public HashMap submit_wait_fetch_results()

in taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshToolInvocation.java [256:369]

• 106 lines of code
• 19 McCabe index (conditional complexity)

	public HashMap<String, Object> submit_wait_fetch_results(
			ReferenceService referenceService) throws InvocationException {
		while (!running.isClosed()) {
			try {
				Thread.sleep(1000);
			} catch (InterruptedException e) {
				throw new InvocationException("Invocation interrupted:"
						+ e.getMessage());
			}
		}

		int exitcode = running.getExitStatus();
		if (!usecase.getValidReturnCodes().contains(exitcode)) {
			try {
				throw new InvocationException("Invalid exit code " + exitcode
						+ ":" + stderr_buf.toString("US-ASCII"));
			} catch (UnsupportedEncodingException e) {
				throw new InvocationException("Invalid exit code " + exitcode
						+ ":" + stderr_buf.toString());
			}
		}

		HashMap<String, Object> results = new HashMap<String, Object>();

		results.put("STDOUT", stdout_buf.toByteArray());
		results.put("STDERR", stderr_buf.toByteArray());
		try {
			stdout_buf.close();
			stderr_buf.close();
		} catch (IOException e2) {
			throw new InvocationException(e2);
		}

		try {
			ChannelSftp sftp = SshPool.getSftpPutChannel(workerNode,
					askUserForPw);
			synchronized (getNodeLock(workerNode)) {
				for (Map.Entry<String, ScriptOutput> cur : usecase.getOutputs()
						.entrySet()) {
					ScriptOutput scriptOutput = cur.getValue();
					String fullPath = workerNode.getDirectory() + tmpname + "/"
							+ scriptOutput.getPath();
					try {
						if (sftp.stat(fullPath) != null) {
							SshUrl url = new SshUrl(workerNode);
							url.setSubDirectory(tmpname);
							url.setFileName(scriptOutput.getPath());
							if (scriptOutput.isBinary()) {
								url.setDataNature(ReferencedDataNature.BINARY);
							} else {
								url.setDataNature(ReferencedDataNature.TEXT);
								url.setCharset("UTF-8");
							}
							if (isRetrieveData()) {
								SshReference urlRef = new SshReference(url);
								InputStream is = urlRef.openStream(null);
								AbstractExternalReference ref;
								if (scriptOutput.isBinary()) {
									ref = inlineByteArrayReferenceBuilder
											.createReference(is, null);
								} else {
									ref = inlineStringReferenceBuilder
											.createReference(is, null);
								}
								try {
									is.close();
								} catch (IOException e) {
									throw new InvocationException(e);
								}
								results.put(cur.getKey(), ref);
							} else {
								results.put(cur.getKey(), url);
							}
						} else {
							ErrorDocument ed = referenceService
									.getErrorDocumentService().registerError(
											"No result for " + cur.getKey(), 0,
											getContext());
							results.put(cur.getKey(), ed);
						}
					} catch (SftpException e) {
						ErrorDocument ed = referenceService
								.getErrorDocumentService().registerError(
										"No result for " + cur.getKey(), 0,
										getContext());
						results.put(cur.getKey(), ed);

					}
				}
			}
		} catch (JSchException e1) {
			throw new InvocationException(e1);
		} catch (ErrorDocumentServiceException e) {
			throw new InvocationException(e);
		}

		if (running != null) {
			running.disconnect();
		}
		if (stdInputStream != null) {
			try {
				stdInputStream.close();
			} catch (IOException e) {
				throw new InvocationException(e);
			}
		}

		if (isRetrieveData()) {
			forgetRun();
			deleteDirectory(location, credentialManager);

		}
		return results;
	}