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Merge pull request #1332 from hapifhir/gg-202206-spdx-android 

Gg 202206 spdx android
This commit is contained in:
Grahame Grieve 2023-06-30 14:30:16 +10:00 committed by GitHub
parent 06a1d523a3 dfb0e0d5b9
commit 9aca593990
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GPG Key ID: 4AEE18F83AFDEB23
7 changed files with 8091 additions and 7895 deletions
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41
org.hl7.fhir.convertors/src/main/java/org/hl7/fhir/convertors/misc/VSACImporter.java
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@ -57,6 +57,19 @@ public class VSACImporter extends OIDBasedValueSetImporter {
errs.put(oid, "Expansion: " +e.getMessage());
System.out.println(e.getMessage());
}
if (vs.hasTitle()) {
if (vs.getTitle().equals(vs.getDescription())) {
vs.setTitle(vs.getName());
} else {
System.out.println(oid);
System.out.println(" name: "+vs.getName());
System.out.println(" title: "+vs.getTitle());
System.out.println(" desc: "+vs.getDescription());
}
} else {
vs.setTitle(vs.getName());
}
vs.setName(makeValidName(vs.getName()));
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "ValueSet-" + oid + ".json")), vs);
}
i++;
@ -75,4 +88,32 @@ public class VSACImporter extends OIDBasedValueSetImporter {
new JsonParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(Utilities.path(dest, "other", "OperationOutcome-vsac-errors.json")), oo);
System.out.println("Done. " + i + " ValueSets");
}
private String makeValidName(String name) {
StringBuilder b = new StringBuilder();
boolean upper = true;
for (char ch : name.toCharArray()) {
if (ch == ' ') {
upper = true;
} else if (Character.isAlphabetic(ch)) {
if (upper) {
b.append(Character.toUpperCase(ch));
} else {
b.append(ch);
}
upper = false;
} else if (Character.isDigit(ch)) {
if (b.length() == 0) {
b.append('N');
}
b.append(ch);
} else if (ch == '_' && b.length() != 0) {
b.append(ch);
} else {
upper = true;
}
}
System.out.println(b.toString()+" from "+name);
return b.toString();
}
}

15723
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/model/ImplementationGuide.java
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File diff suppressed because one or more lines are too long

56
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/TextFile.java
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@ -62,13 +62,18 @@ public class TextFile {
List<String> result = new ArrayList<String>();
File file = new CSFile(path);
BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(file),"UTF-8"));
while( reader.ready() )
result.add(reader.readLine());
reader.close();
return result;
FileInputStream fs = new FileInputStream(file);
try {
BufferedReader reader = new BufferedReader(new InputStreamReader(fs,"UTF-8"));
while( reader.ready() )
result.add(reader.readLine());
reader.close();
return result;
} finally {
fs.close();
}
}
public static void writeAllLines(String path, List<String> lines) throws IOException
@ -141,12 +146,22 @@ public class TextFile {
}
public static String fileToString(File f) throws FileNotFoundException, IOException {
return streamToString(new FileInputStream(f));
FileInputStream fs = new FileInputStream(f);
try {
return streamToString(fs);
} finally {
fs.close();
}
}
public static String fileToString(String src) throws FileNotFoundException, IOException {
return streamToString(new FileInputStream(new CSFile(src)));
}
FileInputStream fs = new FileInputStream(new CSFile(src));
try {
return streamToString(fs);
} finally {
fs.close();
}
}
public static String streamToString(InputStream input) throws IOException {
InputStreamReader sr = new InputStreamReader(input, "UTF-8");
@ -205,7 +220,12 @@ public class TextFile {
}
public static byte[] fileToBytes(String srcFile) throws FileNotFoundException, IOException {
return streamToBytes(new FileInputStream(new CSFile(srcFile)));
FileInputStream fs = new FileInputStream(new CSFile(srcFile));
try {
return streamToBytes(fs);
} finally {
fs.close();
}
}
/**
@ -218,11 +238,21 @@ public class TextFile {
* @throws IOException
*/
public static byte[] fileToBytesNCS(String srcFile) throws FileNotFoundException, IOException {
return streamToBytes(new FileInputStream(new File(srcFile)));
FileInputStream fs = new FileInputStream(new File(srcFile));
try {
return streamToBytes(fs);
} finally {
fs.close();
}
}
public static byte[] fileToBytes(File file) throws FileNotFoundException, IOException {
return streamToBytes(new FileInputStream(file));
FileInputStream fs = new FileInputStream(file);
try {
return streamToBytes(fs);
} finally {
fs.close();
}
}
public static String bytesToString(byte[] bs) throws IOException {

26
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/Utilities.java
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@ -2033,4 +2033,30 @@ public class Utilities {
return i == 0 ? "" : s.substring(0, i+1);
}
public static void renameDirectory(String source, String dest) throws FHIRException, IOException {
File src = new File(source);
File dst = new File(dest);
if (!src.renameTo(dst)) {
int i = 0;
do {
try {
Thread.sleep(20);
} catch (Exception e) {
// nothing
}
System.gc();
i++;
} while (!src.renameTo(dst) && i < 10);
if (src.exists()) {
copyDirectory(source, dest, null);
try {
src.delete();
} catch (Exception e) {
// nothing
}
}
}
}
}

37
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/FilesystemPackageCacheManager.java
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@ -23,6 +23,7 @@ import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import java.util.UUID;
import org.apache.commons.io.FileUtils;
import org.hl7.fhir.exceptions.FHIRException;
@ -421,7 +422,9 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
public NpmPackage addPackageToCache(String id, String version, InputStream packageTgzInputStream, String sourceDesc) throws IOException {
checkValidVersionString(version, id);
NpmPackage npm = NpmPackage.fromPackage(packageTgzInputStream, sourceDesc, true);
String uuid = UUID.randomUUID().toString().toLowerCase();
String tempDir = Utilities.path(cacheFolder, uuid);
NpmPackage npm = NpmPackage.extractFromTgz(packageTgzInputStream, sourceDesc, tempDir, minimalMemory);
if (progress) {
log("");
@ -450,40 +453,18 @@ public class FilesystemPackageCacheManager extends BasePackageCacheManager imple
} catch (Throwable t) {
log("Unable to clear directory: "+packRoot+": "+t.getMessage()+" - this may cause problems later");
}
int i = 0;
int c = 0;
int size = 0;
for (Entry<String, NpmPackageFolder> e : npm.getFolders().entrySet()) {
String dir = e.getKey().equals("package") ? Utilities.path(packRoot, "package") : Utilities.path(packRoot, "package", e.getKey());
if (!(new File(dir).exists()))
Utilities.createDirectory(dir);
for (Entry<String, byte[]> fe : e.getValue().getContent().entrySet()) {
String fn = Utilities.path(dir, Utilities.cleanFileName(fe.getKey()));
byte[] cnt = fe.getValue();
TextFile.bytesToFile(cnt, fn);
size = size + cnt.length;
i++;
if (progress && i % 50 == 0) {
c++;
logn(".");
if (c == 120) {
log("");
logn(" ");
c = 2;
}
}
}
}
Utilities.renameDirectory(tempDir, packRoot);
IniFile ini = new IniFile(Utilities.path(cacheFolder, "packages.ini"));
ini.setTimeStampFormat("yyyyMMddhhmmss");
ini.setTimestampProperty("packages", id + "#" + v, Timestamp.from(Instant.now()), null);
ini.setIntegerProperty("package-sizes", id + "#" + v, size, null);
ini.setIntegerProperty("package-sizes", id + "#" + v, npm.getSize(), null);
ini.save();
if (progress)
log(" done.");
} else {
Utilities.clearDirectory(tempDir);
new File(tempDir).delete();
}
if (!id.equals(npm.getNpm().asString("name")) || !v.equals(npm.getNpm().asString("version"))) {
if (!id.equals(npm.getNpm().asString("name"))) {

72
org.hl7.fhir.utilities/src/main/java/org/hl7/fhir/utilities/npm/NpmPackage.java
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@ -36,6 +36,7 @@ import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
@ -295,6 +296,7 @@ public class NpmPackage {
private boolean changedByLoader; // internal qa only!
private Map<String, Object> userData;
private boolean minimalMemory;
private int size;
/**
* Constructor
@ -443,7 +445,64 @@ public class NpmPackage {
res.readStream(tgz, desc, progress);
return res;
}
public static NpmPackage extractFromTgz(InputStream tgz, String desc, String tempDir, boolean minimal) throws IOException {
String dest = Utilities.path(tempDir, "package");
Utilities.createDirectory(dest);
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.startsWith("package/")) {
n = n.substring(8);
}
if (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(dest, dir));
}
} else {
int count;
byte data[] = new byte[BUFFER_SIZE];
String filename = Utilities.path(dest, 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 {
@ -1302,6 +1361,17 @@ public class NpmPackage {
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;
}
}

31
org.hl7.fhir.utilities/src/test/java/org/hl7/fhir/utilities/npm/MinimalMemoryTests.java Normal file
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@ -0,0 +1,31 @@
package org.hl7.fhir.utilities.npm;
import static org.junit.jupiter.api.Assertions.assertEquals;
import java.io.IOException;
import java.io.File;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.utilities.Utilities;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.Test;
public class MinimalMemoryTests {
@Test
public void testFetch() throws IOException {
File folder = new File(Utilities.path("[tmp]", ".fhir-mm"));
if (folder.exists()) {
Utilities.clearDirectory(folder.getAbsolutePath());
} else {
Utilities.createDirectory(folder.getAbsolutePath());
}
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(folder.getAbsolutePath());
pcm.setMinimalMemory(true);
NpmPackage npm = pcm.loadPackage("hl7.fhir.us.core", "5.0.0");
Assertions.assertTrue(npm.isMinimalMemory());
}
}