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Hack to handle special characters so we can release
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@rlreamy
rlreamy committed Sep 20, 2019
1 parent 7bec84a commit 359b087
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Showing 5 changed files with 124 additions and 34 deletions.
3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -14,3 +14,6 @@ out
.idea
.settings
.classpath
tokens
*credentials.json

35 changes: 23 additions & 12 deletions src/main/java/org/kpmp/RegenerateZipFiles.java
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Expand Up @@ -5,15 +5,19 @@
import java.time.LocalDateTime;
import java.time.ZoneId;
import java.time.temporal.ChronoUnit;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

import org.json.JSONObject;
import org.kpmp.externalProcess.CommandBuilder;
import org.kpmp.externalProcess.ProcessExecutor;
import org.kpmp.packages.CustomPackageRepository;
import org.kpmp.packages.FilePathHelper;
import org.kpmp.packages.PackageKeys;
import org.kpmp.zip.ZipService;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
Expand All @@ -30,14 +34,16 @@ public class RegenerateZipFiles implements CommandLineRunner {
private CommandBuilder commandBuilder;
private ProcessExecutor processExecutor;
private final Logger log = LoggerFactory.getLogger(this.getClass());
private ZipService zipService;

@Autowired
public RegenerateZipFiles(CustomPackageRepository packageRepository, CommandBuilder commandBuilder,
FilePathHelper pathHelper, ProcessExecutor processExecutor) {
FilePathHelper pathHelper, ProcessExecutor processExecutor, ZipService zipService) {
this.packageRepository = packageRepository;
this.commandBuilder = commandBuilder;
this.pathHelper = pathHelper;
this.processExecutor = processExecutor;
this.zipService = zipService;
}

public static void main(String[] args) {
Expand All @@ -59,18 +65,23 @@ public void run(String... args) throws Exception {
try {
File existingZipFile = new File(zipFileName);
existingZipFile.delete();
String[] zipCommand = commandBuilder.buildZipCommand(packageId, packageMetadata);
boolean success = processExecutor.executeProcess(zipCommand);
if (success) {
LocalDateTime start = LocalDateTime.ofInstant(startRezipTime.toInstant(),
ZoneId.systemDefault());
LocalDateTime end = LocalDateTime.ofInstant(new Date().toInstant(), ZoneId.systemDefault());
long totalTime = ChronoUnit.SECONDS.between(start, end);
log.info("Timing: " + totalTime + " seconds");
packageRepository.updateField(packageId, PackageKeys.REGENERATE_ZIP.getKey(), false);
} else {
log.error("Unable to zip files for package " + packageId);
// String[] zipCommand = commandBuilder.buildZipCommand(packageId, packageMetadata);
// boolean success = processExecutor.executeProcess(zipCommand);
String packagePath = pathHelper.getPackagePath(packageId);
List<String> fileNames = pathHelper.getFilenames(packagePath);
List<String> filePaths = new ArrayList<>();
for (String fileName : fileNames) {
filePaths.add(packagePath + File.separator + fileName);
}

Map<String, String> additionalData = new HashMap<String, String>();
additionalData.put("metadata.json", packageMetadata);
zipService.createZipFile(zipFileName, filePaths, additionalData);
LocalDateTime start = LocalDateTime.ofInstant(startRezipTime.toInstant(), ZoneId.systemDefault());
LocalDateTime end = LocalDateTime.ofInstant(new Date().toInstant(), ZoneId.systemDefault());
long totalTime = ChronoUnit.SECONDS.between(start, end);
log.info("Timing: " + totalTime + " seconds");
packageRepository.updateField(packageId, PackageKeys.REGENERATE_ZIP.getKey(), false);
} catch (IOException e) {
log.error("Unable to delete file, invalid permissions: " + zipFileName);
}
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53 changes: 32 additions & 21 deletions src/main/java/org/kpmp/packages/PackageService.java
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Expand Up @@ -12,6 +12,7 @@
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

Expand All @@ -24,6 +25,7 @@
import org.kpmp.packages.state.State;
import org.kpmp.packages.state.StateHandlerService;
import org.kpmp.users.User;
import org.kpmp.zip.ZipService;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.stereotype.Service;
Expand All @@ -49,17 +51,20 @@ public class PackageService {
private CommandBuilder commandBuilder;
private ProcessExecutor processExecutor;

private ZipService zipService;

@Autowired
public PackageService(PackageFileHandler packageFileHandler, FilePathHelper filePathHelper,
CustomPackageRepository packageRepository, StateHandlerService stateHandler, CommandBuilder commandBuilder,
ProcessExecutor processExecutor, LoggingService logger) {
ProcessExecutor processExecutor, LoggingService logger, ZipService zipService) {
this.filePathHelper = filePathHelper;
this.packageFileHandler = packageFileHandler;
this.packageRepository = packageRepository;
this.stateHandler = stateHandler;
this.commandBuilder = commandBuilder;
this.processExecutor = processExecutor;
this.logger = logger;
this.zipService = zipService;
}

public List<PackageView> findAllPackages() throws JSONException, IOException {
Expand Down Expand Up @@ -127,27 +132,33 @@ public void createZipFile(String packageId, String origin, User user) throws Exc
public void run() {
try {
String packageMetadata = packageRepository.getJSONByPackageId(packageId);
String[] zipCommand = commandBuilder.buildZipCommand(packageId, packageMetadata);
boolean success = processExecutor.executeProcess(zipCommand);
if (success) {
logger.logInfoMessage(PackageService.class, null, packageId,
PackageService.class.getSimpleName() + ".createZipFile",
zipPackage.format(new Object[] { "Zip file created for package: ", packageId }));
long zipDuration = calculateDurationInSeconds(finishUploadTime, new Date());
logger.logInfoMessage(PackageService.class, user, packageId,
PackageService.class.getSimpleName() + ".createZipFile",
zipTiming.format(new Object[] { packageInfo.getCreatedAt(), user.toString(), packageId,
packageInfo.getAttachments().size(), displaySize, zipDuration + " seconds" }));

stateHandler.sendStateChange(packageId, uploadSucceededState);

stateHandler.sendNotification(packageId, packageInfo.getPackageType(),
packageInfo.getCreatedAt(), packageInfo.getSubmitter().getFirstName(),
packageInfo.getSubmitter().getLastName(), packageInfo.getSubjectId(), origin);
} else {
logger.logErrorMessage(PackageService.class, user, packageId,
PackageService.class.getSimpleName(), "Unable to zip package");
// String[] zipCommand = commandBuilder.buildZipCommand(packageId, packageMetadata);
String zipFileName = filePathHelper.getZipFileName(packageId);
String packagePath = filePathHelper.getPackagePath(packageId);
List<String> fileNames = filePathHelper.getFilenames(packagePath);
List<String> filePaths = new ArrayList<>();
for (String fileName : fileNames) {
filePaths.add(packagePath + File.separator + fileName);
}

Map<String, String> additionalData = new HashMap<String, String>();
additionalData.put("metadata.json", packageMetadata);
zipService.createZipFile(zipFileName, filePaths, additionalData);

logger.logInfoMessage(PackageService.class, null, packageId,
PackageService.class.getSimpleName() + ".createZipFile",
zipPackage.format(new Object[] { "Zip file created for package: ", packageId }));
long zipDuration = calculateDurationInSeconds(finishUploadTime, new Date());
logger.logInfoMessage(PackageService.class, user, packageId,
PackageService.class.getSimpleName() + ".createZipFile",
zipTiming.format(new Object[] { packageInfo.getCreatedAt(), user.toString(), packageId,
packageInfo.getAttachments().size(), displaySize, zipDuration + " seconds" }));

stateHandler.sendStateChange(packageId, uploadSucceededState);

stateHandler.sendNotification(packageId, packageInfo.getPackageType(), packageInfo.getCreatedAt(),
packageInfo.getSubmitter().getFirstName(), packageInfo.getSubmitter().getLastName(),
packageInfo.getSubjectId(), origin);
} catch (Exception e) {
logger.logErrorMessage(PackageService.class, user, packageId, PackageService.class.getSimpleName(),
e.getMessage());
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62 changes: 62 additions & 0 deletions src/main/java/org/kpmp/zip/ZipService.java
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@@ -0,0 +1,62 @@
package org.kpmp.zip;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.nio.charset.StandardCharsets;
import java.util.List;
import java.util.Map;
import java.util.Set;

import org.apache.commons.compress.archivers.zip.ZipArchiveEntry;
import org.apache.commons.compress.archivers.zip.ZipArchiveOutputStream;
import org.springframework.stereotype.Component;

@Component
public class ZipService {

private static final String TMP_FILE_EXTENSION = ".tmp";

public void createZipFile(String zipFilePath, List<String> filePaths, Map<String, String> additionalFileInformation)
throws IOException {
File tempZipFileHandle = new File(zipFilePath + TMP_FILE_EXTENSION);
try (ZipArchiveOutputStream zipFile = new ZipArchiveOutputStream(new File(zipFilePath))) {
zipFile.setMethod(ZipArchiveOutputStream.DEFLATED);
zipFile.setEncoding(StandardCharsets.UTF_8.name());
for (String filePath : filePaths) {
File file = new File(filePath);
ZipArchiveEntry entry = new ZipArchiveEntry(file.getName());
entry.setSize(file.length());
zipFile.putArchiveEntry(entry);
try (FileInputStream fileInputStream = new FileInputStream(file)) {
try (BufferedInputStream bufferedInputStream = new BufferedInputStream(fileInputStream)) {
byte[] buffer = new byte[32768];
int data = 0;
while ((data = bufferedInputStream.read(buffer, 0, buffer.length)) != -1) {
zipFile.write(buffer, 0, data);
}
zipFile.flush();
bufferedInputStream.close();
}
fileInputStream.close();
}
zipFile.closeArchiveEntry();
}

Set<String> keys = additionalFileInformation.keySet();
for (String additionalFileName : keys) {
ZipArchiveEntry additionalEntry = new ZipArchiveEntry(additionalFileName);
String additionaFileContents = additionalFileInformation.get(additionalFileName);
additionalEntry.setSize(additionaFileContents.getBytes().length);
zipFile.putArchiveEntry(additionalEntry);
zipFile.write(additionaFileContents.getBytes(StandardCharsets.UTF_8));
zipFile.closeArchiveEntry();
}

File zipFileHandle = new File(zipFilePath);
tempZipFileHandle.renameTo(zipFileHandle);
}
}

}
5 changes: 4 additions & 1 deletion src/test/java/org/kpmp/packages/PackageServiceTest.java
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Expand Up @@ -30,6 +30,7 @@
import org.kpmp.packages.state.State;
import org.kpmp.packages.state.StateHandlerService;
import org.kpmp.users.User;
import org.kpmp.zip.ZipService;
import org.mockito.Mock;
import org.mockito.MockitoAnnotations;
import org.slf4j.LoggerFactory;
Expand Down Expand Up @@ -57,12 +58,14 @@ public class PackageServiceTest {
private CommandBuilder commandBuilder;
@Mock
private ProcessExecutor processExecutor;
@Mock
private ZipService zipWorker;

@Before
public void setUp() throws Exception {
MockitoAnnotations.initMocks(this);
service = new PackageService(packageFileHandler, filePathHelper, packageRepository, stateHandlerService,
commandBuilder, processExecutor, logger);
commandBuilder, processExecutor, logger, zipWorker);
ReflectionTestUtils.setField(service, "uploadSucceededState", "UPLOAD_SUCCEEDED");
}

Expand Down

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