protected void readAlignments(BufferedReader stdInput, InputStream errorStream)
throws IOException {
String outLine;
SAMAlignmentReader alignmentReader = new SAMAlignmentReader();
while ((outLine = stdInput.readLine()) != null) {
if (logger.isDebugEnabled()) {
logger.debug("LINE: " + outLine);
}
if (outLine.startsWith("@")) {
logger.debug("SAM HEADER LINE: " + outLine);
continue;
}
String readPairId = outLine.substring(0, outLine.indexOf('\t'));
if (readPairId.endsWith("/1") || readPairId.endsWith("/2")) {
readPairId = readPairId.substring(0, readPairId.length() - 2);
}
AlignmentRecord alignment = alignmentReader.parseRecord(outLine);
if (!alignment.isMapped()) {
continue;
}
getOutput().collect(new Text(readPairId), new Text(outLine));
}
String errLine;
BufferedReader errorReader = new BufferedReader(new InputStreamReader(errorStream));
while ((errLine = errorReader.readLine()) != null) {
logger.error("ERROR: " + errLine);
}
}
/**
* Generates an SHA-1 digest hash of the string: clearTextID+"-"+function or: clearTextID if
* function was blank.
*
* <p>Note that the SHA-1 used only creates a 20 byte hash.
*
* <p>
*
* @param clearTextID A string that is to be hashed. This can be any string used for hashing or
* hiding data.
* @param function A function related to the clearTextID string. This is used to create a hash
* associated with clearTextID so that it is a uique code.
* @return array of bytes containing the hash of the string: clearTextID+"-"+function or
* clearTextID if function was blank. Can return null if SHA-1 does not exist on platform.
*/
public final byte[] generateHash(String clearTextID, String function) {
String id;
if (function == null) {
id = clearTextID;
} else {
id = clearTextID + functionSeperator + function;
}
byte[] buffer = id.getBytes();
MessageDigest algorithm = null;
try {
algorithm = MessageDigest.getInstance(algorithmType);
} catch (Exception e) {
LOG.error("Cannot load selected Digest Hash implementation", e);
return null;
}
// Generate the digest.
algorithm.reset();
algorithm.update(buffer);
try {
byte[] digest1 = algorithm.digest();
return digest1;
} catch (Exception de) {
LOG.error("Failed to creat a digest.", de);
return null;
}
}
public Graph(WeightedBVGraph graph, String[] names) {
org.apache.log4j.Logger logger =
org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph");
logger.setLevel(org.apache.log4j.Level.FATAL);
if (names.length != graph.numNodes())
throw new Error("Problem with the list of names for the nodes in the graph.");
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
this.graph = graph;
WeightedArcSet list = new WeightedArcSet();
ArcLabelledNodeIterator it = graph.nodeIterator();
while (it.hasNext()) {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
Integer aux1 = it.nextInt();
Integer aux2 = null;
ArcLabelledNodeIterator.LabelledArcIterator suc = it.successors();
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
WeightedArc arc = (WeightedArc) cons[0].newInstance(aux2, aux1, suc.label().getFloat());
list.add(arc);
this.nodes.put(aux1, names[aux1]);
this.nodes.put(aux2, names[aux2]);
this.nodesReverse.put(names[aux1], aux1);
this.nodesReverse.put(names[aux2], aux2);
} catch (Exception ex) {
throw new Error(ex);
}
}
reverse = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
numArcs = list.size();
iterator = nodeIterator();
try {
File auxFile = File.createTempFile("graph" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
String basename = auxFile.getAbsolutePath();
store(basename);
} catch (IOException ex) {
throw new Error(ex);
}
commit();
}
public final String readCommand(byte[] b)
throws IOException, InterruptedException, MessagingNetworkException {
InputStream is = getInputStream();
synchronized (is) {
long abortTime =
System.currentTimeMillis() + 1000 * MSNMessagingNetwork.REQPARAM_SOCKET_TIMEOUT_SECONDS;
int ofs = 0;
boolean d = false;
for (; ; ) {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
int by = is.read();
if (by == -1) throw new IOException("unexpected EOF");
if (by == 10 && d) break;
d = (by == 13);
if (ofs < b.length) {
b[ofs++] = (byte) by;
}
if (System.currentTimeMillis() > abortTime) throw new IOException("connection timed out");
/*
if (len >= buffer.length)
{
...
return ...;
}
int pos = findCRLF();
if (pos != -1) break;
fill(is, abortTime);
*/
}
if (b[ofs - 1] == 13) --ofs;
String line = new String(b, 0, ofs, "ASCII");
if (StringUtil.startsWith(line, "MSG")) {
StringTokenizer st = new StringTokenizer(line);
String len_s = null;
while (st.hasMoreTokens()) {
len_s = st.nextToken();
}
if (len_s == null) throw new AssertException("len_s is null");
int len;
try {
len = Integer.parseInt(len_s);
} catch (NumberFormatException ex) {
ServerConnection.throwProtocolViolated("MSG length must be int");
len = 0;
}
String msg = readMSG(len);
line = line + "\r\n" + msg;
}
if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("S: " + line);
return line;
}
}
public final void writeASCII(String s) throws IOException {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
OutputStream os = getOutputStream();
synchronized (os) {
if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("C: " + s);
os.write(s.getBytes("ASCII"));
os.write((byte) 13);
os.write((byte) 10);
os.flush();
}
}
protected void waitForOpenSlot(int maxProcessesOnNode, Reporter reporter)
throws IOException, InterruptedException {
while (true) {
// sleep for a random length of time between 0 and 60 seconds
long sleepTime = (long) (Math.random() * 1000 * 60);
logger.info("sleeping for " + sleepTime);
Thread.sleep(sleepTime);
int numRunningMappers = getNumRunningMappers();
logger.info("num running mappers: " + numRunningMappers);
if (numRunningMappers < maxProcessesOnNode) return;
reporter.progress();
}
}
/**
* UTF byte count is appended to the asciiPrefix, then UTF bytes are appended to the result; the
* final result is sent.
*/
public final void writeMSG(String asciiPrefix, String msgBody) throws IOException {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
OutputStream os = getOutputStream();
synchronized (os) {
byte[] utfBytes = msgBody.getBytes("UTF-8");
asciiPrefix = asciiPrefix + ' ' + utfBytes.length;
if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("C: " + asciiPrefix + "\r\n" + msgBody);
os.write(asciiPrefix.getBytes("ASCII"));
os.write((byte) 13);
os.write((byte) 10);
os.write(utfBytes);
os.flush();
}
}
public class Underlay extends AbstractConsoleCommand {
private static org.apache.log4j.Logger log = org.apache.log4j.Logger.getLogger(Underlay.class);
private final UnderlayLocator underlayLocator;
public Underlay(
List<String> args,
String host,
String currentDir,
ResourceFactory resourceFactory,
DeploymentService deploymentService,
UnderlayLocator underlayLocator) {
super(args, host, currentDir, resourceFactory);
this.underlayLocator = underlayLocator;
}
@Override
public Result execute() {
Folder cur;
try {
cur = currentResource();
} catch (NotAuthorizedException | BadRequestException ex) {
return result("can't lookup current resource", ex);
}
if (cur == null) {
return result("current dir not found: " + currentDir);
}
String cmd = args.get(0);
args.remove(0);
switch (cmd) {
case "add":
return doAdd(cur.getHost());
case "remove":
return doRemove(cur.getHost());
default:
return result("Unknown command: " + cmd);
}
}
private Result doAdd(Host currentHost) {
UnderlayVector v = new UnderlayVector();
v.setGroupId(args.get(0));
v.setArtifcatId(args.get(1));
v.setVersion(args.get(2));
List<UnderlayVector> vectors = currentHost.getUnderlayVectors();
if (vectors == null) {
vectors = new ArrayList<>();
}
Iterator<UnderlayVector> it = vectors.iterator();
while (it.hasNext()) {
UnderlayVector oldV = it.next();
// if( oldV.getGroupId().equals(v.getGroupId()))
}
return null;
}
private Result doRemove(Host currentHost) {
throw new UnsupportedOperationException("Not yet implemented");
}
}
public void addHostKey(byte[] key) throws JSchException {
HostKeyRepository hkr = this.jsch.getHostKeyRepository();
HostKey hk = new HostKey(this.host, key);
UserInfo userInfo = new MyUserInfo();
hkr.add(hk, userInfo);
log.info("hostkey added");
}
protected void setValidationErrorMessage(
List<org.kuali.coeus.s2sgen.api.core.AuditError> errors) {
if (errors != null) {
LOG.info("Error list size:" + errors.size() + errors.toString());
List<org.kuali.rice.krad.util.AuditError> auditErrors = new ArrayList<>();
for (org.kuali.coeus.s2sgen.api.core.AuditError error : errors) {
auditErrors.add(
new org.kuali.rice.krad.util.AuditError(
error.getErrorKey(),
Constants.GRANTS_GOV_GENERIC_ERROR_KEY,
error.getLink(),
new String[] {error.getMessageKey()}));
}
if (!auditErrors.isEmpty()) {
getGlobalVariableService()
.getAuditErrorMap()
.put(
"grantsGovAuditErrors",
new AuditCluster(
Constants.GRANTS_GOV_OPPORTUNITY_PANEL,
auditErrors,
Constants.GRANTSGOV_ERRORS));
}
}
}
public Session getSession(String host, Integer port, String user, Boolean hostKeyChecking)
throws JSchException {
if (this.session != null) return this.session;
this.setHost(host);
this.setUser(user);
this.session = jsch.getSession(user, host, port);
java.util.Properties config = new java.util.Properties();
if (hostKeyChecking) {
log.info("strict host key checking enabled");
config.put("StrictHostKeyChecking", "yes");
} else {
log.info("strict host key checking disabled");
config.put("StrictHostKeyChecking", "no");
}
session.setConfig(config);
return session;
}
protected String printErrorStream(InputStream errorStream) throws IOException {
String outLine;
BufferedReader stdErr = new BufferedReader(new InputStreamReader(errorStream));
String firstErrorLine = null;
while ((outLine = stdErr.readLine()) != null) {
if (firstErrorLine == null) firstErrorLine = outLine;
logger.error(outLine);
}
return firstErrorLine;
}
/**
* Generates a Base64 encoded string of an SHA-1 digest hash of the string:
* clearTextID+"-"+function or: clearTextID if function was blank.
*
* <p>
*
* @param clearTextID A string that is to be hashed. This can be any string used for hashing or
* hiding data.
* @param function A function related to the clearTextID string. This is used to create a hash
* associated with clearTextID so that it is a uique code.
* @return Base64 encoded string containing the hash of the string: clearTextID+"-"+function or
* clearTextID if function was blank.
*/
public final String generateHashString(String clearTextID, String function) {
try {
java.io.StringWriter base64 = new java.io.StringWriter();
net.jxta.impl.util.BASE64OutputStream encode =
new net.jxta.impl.util.BASE64OutputStream(base64);
encode.write(generateHash(clearTextID, function));
encode.close();
return base64.toString();
} catch (Exception failed) {
LOG.error("Unable to encode hash value.", failed);
throw new RuntimeException("Unable to encode hash value.");
}
}
@Transactional
@RequestMapping(
value = "/proposalDevelopment",
params = {"methodToCall=refreshSubmissionDetails"})
public ModelAndView refreshSubmissionDetails(ProposalDevelopmentDocumentForm form)
throws Exception {
ProposalDevelopmentDocument document = form.getProposalDevelopmentDocument();
try {
getS2sSubmissionService().refreshGrantsGov(document);
} catch (S2sCommunicationException ex) {
LOG.error(ex.getMessage(), ex);
getGlobalVariableService()
.getMessageMap()
.putError(Constants.NO_FIELD, ex.getErrorKey(), ex.getMessage());
}
return getRefreshControllerService().refresh(form);
}
@Transactional
@RequestMapping(
value = "/proposalDevelopment",
params = {"methodToCall=addUserAttachedForm"})
public ModelAndView addUserAttachedForm(
@ModelAttribute("KualiForm") ProposalDevelopmentDocumentForm form) throws Exception {
S2sUserAttachedForm s2sUserAttachedForm = form.getS2sUserAttachedForm();
ProposalDevelopmentDocument proposalDevelopmentDocument = form.getProposalDevelopmentDocument();
MultipartFile userAttachedFormFile = s2sUserAttachedForm.getNewFormFile();
s2sUserAttachedForm.setNewFormFileBytes(userAttachedFormFile.getBytes());
s2sUserAttachedForm.setFormFileName(userAttachedFormFile.getOriginalFilename());
s2sUserAttachedForm.setProposalNumber(
proposalDevelopmentDocument.getDevelopmentProposal().getProposalNumber());
try {
List<S2sUserAttachedForm> userAttachedForms =
getS2sUserAttachedFormService()
.extractNSaveUserAttachedForms(proposalDevelopmentDocument, s2sUserAttachedForm);
proposalDevelopmentDocument
.getDevelopmentProposal()
.getS2sUserAttachedForms()
.addAll(userAttachedForms);
form.setS2sUserAttachedForm(new S2sUserAttachedForm());
} catch (S2SException ex) {
LOG.error(ex.getMessage(), ex);
if (ex.getTabErrorKey() != null) {
if (getGlobalVariableService()
.getMessageMap()
.getErrorMessagesForProperty(ex.getTabErrorKey())
== null) {
getGlobalVariableService()
.getMessageMap()
.putError(ex.getTabErrorKey(), ex.getErrorKey(), ex.getParams());
}
} else {
getGlobalVariableService()
.getMessageMap()
.putError(Constants.NO_FIELD, ex.getErrorKey(), ex.getMessageWithParams());
}
}
return super.save(form);
}
private void splitRead(LongWritable key, String line, Writer writer) throws IOException {
String[] fields = line.split("\t");
if (fields[1].length() != fields[3].length()) {
logger.warn("Warning; mismatching seq and qual lengths in record " + key.toString() + "!");
logger.warn("Seq:");
logger.warn(fields[1]);
logger.warn("Qual:");
logger.warn(fields[3]);
logger.warn("DONE WARNING");
}
writer.write(fields[0] + "\n");
writer.write(fields[1] + "\n");
writer.write(fields[2] + "\n");
writer.write(fields[3] + "\n");
}
/**
* Compares a clear text code or ID with a candidate hash code. This is used to confirm that the
* clearTextID can be successfully converted to the hash.
*
* @param clearTextID A string that is to be hashed. This can be any string used for hashing or
* hiding data.
* @param testHash A string of hashed string.
* @return true if the hash created from clearTextID is equal to the testHash string.Can return
* false if SHA-1 does not exist on platform.
*/
public final boolean test(String clearTextID, String testHash) {
byte[] digest1 = generateHash(clearTextID);
byte[] digest2;
try {
java.io.ByteArrayOutputStream bos = new java.io.ByteArrayOutputStream();
net.jxta.impl.util.BASE64InputStream decoder =
new net.jxta.impl.util.BASE64InputStream(new java.io.StringReader(testHash));
while (true) {
int c = decoder.read();
if (-1 == c) {
break;
}
bos.write(c);
}
digest2 = bos.toByteArray();
} catch (Exception e) {
LOG.error("Failed to create a digest.", e);
return false;
}
if (digest1.length != digest2.length) {
// Not a match! because of length.
return false;
}
for (int i = 0; i < digest1.length; i++) {
if (digest1[i] != digest2[i]) {
// Not a match because of byte:"+i+" did not match
return false;
}
}
// Match was ok
return true;
}
public ChannelExec getExecutionChannel() throws JSchException {
Channel channel = session.openChannel("exec");
log.info("opening execution channel");
return (ChannelExec) channel;
}
public ChannelSftp getSftpChannel() throws JSchException {
Channel channel = session.openChannel("sftp");
log.info("opening sftp channel");
return (ChannelSftp) channel;
}
@Override
public Integer call() {
int exitstatus = Integer.MAX_VALUE;
Boolean useIdentityFile = null;
String credentials = null;
String userName = nodeCredentials.getUsername();
if (nodeCredentials instanceof LoginCredentialsPassword) {
useIdentityFile = false;
credentials = ((LoginCredentialsPassword) nodeCredentials).getPassword();
} else if (nodeCredentials instanceof LoginCredentialsPrivateKey) {
useIdentityFile = true;
credentials = ((LoginCredentialsPrivateKey) nodeCredentials).getKey().getKeyPath();
}
ChannelExec c = null;
SshClient ssh = null;
try {
ssh = new SshClient();
ssh.createSession(nodeAddress, userName, false);
log.info("connecting with username: "******"connecting using identity file: " + credentials);
} else {
log.info("connecting using password: "******"executing command: " + command);
c.connect();
new Thread(
new Runnable() {
public void run() {
String line;
BufferedReader bufferedInputReader =
new BufferedReader(new InputStreamReader(is));
try {
while ((line = bufferedInputReader.readLine()) != null) {
output.append(line);
synchronized (timeStamp) {
timeStamp = System.currentTimeMillis();
}
}
} catch (IOException e) {
e.printStackTrace();
}
}
})
.start();
new Thread(
new Runnable() {
public void run() {
String line;
BufferedReader bufferedErrorReader =
new BufferedReader(new InputStreamReader(err));
try {
while ((line = bufferedErrorReader.readLine()) != null) {
error.append(line);
synchronized (timeStamp) {
timeStamp = System.currentTimeMillis();
}
}
} catch (IOException e) {
e.printStackTrace();
}
}
})
.start();
while (!c.isClosed()) {
synchronized (this.timeStamp) {
if (System.currentTimeMillis() - this.timeStamp > MAXIMUM_WAITING_TIME_INACTIVITY) {
log.warn("command execution seems inactive, canceling!");
break;
}
}
log.info("waiting for command to finish.");
try {
Thread.sleep(SshClient.DEFAULT_WAITING_TIME_PER_CYCLE);
} catch (InterruptedException e) {
e.printStackTrace();
}
}
exitstatus = c.getExitStatus();
} catch (JSchException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
} finally {
if (c != null) {
c.disconnect();
}
if (ssh != null) {
try {
ssh.disconnectSession();
} catch (JSchException e) {
e.printStackTrace();
}
}
}
return exitstatus;
}
public Graph(String file) throws IOException {
org.apache.log4j.Logger logger =
org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph");
logger.setLevel(org.apache.log4j.Level.FATAL);
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
String aux = null;
Float weight = (float) 1.0;
WeightedArcSet list = new WeightedArcSet();
BufferedReader br;
try {
br =
new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(file))));
} catch (Exception ex) {
br = new BufferedReader(new FileReader(file));
}
while ((aux = br.readLine()) != null)
try {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
String parts[] = aux.split("\t");
String l1 = new String(parts[0]);
String l2 = new String(parts[1]);
if (!nodesReverse.containsKey(l1)) {
nodesReverse.put(l1, nodesReverse.size());
nodes.put(nodes.size(), l1);
}
if (!nodesReverse.containsKey(l2)) {
nodesReverse.put(l2, nodesReverse.size());
nodes.put(nodes.size(), l2);
}
if (parts.length == 3) weight = new Float(parts[2]);
list.add(
(WeightedArc) cons[0].newInstance(nodesReverse.get(l1), nodesReverse.get(l2), weight));
} catch (Exception ex) {
throw new Error(ex);
}
this.graph = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
br.close();
list = new WeightedArcSet();
br = new BufferedReader(new FileReader(file));
while ((aux = br.readLine()) != null)
try {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
String parts[] = aux.split("\t");
String l1 = new String(parts[0]);
String l2 = new String(parts[1]);
if (parts.length == 3) weight = new Float(parts[2]);
list.add(
(WeightedArc) cons[0].newInstance(nodesReverse.get(l2), nodesReverse.get(l1), weight));
} catch (Exception ex) {
throw new Error(ex);
}
br.close();
this.reverse = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
numArcs = list.size();
iterator = nodeIterator();
try {
File auxFile = File.createTempFile("graph" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
String basename = auxFile.getAbsolutePath();
store(basename);
} catch (IOException ex) {
throw new Error(ex);
}
commit();
}
public Graph(BVGraph graph) {
org.apache.log4j.Logger logger =
org.apache.log4j.Logger.getLogger("it.unimi.dsi.webgraph.ImmutableGraph");
logger.setLevel(org.apache.log4j.Level.FATAL);
try {
File auxFile = File.createTempFile("graph-maps-" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
RecordManager recMan = RecordManagerFactory.createRecordManager(auxFile.getAbsolutePath());
nodes = recMan.hashMap("nodes");
nodesReverse = recMan.hashMap("nodesReverse");
} catch (IOException ex) {
throw new Error(ex);
}
nodes.clear();
nodesReverse.clear();
Constructor[] cons = WeightedArc.class.getDeclaredConstructors();
for (int i = 0; i < cons.length; i++) cons[i].setAccessible(true);
Integer aux1 = null;
WeightedArcSet list = new WeightedArcSet();
it.unimi.dsi.webgraph.NodeIterator it = graph.nodeIterator();
while ((aux1 = it.nextInt()) != null) {
LazyIntIterator suc = it.successors();
Integer aux2 = null;
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
if (commit++ % COMMIT_SIZE == 0) {
list.commit();
}
list.add((WeightedArc) cons[0].newInstance(aux1, aux2, (float) 1.0));
} catch (Exception ex) {
throw new Error(ex);
}
}
this.graph = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
list = new WeightedArcSet();
it = graph.nodeIterator();
while ((aux1 = it.nextInt()) != null) {
LazyIntIterator suc = it.successors();
Integer aux2 = null;
while ((aux2 = suc.nextInt()) != null && aux2 >= 0 && (aux2 < graph.numNodes()))
try {
if (commit++ % COMMIT_SIZE == 0) {
commit();
list.commit();
}
list.add((WeightedArc) cons[0].newInstance(aux2, aux1, (float) 1.0));
this.nodes.put(aux1, "" + aux1);
this.nodes.put(aux2, "" + aux2);
this.nodesReverse.put("" + aux1, aux1);
this.nodesReverse.put("" + aux2, aux2);
} catch (Exception ex) {
throw new Error(ex);
}
}
this.reverse = new WeightedBVGraph(list.toArray(new WeightedArc[0]));
numArcs = list.size();
iterator = nodeIterator();
try {
File auxFile = File.createTempFile("graph" + System.currentTimeMillis(), "aux");
auxFile.deleteOnExit();
String basename = auxFile.getAbsolutePath();
store(basename);
} catch (IOException ex) {
throw new Error(ex);
}
commit();
}
public class SshClient {
public static long DEFAULT_WAITING_TIME_PER_CYCLE = 1000;
public static long MAXIMUM_WAITING_TIME_INACTIVITY = 10000;
private static org.apache.log4j.Logger log = org.apache.log4j.Logger.getLogger("SshClient");
protected String host = null;
protected Integer port = null;
protected String user = null;
protected final JSch jsch;
protected String knownHostsFile = null;
protected Session session = null;;
public SshClient() throws JSchException {
this.jsch = new JSch();
}
public SshClient(String knownHostsFile) throws JSchException {
this.knownHostsFile = knownHostsFile;
this.jsch = new JSch();
jsch.setKnownHosts(this.knownHostsFile);
}
public void addIdentityFile(String identityFileName) throws JSchException {
this.jsch.addIdentity(identityFileName);
}
public void setHost(String host) {
this.host = host;
}
public void setPort(Integer port) {
this.port = port;
}
public void setUser(String user) {
this.user = user;
}
public void createSession(String host, String user, Boolean hostKeyChecking)
throws JSchException {
log.info("creating session");
this.session = this.getSession(host, user, hostKeyChecking);
}
public void createSession(String host, Integer port, String user, Boolean hostKeyChecking)
throws JSchException {
log.info("creating session");
this.session = this.getSession(host, port, user, hostKeyChecking);
}
public Session getSession(String host, String user, Boolean hostKeyChecking)
throws JSchException {
return this.getSession(host, 22, user, hostKeyChecking);
}
public Session getSession(String host, Integer port, String user, Boolean hostKeyChecking)
throws JSchException {
if (this.session != null) return this.session;
this.setHost(host);
this.setUser(user);
this.session = jsch.getSession(user, host, port);
java.util.Properties config = new java.util.Properties();
if (hostKeyChecking) {
log.info("strict host key checking enabled");
config.put("StrictHostKeyChecking", "yes");
} else {
log.info("strict host key checking disabled");
config.put("StrictHostKeyChecking", "no");
}
session.setConfig(config);
return session;
}
public void setSessionPassword(String pw) {
log.info("password set");
this.session.setPassword(pw);
}
public void connectSession() throws JSchException {
log.info("connecting session");
this.session.connect();
}
public void disconnectSession() throws JSchException {
log.info("disconnecting session");
this.session.disconnect();
}
public ChannelExec getExecutionChannel() throws JSchException {
Channel channel = session.openChannel("exec");
log.info("opening execution channel");
return (ChannelExec) channel;
}
public ChannelShell getShellChannel() throws JSchException {
Channel channel = session.openChannel("shell");
log.info("opening shell channel");
return (ChannelShell) channel;
}
public ChannelSftp getSftpChannel() throws JSchException {
Channel channel = session.openChannel("sftp");
log.info("opening sftp channel");
return (ChannelSftp) channel;
}
public void listKnownHosts() {
HostKeyRepository hkr = this.jsch.getHostKeyRepository();
HostKey[] hks = hkr.getHostKey();
if (hks != null) {
System.out.println("Host keys in " + hkr.getKnownHostsRepositoryID());
for (int i = 0; i < hks.length; i++) {
HostKey hk = hks[i];
System.out.println(hk.getHost() + " " + hk.getType() + " " + hk.getFingerPrint(jsch));
}
System.out.println("");
}
}
public void addHostKey(byte[] key) throws JSchException {
HostKeyRepository hkr = this.jsch.getHostKeyRepository();
HostKey hk = new HostKey(this.host, key);
UserInfo userInfo = new MyUserInfo();
hkr.add(hk, userInfo);
log.info("hostkey added");
}
/**
* Executes the specified command on the specified host, using loginCredentials.
*
* <p>The function can't respond to requests on the default input! If a command waits for an
* input, the execution will be terminated after a certain waiting time without changes to stderr
* or stdin.
*
* @param nodeAddress
* @param nodeCredentials
* @param command
* @return
*/
public CommandExecution getCommandExecutor(
String nodeAddress, LoginCredentials nodeCredentials, String command) {
return new CommandExecution(nodeAddress, nodeCredentials, command);
}
public static ChannelExec getExecutionChannel(Session session, String cmd) throws JSchException {
Channel channel = session.openChannel("exec");
((ChannelExec) channel).setCommand(cmd);
return ((ChannelExec) channel);
}
public static class CommandExecution implements Callable<Integer> {
protected static ExecutorService executor = Executors.newFixedThreadPool(4);
protected StringBuffer output = new StringBuffer();
protected StringBuffer error = new StringBuffer();
private Long timeStamp = System.currentTimeMillis();
private String nodeAddress;
private LoginCredentials nodeCredentials;
private String command;
public CommandExecution(String nodeAddress, LoginCredentials nodeCredentials, String command) {
this.nodeAddress = nodeAddress;
this.nodeCredentials = nodeCredentials;
this.command = command;
}
public Future<Integer> execute() {
if (executor == null) executor = Executors.newFixedThreadPool(4);
if (executor.isShutdown()) executor = Executors.newFixedThreadPool(4);
ExecutorCompletionService<Integer> commandExecutor =
new ExecutorCompletionService<Integer>(executor);
return commandExecutor.submit(this);
}
public void shutdown() {
if (!executor.isShutdown()) executor.shutdown();
}
@Override
public Integer call() {
int exitstatus = Integer.MAX_VALUE;
Boolean useIdentityFile = null;
String credentials = null;
String userName = nodeCredentials.getUsername();
if (nodeCredentials instanceof LoginCredentialsPassword) {
useIdentityFile = false;
credentials = ((LoginCredentialsPassword) nodeCredentials).getPassword();
} else if (nodeCredentials instanceof LoginCredentialsPrivateKey) {
useIdentityFile = true;
credentials = ((LoginCredentialsPrivateKey) nodeCredentials).getKey().getKeyPath();
}
ChannelExec c = null;
SshClient ssh = null;
try {
ssh = new SshClient();
ssh.createSession(nodeAddress, userName, false);
log.info("connecting with username: "******"connecting using identity file: " + credentials);
} else {
log.info("connecting using password: "******"executing command: " + command);
c.connect();
new Thread(
new Runnable() {
public void run() {
String line;
BufferedReader bufferedInputReader =
new BufferedReader(new InputStreamReader(is));
try {
while ((line = bufferedInputReader.readLine()) != null) {
output.append(line);
synchronized (timeStamp) {
timeStamp = System.currentTimeMillis();
}
}
} catch (IOException e) {
e.printStackTrace();
}
}
})
.start();
new Thread(
new Runnable() {
public void run() {
String line;
BufferedReader bufferedErrorReader =
new BufferedReader(new InputStreamReader(err));
try {
while ((line = bufferedErrorReader.readLine()) != null) {
error.append(line);
synchronized (timeStamp) {
timeStamp = System.currentTimeMillis();
}
}
} catch (IOException e) {
e.printStackTrace();
}
}
})
.start();
while (!c.isClosed()) {
synchronized (this.timeStamp) {
if (System.currentTimeMillis() - this.timeStamp > MAXIMUM_WAITING_TIME_INACTIVITY) {
log.warn("command execution seems inactive, canceling!");
break;
}
}
log.info("waiting for command to finish.");
try {
Thread.sleep(SshClient.DEFAULT_WAITING_TIME_PER_CYCLE);
} catch (InterruptedException e) {
e.printStackTrace();
}
}
exitstatus = c.getExitStatus();
} catch (JSchException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
} finally {
if (c != null) {
c.disconnect();
}
if (ssh != null) {
try {
ssh.disconnectSession();
} catch (JSchException e) {
e.printStackTrace();
}
}
}
return exitstatus;
}
}
public static void main(String[] args) throws JSchException {
SshClient ssh = new SshClient();
CommandExecution exec =
ssh.getCommandExecutor(
ChefNodeManager.DEFAULT_CHEF_HOST,
new LoginCredentialsPassword("chef login creds", "root", "redundant"),
// "ps aux");
"knife bootstrap 23.20.100.107 -i /tmp/creds3268697130713915657.tmp -x ubuntu --sudo --no-host-key-verify -d ubuntu10.04-apt -N mytestNode1");
Future<Integer> result = exec.execute();
System.out.println("result: " + result);
exec.shutdown();
}
public static class MyUserInfo implements UserInfo, UIKeyboardInteractive {
public String getPassword() {
return passwd;
}
public boolean promptYesNo(String str) {
Object[] options = {"yes", "no"};
int foo =
JOptionPane.showOptionDialog(
null,
str,
"Warning",
JOptionPane.DEFAULT_OPTION,
JOptionPane.WARNING_MESSAGE,
null,
options,
options[0]);
return foo == 0;
}
String passwd;
JTextField passwordField = (JTextField) new JPasswordField(20);
public String getPassphrase() {
return null;
}
public boolean promptPassphrase(String message) {
return true;
}
public boolean promptPassword(String message) {
Object[] ob = {passwordField};
int result = JOptionPane.showConfirmDialog(null, ob, message, JOptionPane.OK_CANCEL_OPTION);
if (result == JOptionPane.OK_OPTION) {
passwd = passwordField.getText();
return true;
} else {
return false;
}
}
public void showMessage(String message) {
JOptionPane.showMessageDialog(null, message);
}
final GridBagConstraints gbc =
new GridBagConstraints(
0,
0,
1,
1,
1,
1,
GridBagConstraints.NORTHWEST,
GridBagConstraints.NONE,
new Insets(0, 0, 0, 0),
0,
0);
private Container panel;
public String[] promptKeyboardInteractive(
String destination, String name, String instruction, String[] prompt, boolean[] echo) {
panel = new JPanel();
panel.setLayout(new GridBagLayout());
gbc.weightx = 1.0;
gbc.gridwidth = GridBagConstraints.REMAINDER;
gbc.gridx = 0;
panel.add(new JLabel(instruction), gbc);
gbc.gridy++;
gbc.gridwidth = GridBagConstraints.RELATIVE;
JTextField[] texts = new JTextField[prompt.length];
for (int i = 0; i < prompt.length; i++) {
gbc.fill = GridBagConstraints.NONE;
gbc.gridx = 0;
gbc.weightx = 1;
panel.add(new JLabel(prompt[i]), gbc);
gbc.gridx = 1;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.weighty = 1;
if (echo[i]) {
texts[i] = new JTextField(20);
} else {
texts[i] = new JPasswordField(20);
}
panel.add(texts[i], gbc);
gbc.gridy++;
}
if (JOptionPane.showConfirmDialog(
null,
panel,
destination + ": " + name,
JOptionPane.OK_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE)
== JOptionPane.OK_OPTION) {
String[] response = new String[prompt.length];
for (int i = 0; i < prompt.length; i++) {
response[i] = texts[i].getText();
}
return response;
} else {
return null; // cancel
}
}
}
}
public void createSession(String host, Integer port, String user, Boolean hostKeyChecking)
throws JSchException {
log.info("creating session");
this.session = this.getSession(host, port, user, hostKeyChecking);
}
/**
* This is a utility class used to create pipe advertisement named and BinaryID for the pipeID to
* create a private address space that can be hosted in the public discovery system or sent over
* unencrypted channeds without revealing their intent or purpose.
*
* <p>We use a one-way hashing algorythum to create an ID from private information like a user's
* social security number or a user's email address. We search for the pipe by with this private
* information securly by creating the matching hash using the same methods.
*
* <p>The purpose of this system is to create a way to search for a pipe (or other BinaryID based
* system) without exposing the pipe owner's clearTextID while allowing for people that know what
* they are looking for to find the right pipe. The system also has the ability to create pipes that
* have a specific purpose. For example, the email address is appended with a function name. Say you
* have a pipe for messages and one for administrative purposes. You would supply the email and a
* string for the function. The same combination can be created by another peer to search for either
* of these pipes.
*
* <p>This implementation uses the "SHA-1" algorythum. This was selected for relitive speed. It is
* used as a one-way conversion that cannot be reversed engineered to create the original string.
* This allows you to publish the hash without the possibility of the contents being decoded. This
* allows for public indexing of data that is only known by the parties involved.
*
* <p>Note that this can also be used to generate safe password verification hash codes. Sample
* useage: <code>
* String clearTextID = "*****@*****.**";
* String function = "eventPipe";
* System.out.println("clear text ID: "+clearTextID);
* System.out.println("function text: "+function);
* String digest1 = DigestID.generateHashString(clearTextID, function);
* String digest2 = DigestID.generateHashString(clearTextID);
* System.out.println("Digest1: '"+digest1+"'");
* System.out.println("Digest2: '"+digest2+"'");
* System.out.println("test1: "+DigestID.test(clearTextID, function,digest1));
* System.out.println("test2: "+DigestID.test(clearTextID, digest2));
* System.out.println("Digest1 != Digest2: "+DigestID.test(clearTextID, function,digest2));
* </code>
*
* <p>To use an algorythum other than SHA-1, you will need stronger encyption. The BouncyCastle that
* comes with JXTA is just a minimum implimentation so a good choice is the normal bouncy castle (it
* is much larger, nearing a meg, which is why it is not a part of the normal JXTA distribution. The
* full version of bouncy includes SHA-128, SHA-256, SHA-384, and SHA-512.
*
* <p>Here is how you create a provider from the full version of Bouncy. Once you do this, you can
* access the extended Digest ecryption levels. <code>
* provider = new org.bouncycastle.jce.provider.BouncyCastleProvider();
* System.out.println("provider:"+provider.getName());
* Security.addProvider(provider);
* </code>
*
* <p>Security Note
*
* <p>
*
* <p>This class should have all of its fields and properties marked as 'final' to prevent
* overriding the default behavior. Failure to do so could allow a less scrupulous person to cause
* the BinaryID or hash codes to contain the original information. Note that the class itself is not
* final to allow for additional convienience methods to be added. There a no methods for creating
* ModuleClassBinaryID, ModuleSpecBinaryID, or CodatID because this is meant for general' use, not
* for extending platform (you can write your own using similar code).
*
* <p>
*
* @version $Revision: 1.1 $
* @author Daniel Brookshier <a HREF="mailto:[email protected]">[email protected]</a>
*/
public class DigestTool {
private static final org.apache.log4j.Logger LOG =
org.apache.log4j.Logger.getLogger(DigestTool.class.getName());
/** varaible used for conditional compile of debug printing. */
public static final boolean debug = true;
/**
* Defualt SHA-1 digest algorithm type. This is a 20 byte hash function (note: that MD5 is only 16
* so we don't use it).
*/
public static final String SHAOne = "SHA-1";
/**
* SHA-128 digest algorithm type. This is a 128 bit hash function (note: must have another
* provider registered to use).
*/
public static final String SHA128 = "SHA-128";
/**
* SHA-256 digest algorithm type. This is a 256 bit hash function (note: must have another
* provider registered to use).
*/
public static final String SHA256 = "SHA-256";
/**
* SHA-384 digest algorithm type. This is a 384 bit hash function (note: must have another
* provider registered to use).
*/
public static final String SHA384 = "SHA-384";
/**
* SHA-512 digest algorithm type. This is a 512 bit hash function (note: must have another
* provider registered to use).
*/
public static final String SHA512 = "SHA-512";
/** Tilde character used to seperate candidate strings from a function. */
public final String functionSeperator = "~";
String algorithmType;
public DigestTool() {
algorithmType = SHAOne;
}
public DigestTool(String algorithmType) {
this.algorithmType = algorithmType;
}
/**
* Create a PipeID based on the BinaryID type with a digest of the clearTextID and function.
*
* @param peerGroupID Parent peer group ID.
* @param clearTextID String used as the significant part of the address
* @param function String used to diferentiate different clearTextID addresses (can be null).
* @return PipeBinaryID with the digest hash of the string: clearTextID+"~"+function.
*/
public final PipeBinaryID createPipeID(
net.jxta.peergroup.PeerGroupID peerGroupID, String clearTextID, String function) {
byte[] digest = generateHash(clearTextID, function);
PipeBinaryID pipe = new PipeBinaryID(peerGroupID, digest, false);
return pipe;
}
/**
* Create a PeerGroupID based on the BinaryID type with a digest of the clearTextID and function.
*
* @param peerGroupID Parent peer group ID.
* @param clearTextID String used as the significant part of the address
* @param function String used to diferentiate different clearTextID addresses (can be null).
* @return PeerGroupBinaryID with the digest hash of the string: clearTextID+"~"+function.
*/
public final PeerGroupBinaryID createPeerGroupID(
net.jxta.peergroup.PeerGroupID parentPeerGroupID, String clearTextID, String function) {
byte[] digest = generateHash(clearTextID, function);
PeerGroupBinaryID peerGroupID = new PeerGroupBinaryID(parentPeerGroupID, digest, false);
return peerGroupID;
}
/**
* Create a PeerID based on the BinaryID type with a digest of the clearTextID and function.
*
* @param peerGroupID Parent peer group ID.
* @param clearTextID String used as the significant part of the address
* @param function String used to diferentiate different clearTextID addresses (can be null).
* @return PeerBinaryID with the digest hash of the string: clearTextID+"~"+function.
*/
public final PeerBinaryID createPeerID(
net.jxta.peergroup.PeerGroupID peerGroupID, String clearTextID, String function) {
byte[] digest = generateHash(clearTextID, function);
PeerBinaryID peerID = new PeerBinaryID(peerGroupID, digest, false);
return peerID;
}
/**
* Creates a new instance of DigestPipe. Because this is a utility, this is private to prevent
* construction.
*/
/**
* Generates a Base64 encoded string of an SHA-1 digest hash of the string: clearTextID.
*
* <p>
*
* @param clearTextID A string that is to be hashed. This can be any string used for hashing or
* hiding data.
* @return Base64 encoded string containing the hash of the string: clearTextID.
*/
public final String generateHashString(String clearTextID) {
try {
java.io.StringWriter base64 = new java.io.StringWriter();
net.jxta.impl.util.BASE64OutputStream encode =
new net.jxta.impl.util.BASE64OutputStream(base64);
encode.write(generateHash(clearTextID));
encode.close();
return base64.toString();
} catch (Exception failed) {
LOG.error("Unable to encode hash value.", failed);
throw new RuntimeException("Unable to encode hash value.");
}
}
/**
* Generates a Base64 encoded string of an SHA-1 digest hash of the string:
* clearTextID+"-"+function or: clearTextID if function was blank.
*
* <p>
*
* @param clearTextID A string that is to be hashed. This can be any string used for hashing or
* hiding data.
* @param function A function related to the clearTextID string. This is used to create a hash
* associated with clearTextID so that it is a uique code.
* @return Base64 encoded string containing the hash of the string: clearTextID+"-"+function or
* clearTextID if function was blank.
*/
public final String generateHashString(String clearTextID, String function) {
try {
java.io.StringWriter base64 = new java.io.StringWriter();
net.jxta.impl.util.BASE64OutputStream encode =
new net.jxta.impl.util.BASE64OutputStream(base64);
encode.write(generateHash(clearTextID, function));
encode.close();
return base64.toString();
} catch (Exception failed) {
LOG.error("Unable to encode hash value.", failed);
throw new RuntimeException("Unable to encode hash value.");
}
}
/**
* Generates a SHA-1 digest hash of the string: clearTextID.
*
* <p>
*
* @param clearTextID A string that is to be hashed. This can be any string used for hashing or
* hiding data.
* @return String containing the hash of the string: clearTextID.
*/
public final byte[] generateHash(String clearTextID) {
return generateHash(clearTextID, null);
}
/**
* Generates an SHA-1 digest hash of the string: clearTextID+"-"+function or: clearTextID if
* function was blank.
*
* <p>Note that the SHA-1 used only creates a 20 byte hash.
*
* <p>
*
* @param clearTextID A string that is to be hashed. This can be any string used for hashing or
* hiding data.
* @param function A function related to the clearTextID string. This is used to create a hash
* associated with clearTextID so that it is a uique code.
* @return array of bytes containing the hash of the string: clearTextID+"-"+function or
* clearTextID if function was blank. Can return null if SHA-1 does not exist on platform.
*/
public final byte[] generateHash(String clearTextID, String function) {
String id;
if (function == null) {
id = clearTextID;
} else {
id = clearTextID + functionSeperator + function;
}
byte[] buffer = id.getBytes();
MessageDigest algorithm = null;
try {
algorithm = MessageDigest.getInstance(algorithmType);
} catch (Exception e) {
LOG.error("Cannot load selected Digest Hash implementation", e);
return null;
}
// Generate the digest.
algorithm.reset();
algorithm.update(buffer);
try {
byte[] digest1 = algorithm.digest();
return digest1;
} catch (Exception de) {
LOG.error("Failed to creat a digest.", de);
return null;
}
}
/**
* Generates an SHA-1 digest hash of the string: clearTextID.
*
* <p>
*
* @param clearTextID A string that is to be hashed. This can be any string used for hashing or
* hiding data.
* @return String containing the hash of the string: clearTextID.
*/
public final boolean test(String clearTextID, String function, String testHash) {
String id = clearTextID + functionSeperator + function;
return test(id, testHash);
}
/**
* Compares a clear text code or ID with a candidate hash code. This is used to confirm that the
* clearTextID can be successfully converted to the hash.
*
* @param clearTextID A string that is to be hashed. This can be any string used for hashing or
* hiding data.
* @param testHash A string of hashed string.
* @return true if the hash created from clearTextID is equal to the testHash string.Can return
* false if SHA-1 does not exist on platform.
*/
public final boolean test(String clearTextID, String testHash) {
byte[] digest1 = generateHash(clearTextID);
byte[] digest2;
try {
java.io.ByteArrayOutputStream bos = new java.io.ByteArrayOutputStream();
net.jxta.impl.util.BASE64InputStream decoder =
new net.jxta.impl.util.BASE64InputStream(new java.io.StringReader(testHash));
while (true) {
int c = decoder.read();
if (-1 == c) {
break;
}
bos.write(c);
}
digest2 = bos.toByteArray();
} catch (Exception e) {
LOG.error("Failed to create a digest.", e);
return false;
}
if (digest1.length != digest2.length) {
// Not a match! because of length.
return false;
}
for (int i = 0; i < digest1.length; i++) {
if (digest1[i] != digest2[i]) {
// Not a match because of byte:"+i+" did not match
return false;
}
}
// Match was ok
return true;
}
/**
* Compares a clear text code or ID with a candidate hash code. This is used to confirm that the
* clearTextID can be successfully converted to the hash.
*
* @param clearTextID A string that is to be hashed. This can be any string used for hashing or
* hiding data.
* @param testHash A string of hashed string.
* @return true if the hash created from clearTextID is equal to the testHash string.Can return
* false if SHA-1 does not exist on platform.
*/
public final boolean test(String clearTextID, byte[] testHash) {
byte[] digest1 = generateHash(clearTextID);
if (digest1.length != testHash.length) {
// Not a match! because of length.
return false;
}
for (int i = 0; i < testHash.length; i++) {
if (digest1[i] != testHash[i]) {
// Not a match because of byte:"+i+" did not match
return false;
}
}
// Match was ok
return true;
}
}
public abstract class Connection {
private static final boolean TRAKTOR_USED = false;
private static final org.apache.log4j.Logger CAT =
org.apache.log4j.Logger.getLogger(Connection.class.getName());
private Frame traktor;
private static boolean traktorConnectionDown = false;
/**
* Creates a new connection to the specified host of specified type. <br>
* <br>
* type: Type of connection to create <br>
* destination: Host to connect to (in "host:port" or "host" syntax)
*/
public Connection(java.net.InetAddress host, int port, PluginContext ctx)
throws MessagingNetworkException, java.io.IOException {
if (TRAKTOR_USED) {
if (traktorConnectionDown) throw new IOException("network is down");
traktor = new Frame("" + host + ":" + port + " - Traktor");
final Checkbox c = new Checkbox("break this & ALL future connections");
c.setState(traktorConnectionDown);
c.addItemListener(
new ItemListener() {
public void itemStateChanged(ItemEvent e) {
traktorConnectionDown = c.getState();
try {
if (traktorConnectionDown) closeSocket();
} catch (Exception ex) {
}
}
});
traktor.add(c);
traktor.setSize(100, 50);
traktor.setLocation(230, 450);
traktor.setVisible(true);
} else {
traktor = null;
}
}
public final int available() throws IOException {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
if (isClosed()) throw new IOException("connection closed");
return getInputStream().available();
}
public abstract void closeSocket();
public final void flush() throws IOException, MessagingNetworkException {
OutputStream os = getOutputStream();
synchronized (os) {
os.flush();
}
}
protected final java.io.InputStream getInputStream() throws IOException {
if (isClosed()) throw new IOException("connection closed");
InputStream is = getInputStream0();
if (is == null) throw new IOException("connection closed");
return is;
}
protected abstract java.io.InputStream getInputStream0() throws IOException;
protected final java.io.OutputStream getOutputStream() throws IOException {
if (isClosed()) {
if (TRAKTOR_USED && traktor != null && !traktorConnectionDown) {
traktor.dispose();
traktor = null;
}
throw new IOException("connection closed");
}
OutputStream os = getOutputStream0();
if (os == null) throw new IOException("connection closed");
return os;
}
protected abstract java.io.OutputStream getOutputStream0() throws IOException;
public abstract boolean isClosed();
/*
private byte[] buf = new byte[8192];
private int ofs = 0;
private int len = 0;
private void fill(InputStream is, long abortTime)
throws IOException
{
for (;;)
{
if (System.currentTimeMillis() > abortTime) throw new IOException("connection timed out");
int av = is.available();
if (av == 0)
{
try
{
Thread.currentThread().sleep(100);
}
catch (InterruptedException ex)
{
throw new InterruptedIOException();
}
continue;
}
int capacity = buf.length - len;
if (av > capacity) av = capacity;
int rc = capacity - ofs;
int pos = ofs + len;
if (rc >= av)
{
int read = is.read(buf, pos, av);
if (read < 0) read = 0;
len += read;
return;
}
//rc < av
while (rc > 0)
{
int read = is.read(buf, ofs, rc);
if (read < 0) read = 0;
len += read;
rc -= read;
if (System.currentTimeMillis() > abortTime) throw new IOException("connection timed out");
}
//rc <= 0
//case 1, when buf.length-1 >= ofs+len-1 (=> rc > 0)
//cells ofs, ..., ofs+len-1 are filled
//case 2, when buf.length-1 < ofs+len-1 (<=> buf.length-1 <= ofs+len-2)
//cells ofs, ..., buf.length-1 are filled
//cells 0, ..., ofs+len-2 - (buf.length-1) are filled, too
int lm = ofs+len-1 - buf.length;
if (lm > av) lm = av;
rc = 0;
while (lm > 0)
{
int read = is.read(buf, ofs, rc);
if (read < 0) read = 0;
len += read;
rc -= read;
if (System.currentTimeMillis() > abortTime) throw new IOException("connection timed out");
}
}
}
*/
public final String readCommand(byte[] b)
throws IOException, InterruptedException, MessagingNetworkException {
InputStream is = getInputStream();
synchronized (is) {
long abortTime =
System.currentTimeMillis() + 1000 * MSNMessagingNetwork.REQPARAM_SOCKET_TIMEOUT_SECONDS;
int ofs = 0;
boolean d = false;
for (; ; ) {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
int by = is.read();
if (by == -1) throw new IOException("unexpected EOF");
if (by == 10 && d) break;
d = (by == 13);
if (ofs < b.length) {
b[ofs++] = (byte) by;
}
if (System.currentTimeMillis() > abortTime) throw new IOException("connection timed out");
/*
if (len >= buffer.length)
{
...
return ...;
}
int pos = findCRLF();
if (pos != -1) break;
fill(is, abortTime);
*/
}
if (b[ofs - 1] == 13) --ofs;
String line = new String(b, 0, ofs, "ASCII");
if (StringUtil.startsWith(line, "MSG")) {
StringTokenizer st = new StringTokenizer(line);
String len_s = null;
while (st.hasMoreTokens()) {
len_s = st.nextToken();
}
if (len_s == null) throw new AssertException("len_s is null");
int len;
try {
len = Integer.parseInt(len_s);
} catch (NumberFormatException ex) {
ServerConnection.throwProtocolViolated("MSG length must be int");
len = 0;
}
String msg = readMSG(len);
line = line + "\r\n" + msg;
}
if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("S: " + line);
return line;
}
}
private final String readMSG(final int len)
throws IOException, InterruptedException, MessagingNetworkException {
if (len > 65000)
ServerConnection.throwProtocolViolated("incoming message is too long: " + len + " bytes");
byte[] b = new byte[len];
InputStream is = getInputStream();
synchronized (is) {
long abortTime =
System.currentTimeMillis() + 1000 * MSNMessagingNetwork.REQPARAM_SOCKET_TIMEOUT_SECONDS;
int ofs = 0;
while (ofs < len) {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
int read = is.read(b, ofs, len - ofs);
if (read < 0) read = 0;
ofs += read;
if (System.currentTimeMillis() > abortTime) throw new IOException("connection timed out");
/*
if (len >= buffer.length)
{
...
return ...;
}
int pos = findCRLF();
if (pos != -1) break;
fill(is, abortTime);
*/
}
String msg = new String(b, 0, len, "UTF-8");
return msg;
}
}
public final void writeASCII(String s) throws IOException {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
OutputStream os = getOutputStream();
synchronized (os) {
if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("C: " + s);
os.write(s.getBytes("ASCII"));
os.write((byte) 13);
os.write((byte) 10);
os.flush();
}
}
/**
* UTF byte count is appended to the asciiPrefix, then UTF bytes are appended to the result; the
* final result is sent.
*/
public final void writeMSG(String asciiPrefix, String msgBody) throws IOException {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
OutputStream os = getOutputStream();
synchronized (os) {
byte[] utfBytes = msgBody.getBytes("UTF-8");
asciiPrefix = asciiPrefix + ' ' + utfBytes.length;
if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("C: " + asciiPrefix + "\r\n" + msgBody);
os.write(asciiPrefix.getBytes("ASCII"));
os.write((byte) 13);
os.write((byte) 10);
os.write(utfBytes);
os.flush();
}
}
}
public class Deploy extends AbstractConsoleCommand {
private static org.apache.log4j.Logger log = org.apache.log4j.Logger.getLogger(Deploy.class);
private final DeploymentService deploymentService;
private final UnderlayLocator underlayLocator;
private String mavenRoot;
public Deploy(
List<String> args,
String host,
String currentDir,
ResourceFactory resourceFactory,
DeploymentService deploymentService,
UnderlayLocator underlayLocator) {
super(args, host, currentDir, resourceFactory);
this.deploymentService = deploymentService;
this.underlayLocator = underlayLocator;
}
@Override
public Result execute() {
Folder cur;
try {
cur = currentResource();
} catch (NotAuthorizedException | BadRequestException ex) {
return result("can't lookup current resource", ex);
}
if (cur == null) {
return result("current dir not found: " + currentDir);
}
String deployUrl = "";
if (cur instanceof Folder) {
Folder col = cur;
try {
if (args.size() == 1) {
deployUrl = args.get(0);
return deploySimple(deployUrl, col);
} else if (args.size() >= 3) {
String s = args.get(0);
boolean isUnderlay = false;
if (s.equals("-underlay")) {
isUnderlay = true;
args.remove(0);
}
if (mavenRoot == null || mavenRoot.length() == 0) {
return result("Cant deploy maven spec, no maven root has been configred");
}
String group = args.get(0);
String artifact = args.get(1);
String version = args.get(2);
deployUrl =
mavenRoot
+ "/"
+ group.replace(".", "/")
+ "/"
+ artifact
+ "/"
+ version
+ "/"
+ artifact
+ "-"
+ version
+ ".war";
log.info("Built maven URL: " + deployUrl);
if (isUnderlay) {
UnderlayVector v = new UnderlayVector();
v.setArtifcatId(artifact);
v.setGroupId(group);
v.setVersion(version);
return deployUnderlay(deployUrl, v);
} else {
return deploySimple(deployUrl, col);
}
} else {
return result(
"Invalid number of arguments. Either give single URL or 3 arguments for a maven vector group artifact id");
}
} catch (MalformedURLException ex) {
return result("Bad url: " + deployUrl);
} catch (Exception ex) {
return result("Exception deploying: " + deployUrl, ex);
}
} else {
return result("not a collection: " + cur.getHref());
}
}
private Result deployUnderlay(String deployUrl, UnderlayVector v)
throws MalformedURLException, IOException, Exception {
try {
VfsTransactionManager.setRollbackOnly(true);
Host underlayHost = underlayLocator.createUnderlay(v);
return deploySimple(deployUrl, underlayHost);
} finally {
VfsTransactionManager.setRollbackOnly(false);
}
}
private Result deploySimple(String deployUrl, Folder currentFolder)
throws MalformedURLException, IOException, Exception {
URL url = new URL(deployUrl);
try (InputStream in = url.openStream();
BufferedInputStream bufIn = new BufferedInputStream(in)) {
VfsTransactionManager.setRollbackOnly(true);
Path path = Path.path(url.getPath());
File deployWar = File.createTempFile("ettrema-deploy", path.getName());
try (FileOutputStream fout = new FileOutputStream(deployWar);
BufferedOutputStream bufOut = new BufferedOutputStream(fout)) {
StreamUtils.readTo(bufIn, bufOut);
bufOut.flush();
fout.flush();
}
String deployName = findDeployName(path);
deploymentService.deploy(deployWar, deployName, currentFolder.getWeb());
VfsTransactionManager.setRollbackOnly(false);
commit();
return result("Deployed ok: " + deployName);
} finally {
VfsTransactionManager.setRollbackOnly(false);
}
}
private String findDeployName(Path p) {
String s = p.getName(); // eg issues-web-1.0.war
int pos = s.lastIndexOf("-");
s = s.substring(0, pos);
return s;
}
public String getMavenRoot() {
return mavenRoot;
}
public void setMavenRoot(String mavenRoot) {
this.mavenRoot = mavenRoot;
}
}
@Controller
public class ProposalDevelopmentS2SController extends ProposalDevelopmentControllerBase {
private static final String CONTENT_TYPE_XML = "text/xml";
private static final String CONTENT_TYPE_PDF = "application/pdf";
private static final org.apache.log4j.Logger LOG =
org.apache.log4j.Logger.getLogger(ProposalDevelopmentS2SController.class);
@Autowired
@Qualifier("s2sSubmissionService")
private S2sSubmissionService s2sSubmissionService;
@Autowired
@Qualifier("s2sUserAttachedFormService")
private S2sUserAttachedFormService s2sUserAttachedFormService;
@Autowired
@Qualifier("userAttachedFormService")
private UserAttachedFormService userAttachedFormService;
@Autowired
@Qualifier("globalVariableService")
private GlobalVariableService globalVariableService;
@Autowired
@Qualifier("formPrintService")
private FormPrintService formPrintService;
@Autowired
@Qualifier("parameterService")
private ParameterService parameterService;
@Autowired
@Qualifier("proposalTypeService")
private ProposalTypeService proposalTypeService;
@Autowired
@Qualifier("proposalDevelopmentDocumentViewAuthorizer")
private ProposalDevelopmentDocumentViewAuthorizer proposalDevelopmentDocumentViewAuthorizer;
private static final String ERROR_NO_GRANTS_GOV_FORM_SELECTED =
"error.proposalDevelopment.no.grants.gov.form.selected";
@Transactional
@RequestMapping(
value = "/proposalDevelopment",
params = {"methodToCall=refresh", "refreshCaller=S2sOpportunity-LookupView"})
public ModelAndView refresh(
@ModelAttribute("KualiForm") ProposalDevelopmentDocumentForm form,
BindingResult result,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
ProposalDevelopmentDocument document = form.getProposalDevelopmentDocument();
DevelopmentProposal proposal = document.getDevelopmentProposal();
if (form.getNewS2sOpportunity() != null
&& StringUtils.isNotEmpty(form.getNewS2sOpportunity().getOpportunityId())) {
proposal.setS2sOpportunity(form.getNewS2sOpportunity());
proposal.getS2sOpportunity().setDevelopmentProposal(proposal);
// Set default S2S Submission Type
if (StringUtils.isBlank(form.getNewS2sOpportunity().getS2sSubmissionTypeCode())) {
String defaultS2sSubmissionTypeCode =
getProposalTypeService().getDefaultSubmissionTypeCode(proposal.getProposalTypeCode());
proposal.getS2sOpportunity().setS2sSubmissionTypeCode(defaultS2sSubmissionTypeCode);
getDataObjectService()
.wrap(proposal.getS2sOpportunity())
.fetchRelationship("s2sSubmissionType");
}
final String opportunityTitle = form.getNewS2sOpportunity().getOpportunityTitle();
String trimmedTitle =
StringUtils.substring(
opportunityTitle, 0, ProposalDevelopmentConstants.S2sConstants.OPP_TITLE_MAX_LENGTH);
// Set Opportunity Title and Opportunity ID in the Sponsor & Program Information section
proposal.setProgramAnnouncementTitle(trimmedTitle);
proposal.setCfdaNumber(form.getNewS2sOpportunity().getCfdaNumber());
proposal.setProgramAnnouncementNumber(form.getNewS2sOpportunity().getOpportunityId());
form.setNewS2sOpportunity(new S2sOpportunity());
}
S2sOpportunity s2sOpportunity = proposal.getS2sOpportunity();
try {
if (s2sOpportunity != null && s2sOpportunity.getSchemaUrl() != null) {
List<String> missingMandatoryForms =
s2sSubmissionService.setMandatoryForms(proposal, s2sOpportunity);
if (!CollectionUtils.isEmpty(missingMandatoryForms)) {
globalVariableService
.getMessageMap()
.putError(
Constants.NO_FIELD,
KeyConstants.ERROR_IF_OPPORTUNITY_ID_IS_INVALID,
s2sOpportunity.getOpportunityId(),
StringUtils.join(missingMandatoryForms, ","));
proposal.setS2sOpportunity(null);
}
}
} catch (S2sCommunicationException ex) {
if (ex.getErrorKey().equals(KeyConstants.ERROR_GRANTSGOV_NO_FORM_ELEMENT)) {
ex.setMessage(s2sOpportunity.getOpportunityId());
}
globalVariableService
.getMessageMap()
.putError(Constants.NO_FIELD, ex.getErrorKey(), ex.getMessageWithParams());
proposal.setS2sOpportunity(new S2sOpportunity());
}
super.save(form, result, request, response);
return getRefreshControllerService().refresh(form);
}
@Transactional
@RequestMapping(
value = "/proposalDevelopment",
params = {"methodToCall=clearOpportunity"})
public ModelAndView clearOpportunity(
@ModelAttribute("KualiForm") ProposalDevelopmentDocumentForm form,
BindingResult result,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
((ProposalDevelopmentViewHelperServiceImpl) form.getViewHelperService())
.clearOpportunity(form.getDevelopmentProposal());
return getRefreshControllerService().refresh(form);
}
@Transactional
@RequestMapping(
value = "/proposalDevelopment",
params = {"methodToCall=printFormsXml"})
public ModelAndView printFormsXml(
@ModelAttribute("KualiForm") ProposalDevelopmentDocumentForm form,
HttpServletResponse response)
throws Exception {
form.getDevelopmentProposal().setGrantsGovSelectFlag(true);
return printForms(form, response);
}
@Transactional
@RequestMapping(
value = "/proposalDevelopment",
params = {"methodToCall=printForms"})
public ModelAndView printForms(
@ModelAttribute("KualiForm") ProposalDevelopmentDocumentForm form,
HttpServletResponse response)
throws Exception {
ProposalDevelopmentDocument proposalDevelopmentDocument = form.getProposalDevelopmentDocument();
proposalDevelopmentDocumentViewAuthorizer.initializeDocumentAuthorizerIfNecessary(
form.getProposalDevelopmentDocument());
if (!((ProposalDevelopmentDocumentAuthorizer)
proposalDevelopmentDocumentViewAuthorizer.getDocumentAuthorizer())
.isAuthorizedToPrint(
proposalDevelopmentDocument, globalVariableService.getUserSession().getPerson())) {
throw new AuthorizationException(
globalVariableService.getUserSession().getPrincipalName(), "printForms", "Proposal");
}
if (proposalDevelopmentDocument.getDevelopmentProposal().getSelectedS2sOppForms().isEmpty()) {
getGlobalVariableService()
.getMessageMap()
.putError("noKey", ERROR_NO_GRANTS_GOV_FORM_SELECTED);
return getModelAndViewService().getModelAndView(form);
}
FormPrintResult formPrintResult = getFormPrintService().printForm(proposalDevelopmentDocument);
setValidationErrorMessage(formPrintResult.getErrors());
KcFile attachmentDataSource = formPrintResult.getFile();
if (((attachmentDataSource == null
|| attachmentDataSource.getData() == null
|| attachmentDataSource.getData().length == 0)
&& !proposalDevelopmentDocument.getDevelopmentProposal().getGrantsGovSelectFlag())
|| CollectionUtils.isNotEmpty(formPrintResult.getErrors())) {
boolean grantsGovErrorExists =
copyAuditErrorsToPage(Constants.GRANTSGOV_ERRORS, "grantsGovFormValidationErrors");
if (grantsGovErrorExists) {
getGlobalVariableService()
.getMessageMap()
.putError(
"grantsGovFormValidationErrors",
KeyConstants.VALIDATTION_ERRORS_BEFORE_GRANTS_GOV_SUBMISSION);
}
proposalDevelopmentDocument.getDevelopmentProposal().setGrantsGovSelectFlag(false);
return getModelAndViewService().getModelAndView(form);
}
if (proposalDevelopmentDocument.getDevelopmentProposal().getGrantsGovSelectFlag()) {
File grantsGovXmlDirectoryFile =
getS2sSubmissionService().getGrantsGovSavedFile(proposalDevelopmentDocument);
byte[] bytes = new byte[(int) grantsGovXmlDirectoryFile.length()];
FileInputStream fileInputStream = new FileInputStream(grantsGovXmlDirectoryFile);
fileInputStream.read(bytes);
int size = bytes.length;
try (ByteArrayOutputStream outputStream = new ByteArrayOutputStream(size)) {
outputStream.write(bytes);
ControllerFileUtils.streamOutputToResponse(
response,
outputStream,
"binary/octet-stream",
grantsGovXmlDirectoryFile.getName(),
size);
response.flushBuffer();
}
proposalDevelopmentDocument.getDevelopmentProposal().setGrantsGovSelectFlag(false);
return getModelAndViewService().getModelAndView(form);
}
ControllerFileUtils.streamToResponse(attachmentDataSource, response);
return getModelAndViewService().getModelAndView(form);
}
protected void setValidationErrorMessage(
List<org.kuali.coeus.s2sgen.api.core.AuditError> errors) {
if (errors != null) {
LOG.info("Error list size:" + errors.size() + errors.toString());
List<org.kuali.rice.krad.util.AuditError> auditErrors = new ArrayList<>();
for (org.kuali.coeus.s2sgen.api.core.AuditError error : errors) {
auditErrors.add(
new org.kuali.rice.krad.util.AuditError(
error.getErrorKey(),
Constants.GRANTS_GOV_GENERIC_ERROR_KEY,
error.getLink(),
new String[] {error.getMessageKey()}));
}
if (!auditErrors.isEmpty()) {
getGlobalVariableService()
.getAuditErrorMap()
.put(
"grantsGovAuditErrors",
new AuditCluster(
Constants.GRANTS_GOV_OPPORTUNITY_PANEL,
auditErrors,
Constants.GRANTSGOV_ERRORS));
}
}
}
protected boolean copyAuditErrorsToPage(String auditClusterCategory, String errorkey) {
boolean auditClusterFound = false;
Iterator<String> iter = getGlobalVariableService().getAuditErrorMap().keySet().iterator();
while (iter.hasNext()) {
String errorKey = (String) iter.next();
AuditCluster auditCluster = getGlobalVariableService().getAuditErrorMap().get(errorKey);
if (auditClusterCategory == null
|| StringUtils.equalsIgnoreCase(auditCluster.getCategory(), auditClusterCategory)) {
auditClusterFound = true;
for (Object error : auditCluster.getAuditErrorList()) {
AuditError auditError = (AuditError) error;
getGlobalVariableService()
.getMessageMap()
.putError(
errorKey == null ? auditError.getErrorKey() : errorKey,
auditError.getMessageKey(),
auditError.getParams());
}
}
}
return auditClusterFound;
}
@Transactional
@RequestMapping(
value = "/proposalDevelopment",
params = {"methodToCall=addUserAttachedForm"})
public ModelAndView addUserAttachedForm(
@ModelAttribute("KualiForm") ProposalDevelopmentDocumentForm form) throws Exception {
S2sUserAttachedForm s2sUserAttachedForm = form.getS2sUserAttachedForm();
ProposalDevelopmentDocument proposalDevelopmentDocument = form.getProposalDevelopmentDocument();
MultipartFile userAttachedFormFile = s2sUserAttachedForm.getNewFormFile();
s2sUserAttachedForm.setNewFormFileBytes(userAttachedFormFile.getBytes());
s2sUserAttachedForm.setFormFileName(userAttachedFormFile.getOriginalFilename());
s2sUserAttachedForm.setProposalNumber(
proposalDevelopmentDocument.getDevelopmentProposal().getProposalNumber());
try {
List<S2sUserAttachedForm> userAttachedForms =
getS2sUserAttachedFormService()
.extractNSaveUserAttachedForms(proposalDevelopmentDocument, s2sUserAttachedForm);
proposalDevelopmentDocument
.getDevelopmentProposal()
.getS2sUserAttachedForms()
.addAll(userAttachedForms);
form.setS2sUserAttachedForm(new S2sUserAttachedForm());
} catch (S2SException ex) {
LOG.error(ex.getMessage(), ex);
if (ex.getTabErrorKey() != null) {
if (getGlobalVariableService()
.getMessageMap()
.getErrorMessagesForProperty(ex.getTabErrorKey())
== null) {
getGlobalVariableService()
.getMessageMap()
.putError(ex.getTabErrorKey(), ex.getErrorKey(), ex.getParams());
}
} else {
getGlobalVariableService()
.getMessageMap()
.putError(Constants.NO_FIELD, ex.getErrorKey(), ex.getMessageWithParams());
}
}
return super.save(form);
}
@Transactional
@RequestMapping(
value = "/proposalDevelopment",
params = {"methodToCall=viewUserAttachedFormXML"})
public ModelAndView viewUserAttachedFormXML(
ProposalDevelopmentDocumentForm form,
HttpServletResponse response,
@RequestParam("selectedLine") String selectedLine)
throws Exception {
DevelopmentProposal developmentProposal = form.getDevelopmentProposal();
List<S2sUserAttachedForm> s2sAttachedForms = developmentProposal.getS2sUserAttachedForms();
S2sUserAttachedForm selectedForm = s2sAttachedForms.get(Integer.parseInt(selectedLine));
S2sUserAttachedFormFileContract userAttachedFormFile =
getUserAttachedFormService().findUserAttachedFormFile(selectedForm);
if (userAttachedFormFile != null) {
ControllerFileUtils.streamToResponse(
userAttachedFormFile.getXmlFile().getBytes(),
selectedForm.getFormName() + ".xml",
CONTENT_TYPE_XML,
response);
} else {
return getModelAndViewService().getModelAndView(form);
}
return null;
}
@Transactional
@RequestMapping(
value = "/proposalDevelopment",
params = {"methodToCall=viewUserAttachedFormPDF"})
public ModelAndView viewUserAttachedFormPDF(
ProposalDevelopmentDocumentForm form,
HttpServletResponse response,
@RequestParam("selectedLine") String selectedLine)
throws Exception {
DevelopmentProposal developmentProposal = form.getDevelopmentProposal();
List<S2sUserAttachedForm> s2sAttachedForms = developmentProposal.getS2sUserAttachedForms();
S2sUserAttachedForm selectedForm = s2sAttachedForms.get(Integer.parseInt(selectedLine));
S2sUserAttachedFormFileContract userAttachedFormFile =
getUserAttachedFormService().findUserAttachedFormFile(selectedForm);
if (userAttachedFormFile != null) {
ControllerFileUtils.streamToResponse(
userAttachedFormFile.getFormFile(),
selectedForm.getFormFileName(),
CONTENT_TYPE_PDF,
response);
} else {
return getModelAndViewService().getModelAndView(form);
}
return null;
}
@Transactional
@RequestMapping(
value = "/proposalDevelopment",
params = {"methodToCall=deleteUserAttachedForm"})
public ModelAndView deleteUserAttachedForm(
ProposalDevelopmentDocumentForm form,
HttpServletResponse response,
@RequestParam("selectedLine") String selectedLine)
throws Exception {
S2sUserAttachedForm deleteForm =
form.getDevelopmentProposal()
.getS2sUserAttachedForms()
.remove(Integer.parseInt(selectedLine));
getDataObjectService().delete(deleteForm);
getS2sUserAttachedFormService()
.resetFormAvailability(form.getProposalDevelopmentDocument(), deleteForm.getNamespace());
return getModelAndViewService().getModelAndView(form);
}
@Transactional
@RequestMapping(
value = "/proposalDevelopment",
params = {"methodToCall=refreshSubmissionDetails"})
public ModelAndView refreshSubmissionDetails(ProposalDevelopmentDocumentForm form)
throws Exception {
ProposalDevelopmentDocument document = form.getProposalDevelopmentDocument();
try {
getS2sSubmissionService().refreshGrantsGov(document);
} catch (S2sCommunicationException ex) {
LOG.error(ex.getMessage(), ex);
getGlobalVariableService()
.getMessageMap()
.putError(Constants.NO_FIELD, ex.getErrorKey(), ex.getMessage());
}
return getRefreshControllerService().refresh(form);
}
@Transactional
@RequestMapping(value = "/proposalDevelopment", params = "methodToCall=saveUserAttachedForm")
public ModelAndView saveUserAttachedForm(
@ModelAttribute("KualiForm") ProposalDevelopmentDocumentForm form) throws Exception {
final String selectedCollectionPath =
form.getActionParamaterValue(UifParameters.SELECTED_COLLECTION_PATH);
String selectedLine = form.getActionParamaterValue(UifParameters.SELECTED_LINE_INDEX);
if (form.getEditableCollectionLines().containsKey(selectedCollectionPath)) {
form.getEditableCollectionLines().get(selectedCollectionPath).remove(selectedLine);
}
return super.save(form);
}
public S2sSubmissionService getS2sSubmissionService() {
return s2sSubmissionService;
}
public void setS2sSubmissionService(S2sSubmissionService s2sSubmissionService) {
this.s2sSubmissionService = s2sSubmissionService;
}
public GlobalVariableService getGlobalVariableService() {
return globalVariableService;
}
public void setGlobalVariableService(GlobalVariableService globalVariableService) {
this.globalVariableService = globalVariableService;
}
public FormPrintService getFormPrintService() {
return formPrintService;
}
public void setFormPrintService(FormPrintService formPrintService) {
this.formPrintService = formPrintService;
}
public ParameterService getParameterService() {
return parameterService;
}
public void setParameterService(ParameterService parameterService) {
this.parameterService = parameterService;
}
public S2sUserAttachedFormService getS2sUserAttachedFormService() {
return s2sUserAttachedFormService;
}
public void setS2sUserAttachedFormService(S2sUserAttachedFormService s2sUserAttachedFormService) {
this.s2sUserAttachedFormService = s2sUserAttachedFormService;
}
public UserAttachedFormService getUserAttachedFormService() {
return userAttachedFormService;
}
public void setUserAttachedFormService(UserAttachedFormService userAttachedFormService) {
this.userAttachedFormService = userAttachedFormService;
}
public ProposalTypeService getProposalTypeService() {
return proposalTypeService;
}
public void setProposalTypeService(ProposalTypeService proposalTypeService) {
this.proposalTypeService = proposalTypeService;
}
public ProposalDevelopmentDocumentViewAuthorizer getProposalDevelopmentDocumentViewAuthorizer() {
return proposalDevelopmentDocumentViewAuthorizer;
}
public void setProposalDevelopmentDocumentViewAuthorizer(
ProposalDevelopmentDocumentViewAuthorizer proposalDevelopmentDocumentViewAuthorizer) {
this.proposalDevelopmentDocumentViewAuthorizer = proposalDevelopmentDocumentViewAuthorizer;
}
}
@Override
public Result execute() {
Folder cur;
try {
cur = currentResource();
} catch (NotAuthorizedException | BadRequestException ex) {
return result("can't lookup current resource", ex);
}
if (cur == null) {
return result("current dir not found: " + currentDir);
}
String deployUrl = "";
if (cur instanceof Folder) {
Folder col = cur;
try {
if (args.size() == 1) {
deployUrl = args.get(0);
return deploySimple(deployUrl, col);
} else if (args.size() >= 3) {
String s = args.get(0);
boolean isUnderlay = false;
if (s.equals("-underlay")) {
isUnderlay = true;
args.remove(0);
}
if (mavenRoot == null || mavenRoot.length() == 0) {
return result("Cant deploy maven spec, no maven root has been configred");
}
String group = args.get(0);
String artifact = args.get(1);
String version = args.get(2);
deployUrl =
mavenRoot
+ "/"
+ group.replace(".", "/")
+ "/"
+ artifact
+ "/"
+ version
+ "/"
+ artifact
+ "-"
+ version
+ ".war";
log.info("Built maven URL: " + deployUrl);
if (isUnderlay) {
UnderlayVector v = new UnderlayVector();
v.setArtifcatId(artifact);
v.setGroupId(group);
v.setVersion(version);
return deployUnderlay(deployUrl, v);
} else {
return deploySimple(deployUrl, col);
}
} else {
return result(
"Invalid number of arguments. Either give single URL or 3 arguments for a maven vector group artifact id");
}
} catch (MalformedURLException ex) {
return result("Bad url: " + deployUrl);
} catch (Exception ex) {
return result("Exception deploying: " + deployUrl, ex);
}
} else {
return result("not a collection: " + cur.getHref());
}
}
public ChannelShell getShellChannel() throws JSchException {
Channel channel = session.openChannel("shell");
log.info("opening shell channel");
return (ChannelShell) channel;
}
