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Improve command-line argument for extracting resources #728

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merged 5 commits into from
Feb 20, 2024
Merged

Improve command-line argument for extracting resources #728

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ade16d7
Support extracting from embedded build for remote pipeline scenarios
labkey-jeckels Feb 12, 2024
550fa94
Change command-line arg
labkey-jeckels Feb 14, 2024
ce8ba36
Merge branch 'develop' into fb_embedded_pipelineExtract
labkey-jeckels Feb 19, 2024
2321ce3
Fail when we don't find distribution.zip
labkey-jeckels Feb 19, 2024
ec59a6b
Merge branch 'develop' into fb_embedded_pipelineExtract
labkey-jeckels Feb 19, 2024
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149 changes: 149 additions & 0 deletions server/embedded/src/org/labkey/embedded/EmbeddedExtractor.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,149 @@
package org.labkey.embedded;

import org.labkey.bootstrap.ConfigException;

import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.Arrays;
import java.util.jar.JarFile;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;

public class EmbeddedExtractor
{
private static final int BUFFER_SIZE = 1024 * 64;

private void extractExecutableJar(File jarFilePath, File destDirectory, boolean remotePipeline)
{
try
{
try (JarFile jar = new JarFile(jarFilePath))
{
boolean foundDistributionZip = false;
var entries = jar.entries();
while (entries.hasMoreElements())
{
var entry = entries.nextElement();
var entryName = entry.getName();

if ("labkey/distribution.zip".equals(entryName))
{
foundDistributionZip = true;
try (var distInputStream = jar.getInputStream(entry))
{
extractZip(distInputStream, destDirectory);
}
}
if (remotePipeline)
{
if (entry.getName().contains("labkeyBootstrap") && entry.getName().toLowerCase().endsWith(".jar"))
{
try (var in = jar.getInputStream(entry))
{
extractFile(in, new File(destDirectory, "labkeyBootstrap.jar"));
}
}
if (entry.getName().contains("tomcat-servlet-api") && entry.getName().toLowerCase().endsWith(".jar"))
{
File pipelineLib = new File(destDirectory, "pipeline-lib");
if (!pipelineLib.exists())
{
if (!pipelineLib.mkdirs())
{
throw new ConfigException("Failed to create directory " + pipelineLib + " Please check file system permissions");
}
}
try (var in = jar.getInputStream(entry))
{
extractFile(in, new File(pipelineLib, "servletApi.jar"));
}
}
}
}

if (!foundDistributionZip)
{
throw new ConfigException("Unable to find distribution zip required to run LabKey Server.");
}
}
}
catch (IOException | ConfigException e)
{
throw new RuntimeException(e);
}
}

public void extractExecutableJarFromDir(File currentDir, File destDir, boolean remotePipeline) throws ConfigException
{
File[] files = currentDir.listFiles(file -> {
String name = file.getName().toLowerCase();
return name.endsWith(".jar") && !name.contains("labkeybootstrap");
});

if (files == null)
{
throw new ConfigException("Executable jar not found.");
}

// only 1 jar should be there
if (files.length == 1)
{
extractExecutableJar(files[0], destDir, remotePipeline);
}
else
{
throw new ConfigException("Multiple jars found - " + Arrays.asList(files) + ". Must provide only one jar.");
}
}

private void extractZip(InputStream zipInputStream, File destDir) throws IOException
{
//noinspection SSBasedInspection
if (!destDir.exists() && !destDir.mkdirs())
{
throw new IOException("Failed to create directory " + destDir + " - please check file system permissions");
}
try (ZipInputStream zipIn = new ZipInputStream(zipInputStream))
{
ZipEntry entry = zipIn.getNextEntry();
// iterates over entries in the zip file
while (entry != null)
{
File filePath = new File(destDir, entry.getName());
if (!entry.isDirectory())
{
// if the entry is a file, extracts it
extractFile(zipIn, filePath);
}
else
{
// if the entry is a directory, make the directory
//noinspection SSBasedInspection
if (!filePath.exists() && !filePath.mkdirs())
{
throw new IOException("Failed to create directory " + filePath + " - please check file system permissions");
}
}
zipIn.closeEntry();
entry = zipIn.getNextEntry();
}
}
}

private static void extractFile(InputStream zipIn, File filePath) throws IOException
{
try (BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(filePath)))
{
byte[] bytesIn = new byte[BUFFER_SIZE];
int read;
while ((read = zipIn.read(bytesIn)) != -1)
{
bos.write(bytesIn, 0, read);
}
}
}

}
8 changes: 8 additions & 0 deletions server/embedded/src/org/labkey/embedded/LabKeyServer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
import org.springframework.context.annotation.Configuration;
import org.springframework.validation.annotation.Validated;

import java.io.File;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
Expand All @@ -37,6 +38,13 @@ public class LabKeyServer

public static void main(String[] args)
{
if (args.length > 0 && args[0].equalsIgnoreCase("-extract"))
{
File currentDir = new File("").getAbsoluteFile();
new EmbeddedExtractor().extractExecutableJarFromDir(currentDir, currentDir, true);
return;
}

// Issue 40038: Ride-or-die Mode - default to shutting down by default in embedded deployment scenario
if (System.getProperty(TERMINATE_ON_STARTUP_FAILURE) == null)
{
Expand Down
145 changes: 9 additions & 136 deletions server/embedded/src/org/labkey/embedded/LabKeyTomcatServletWebServerFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,19 +14,10 @@
import org.springframework.boot.web.servlet.ServletContextInitializer;

import javax.sql.DataSource;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.jar.JarFile;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;

import static org.labkey.embedded.LabKeyServer.SERVER_GUID_PARAMETER_NAME;
import static org.labkey.embedded.LabKeyServer.SERVER_SSL_KEYSTORE;
Expand All @@ -36,8 +27,6 @@ class LabKeyTomcatServletWebServerFactory extends TomcatServletWebServerFactory
private static final Log LOG = LogFactory.getLog(LabKeyTomcatServletWebServerFactory.class);
private final LabKeyServer _server;

private static final int BUFFER_SIZE = 4096;

public LabKeyTomcatServletWebServerFactory(LabKeyServer server)
{
_server = server;
Expand Down Expand Up @@ -70,26 +59,25 @@ protected TomcatWebServer getTomcatWebServer(Tomcat tomcat)

// for development, point to the local deploy/labkeyWebapp directory in configs/application.properties
boolean webAppLocationPresent = contextProperties.getWebAppLocation() != null;
var webAppLocation = "";
File webAppLocation;

try
{
if (!webAppLocationPresent)
{
final var currentPath = new File("").getAbsolutePath();
var destDirectory = currentPath + "/server";
webAppLocation = destDirectory + "/labkeywebapp";
boolean extracted = new File(webAppLocation).exists();
String jarFilePath = getExecutableJar(currentPath);
final var currentPath = new File("");
var destDirectory = new File(currentPath, "server");
webAppLocation = new File(destDirectory, "labkeywebapp");

if (!extracted)
if (!webAppLocation.exists())
{
extractExecutableJar(destDirectory, jarFilePath);
EmbeddedExtractor extractor = new EmbeddedExtractor();
extractor.extractExecutableJarFromDir(currentPath, destDirectory, false);
}
}
else
{
webAppLocation = contextProperties.getWebAppLocation();
webAppLocation = new File(contextProperties.getWebAppLocation());
}

// Turn off the default web.xml behavior so that we don't stomp over customized values
Expand All @@ -104,7 +92,7 @@ protected TomcatWebServer getTomcatWebServer(Tomcat tomcat)

// Spring Boot's webapp is being deployed to the root. We have to deploy elsewhere in this initial
// call, but can immediately swap it with the desired place
StandardContext context = (StandardContext) tomcat.addWebapp("/labkey", webAppLocation);
StandardContext context = (StandardContext) tomcat.addWebapp("/labkey", webAppLocation.getAbsolutePath());
// set the root path to the context explicitly
context.setPath(contextProperties.getContextPath());

Expand Down Expand Up @@ -375,119 +363,4 @@ private ContextResource getMailResource()

return mailResource;
}

private void extractExecutableJar(String destDirectory, String jarFilePath)
{
try
{
try (JarFile jar = new JarFile(jarFilePath))
{
boolean foundDistributionZip = false;
var entries = jar.entries();
while (entries.hasMoreElements())
{
var entry = entries.nextElement();
var entryName = entry.getName();

if ("labkey/distribution.zip".equals(entryName))
{
foundDistributionZip = true;
try (var distInputStream = jar.getInputStream(entry))
{
extractZip(distInputStream, destDirectory);
}
}
}

if (!foundDistributionZip)
{
throw new ConfigException("Unable to find distribution zip required to run LabKey server.");
}
}
}
catch (IOException | ConfigException e)
{
throw new RuntimeException(e);
}
}

private static String getExecutableJar(String currentPath) throws ConfigException
{
File currentDir = new File(currentPath);
List<String> jarsPresent = new ArrayList<>();

File[] files = currentDir.listFiles();
if (files != null)
{
for (File file : files)
{
if (file.getName().toLowerCase().endsWith(".jar"))
{
jarsPresent.add(file.getName());
}
}
}

if (jarsPresent.isEmpty())
{
throw new ConfigException("Executable jar not found.");
}

// only 1 jar should be there
if (jarsPresent.size() == 1)
{
return jarsPresent.get(0);
}

throw new ConfigException("Multiple jars found - " + jarsPresent + ". Must provide only one jar.");
}

private void extractZip(InputStream zipInputStream, String destDirectory) throws IOException
{
File destDir = new File(destDirectory);
//noinspection SSBasedInspection
if (!destDir.exists() && !destDir.mkdirs())
{
throw new IOException("Failed to create directory " + destDir + " - please check file system permissions");
}
try (ZipInputStream zipIn = new ZipInputStream(zipInputStream))
{
ZipEntry entry = zipIn.getNextEntry();
// iterates over entries in the zip file
while (entry != null)
{
String filePath = destDirectory + File.separator + entry.getName();
if (!entry.isDirectory())
{
// if the entry is a file, extracts it
extractFile(zipIn, filePath);
}
else
{
// if the entry is a directory, make the directory
File dir = new File(filePath);
//noinspection SSBasedInspection
if (!dir.exists() && !dir.mkdirs())
{
throw new IOException("Failed to create directory " + dir + " - please check file system permissions");
}
}
zipIn.closeEntry();
entry = zipIn.getNextEntry();
}
}
}

private static void extractFile(ZipInputStream zipIn, String filePath) throws IOException
{
try (BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(filePath)))
{
byte[] bytesIn = new byte[BUFFER_SIZE];
int read;
while ((read = zipIn.read(bytesIn)) != -1)
{
bos.write(bytesIn, 0, read);
}
}
}
}