());
|
||||
|
||||
zip.closeEntry();
|
||||
}
|
||||
zip.close();
|
||||
res.npm = (JsonObject) new com.google.gson.JsonParser().parse(new String(res.content.get("package/package.json")));
|
||||
if (res.content.containsKey("package/.index.json"))
|
||||
res.readIndexFile((JsonObject) new com.google.gson.JsonParser().parse(new String(res.content.get("package/.index.json"))));
|
||||
return res;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Accessing the contents of the package - get a list of files in a subfolder of the package
|
||||
*
|
||||
* @param folder
|
||||
* @return
|
||||
* @throws IOException
|
||||
*/
|
||||
public List<String> list(String folder) throws IOException {
|
||||
List<String> res = new ArrayList<String>();
|
||||
if (path != null) {
|
||||
File f = new File(Utilities.path(path, folder));
|
||||
if (f.exists() && f.isDirectory())
|
||||
for (String s : f.list())
|
||||
res.add(s);
|
||||
} else {
|
||||
for (String s : content.keySet()) {
|
||||
if (s.startsWith(folder+"/") && !s.substring(folder.length()+2).contains("/"))
|
||||
res.add(s.substring(folder.length()+1));
|
||||
}
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
public List<String> listResources(String... types) throws IOException {
|
||||
List<String> res = new ArrayList<String>();
|
||||
if (this.types.size() > 0) {
|
||||
for (String s : types) {
|
||||
if (this.types.containsKey(s))
|
||||
res.addAll(this.types.get(s));
|
||||
}
|
||||
} else {
|
||||
List<String> files = list("package");
|
||||
for (String s : files) {
|
||||
String[] n = s.split("\\-");
|
||||
if (Utilities.existsInList(n[0], types))
|
||||
res.add(s);
|
||||
}
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
/**
|
||||
* Copies all the files in the package folder [folder] to the nominated dest,
|
||||
* and returns a list of all the file names copied
|
||||
*
|
||||
* @param folder
|
||||
* @return
|
||||
* @throws IOException
|
||||
*/
|
||||
public List<String> copyTo(String folder, String dest) throws IOException {
|
||||
List<String> res = new ArrayList<String>();
|
||||
if (path != null) {
|
||||
copyToDest(Utilities.path(path, folder), Utilities.path(path, folder), dest, res);
|
||||
} else {
|
||||
for (Entry<String, byte[]> e : content.entrySet()) {
|
||||
if (e.getKey().startsWith(folder+"/")) {
|
||||
String s = e.getKey().substring(folder.length()+1);
|
||||
res.add(s);
|
||||
String dst = Utilities.path(dest, s);
|
||||
String dstDir = Utilities.getDirectoryForFile(dst);
|
||||
Utilities.createDirectory(dstDir);
|
||||
TextFile.bytesToFile(e.getValue(), dst);
|
||||
}
|
||||
}
|
||||
}
|
||||
return res;
|
||||
}
|
||||
|
||||
private void copyToDest(String base, String folder, String dest, List<String> res) throws IOException {
|
||||
for (File f : new File(folder).listFiles()) {
|
||||
if (f.isDirectory()) {
|
||||
copyToDest(base, f.getAbsolutePath(), Utilities.path(dest, f.getName()), res);
|
||||
} else {
|
||||
String dst = Utilities.path(dest, f.getName());
|
||||
FileUtils.copyFile(f, new File(dst), true);
|
||||
res.add(f.getAbsolutePath().substring(base.length()+1));
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* get a stream that contains the contents of one of the files in a folder
|
||||
*
|
||||
* @param folder
|
||||
* @param file
|
||||
* @return
|
||||
* @throws IOException
|
||||
*/
|
||||
public InputStream load(String folder, String file) throws IOException {
|
||||
if (content.containsKey(folder+"/"+file))
|
||||
return new ByteArrayInputStream(content.get(folder+"/"+file));
|
||||
else {
|
||||
File f = new File(Utilities.path(path, folder, file));
|
||||
if (f.exists())
|
||||
return new FileInputStream(f);
|
||||
throw new IOException("Unable to find the file "+folder+"/"+file+" in the package "+name());
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* Handle to the package json file
|
||||
*
|
||||
* @return
|
||||
*/
|
||||
public JsonObject getNpm() {
|
||||
return npm;
|
||||
}
|
||||
|
||||
/**
|
||||
* convenience method for getting the package name
|
||||
* @return
|
||||
*/
|
||||
public String name() {
|
||||
return npm.get("name").getAsString();
|
||||
}
|
||||
|
||||
public String date() {
|
||||
return npm.has("date") ? npm.get("date").getAsString() : null;
|
||||
}
|
||||
|
||||
public String canonical() {
|
||||
return npm.has("canonical") ? npm.get("canonical").getAsString() : null;
|
||||
}
|
||||
|
||||
/**
|
||||
* convenience method for getting the package version
|
||||
* @return
|
||||
*/
|
||||
public String version() {
|
||||
return npm.get("version").getAsString();
|
||||
}
|
||||
|
||||
/**
|
||||
* convenience method for getting the package fhir version
|
||||
* @return
|
||||
*/
|
||||
public String fhirVersion() {
|
||||
if ("hl7.fhir.core".equals(npm.get("name").getAsString()))
|
||||
return npm.get("version").getAsString();
|
||||
else if (npm.get("name").getAsString().startsWith("hl7.fhir.r2.") || npm.get("name").getAsString().startsWith("hl7.fhir.r2b.") || npm.get("name").getAsString().startsWith("hl7.fhir.r3.") || npm.get("name").getAsString().startsWith("hl7.fhir.r4.") || npm.get("name").getAsString().startsWith("hl7.fhir.r5."))
|
||||
return npm.get("version").getAsString();
|
||||
else {
|
||||
JsonObject dep = npm.getAsJsonObject("dependencies");
|
||||
if (dep == null)
|
||||
throw new FHIRException("no dependencies found in the Package definition");
|
||||
for (Entry<String, JsonElement> e : dep.entrySet()) {
|
||||
if (Utilities.existsInList(e.getKey(), "hl7.fhir.r2.core", "hl7.fhir.r2b.core", "hl7.fhir.r3.core", "hl7.fhir.r4.core"))
|
||||
return e.getValue().getAsString();
|
||||
if (Utilities.existsInList(e.getKey(), "hl7.fhir.core")) // while all packages are updated
|
||||
return e.getValue().getAsString();
|
||||
}
|
||||
if (npm.has("fhirVersions")) {
|
||||
return npm.getAsJsonArray("fhirVersions").get(0).getAsString();
|
||||
}
|
||||
// legacy simplifier support:
|
||||
if (dep.has("simplifier.core.r4"))
|
||||
return "4.0";
|
||||
if (dep.has("simplifier.core.r3"))
|
||||
return "3.0";
|
||||
if (dep.has("simplifier.core.r2"))
|
||||
return "2.0";
|
||||
throw new FHIRException("no core dependency or FHIR Version found in the Package definition");
|
||||
}
|
||||
}
|
||||
|
||||
public String summary() {
|
||||
if (path != null)
|
||||
return path;
|
||||
else
|
||||
return "memory";
|
||||
}
|
||||
|
||||
public boolean isType(PackageType template) {
|
||||
return template.getCode().equals(type());
|
||||
}
|
||||
|
||||
public String type() {
|
||||
return npm.get("type").getAsString();
|
||||
}
|
||||
|
||||
public String description() {
|
||||
return npm.has("description") ? npm.get("description").getAsString() : null;
|
||||
}
|
||||
|
||||
public String getPath() {
|
||||
return path;
|
||||
}
|
||||
|
||||
public IniFile getCache() {
|
||||
return cache;
|
||||
}
|
||||
|
||||
/**
|
||||
* only for use by the package manager itself
|
||||
*
|
||||
* @param path
|
||||
*/
|
||||
public void setPath(String path) {
|
||||
this.path = path;
|
||||
}
|
||||
|
||||
public String getWebLocation() {
|
||||
if (npm.has("url"))
|
||||
return npm.get("url").getAsString();
|
||||
else
|
||||
return npm.get("canonical").getAsString();
|
||||
}
|
||||
|
||||
public boolean hasFile(String folder, String name) throws IOException {
|
||||
String file = folder+"/"+name;
|
||||
return content.containsKey(file);
|
||||
}
|
||||
|
||||
public InputStream loadResource(String type, String id) throws IOException {
|
||||
String file = type+"-"+id+".json";
|
||||
if (content.containsKey("package/"+file))
|
||||
return new ByteArrayInputStream(content.get("package/"+file));
|
||||
else {
|
||||
File f = new File(Utilities.path(path, "package", file));
|
||||
if (f.exists())
|
||||
return new FileInputStream(f);
|
||||
else
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
/** special case when playing around inside the package **/
|
||||
public Map<String, byte[]> getContent() {
|
||||
return content;
|
||||
}
|
||||
|
||||
public static NpmPackage fromFolder(String folder, String... exemptions) throws IOException {
|
||||
return fromFolder(folder, null, exemptions);
|
||||
}
|
||||
|
||||
public static NpmPackage fromFolder(String folder, PackageType defType, String... exemptions) throws IOException {
|
||||
NpmPackage res = new NpmPackage(null);
|
||||
loadFiles(res, folder, new File(folder), exemptions);
|
||||
if (!res.content.containsKey("package/package.json") && defType != null)
|
||||
res.content.put("package/package.json", TextFile.stringToBytes("{ \"type\" : \""+defType.getCode()+"\"}", false));
|
||||
res.npm = (JsonObject) new com.google.gson.JsonParser().parse(new String(res.content.get("package/package.json")));
|
||||
return res;
|
||||
}
|
||||
|
||||
private static void loadFiles(NpmPackage res, String base, File folder, String... exemptions) throws FileNotFoundException, IOException {
|
||||
for (File f : folder.listFiles()) {
|
||||
if (!f.getName().equals(".git") || !Utilities.existsInList(f.getName(), exemptions)) {
|
||||
if (f.isDirectory())
|
||||
loadFiles(res, base, f);
|
||||
else {
|
||||
String name = f.getAbsolutePath().substring(base.length()+1).replace("\\", "/");
|
||||
byte[] cnt = TextFile.fileToBytes(f);
|
||||
res.content.put(name, cnt);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
public void unPack(String dir) throws IOException {
|
||||
for (String s : content.keySet()) {
|
||||
String fn = Utilities.path(dir, s);
|
||||
String dn = Utilities.getDirectoryForFile(fn);
|
||||
Utilities.createDirectory(dn);
|
||||
TextFile.bytesToFile(content.get(s), fn);
|
||||
}
|
||||
if (path != null)
|
||||
FileUtils.copyDirectory(new File(path), new File(dir));
|
||||
}
|
||||
|
||||
public void save(OutputStream stream) throws IOException {
|
||||
TarArchiveOutputStream tar;
|
||||
ByteArrayOutputStream OutputStream;
|
||||
BufferedOutputStream bufferedOutputStream;
|
||||
GzipCompressorOutputStream gzipOutputStream;
|
||||
|
||||
OutputStream = new ByteArrayOutputStream();
|
||||
bufferedOutputStream = new BufferedOutputStream(OutputStream);
|
||||
gzipOutputStream = new GzipCompressorOutputStream(bufferedOutputStream);
|
||||
tar = new TarArchiveOutputStream(gzipOutputStream);
|
||||
|
||||
NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();
|
||||
indexer.start();
|
||||
|
||||
for (String s : content.keySet()) {
|
||||
byte[] b = content.get(s);
|
||||
if (s.startsWith("package/")) {
|
||||
indexer.seeFile(tail(s), b);
|
||||
}
|
||||
if (!s.endsWith(".index.json") && !s.equals("package/package.json")) {
|
||||
TarArchiveEntry entry = new TarArchiveEntry(s);
|
||||
entry.setSize(b.length);
|
||||
tar.putArchiveEntry(entry);
|
||||
tar.write(b);
|
||||
tar.closeArchiveEntry();
|
||||
}
|
||||
}
|
||||
byte[] cnt = new GsonBuilder().setPrettyPrinting().create().toJson(npm).getBytes(Charset.forName("UTF-8"));
|
||||
TarArchiveEntry entry = new TarArchiveEntry("package/package.json");
|
||||
entry.setSize(cnt.length);
|
||||
tar.putArchiveEntry(entry);
|
||||
tar.write(cnt);
|
||||
tar.closeArchiveEntry();
|
||||
|
||||
cnt = indexer.build().getBytes(Charset.forName("UTF-8"));
|
||||
entry = new TarArchiveEntry("package/.index.json");
|
||||
entry.setSize(cnt.length);
|
||||
tar.putArchiveEntry(entry);
|
||||
tar.write(cnt);
|
||||
tar.closeArchiveEntry();
|
||||
|
||||
tar.finish();
|
||||
tar.close();
|
||||
gzipOutputStream.close();
|
||||
bufferedOutputStream.close();
|
||||
OutputStream.close();
|
||||
byte[] b = OutputStream.toByteArray();
|
||||
stream.write(b);
|
||||
}
|
||||
|
||||
private String tail(String s) {
|
||||
return s.substring(s.lastIndexOf("/")+1);
|
||||
}
|
||||
|
||||
public List<String> dependencies() {
|
||||
List<String> res = new ArrayList<>();
|
||||
if (npm.has("dependencies")) {
|
||||
for (Entry<String, JsonElement> e : npm.getAsJsonObject("dependencies").entrySet()) {
|
||||
res.add(e.getKey()+"#"+e.getValue().getAsString());
|
||||
}
|
||||
}
|
||||
return res;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -149,6 +149,7 @@ import org.hl7.fhir.r5.utils.ValidationProfileSet;
|
||||
import org.hl7.fhir.utilities.IniFile;
|
||||
import org.hl7.fhir.utilities.TextFile;
|
||||
import org.hl7.fhir.utilities.Utilities;
|
||||
import org.hl7.fhir.utilities.VersionUtilities;
|
||||
import org.hl7.fhir.utilities.cache.NpmPackage;
|
||||
import org.hl7.fhir.utilities.cache.PackageCacheManager;
|
||||
import org.hl7.fhir.utilities.cache.ToolsVersion;
|
||||
@ -310,6 +311,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
||||
private PackageCacheManager pcm;
|
||||
private PrintWriter mapLog;
|
||||
private boolean debug;
|
||||
private Set<String> loadedIgs = new HashSet<>();
|
||||
|
||||
private class AsteriskFilter implements FilenameFilter {
|
||||
String dir;
|
||||
@ -403,7 +405,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
||||
}
|
||||
|
||||
private void loadDefinitions(String src, boolean recursive) throws Exception {
|
||||
Map<String, byte[]> source = loadIgSource(src, recursive);
|
||||
Map<String, byte[]> source = loadIgSource(src, recursive, true);
|
||||
if (version == null)
|
||||
version = getVersionFromPack(source);
|
||||
context = SimpleWorkerContext.fromDefinitions(source, loaderForVersion());
|
||||
@ -478,7 +480,9 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
||||
return TextFile.fileToBytes(src);
|
||||
}
|
||||
|
||||
private Map<String, byte[]> loadIgSource(String src, boolean recursive) throws Exception {
|
||||
/** explore should be true if we're trying to load an -ig parameter, and false if we're loading source **/
|
||||
|
||||
private Map<String, byte[]> loadIgSource(String src, boolean recursive, boolean explore) throws Exception {
|
||||
// src can be one of the following:
|
||||
// - a canonical url for an ig - this will be converted to a package id and loaded into the cache
|
||||
// - a package id for an ig - this will be loaded into the cache
|
||||
@ -494,7 +498,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
||||
if (!Utilities.noString(pid))
|
||||
return fetchByPackage(pid+(v == null ? "" : "#"+v));
|
||||
else
|
||||
return fetchFromUrl(src+(v == null ? "" : "|"+v));
|
||||
return fetchFromUrl(src+(v == null ? "" : "|"+v), explore);
|
||||
}
|
||||
|
||||
File f = new File(src);
|
||||
@ -526,7 +530,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
||||
}
|
||||
|
||||
|
||||
private Map<String, byte[]> fetchFromUrl(String src) throws Exception {
|
||||
private Map<String, byte[]> fetchFromUrl(String src, boolean explore) throws Exception {
|
||||
if (src.endsWith(".tgz"))
|
||||
return loadPackage(fetchFromUrlSpecific(src, false), src);
|
||||
if (src.endsWith(".pack"))
|
||||
@ -534,18 +538,21 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
||||
if (src.endsWith("igpack.zip"))
|
||||
return readZip(fetchFromUrlSpecific(src, false));
|
||||
|
||||
InputStream stream = fetchFromUrlSpecific(Utilities.pathURL(src, "package.tgz"), true);
|
||||
if (stream != null)
|
||||
return loadPackage(stream, Utilities.pathURL(src, "package.tgz"));
|
||||
// todo: these options are deprecated - remove once all IGs have been rebuilt post R4 technical correction
|
||||
stream = fetchFromUrlSpecific(Utilities.pathURL(src, "igpack.zip"), true);
|
||||
if (stream != null)
|
||||
return readZip(stream);
|
||||
stream = fetchFromUrlSpecific(Utilities.pathURL(src, "validator.pack"), true);
|
||||
if (stream != null)
|
||||
return readZip(stream);
|
||||
stream = fetchFromUrlSpecific(Utilities.pathURL(src, "validator.pack"), true);
|
||||
//// -----
|
||||
InputStream stream = null;
|
||||
if (explore) {
|
||||
stream = fetchFromUrlSpecific(Utilities.pathURL(src, "package.tgz"), true);
|
||||
if (stream != null)
|
||||
return loadPackage(stream, Utilities.pathURL(src, "package.tgz"));
|
||||
// todo: these options are deprecated - remove once all IGs have been rebuilt post R4 technical correction
|
||||
stream = fetchFromUrlSpecific(Utilities.pathURL(src, "igpack.zip"), true);
|
||||
if (stream != null)
|
||||
return readZip(stream);
|
||||
stream = fetchFromUrlSpecific(Utilities.pathURL(src, "validator.pack"), true);
|
||||
if (stream != null)
|
||||
return readZip(stream);
|
||||
stream = fetchFromUrlSpecific(Utilities.pathURL(src, "validator.pack"), true);
|
||||
//// -----
|
||||
}
|
||||
|
||||
// ok, having tried all that... now we'll just try to access it directly
|
||||
byte[] cnt;
|
||||
@ -612,11 +619,21 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
||||
|
||||
}
|
||||
|
||||
private Map<String, byte[]> loadPackage(InputStream stream, String name) throws FileNotFoundException, IOException {
|
||||
private Map<String, byte[]> loadPackage(InputStream stream, String name) throws Exception {
|
||||
return loadPackage(NpmPackage.fromPackage(stream));
|
||||
}
|
||||
|
||||
public Map<String, byte[]> loadPackage(NpmPackage pi) throws IOException {
|
||||
public Map<String, byte[]> loadPackage(NpmPackage pi) throws Exception {
|
||||
loadedIgs.add(pi.name()+"#"+pi.version());
|
||||
for (String s : pi.dependencies()) {
|
||||
if (!loadedIgs.contains(s)) {
|
||||
if (!VersionUtilities.isCorePackage(s)) {
|
||||
System.out.println("+ .. load IG from "+s);
|
||||
fetchByPackage(s);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
Map<String, byte[]> res = new HashMap<String, byte[]>();
|
||||
for (String s : pi.listResources("CodeSystem", "ConceptMap", "ImplementationGuide", "CapabilityStatement", "Conformance", "StructureMap", "ValueSet", "StructureDefinition")) {
|
||||
res.put(s, TextFile.streamToBytes(pi.load("package", s)));
|
||||
@ -772,7 +789,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
||||
|
||||
public void loadIg(String src, boolean recursive) throws IOException, FHIRException, Exception {
|
||||
String canonical = null;
|
||||
Map<String, byte[]> source = loadIgSource(src, recursive);
|
||||
Map<String, byte[]> source = loadIgSource(src, recursive, true);
|
||||
String version = Constants.VERSION;
|
||||
if (this.version != null)
|
||||
version = this.version;
|
||||
@ -893,7 +910,7 @@ public class ValidationEngine implements IValidatorResourceFetcher {
|
||||
}
|
||||
|
||||
public Content loadContent(String source, String opName) throws Exception {
|
||||
Map<String, byte[]> s = loadIgSource(source, false);
|
||||
Map<String, byte[]> s = loadIgSource(source, false, false);
|
||||
Content res = new Content();
|
||||
if (s.size() != 1)
|
||||
throw new Exception("Unable to find resource " + source + " to "+opName);
|
||||
|
||||
@ -513,7 +513,7 @@ public class Validator {
|
||||
validator.setVersion(sv);
|
||||
for (String src : igs) {
|
||||
System.out.println("+ .. load IG from "+src);
|
||||
validator.loadIg(src, recursive);
|
||||
validator.loadIg(src, recursive);
|
||||
}
|
||||
validator.setQuestionnaires(questionnaires);
|
||||
validator.setNative(doNative);
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user