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Builds the hapi fhir utilities. Requires the hapi-fhir-base be built first and be excluded
from any other poms requiring it.
The newest version!
package org.hl7.fhir.utilities.npm;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.io.BufferedOutputStream;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.charset.StandardCharsets;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.UUID;
import java.util.zip.Deflater;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import javax.annotation.Nonnull;
import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream;
import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
import org.apache.commons.compress.compressors.gzip.GzipCompressorOutputStream;
import org.apache.commons.compress.compressors.gzip.GzipParameters;
import org.hl7.fhir.exceptions.FHIRException;
import org.hl7.fhir.utilities.ByteProvider;
import org.hl7.fhir.utilities.CommaSeparatedStringBuilder;
import org.hl7.fhir.utilities.SimpleHTTPClient;
import org.hl7.fhir.utilities.SimpleHTTPClient.HTTPResult;
import org.hl7.fhir.utilities.TextFile;
import org.hl7.fhir.utilities.Utilities;
import org.hl7.fhir.utilities.json.JsonException;
import org.hl7.fhir.utilities.json.model.JsonArray;
import org.hl7.fhir.utilities.json.model.JsonElement;
import org.hl7.fhir.utilities.json.model.JsonObject;
import org.hl7.fhir.utilities.json.model.JsonProperty;
import org.hl7.fhir.utilities.json.parser.JsonParser;
import org.hl7.fhir.utilities.npm.PackageGenerator.PackageType;
/**
* info and loader for a package
*
* Packages may exist on disk in the cache, or purely in memory when they are loaded on the fly
*
* Packages are contained in subfolders (see the package spec). The FHIR resources will be in "package"
*
* @author Grahame Grieve
*
*/
public class NpmPackage {
public interface ITransformingLoader {
byte[] load(File f);
}
public class PackageResourceInformationSorter implements Comparator {
@Override
public int compare(PackageResourceInformation o1, PackageResourceInformation o2) {
return o1.filename.compareTo(o2.filename);
}
}
public class PackageResourceInformation {
private String id;
private String resourceType;
private String url;
private String version;
private String filename;
private String supplements;
private String stype;
private String derivation;
private String content;
public PackageResourceInformation(String root, JsonObject fi) throws IOException {
super();
id = fi.asString("id");
resourceType = fi.asString("resourceType");
url = fi.asString("url");
version = fi.asString("version");
filename = Utilities.path(root, fi.asString("filename"));
supplements = fi.asString("supplements");
stype = fi.asString("type");
derivation = fi.asString("derivation");
content = fi.asString("content");
}
public String getId() {
return id;
}
public String getResourceType() {
return resourceType;
}
public String getStatedType() {
return stype;
}
public String getUrl() {
return url;
}
public String getVersion() {
return version;
}
public String getFilename() {
return filename;
}
public String getSupplements() {
return supplements;
}
public boolean hasId() {
return !Utilities.noString(id);
}
public String getDerivation() {
return derivation;
}
public String getContent() {
return content;
}
}
public class IndexVersionSorter implements Comparator {
@Override
public int compare(JsonObject o0, JsonObject o1) {
String v0 = o0.asString("version");
String v1 = o1.asString("version");
return v0.compareTo(v1);
}
}
public static boolean isValidName(String pid) {
return pid.matches("^[a-z][a-zA-Z0-9]*(\\.[a-z][a-zA-Z0-9\\-]*)+$");
}
public static boolean isValidVersion(String ver) {
return ver.matches("^[0-9]+\\.[0-9]+\\.[0-9]+$");
}
public class NpmPackageFolder {
private String folderName;
private Map> types;
private Map content;
private JsonObject cachedIndex;
private File folder;
public NpmPackageFolder(String folderName) {
super();
this.folderName = folderName;
if (!minimalMemory) {
types = new HashMap<>();
content = new HashMap<>();
}
}
private String fn(String name) throws IOException {
return Utilities.path(folder.getAbsolutePath(), name);
}
public Map> getTypes() throws JsonException, IOException {
if (minimalMemory) {
Map> typeMap = new HashMap<>();
readIndex(JsonParser.parseObjectFromFile(fn(".index.json")), typeMap);
return typeMap;
} else {
return types;
}
}
public String getFolderName() {
return folderName;
}
public String getFolderPath() {
return folder == null ? null : folder.getAbsolutePath();
}
public boolean readIndex(JsonObject index, Map> typeMap) {
if (!index.has("index-version") || (index.asInteger("index-version") != NpmPackageIndexBuilder.CURRENT_INDEX_VERSION)) {
return false;
}
if (!minimalMemory) {
this.cachedIndex = index;
}
for (JsonObject file : index.getJsonObjects("files")) {
String type = file.asString("resourceType");
String name = file.asString("filename");
if (!typeMap.containsKey(type))
typeMap.put(type, new ArrayList<>());
typeMap.get(type).add(name);
}
return true;
}
public List listFiles() {
List res = new ArrayList<>();
if (folder != null) {
for (File f : folder.listFiles()) {
if (!f.isDirectory() && !Utilities.existsInList(f.getName(), "package.json", ".index.json", ".index.db", ".oids.json", ".oids.db")) {
res.add(f.getName());
}
}
} else {
for (String s : content.keySet()) {
if (!Utilities.existsInList(s, "package.json", ".index.json", ".index.db", ".oids.json", ".oids.db")) {
res.add(s);
}
}
}
Collections.sort(res);
return res;
}
public Map getContent() {
assert !minimalMemory;
return content;
}
public byte[] fetchFile(String file) throws FileNotFoundException, IOException {
if (folder != null) {
File f = new File(Utilities.path(folder.getAbsolutePath(), file));
if (f.exists()) {
return TextFile.fileToBytes(f);
} else {
return null;
}
} else {
return content.get(file);
}
}
public ByteProvider getProvider(String file) throws FileNotFoundException, IOException {
if (folder != null) {
File f = new File(Utilities.path(folder.getAbsolutePath(), file));
if (f.exists()) {
return ByteProvider.forFile(f);
} else {
return null;
}
} else {
return ByteProvider.forBytes(content.get(file));
}
}
public boolean hasFile(String file) throws IOException {
if (folder != null) {
return new File(Utilities.path(folder.getAbsolutePath(), file)).exists();
} else {
return content.containsKey(file);
}
}
public String dump() {
return folderName + " ("+ (folder == null ? "null" : folder.toString())+")"+(minimalMemory ? "" : " | "+Boolean.toString(cachedIndex != null)+" | "+content.size()+" | "+types.size());
}
public void removeFile(String n) throws IOException {
if (folder != null) {
new File(Utilities.path(folder.getAbsolutePath(), n)).delete();
} else {
content.remove(n);
}
changedByLoader = true;
}
public JsonObject index() throws IOException {
if (cachedIndex != null) {
return cachedIndex;
} else if (folder == null) {
return null;
} else {
File ij = new File(fn(".index.json"));
if (ij.exists()) {
return JsonParser.parseObject(ij);
} else {
return null;
}
}
}
public JsonObject oidIndex() throws IOException {
if (folder == null) {
return null;
} else {
File ij = new File(fn(".oids.json"));
if (ij.exists()) {
return JsonParser.parseObject(ij);
} else {
return null;
}
}
}
}
private String path;
private JsonObject npm;
private Map folders = new HashMap<>();
private boolean changedByLoader; // internal qa only!
private Map userData;
private boolean minimalMemory;
private int size;
private boolean warned = false;
/**
* Constructor
*/
private NpmPackage() {
super();
}
/**
* Factory method that parses a package from an extracted folder
*/
public static NpmPackage fromFolder(String path) throws IOException {
NpmPackage res = new NpmPackage();
res.loadFiles(path, new File(path));
res.checkIndexed(path);
return res;
}
/**
* Factory method that parses a package from an extracted folder
*/
public static NpmPackage fromFolderMinimal(String path) throws IOException {
NpmPackage res = new NpmPackage();
res.minimalMemory = true;
res.loadFiles(path, new File(path));
res.checkIndexed(path);
return res;
}
/**
* Factory method that starts a new empty package using the given PackageGenerator to create the manifest
*/
public static NpmPackage empty(PackageGenerator thePackageGenerator) {
NpmPackage retVal = new NpmPackage();
retVal.npm = thePackageGenerator.getRootJsonObject();
return retVal;
}
/**
* Factory method that starts a new empty package using the given PackageGenerator to create the manifest
*/
public static NpmPackage empty() {
NpmPackage retVal = new NpmPackage();
return retVal;
}
public Map getUserData() {
if (userData == null) {
userData = new HashMap<>();
}
return userData;
}
public void loadFiles(String path, File source, String... exemptions) throws FileNotFoundException, IOException {
this.npm = JsonParser.parseObject(TextFile.fileToString(Utilities.path(path, "package", "package.json")));
this.path = path;
File dir = new File(path);
for (File f : dir.listFiles()) {
if (!isInternalExemptFile(f) && !Utilities.existsInList(f.getName(), exemptions)) {
if (f.isDirectory()) {
String d = f.getName();
if (!d.equals("package")) {
d = Utilities.path("package", d);
}
File ij = new File(Utilities.path(f.getAbsolutePath(), ".index.json"));
NpmPackageFolder folder = this.new NpmPackageFolder(d);
folder.folder = f;
this.folders.put(d, folder);
if (ij.exists() || !minimalMemory) {
if (!minimalMemory) {
try {
if (!ij.exists() || !folder.readIndex(JsonParser.parseObject(ij), folder.getTypes())) {
indexFolder(folder.getFolderName(), folder);
}
} catch (Exception e) {
throw new IOException("Error parsing "+ij.getAbsolutePath()+": "+e.getMessage(), e);
}
}
}
loadSubFolders(dir.getAbsolutePath(), f);
} else {
NpmPackageFolder folder = this.new NpmPackageFolder(Utilities.path("package", "$root"));
folder.folder = dir;
this.folders.put(Utilities.path("package", "$root"), folder);
}
}
}
}
public static boolean isInternalExemptFile(File f) {
return Utilities.existsInList(f.getName(), ".git", ".svn", ".DS_Store") || Utilities.existsInList(f.getName(), "package-list.json") ||
Utilities.endsWithInList(f.getName(), ".tgz");
}
private void loadSubFolders(String rootPath, File dir) throws IOException {
for (File f : dir.listFiles()) {
if (f.isDirectory()) {
String d = f.getAbsolutePath().substring(rootPath.length()+1);
if (!d.startsWith("package")) {
d = Utilities.path("package", d);
}
NpmPackageFolder folder = this.new NpmPackageFolder(d);
folder.folder = f;
this.folders.put(d, folder);
File ij = new File(Utilities.path(f.getAbsolutePath(), ".index.json"));
if (ij.exists() || !minimalMemory) {
try {
if (!ij.exists() || !folder.readIndex(JsonParser.parseObject(ij), folder.getTypes())) {
indexFolder(folder.getFolderName(), folder);
}
} catch (Exception e) {
throw new IOException("Error parsing "+ij.getAbsolutePath()+": "+e.getMessage(), e);
}
}
loadSubFolders(rootPath, f);
}
}
}
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 = JsonParser.parseObject(new String(res.folders.get("package").fetchFile("package.json")));
return res;
}
private static final int BUFFER_SIZE = 1024;
public static @Nonnull NpmPackage fromPackage(InputStream tgz) throws IOException {
return fromPackage(tgz, null, false);
}
public static NpmPackage fromPackage(InputStream tgz, String desc) throws IOException {
return fromPackage(tgz, desc, false);
}
public static NpmPackage fromPackage(InputStream tgz, String desc, boolean progress) throws IOException {
NpmPackage res = new NpmPackage();
res.readStream(tgz, desc, progress);
return res;
}
public static NpmPackage extractFromTgz(InputStream tgz, String desc, String tempDir, boolean minimal) throws IOException {
Utilities.createDirectory(tempDir);
int size = 0;
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;
while ((entry = (TarArchiveEntry) tarIn.getNextEntry()) != null) {
String n = entry.getName();
if (n.contains("/..") || n.contains("../")) {
throw new RuntimeException("Entry with an illegal name: " + n);
}
if (entry.isDirectory()) {
if (!Utilities.noString(n)) {
String dir = n.substring(0, n.length()-1);
Utilities.createDirectory(Utilities.path(tempDir, dir));
}
} else {
int count;
byte data[] = new byte[BUFFER_SIZE];
String filename = Utilities.path(tempDir, n);
String folder = Utilities.getDirectoryForFile(filename);
Utilities.createDirectory(folder);
FileOutputStream fos = new FileOutputStream(filename);
try (BufferedOutputStream dst = new BufferedOutputStream(fos, BUFFER_SIZE)) {
while ((count = tarIn.read(data, 0, BUFFER_SIZE)) != -1) {
dst.write(data, 0, count);
size = size + count;
}
}
fos.close();
}
}
}
try {
NpmPackage npm = NpmPackage.fromFolderMinimal(tempDir);
npm.setSize(size);
if (!minimal) {
npm.checkIndexed(desc);
}
return npm;
} catch (Exception e) {
throw new IOException("Error parsing "+(desc == null ? "" : desc+"#")+"package/package.json: "+e.getMessage(), e);
}
}
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 (n.contains("..")) {
throw new RuntimeException("Entry with an illegal name: " + n);
}
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 = JsonParser.parseObject(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);
}
public void loadFile(String n, byte[] data) throws IOException {
String dir = n.contains("/") ? n.substring(0, n.lastIndexOf("/")) : "$root";
if (dir.startsWith("package/")) {
dir = dir.substring(8);
}
n = n.substring(n.lastIndexOf("/")+1);
NpmPackageFolder index = folders.get(dir);
if (index == null) {
index = new NpmPackageFolder(dir);
folders.put(dir, index);
}
index.content.put(n, data);
}
private void checkIndexed(String desc) throws IOException {
for (NpmPackageFolder folder : folders.values()) {
JsonObject index = folder.index();
if (index == null || index.forceArray("files").size() == 0) {
indexFolder(desc, folder);
}
}
}
public void indexFolder(String desc, NpmPackageFolder folder) throws FileNotFoundException, IOException {
List remove = new ArrayList<>();
NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();
indexer.start(folder.folder != null ? Utilities.path(folder.folder.getAbsolutePath(), ".index.db") : null);
for (String n : folder.listFiles()) {
if (!indexer.seeFile(n, folder.fetchFile(n))) {
remove.add(n);
}
}
for (String n : remove) {
folder.removeFile(n);
}
String json = indexer.build();
try {
if (!minimalMemory) {
folder.readIndex(JsonParser.parseObject(json), folder.getTypes());
}
if (folder.folder != null) {
TextFile.stringToFile(json, Utilities.path(folder.folder.getAbsolutePath(), ".index.json"));
}
} catch (Exception e) {
TextFile.stringToFile(json, Utilities.path("[tmp]", ".index.json"));
throw new IOException("Error parsing "+(desc == null ? "" : desc+"#")+"package/"+folder.folderName+"/.index.json: "+e.getMessage(), e);
}
}
public static NpmPackage fromZip(InputStream stream, boolean dropRootFolder, String desc) throws IOException {
NpmPackage res = new NpmPackage();
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.loadFile(ze.getName().substring(ze.getName().indexOf("/")+1), bytes.toByteArray());
} else {
res.loadFile(ze.getName(), bytes.toByteArray());
}
}
zip.closeEntry();
}
zip.close();
try {
res.npm = JsonParser.parseObject(res.folders.get("package").fetchFile("package.json"));
} catch (Exception e) {
throw new IOException("Error parsing "+(desc == null ? "" : desc+"#")+"package/package.json: "+e.getMessage(), e);
}
res.checkIndexed(desc);
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 list(String folder) throws IOException {
List res = new ArrayList();
if (folders.containsKey(folder)) {
for (String s : folders.get(folder).listFiles()) {
if (!s.startsWith(".")) {
res.add(s);
}
}
} else if (folders.containsKey(Utilities.path("package", folder))) {
for (String s : folders.get(Utilities.path("package", folder)).listFiles()) {
if (!s.startsWith(".")) {
res.add(s);
}
}
}
return res;
}
public List listResources(String... types) throws IOException {
return listResources(Utilities.strings(types));
}
public List listResources(List types) throws IOException {
List res = new ArrayList();
NpmPackageFolder folder = folders.get("package");
if (types.size() == 0) {
for (String s : folder.types.keySet()) {
if (folder.types.containsKey(s)) {
res.addAll(folder.types.get(s));
}
}
} else {
for (String s : types) {
if (folder.types.containsKey(s)) {
res.addAll(folder.types.get(s));
}
}
}
Collections.sort(res);
return res;
}
public List listIndexedResources(String... types) throws IOException {
return listIndexedResources(Utilities.strings(types));
}
public List listIndexedResources(List types) throws IOException {
List res = new ArrayList();
for (NpmPackageFolder folder : folders.values()) {
JsonObject index = folder.index();
if (index != null) {
for (JsonObject fi : index.getJsonObjects("files")) {
if (Utilities.existsInList(fi.asString("resourceType"), types) || types.isEmpty()) {
res.add(new PackageResourceInformation(folder.folder == null ? "@"+folder.getFolderName() : folder.folder.getAbsolutePath(), fi));
}
}
}
}
// Collections.sort(res, new PackageResourceInformationSorter());
return res;
}
/**
* use the name from listResources()
*
* @param file
* @return
* @throws IOException
*/
public InputStream loadResource(String file) throws IOException {
NpmPackageFolder folder = folders.get("package");
return new ByteArrayInputStream(folder.fetchFile(file));
}
/**
* get a stream that contains the contents of a resource in the base folder, by it's canonical URL
*
* @param canonical - the canonical URL of the resource (exact match only)
* @return null if it is not found
* @throws IOException
*/
public InputStream loadByCanonical(String canonical) throws IOException {
return loadByCanonicalVersion("package", canonical, null);
}
/**
* get a stream that contains the contents of a resource in the nominated folder, by it's canonical URL
*
* @param folder - one of the folders in the package (main folder is "package")
* @param canonical - the canonical URL of the resource (exact match only)
* @return null if it is not found
* @throws IOException
*/
public InputStream loadByCanonical(String folder, String canonical) throws IOException {
return loadByCanonicalVersion(folder, canonical, null);
}
/**
* get a stream that contains the contents of a resource in the base folder, by it's canonical URL
*
* @param canonical - the canonical URL of the resource (exact match only)
* @param version - the specified version (or null if the most recent)
*
* @return null if it is not found
* @throws IOException
*/
public InputStream loadByCanonicalVersion(String canonical, String version) throws IOException {
return loadByCanonicalVersion("package", canonical, version);
}
/**
* get a stream that contains the contents of a resource in the nominated folder, by it's canonical URL
*
* @param folder - one of the folders in the package (main folder is "package")
* @param canonical - the canonical URL of the resource (exact match only)
* @param version - the specified version (or null if the most recent)
*
* @return null if it is not found
* @throws IOException
*/
public InputStream loadByCanonicalVersion(String folder, String canonical, String version) throws IOException {
NpmPackageFolder f = folders.get(folder);
List matches = new ArrayList<>();
for (JsonObject file : f.index().getJsonObjects("files")) {
if (canonical.equals(file.asString("url"))) {
if (version != null && version.equals(file.asString("version"))) {
return load("package", file.asString("filename"));
} else if (version == null) {
matches.add(file);
}
}
if (matches.size() > 0) {
if (matches.size() == 1) {
return load("package", matches.get(0).asString("filename"));
} else {
Collections.sort(matches, new IndexVersionSorter());
return load("package", matches.get(matches.size()-1).asString("filename"));
}
}
}
return null;
}
/**
* get a stream that contains the contents of one of the files in the base package
*
* @param file
* @return
* @throws IOException
*/
public InputStream load(String file) throws IOException {
return load("package", file);
}
/**
* 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 {
NpmPackageFolder f = folders.get(folder);
if (f == null) {
f = folders.get(Utilities.path("package", folder));
}
if (f != null && f.hasFile(file)) {
return new ByteArrayInputStream(f.fetchFile(file));
} else {
throw new IOException("Unable to find the file "+folder+"/"+file+" in the package "+name());
}
}
/**
* get a stream that contains the contents of one of the files in a folder
*
* @param folder
* @param file
* @return
* @throws IOException
*/
public ByteProvider getProvider(String folder, String file) throws IOException {
NpmPackageFolder f = folders.get(folder);
if (f == null) {
f = folders.get(Utilities.path("package", folder));
}
if (f != null && f.hasFile(file)) {
return f.getProvider(file);
} else {
throw new IOException("Unable to find the file "+folder+"/"+file+" in the package "+name());
}
}
public boolean hasFile(String folder, String file) throws IOException {
NpmPackageFolder f = folders.get(folder);
if (f == null) {
f = folders.get(Utilities.path("package", folder));
}
return f != null && f.hasFile(file);
}
/**
* Handle to the package json file
*
* @return
*/
public JsonObject getNpm() {
return npm;
}
/**
* should only use this when npm == null
*
* @param npm
*/
public void setNpm(JsonObject npm) {
this.npm = npm;
}
/**
* convenience method for getting the package name
* @return
*/
public String name() {
return npm.asString("name");
}
/**
* convenience method for getting the package id (which in NPM language is the same as the name)
* @return
*/
public String id() {
return npm.asString("name");
}
public String date() {
return npm.asString("date");
}
public String canonical() {
return npm.asString("canonical");
}
/**
* convenience method for getting the package version
* @return
*/
public String version() {
return npm.asString("version");
}
/**
* convenience method for getting the package fhir version
* @return
*/
public String fhirVersion() {
if ("hl7.fhir.core".equals(npm.asString("name")))
return npm.asString("version");
else if (npm.asString("name").startsWith("hl7.fhir.r2.") || npm.asString("name").startsWith("hl7.fhir.r2b.") || npm.asString("name").startsWith("hl7.fhir.r3.") ||
npm.asString("name").startsWith("hl7.fhir.r4.") || npm.asString("name").startsWith("hl7.fhir.r4b.") || npm.asString("name").startsWith("hl7.fhir.r5."))
return npm.asString("version");
else {
JsonObject dep = null;
if (npm.hasObject("dependencies")) {
dep = npm.getJsonObject("dependencies");
if (dep != null) {
for (JsonProperty e : dep.getProperties()) {
if (Utilities.existsInList(e.getName(), "hl7.fhir.r2.core", "hl7.fhir.r2b.core", "hl7.fhir.r3.core", "hl7.fhir.r4.core"))
return e.getValue().asString();
if (Utilities.existsInList(e.getName(), "hl7.fhir.core")) // while all packages are updated
return e.getValue().asString();
}
}
}
if (npm.hasArray("fhirVersions")) {
JsonArray e = npm.getJsonArray("fhirVersions");
if (e.size() > 0) {
return e.getItems().get(0).asString();
}
}
if (dep != null) {
// 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()) || template.getOldCode().equals(type()) ;
}
public String type() {
return npm.asString("type");
}
public String description() {
return npm.asString("description");
}
public String getPath() {
return path;
}
public List dependencies() {
List res = new ArrayList<>();
if (npm.has("dependencies")) {
for (JsonProperty e : npm.getJsonObject("dependencies").getProperties()) {
res.add(e.getName()+"#"+e.getValue().asString());
}
}
return res;
}
public String homepage() {
return npm.asString("homepage");
}
public String url() {
return npm.asString("url");
}
public String title() {
return npm.asString("title");
}
public String toolsVersion() {
return npm.asString("tools-version");
}
public String license() {
return npm.asString("license");
}
// /**
// * only for use by the package manager itself
// *
// * @param path
// */
// public void setPath(String path) {
// this.path = path;
// }
public String getWebLocation() {
if (npm.hasPrimitive("url")) {
return PackageHacker.fixPackageUrl(npm.asString("url"));
} else {
return npm.asString("canonical");
}
}
public InputStream loadResource(String type, String id) throws IOException {
NpmPackageFolder f = folders.get("package");
JsonArray files = f.index().getJsonArray("files");
for (JsonElement e : files.getItems()) {
JsonObject i = (JsonObject) e;
if (type.equals(i.asString("resourceType")) && id.equals(i.asString("id"))) {
return load("package", i.asString("filename"));
}
}
return null;
}
public InputStream loadExampleResource(String type, String id) throws IOException {
NpmPackageFolder f = folders.get("example");
if (f == null) {
f = folders.get("package/example");
}
if (f != null) {
JsonArray files = f.index().getJsonArray("files");
for (JsonElement e : files.getItems()) {
JsonObject i = (JsonObject) e;
if (type.equals(i.asString("resourceType")) && id.equals(i.asString("id"))) {
return load("example", i.asString("filename"));
}
}
}
return null;
}
/** special case when playing around inside the package **/
public Map getFolders() {
return folders;
}
public void save(File directory) throws IOException {
assert !minimalMemory;
File dir = new File(Utilities.path(directory.getAbsolutePath(), name()));
if (!dir.exists()) {
Utilities.createDirectory(dir.getAbsolutePath());
} else {
Utilities.clearDirectory(dir.getAbsolutePath());
}
for (NpmPackageFolder folder : folders.values()) {
String n = folder.folderName;
File pd = new File(Utilities.path(dir.getAbsolutePath(), n));
if (!pd.exists()) {
Utilities.createDirectory(pd.getAbsolutePath());
}
NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();
indexer.start(Utilities.path(dir.getAbsolutePath(), n, ".index.db"));
for (String s : folder.content.keySet()) {
byte[] b = folder.content.get(s);
indexer.seeFile(s, b);
if (!s.equals(".index.json") && !s.equals("package.json")) {
TextFile.bytesToFile(b, Utilities.path(dir.getAbsolutePath(), n, s));
}
}
byte[] cnt = indexer.build().getBytes(StandardCharsets.UTF_8);
TextFile.bytesToFile(cnt, Utilities.path(dir.getAbsolutePath(), n, ".index.json"));
}
byte[] cnt = TextFile.stringToBytes(JsonParser.compose(npm, true));
TextFile.bytesToFile(cnt, Utilities.path(dir.getAbsolutePath(), "package", "package.json"));
}
public void save(OutputStream stream) throws IOException {
assert !minimalMemory;
TarArchiveOutputStream tar;
// ByteArrayOutputStream OutputStream;
// BufferedOutputStream bufferedOutputStream;
GzipCompressorOutputStream gzipOutputStream;
// OutputStream = new ByteArrayOutputStream();
// bufferedOutputStream = new BufferedOutputStream(OutputStream);
GzipParameters gp = new GzipParameters();
gp.setCompressionLevel(Deflater.BEST_COMPRESSION);
gzipOutputStream = new GzipCompressorOutputStream(stream, gp);
tar = new TarArchiveOutputStream(gzipOutputStream);
for (NpmPackageFolder folder : folders.values()) {
String n = folder.folderName;
if (!"package".equals(n) && !(n.startsWith("package/") || n.startsWith("package\\"))) {
n = "package/"+n;
}
NpmPackageIndexBuilder indexer = new NpmPackageIndexBuilder();
String filename = Utilities.path("[tmp]", "tmp-"+UUID.randomUUID().toString()+".db");
indexer.start(filename);
for (String s : folder.content.keySet()) {
byte[] b = folder.content.get(s);
String name = n+"/"+s;
if (b == null) {
System.out.println(name+" is null");
} else {
indexer.seeFile(s, b);
if (!s.equals(".index.json") && !s.equals(".index.db") && !s.equals("package.json")) {
TarArchiveEntry entry = new TarArchiveEntry(name);
entry.setSize(b.length);
tar.putArchiveEntry(entry);
tar.write(b);
tar.closeArchiveEntry();
}
}
}
byte[] cnt = indexer.build().getBytes(StandardCharsets.UTF_8);
TarArchiveEntry entry = new TarArchiveEntry(n+"/.index.json");
entry.setSize(cnt.length);
tar.putArchiveEntry(entry);
tar.write(cnt);
tar.closeArchiveEntry();
var file = new File(filename);
if (file.exists()) {
cnt = TextFile.fileToBytes(file);
file.delete();
entry = new TarArchiveEntry(n+"/.index.db");
entry.setSize(cnt.length);
tar.putArchiveEntry(entry);
tar.write(cnt);
tar.closeArchiveEntry();
}
}
byte[] cnt = TextFile.stringToBytes(JsonParser.compose(npm, true));
TarArchiveEntry entry = new TarArchiveEntry("package/package.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);
}
/**
* Keys are resource type names, values are filenames
*/
public Map> getTypes() {
return folders.get("package").types;
}
public String fhirVersionList() {
if (npm.has("fhirVersions")) {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
if (npm.hasArray("fhirVersions")) {
for (String n : npm.getJsonArray("fhirVersions").asStrings()) {
b.append(n);
}
}
if (npm.hasPrimitive("fhirVersions")) {
b.append(npm.asString("fhirVersions"));
}
return b.toString();
} else
return "";
}
public String dependencySummary() {
if (npm.has("dependencies")) {
CommaSeparatedStringBuilder b = new CommaSeparatedStringBuilder();
for (JsonProperty e : npm.getJsonObject("dependencies").getProperties()) {
b.append(e.getName()+"#"+e.getValue().asString());
}
return b.toString();
} else
return "";
}
public void unPack(String dir) throws IOException {
unPack (dir, false, new ArrayList<>());
}
public void unPackWithAppend(String dir, List files) throws IOException {
unPack (dir, true, files);
}
public void unPack(String dir, boolean withAppend) throws IOException {
unPack (dir, withAppend, new ArrayList<>());
}
public void unPack(String dir, boolean withAppend, List files) throws IOException {
assert !minimalMemory;
for (NpmPackageFolder folder : folders.values()) {
String dn = folder.getFolderName();
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));
f = new File(appendFn);
files.add(f.getAbsolutePath());
if (f.exists())
TextFile.appendBytesToFile(folder.fetchFile(s), appendFn);
else
TextFile.bytesToFile(folder.fetchFile(s), appendFn);
} else
files.add(f.getAbsolutePath());
TextFile.bytesToFile(folder.fetchFile(s), fn);
}
}
}
public void debugDump(String purpose) {
// System.out.println("Debug Dump of Package for '"+purpose+"'. Path = "+path);
// System.out.println(" npm = "+name()+"#"+version()+", canonical = "+canonical());
// System.out.println(" folders = "+folders.size());
// for (String s : sorted(folders.keySet())) {
// NpmPackageFolder folder = folders.get(s);
// System.out.println(" "+folder.dump());
// }
}
private List sorted(Set keys) {
List res = new ArrayList();
res.addAll(keys);
Collections.sort(res);
return res ;
}
public void clearFolder(String folderName) {
NpmPackageFolder folder = folders.get(folderName);
folder.content.clear();
folder.types.clear();
}
public void deleteFolder(String folderName) {
folders.remove(folderName);
}
public void addFile(String folderName, String name, byte[] cnt, String type) {
assert !minimalMemory;
if (!folders.containsKey(folderName)) {
folders.put(folderName, new NpmPackageFolder(folderName));
}
NpmPackageFolder folder = folders.get(folderName);
folder.content.put(name, cnt);
if (!folder.types.containsKey(type))
folder.types.put(type, new ArrayList<>());
folder.types.get(type).add(name);
if ("package".equals(folderName) && "package.json".equals(name)) {
try {
npm = JsonParser.parseObject(cnt);
} catch (IOException e) {
}
}
}
public void loadAllFiles() throws IOException {
for (String folder : folders.keySet()) {
NpmPackageFolder pf = folders.get(folder);
String p = folder.contains("$") ? path : Utilities.path(path, folder);
File file = new File(p);
if (file.exists()) {
for (File f : file.listFiles()) {
if (!f.isDirectory() && !isInternalExemptFile(f)) {
pf.getContent().put(f.getName(), TextFile.fileToBytes(f));
}
}
}
}
}
public void loadAllFiles(ITransformingLoader loader) throws IOException {
for (String folder : folders.keySet()) {
NpmPackageFolder pf = folders.get(folder);
String p = folder.contains("$") ? path : Utilities.path(path, folder);
for (File f : new File(p).listFiles()) {
if (!f.isDirectory() && !isInternalExemptFile(f)) {
pf.getContent().put(f.getName(), loader.load(f));
}
}
}
}
public boolean isChangedByLoader() {
return changedByLoader;
}
public boolean isCore() {
return Utilities.existsInList(npm.asString("type"), "fhir.core", "Core");
}
public boolean isCoreExamples() {
return name().startsWith("hl7.fhir.r") && name().endsWith(".examples");
}
public boolean isTx() {
return npm.asString("name").startsWith("hl7.terminology");
}
public boolean hasCanonical(String url) throws IOException {
if (url == null) {
return false;
}
String u = url.contains("|") ? url.substring(0, url.indexOf("|")) : url;
String v = url.contains("|") ? url.substring(url.indexOf("|")+1) : null;
NpmPackageFolder folder = folders.get("package");
if (folder != null) {
for (JsonObject o : folder.index().getJsonObjects("files")) {
if (u.equals(o.asString("url"))) {
if (v == null || v.equals(o.asString("version"))) {
return true;
}
}
}
}
return false;
}
public boolean canLazyLoad() throws IOException {
for (NpmPackageFolder folder : folders.values()) {
if (folder.folder == null) {
return false;
}
}
if (Utilities.existsInList(name(), "fhir.test.data.r2", "fhir.test.data.r3", "fhir.test.data.r4", "fhir.tx.support.r2", "fhir.tx.support.r3", "fhir.tx.support.r4", "us.nlm.vsac")) {
return true;
}
if (npm.asBoolean("lazy-load")) {
return true;
}
if (!hasFile("other", "spec.internals") && folders.get("package").cachedIndex == null) {
return false;
}
return true;
}
public boolean isNotForPublication() {
return npm.asBoolean("notForPublication");
}
public InputStream load(PackageResourceInformation p) throws FileNotFoundException {
if (p.filename.startsWith("@")) {
String[] pl = p.filename.substring(1).split("\\/");
return new ByteArrayInputStream(folders.get(pl[0]).content.get(pl[1]));
} else {
return new FileInputStream(p.filename);
}
}
public Date dateAsDate() {
try {
String d = date();
if (d == null) {
switch (name()) {
case "hl7.fhir.r2.core": d = "20151024000000"; break;
case "hl7.fhir.r2b.core": d = "20160330000000"; break;
case "hl7.fhir.r3.core": d = "20191024000000"; break;
case "hl7.fhir.r4.core": d = "20191030000000"; break;
case "hl7.fhir.r4b.core": d = "202112200000000"; break;
case "hl7.fhir.r5.core": d = "20211219000000"; break;
default:
return new Date();
}
}
return new SimpleDateFormat("yyyyMMddHHmmss").parse(d);
} catch (ParseException e) {
// this really really shouldn't happen
return new Date();
}
}
public static NpmPackage fromUrl(String source) throws IOException {
SimpleHTTPClient fetcher = new SimpleHTTPClient();
HTTPResult res = fetcher.get(source+"?nocache=" + System.currentTimeMillis());
res.checkThrowException();
return fromPackage(new ByteArrayInputStream(res.getContent()));
}
@Override
public String toString() {
return "NpmPackage "+name()+"#"+version()+" [path=" + path + "]";
}
public String getFilePath(String d) throws IOException {
return Utilities.path(path, "package", d);
}
public boolean isMinimalMemory() {
return minimalMemory;
}
public int getSize() {
return size;
}
public void setSize(int size) {
this.size = size;
}
public boolean isWarned() {
return warned;
}
public void setWarned(boolean warned) {
this.warned = warned;
}
} © 2015 - 2024 Weber Informatics LLC | Privacy Policy