diff --git a/haas-java-client/pom.xml b/haas-java-client/pom.xml
index d5985932ab464218b180599eb843ffd8b5292576..797354f51107a9ff6cec9eb87a77286818f7c6e1 100644
--- a/haas-java-client/pom.xml
+++ b/haas-java-client/pom.xml
@@ -13,7 +13,6 @@
<scm>
<url>https://code.it4i.cz/fiji/haas-java-client.git</url>
<connection>scm:git:https://code.it4i.cz/fiji/haas-java-client.git</connection>
-
</scm>
<build>
<plugins>
@@ -145,6 +144,12 @@
<scope>provided</scope>
</dependency>
</dependencies>
+ <repositories>
+ <repository>
+ <id>it4i</id>
+ <url>https://artifactory.cs.vsb.cz/it4i/</url>
+ </repository>
+ </repositories>
<distributionManagement>
<repository>
<id>it4i</id>
diff --git a/java-scpclient/.classpath b/java-scpclient/.classpath
deleted file mode 100644
index 5e8a55fefbd916a028d5a67f0b8db3fcb3262258..0000000000000000000000000000000000000000
--- a/java-scpclient/.classpath
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<classpath>
- <classpathentry kind="src" output="target/classes" path="src/main/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="src" output="target/test-classes" path="src/test/java">
- <attributes>
- <attribute name="optional" value="true"/>
- <attribute name="maven.pomderived" value="true"/>
- <attribute name="test" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
- <attributes>
- <attribute name="maven.pomderived" value="true"/>
- </attributes>
- </classpathentry>
- <classpathentry kind="output" path="target/classes"/>
-</classpath>
diff --git a/java-scpclient/.gitignore b/java-scpclient/.gitignore
deleted file mode 100644
index b83d22266ac8aa2f8df2edef68082c789727841d..0000000000000000000000000000000000000000
--- a/java-scpclient/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-/target/
diff --git a/java-scpclient/.project b/java-scpclient/.project
deleted file mode 100644
index d077f331a9dd2fefe2abd7536a0d19808e11ef81..0000000000000000000000000000000000000000
--- a/java-scpclient/.project
+++ /dev/null
@@ -1,23 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<projectDescription>
- <name>java-scpclient</name>
- <comment></comment>
- <projects>
- </projects>
- <buildSpec>
- <buildCommand>
- <name>org.eclipse.jdt.core.javabuilder</name>
- <arguments>
- </arguments>
- </buildCommand>
- <buildCommand>
- <name>org.eclipse.m2e.core.maven2Builder</name>
- <arguments>
- </arguments>
- </buildCommand>
- </buildSpec>
- <natures>
- <nature>org.eclipse.jdt.core.javanature</nature>
- <nature>org.eclipse.m2e.core.maven2Nature</nature>
- </natures>
-</projectDescription>
diff --git a/java-scpclient/.settings/org.eclipse.jdt.core.prefs b/java-scpclient/.settings/org.eclipse.jdt.core.prefs
deleted file mode 100644
index b8947ec6fc0a929c7ba04e493e77a2663a75b64e..0000000000000000000000000000000000000000
--- a/java-scpclient/.settings/org.eclipse.jdt.core.prefs
+++ /dev/null
@@ -1,6 +0,0 @@
-eclipse.preferences.version=1
-org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
-org.eclipse.jdt.core.compiler.compliance=1.8
-org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
-org.eclipse.jdt.core.compiler.release=disabled
-org.eclipse.jdt.core.compiler.source=1.8
diff --git a/java-scpclient/.settings/org.eclipse.m2e.core.prefs b/java-scpclient/.settings/org.eclipse.m2e.core.prefs
deleted file mode 100644
index f897a7f1cb2389f85fe6381425d29f0a9866fb65..0000000000000000000000000000000000000000
--- a/java-scpclient/.settings/org.eclipse.m2e.core.prefs
+++ /dev/null
@@ -1,4 +0,0 @@
-activeProfiles=
-eclipse.preferences.version=1
-resolveWorkspaceProjects=true
-version=1
diff --git a/java-scpclient/pom.xml b/java-scpclient/pom.xml
deleted file mode 100644
index c5eaaba52508422fac9b68aea67b6a9ec64d0f1f..0000000000000000000000000000000000000000
--- a/java-scpclient/pom.xml
+++ /dev/null
@@ -1,99 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <groupId>cz.it4i.fiji</groupId>
- <artifactId>java-scpclient</artifactId>
- <version>1.0.0</version>
- <name>Scp client library for Java</name>
- <packaging>jar</packaging>
- <properties>
- <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- </properties>
- <scm>
- <url>https://code.it4i.cz/fiji/haas-java-client.git</url>
- <connection>scm:git:https://code.it4i.cz/fiji/haas-java-client.git</connection>
- </scm>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-compiler-plugin</artifactId>
- <version>3.5.1</version>
- <configuration>
- <source>1.8</source>
- <target>1.8</target>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.codehaus.mojo</groupId>
- <artifactId>buildnumber-maven-plugin</artifactId>
- <version>1.4</version>
- <executions>
- <execution>
- <phase>validate</phase>
- <goals>
- <goal>create</goal>
- </goals>
- </execution>
- </executions>
- <configuration>
- <doCheck>false</doCheck>
- <doUpdate>false</doUpdate>
- </configuration>
- </plugin>
- <plugin>
- <groupId>org.apache.maven.plugins</groupId>
- <artifactId>maven-jar-plugin</artifactId>
- <version>3.1.0</version>
- <configuration>
- <archive>
- <manifest>
- <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
- </manifest>
- <manifestEntries>
- <Implementation-Build>${buildNumber}</Implementation-Build>
- </manifestEntries>
- </archive>
- </configuration>
- </plugin>
- </plugins>
- </build>
- <dependencies>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>3.8.1</version>
- <scope>test</scope>
- </dependency>
- <!-- https://mvnrepository.com/artifact/com.jcraft/jsch -->
- <dependency>
- <groupId>com.jcraft</groupId>
- <artifactId>jsch</artifactId>
- <version>0.1.55</version>
- </dependency>
- <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-api</artifactId>
- <version>1.7.25</version>
- </dependency>
- <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-jdk14 -->
- <dependency>
- <groupId>org.slf4j</groupId>
- <artifactId>slf4j-jdk14</artifactId>
- <version>1.7.25</version>
- <optional>true</optional>
- </dependency>
- </dependencies>
- <distributionManagement>
- <repository>
- <id>it4i</id>
- <url>https://artifactory.cs.vsb.cz/it4i/</url>
- </repository>
- <snapshotRepository>
- <id>it4i</id>
- <url>https://artifactory.cs.vsb.cz/it4i/</url>
- </snapshotRepository>
- </distributionManagement>
-</project>
diff --git a/java-scpclient/src/main/java/cz/it4i/fiji/commons/DoActionEventualy.java b/java-scpclient/src/main/java/cz/it4i/fiji/commons/DoActionEventualy.java
deleted file mode 100644
index d73d9bb74f91d37ba2196169805272c785c1a24e..0000000000000000000000000000000000000000
--- a/java-scpclient/src/main/java/cz/it4i/fiji/commons/DoActionEventualy.java
+++ /dev/null
@@ -1,28 +0,0 @@
-
-package cz.it4i.fiji.commons;
-
-import java.io.Closeable;
-import java.util.Timer;
-import java.util.TimerTask;
-
-public class DoActionEventualy implements Closeable {
-
- private final Timer timer;
-
- public DoActionEventualy(final long timeout, final Runnable runnable) {
- timer = new Timer();
- timer.schedule(new TimerTask() {
-
- @Override
- public void run() {
- runnable.run();
- }
- }, timeout);
- }
-
- @Override
- public void close() {
- timer.cancel();
- }
-
-}
diff --git a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/AbstractBaseSshClient.java b/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/AbstractBaseSshClient.java
deleted file mode 100644
index 793eb82e922be76e5f1b56f20bec76322da6fbc7..0000000000000000000000000000000000000000
--- a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/AbstractBaseSshClient.java
+++ /dev/null
@@ -1,173 +0,0 @@
-
-package cz.it4i.fiji.scpclient;
-
-import com.jcraft.jsch.Identity;
-import com.jcraft.jsch.JSch;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.Session;
-import com.jcraft.jsch.UserInfo;
-
-import java.io.Closeable;
-import java.io.UnsupportedEncodingException;
-import java.lang.reflect.Field;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import cz.it4i.fiji.commons.DoActionEventualy;
-
-public class AbstractBaseSshClient implements Closeable {
-
- protected static final int MAX_NUMBER_OF_CONNECTION_ATTEMPTS = 5;
-
- protected static final long TIMEOUT_BETWEEN_CONNECTION_ATTEMPTS = 500;
-
- private final static Logger log = LoggerFactory.getLogger(
- AbstractBaseSshClient.class);
-
- private String hostName;
- private String username;
- private final JSch jsch = new JSch();
- private Session session;
-
- private int port = 22;
-
- public AbstractBaseSshClient(String hostName, String username,
- byte[] privateKeyFile) throws JSchException
- {
- init(hostName, username, new ByteIdentity(jsch, privateKeyFile));
- }
-
- public AbstractBaseSshClient(String hostName, String username,
- Identity privateKeyFile) throws JSchException
- {
- init(hostName, username, privateKeyFile);
- }
-
- public AbstractBaseSshClient(String hostName, String userName, String keyFile,
- String pass) throws JSchException
- {
- Identity id = IdentityFile.newInstance(keyFile, null, jsch);
- try {
- if (pass != null) {
- id.setPassphrase(pass.getBytes("UTF-8"));
- }
- }
- catch (UnsupportedEncodingException e) {
- throw new RuntimeException(e);
- }
- init(hostName, userName, id);
- }
-
- public void setPort(int port) {
- this.port = port;
- }
-
- @Override
- public void close() {
- if (session != null && session.isConnected()) {
- // log.info("disconnect");
- try (DoActionEventualy actionEventualy = new DoActionEventualy(
- TIMEOUT_BETWEEN_CONNECTION_ATTEMPTS, this::interruptSessionThread))
- {
- session.disconnect();
- }
- }
- session = null;
- }
-
- protected Session getConnectedSession() throws JSchException {
- if (session == null) {
- session = jsch.getSession(username, hostName, port);
-
- UserInfo ui = new P_UserInfo();
-
- session.setUserInfo(ui);
- }
- int connectRetry = 0;
- long timoutBetweenRetry = TIMEOUT_BETWEEN_CONNECTION_ATTEMPTS;
- while (!session.isConnected()) {
- try {
- session.connect();
- }
- catch (JSchException e) {
- if (e.getMessage().contains("Auth fail") || e.getMessage().contains(
- "Packet corrupt"))
- {
- if (connectRetry < MAX_NUMBER_OF_CONNECTION_ATTEMPTS) {
- connectRetry++;
- try {
- Thread.sleep(timoutBetweenRetry);
- timoutBetweenRetry *= 2;
- }
- catch (InterruptedException exc) {
- log.info("Interruption detected");
- throw new JSchException(exc.getMessage(), exc);
- }
- continue;
- }
- e = new AuthFailException(e.getMessage(), e);
- }
- throw e;
- }
- }
- return session;
- }
-
- private void interruptSessionThread() {
- try {
- Field f = session.getClass().getDeclaredField("connectThread");
- if (!f.isAccessible()) {
- f.setAccessible(true);
- Thread thread = (Thread) f.get(session);
- thread.interrupt();
- }
- }
- catch (NoSuchFieldException | SecurityException | IllegalArgumentException
- | IllegalAccessException exc)
- {
- log.error(exc.getMessage(), exc);
- }
- }
-
- private void init(String initHostName, String initUsername,
- Identity privateKeyFile) throws JSchException
- {
- this.hostName = initHostName;
- this.username = initUsername;
- jsch.addIdentity(privateKeyFile, null);
- }
-
- private class P_UserInfo implements UserInfo {
-
- @Override
- public String getPassphrase() {
- return null;
- }
-
- @Override
- public String getPassword() {
- return null;
- }
-
- @Override
- public boolean promptPassword(String message) {
- return false;
- }
-
- @Override
- public boolean promptPassphrase(String message) {
- return false;
- }
-
- @Override
- public boolean promptYesNo(String message) {
- return true;
- }
-
- @Override
- public void showMessage(String message) {}
-
- }
-
-}
diff --git a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/AckowledgementChecker.java b/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/AckowledgementChecker.java
deleted file mode 100644
index 130f800b570364020450f71ce60404c097c52a79..0000000000000000000000000000000000000000
--- a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/AckowledgementChecker.java
+++ /dev/null
@@ -1,46 +0,0 @@
-package cz.it4i.fiji.scpclient;
-
-import java.io.IOException;
-import java.io.InputStream;
-
-public class AckowledgementChecker {
-
- private int lastStatus;
-
- private StringBuilder lastMessage;
-
- public boolean checkAck(InputStream in) throws IOException {
- lastMessage = new StringBuilder();
- return checkAck(in, lastMessage);
- }
-
-
- public String getLastMessage() {
- return lastMessage.toString();
- }
-
-
- public int getLastStatus() {
- return lastStatus;
- }
-
- private boolean checkAck(InputStream in, StringBuilder sb) throws IOException {
- lastStatus = in.read();
- // b may be 0 for success,
- // 1 for error,
- // 2 for fatal error,
- // -1
- if (lastStatus == 0) return true;
- if (lastStatus == -1) return false;
-
- if (lastStatus == 1 || lastStatus == 2) {
- int c;
- do {
- c = in.read();
- sb.append((char) c);
- }
- while (c != '\n');
- }
- return lastStatus == 0;
- }
-}
diff --git a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/AuthFailException.java b/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/AuthFailException.java
deleted file mode 100644
index 31ca062dd2974cc484661ed13c5ef7137e981c1d..0000000000000000000000000000000000000000
--- a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/AuthFailException.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package cz.it4i.fiji.scpclient;
-
-import com.jcraft.jsch.JSchException;
-
-
-public class AuthFailException extends JSchException {
-
- public AuthFailException() {
- }
-
- public AuthFailException(String s) {
- super(s);
- }
-
- public AuthFailException(String s, Throwable e) {
- super(s, e);
- }
-
-}
diff --git a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/ByteIdentity.java b/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/ByteIdentity.java
deleted file mode 100644
index f0e2b728afd0fc5577f63cbb475d72338e8c0259..0000000000000000000000000000000000000000
--- a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/ByteIdentity.java
+++ /dev/null
@@ -1,62 +0,0 @@
-package cz.it4i.fiji.scpclient;
-
-import com.jcraft.jsch.Identity;
-import com.jcraft.jsch.JSch;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.KeyPair;
-
-class ByteIdentity implements Identity{
-
- private KeyPair keyPair;
-
- public ByteIdentity(JSch jsch,byte []prvKey) throws JSchException {
- this.keyPair = KeyPair.load(jsch, prvKey, null);
- }
-
- @Override
- public boolean setPassphrase(byte[] passphrase) throws JSchException {
- return keyPair.decrypt(passphrase);
- }
-
- @Override
- public byte[] getPublicKeyBlob() {
- return keyPair.getPublicKeyBlob();
- }
-
- @Override
- public byte[] getSignature(byte[] data) {
- return keyPair.getSignature(data);
- }
-
- @Override
- public boolean decrypt() {
- return false;
- }
-
- @Override
- public String getAlgName() {
- if(keyPair.getKeyType() == KeyPair.RSA) {
- return "ssh-rsa";
- } else if(keyPair.getKeyType() == KeyPair.DSA) {
- return "ssh-dsa";
- }
- throw new UnsupportedOperationException("Key type:" + keyPair.getKeyType() + " not supported.");
- }
-
- @Override
- public String getName() {
- return keyPair.getPublicKeyComment();
- }
-
- @Override
- public boolean isEncrypted() {
- return keyPair.isEncrypted();
- }
-
- @Override
- public void clear() {
- keyPair.dispose();
- keyPair = null;
- }
-
-}
diff --git a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/IdentityFile.java b/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/IdentityFile.java
deleted file mode 100644
index 8b46514ea6c0f0e1331bf1bd4cfc7371157fc3a4..0000000000000000000000000000000000000000
--- a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/IdentityFile.java
+++ /dev/null
@@ -1,124 +0,0 @@
-package cz.it4i.fiji.scpclient;
-
-import com.jcraft.jsch.Identity;
-import com.jcraft.jsch.IdentityRepository;
-import com.jcraft.jsch.JSch;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.KeyPair;
-
-class IdentityFile implements Identity {
- private KeyPair kpair;
- private String identity;
-
- static IdentityFile newInstance(String prvfile, String pubfile, JSch jsch) throws JSchException {
- KeyPair kpair = KeyPair.load(jsch, prvfile, pubfile);
- return new IdentityFile(prvfile, kpair);
- }
-
- static IdentityFile newInstance(String name, byte[] prvkey, byte[] pubkey, JSch jsch) throws JSchException {
- KeyPair kpair = KeyPair.load(jsch, prvkey, pubkey);
- return new IdentityFile(name, kpair);
- }
-
- private IdentityFile(String name, KeyPair kpair) {
- this.identity = name;
- this.kpair = kpair;
- }
-
- /**
- * Decrypts this identity with the specified pass-phrase.
- *
- * @param passphrase
- * the pass-phrase for this identity.
- * @return <tt>true</tt> if the decryption is succeeded or this identity is not
- * cyphered.
- */
- @Override
- public boolean setPassphrase(byte[] passphrase) throws JSchException {
- return kpair.decrypt(passphrase);
- }
-
- /**
- * Returns the public-key blob.
- *
- * @return the public-key blob
- */
- @Override
- public byte[] getPublicKeyBlob() {
- return kpair.getPublicKeyBlob();
- }
-
- /**
- * Signs on data with this identity, and returns the result.
- *
- * @param data
- * data to be signed
- * @return the signature
- */
- @Override
- public byte[] getSignature(byte[] data) {
- return kpair.getSignature(data);
- }
-
- /**
- * @deprecated This method should not be invoked.
- * @see #setPassphrase(byte[] passphrase)
- */
- @Deprecated
- @Override
- public boolean decrypt() {
- throw new RuntimeException("not implemented");
- }
-
- /**
- * Returns the name of the key algorithm.
- *
- * @return "ssh-rsa" or "ssh-dss"
- */
- @Override
- public String getAlgName() {
- if (kpair.getKeyType() == KeyPair.RSA) {
- return "ssh-rsa";
- } else if (kpair.getKeyType() == KeyPair.DSA) {
- return "ssh-dsa";
- }
- throw new UnsupportedOperationException("Key type:" + kpair.getKeyType() + " not supported.");
- }
-
- /**
- * Returns the name of this identity. It will be useful to identify this object
- * in the {@link IdentityRepository}.
- */
- @Override
- public String getName() {
- return identity;
- }
-
- /**
- * Returns <tt>true</tt> if this identity is cyphered.
- *
- * @return <tt>true</tt> if this identity is cyphered.
- */
- @Override
- public boolean isEncrypted() {
- return kpair.isEncrypted();
- }
-
- /**
- * Disposes internally allocated data, like byte array for the private key.
- */
- @Override
- public void clear() {
- kpair.dispose();
- kpair = null;
- }
-
- /**
- * Returns an instance of {@link KeyPair} used in this {@link Identity}.
- *
- * @return an instance of {@link KeyPair} used in this {@link Identity}.
- */
- public KeyPair getKeyPair() {
- return kpair;
- }
-}
diff --git a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/ScpClient.java b/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/ScpClient.java
deleted file mode 100644
index a89a91a09af30f3d50858ed81e239abb0da9b2da..0000000000000000000000000000000000000000
--- a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/ScpClient.java
+++ /dev/null
@@ -1,418 +0,0 @@
-
-package cz.it4i.fiji.scpclient;
-
-import com.jcraft.jsch.Channel;
-import com.jcraft.jsch.ChannelExec;
-import com.jcraft.jsch.ChannelSftp;
-import com.jcraft.jsch.ChannelSftp.LsEntry;
-import com.jcraft.jsch.Identity;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.SftpException;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InterruptedIOException;
-import java.io.OutputStream;
-import java.nio.channels.ClosedByInterruptException;
-import java.nio.file.Files;
-import java.nio.file.NoSuchFileException;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.util.List;
-import java.util.stream.Collectors;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class ScpClient extends AbstractBaseSshClient {
-
- public static final Logger log = LoggerFactory.getLogger(ScpClient.class);
-
- private static final String NO_SUCH_FILE_OR_DIRECTORY_ERROR_TEXT =
- "No such file or directory";
-
- private static String constructExceptionText(AckowledgementChecker ack) {
- return "Check acknowledgement failed with status: " + ack.getLastStatus() +
- " and message: " + ack.getLastMessage();
- }
-
- private static final int BUFFER_SIZE = 4 * 1024 * 1024; // 4 MB
-
- private final TransferFileProgress dummyProgress =
- new TransferFileProgress()
- {
-
- @Override
- public void dataTransfered(long bytesTransfered) {
-
- }
- };
-
- public ScpClient(String hostName, String username, byte[] privateKeyFile)
- throws JSchException
- {
- super(hostName, username, privateKeyFile);
- }
-
- public ScpClient(String hostName, String username, Identity privateKeyFile)
- throws JSchException
- {
- super(hostName, username, privateKeyFile);
- }
-
- public ScpClient(String hostName, String userName, String keyFile,
- String pass) throws JSchException
- {
- super(hostName, userName, keyFile, pass);
- }
-
- public void download(String lfile, Path rFile) throws JSchException,
- IOException
- {
- download(lfile, rFile, dummyProgress);
- }
-
- public void download(String lfile, Path rfile, TransferFileProgress progress)
- throws JSchException, IOException
- {
- if (!Files.exists(rfile.getParent())) {
- Files.createDirectories(rfile.getParent());
- }
- try (OutputStream os = Files.newOutputStream(rfile)) {
- download(lfile, os, progress);
- }
- }
-
- public void download(String lfile, OutputStream os,
- TransferFileProgress progress) throws JSchException, IOException
- {
- AckowledgementChecker ack = new AckowledgementChecker();
- // exec 'scp -f rfile' remotely
-
- lfile = sanityFileName(lfile);
-
- String command = "scp -f " + lfile;
- Channel channel = getConnectedSession().openChannel("exec");
-
- try {
- ((ChannelExec) channel).setCommand(command);
-
- // get I/O streams for remote scp
- try (OutputStream out = channel.getOutputStream();
- InputStream in = channel.getInputStream())
- {
-
- channel.connect();
-
- byte[] buf = new byte[getBufferSize()];
-
- // send '\0'
- buf[0] = 0;
- out.write(buf, 0, 1);
- out.flush();
-
- while (true) {
- ack.checkAck(in);
- if (ack.getLastStatus() != 'C') {
- break;
- }
-
- // read '0644 '
- in.read(buf, 0, 5);
-
- long filesize = 0L;
- while (true) {
- if (in.read(buf, 0, 1) < 0) {
- // error
- break;
- }
- if (buf[0] == ' ') break;
- filesize = filesize * 10L + buf[0] - '0';
- }
-
- @SuppressWarnings("unused")
- String file = null;
- for (int i = 0;; i++) {
- in.read(buf, i, 1);
- if (buf[i] == (byte) 0x0a) {
- file = new String(buf, 0, i);
- break;
- }
- }
-
- // System.out.println("filesize="+filesize+", file="+file);
-
- // send '\0'
-
- buf[0] = 0;
- out.write(buf, 0, 1);
- out.flush();
-
- // read a content of lfile
- int foo;
- while (true) {
- if (buf.length < filesize) foo = buf.length;
- else foo = (int) filesize;
- foo = in.read(buf, 0, foo);
- if (foo < 0) {
- // error
- break;
- }
- os.write(buf, 0, foo);
- progress.dataTransfered(foo);
- filesize -= foo;
- if (filesize == 0L) break;
- }
-
- if (!ack.checkAck(in)) {
- throw new JSchException(constructExceptionText(ack));
- }
-
- // send '\0'
- buf[0] = 0;
- out.write(buf, 0, 1);
- out.flush();
-
- }
- }
-
- }
- catch (ClosedByInterruptException e) {
- throw new InterruptedIOException();
- }
- finally {
- channel.disconnect();
- }
- }
-
- public void upload(Path file, String rfile) throws JSchException,
- IOException
- {
- upload(file, rfile, dummyProgress);
- }
-
- public void upload(Path file, String rfile, TransferFileProgress progress)
- throws JSchException, IOException
- {
- try (InputStream is = Files.newInputStream(file)) {
- upload(is, rfile, file.toFile().length(), file.toFile().lastModified(),
- progress);
- }
- }
-
- public void upload(InputStream is, String fileName, long length,
- long lastModified, TransferFileProgress progress) throws JSchException,
- IOException
- {
- int noSuchFileExceptionThrown = 0;
- do {
- try {
- scp2Server(is, fileName, length, lastModified, progress);
- break;
- }
- catch (NoSuchFileException e) {
- if (noSuchFileExceptionThrown > MAX_NUMBER_OF_CONNECTION_ATTEMPTS) {
- throw new JSchException(e.getReason());
- }
- if (noSuchFileExceptionThrown > 0) {
- try {
- Thread.sleep(TIMEOUT_BETWEEN_CONNECTION_ATTEMPTS);
- }
- catch (InterruptedException exc) {}
- }
- mkdir(e.getFile());
- noSuchFileExceptionThrown++;
- continue;
- }
- }
- while (true);
- }
-
- public long size(String lfile) throws JSchException, IOException {
- AckowledgementChecker ack = new AckowledgementChecker();
- // exec 'scp -f rfile' remotely
-
- lfile = sanityFileName(lfile);
-
- String command = "scp -f " + lfile;
- Channel channel = getConnectedSession().openChannel("exec");
-
- try {
- ((ChannelExec) channel).setCommand(command);
-
- // get I/O streams for remote scp
- try (OutputStream out = channel.getOutputStream();
- InputStream in = channel.getInputStream())
- {
-
- channel.connect();
-
- byte[] buf = new byte[getBufferSize()];
-
- // send '\0'
- buf[0] = 0;
- out.write(buf, 0, 1);
- out.flush();
-
- while (true) {
- ack.checkAck(in);
- if (ack.getLastStatus() != 'C') {
- break;
- }
-
- // read '0644 '
- in.read(buf, 0, 5);
-
- long filesize = 0L;
- while (true) {
- if (in.read(buf, 0, 1) < 0) {
- // error
- break;
- }
- if (buf[0] == ' ') break;
- filesize = filesize * 10L + buf[0] - '0';
- }
- return filesize;
-
- }
- }
-
- }
- finally {
- channel.disconnect();
- }
- return -1;
- }
-
- @SuppressWarnings("unchecked")
- public List<Long> sizeByLs(String lfile) throws JSchException {
-
- // exec 'scp -f rfile' remotely
- Channel channel = getConnectedSession().openChannel("sftp");
- lfile = sanityFileName(lfile);
- try {
- channel.connect();
- return ((List<LsEntry>) ((ChannelSftp) channel).ls(lfile)).stream().map(
- atr -> atr.getAttrs().getSize()).collect(Collectors.toList());
-
- }
- catch (SftpException e) {
- e.printStackTrace();
- }
- finally {
- channel.disconnect();
- }
- return null;
- }
-
- private int getBufferSize() {
- return BUFFER_SIZE;
- }
-
- private void scp2Server(InputStream is, String fileName, long length,
- long lastModified, TransferFileProgress progress) throws JSchException,
- IOException, InterruptedIOException
- {
- AckowledgementChecker ack = new AckowledgementChecker();
- boolean ptimestamp = false;
- // exec 'scp -t rfile' remotely
-
- fileName = sanityFileName(fileName);
-
- String command = "scp " + (ptimestamp ? "-p" : "") + " -t " + fileName;
- Channel channel = getConnectedSession().openChannel("exec");
- ((ChannelExec) channel).setCommand(command);
- // get I/O streams for remote scp
- try (OutputStream out = channel.getOutputStream();
- InputStream in = channel.getInputStream())
- {
- channel.connect();
- if (!ack.checkAck(in)) {
- throw new JSchException(constructExceptionText(ack));
- }
-
- if (ptimestamp) {
- command = "T " + (lastModified / 1000) + " 0";
- // The access time should be sent here,
- // but it is not accessible with JavaAPI ;-<
- command += (" " + (lastModified / 1000) + " 0\n");
- out.write(command.getBytes());
- out.flush();
- if (!ack.checkAck(in)) {
- throw new JSchException(constructExceptionText(ack));
- }
- }
-
- // send "C0644 filesize filename", where filename should not include '/'
- long filesize = length;
- command = "C0644 " + filesize + " ";
- command += Paths.get(fileName).getFileName().toString();
- command += "\n";
- out.write(command.getBytes());
- out.flush();
- if (!ack.checkAck(in)) {
- if (ack.getLastStatus() == 1 && ack.getLastMessage().contains(
- NO_SUCH_FILE_OR_DIRECTORY_ERROR_TEXT))
- {
- throw new NoSuchFileException(getParent(fileName), null,
- constructExceptionText(ack));
- }
- throw new JSchException(constructExceptionText(ack));
- }
- byte[] buf = new byte[getBufferSize()];
- // send a content of lfile
- while (true) {
- int len = is.read(buf, 0, buf.length);
- if (len <= 0) break;
- out.write(buf, 0, len); // out.flush();
- progress.dataTransfered(len);
- }
- // send '\0'
- buf[0] = 0;
- out.write(buf, 0, 1);
- out.flush();
- if (!ack.checkAck(in)) {
- throw new JSchException(constructExceptionText(ack));
- }
- out.close();
-
- }
- catch (ClosedByInterruptException e) {
- Thread.interrupted();
- throw new InterruptedIOException();
- }
- finally {
- channel.disconnect();
- }
- }
-
- private String sanityFileName(String fileName) {
- fileName = fileName.replace("\"", "\\\\\\\"");
- fileName = fileName.replace("'", "\\\\\\'");
- fileName = "'" + fileName + "'";
- return fileName;
- }
-
- private int mkdir(String file) throws JSchException {
- ChannelExec channel = (ChannelExec) getConnectedSession().openChannel(
- "exec");
- file = sanityFileName(file);
- channel.setCommand("mkdir -p '" + file + "'");
- try {
- channel.connect();
- return channel.getExitStatus();
- }
- finally {
- channel.disconnect();
- }
- }
-
- private String getParent(String fileName) {
- int index = fileName.lastIndexOf('/');
- if (index == -1) {
- return null;
- }
- return fileName.substring(0, index);
- }
-
-}
diff --git a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/SshCommandClient.java b/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/SshCommandClient.java
deleted file mode 100644
index fcfb5ee9a46655cad14e533a6e56a6fbe6970d36..0000000000000000000000000000000000000000
--- a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/SshCommandClient.java
+++ /dev/null
@@ -1,134 +0,0 @@
-
-package cz.it4i.fiji.scpclient;
-
-import com.jcraft.jsch.ChannelExec;
-import com.jcraft.jsch.Identity;
-import com.jcraft.jsch.JSchException;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.util.LinkedList;
-import java.util.List;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-public class SshCommandClient extends AbstractBaseSshClient {
-
- private final static Logger log = LoggerFactory.getLogger(
- SshCommandClient.class);
-
- public SshCommandClient(String hostName, String username,
- byte[] privateKeyFile) throws JSchException
- {
- super(hostName, username, privateKeyFile);
- }
-
- public SshCommandClient(String hostName, String username,
- Identity privateKeyFile) throws JSchException
- {
- super(hostName, username, privateKeyFile);
- }
-
- public SshCommandClient(String hostName, String userName, String keyFile,
- String pass) throws JSchException
- {
- super(hostName, userName, keyFile, pass);
- }
-
- public SshExecutionSession openSshExecutionSession(String command) {
- try {
- ChannelExec channelExec = (ChannelExec) getConnectedSession().openChannel(
- "exec");
-
- channelExec.setCommand(command);
- channelExec.connect();
- return new P_SshExecutionSession(channelExec);
- }
- catch (Exception e) {
- log.error("Error: ", e);
- throw new RuntimeException(e);
- }
- }
-
- public List<String> executeCommand(String command) {
- List<String> result = new LinkedList<>();
- try (SshExecutionSession session = openSshExecutionSession(command)) {
-
- BufferedReader reader = new BufferedReader(new InputStreamReader(session
- .getStdout()));
- BufferedReader errReader = new BufferedReader(new InputStreamReader(
- session.getStderr()));
- String line;
-
- while ((line = reader.readLine()) != null) {
- result.add(line);
- }
- List<String> errors = new LinkedList<>();
- while ((line = errReader.readLine()) != null) {
- errors.add(line);
- }
-
- int exitStatus = session.getExitStatus();
-
- if (exitStatus < 0) {
- log.debug("Done, but exit status not set!");
- }
- else if (exitStatus > 0) {
- log.debug("Done, but with error! ");
- throw new SshExecuteCommandException(exitStatus, result, errors);
- }
- else {
- log.debug("Done!");
- }
- }
- catch (Exception e) {
- log.error("Error: ", e);
- throw new RuntimeException(e);
- }
- return result;
- }
-
- public boolean setPortForwarding(int lport, String rhost, int rport) {
- try {
- getConnectedSession().setPortForwardingL(lport, rhost, rport);
- }
- catch (JSchException exc) {
- log.error("forward", exc);
- return false;
- }
- return true;
- }
-
- private class P_SshExecutionSession implements SshExecutionSession {
-
- private ChannelExec channel;
-
- public P_SshExecutionSession(ChannelExec channel) {
- this.channel = channel;
- }
-
- @Override
- public InputStream getStdout() throws IOException {
- return channel.getInputStream();
- }
-
- @Override
- public InputStream getStderr() throws IOException {
- return channel.getErrStream();
- }
-
- @Override
- public int getExitStatus() {
- return channel.getExitStatus();
- }
-
- @Override
- public void close() {
- channel.disconnect();
- }
-
- }
-}
diff --git a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/SshExecuteCommandException.java b/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/SshExecuteCommandException.java
deleted file mode 100644
index 052ec9d956919268f8ccbd8f8a020ae666063848..0000000000000000000000000000000000000000
--- a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/SshExecuteCommandException.java
+++ /dev/null
@@ -1,36 +0,0 @@
-
-package cz.it4i.fiji.scpclient;
-
-import com.jcraft.jsch.JSchException;
-
-import java.util.List;
-
-public class SshExecuteCommandException extends JSchException {
-
- private int exitStatus;
- private List<String> stdout;
- private List<String> stderr;
-
- public SshExecuteCommandException(int exitStatus, List<String> stdout,
- List<String> stderr)
- {
- super("exitStatus: " + exitStatus + ", error output: " + String.join("\n",
- stderr));
- this.exitStatus = exitStatus;
- this.stdout = stdout;
- this.stderr = stderr;
- }
-
- public int getExitStatus() {
- return exitStatus;
- }
-
- public List<String> getStdout() {
- return stdout;
- }
-
- public List<String> getStderr() {
- return stderr;
- }
-
-}
diff --git a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/SshExecutionSession.java b/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/SshExecutionSession.java
deleted file mode 100644
index 3cb9240672097526d33b60dc35551fc06c6f90b8..0000000000000000000000000000000000000000
--- a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/SshExecutionSession.java
+++ /dev/null
@@ -1,18 +0,0 @@
-
-package cz.it4i.fiji.scpclient;
-
-import java.io.Closeable;
-import java.io.IOException;
-import java.io.InputStream;
-
-public interface SshExecutionSession extends Closeable {
-
- InputStream getStdout() throws IOException;
-
- InputStream getStderr() throws IOException;
-
- int getExitStatus();
-
- @Override
- void close();
-}
diff --git a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/TransferFileProgress.java b/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/TransferFileProgress.java
deleted file mode 100644
index af9f1d45c296b7934a94bb11b9fdb65aea4ff385..0000000000000000000000000000000000000000
--- a/java-scpclient/src/main/java/cz/it4i/fiji/scpclient/TransferFileProgress.java
+++ /dev/null
@@ -1,6 +0,0 @@
-package cz.it4i.fiji.scpclient;
-
-public interface TransferFileProgress {
-
- void dataTransfered(long bytesTransfered);
-}
diff --git a/java-scpclient/src/test/java/TestSCP.java b/java-scpclient/src/test/java/TestSCP.java
deleted file mode 100644
index 6762e37bdb19ce65089570420175d5dc1355139d..0000000000000000000000000000000000000000
--- a/java-scpclient/src/test/java/TestSCP.java
+++ /dev/null
@@ -1,22 +0,0 @@
-import java.io.IOException;
-
-import com.jcraft.jsch.JSchException;
-
-import cz.it4i.fiji.scpclient.ScpClient;
-
-public class TestSCP {
-
- public TestSCP() {
-
- }
-
- public static void main(String[] args) throws JSchException, IOException {
- try(ScpClient scp = new ScpClient("salomon.it4i.cz", "koz01", "/home/koz01/.ssh/it4i_rsa-np", null)) {
-// System.out.println( scp.upload(
-// Paths.get("/home/koz01/Work/vyzkumnik/fiji/work/aaa/spim-data/exampleSingleChannel(9).czi"), "'/home/koz01/exampleSingleChannel(9).czi'"));
- System.out.println( scp.size("'/home/koz01/exampleSingleChannel(9).czi'"));
-
- }
- }
-
-}
diff --git a/pom.xml b/pom.xml
index 458248b841156d3513506d319edac0a253ce5cb5..1bfee22c067d7801f9324e9825ff202d644420b6 100644
--- a/pom.xml
+++ b/pom.xml
@@ -12,7 +12,6 @@
<maven.deploy.skip>true</maven.deploy.skip>
</properties>
<modules>
- <module>java-scpclient</module>
<module>haas-java-client</module>
<module>haas-spim-benchmark</module>
<module>haas-imagej-client</module>