public HashMap submit_wait_fetch

public HashMap submit_wait_fetch_results()

in taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalToolInvocation.java [373:460]
82 lines of code
16 McCabe index (conditional complexity)

	public HashMap<String, Object> submit_wait_fetch_results(ReferenceService referenceService) throws InvocationException {
		ByteArrayOutputStream stdout_buf = new ByteArrayOutputStream();
		ByteArrayOutputStream stderr_buf = new ByteArrayOutputStream();
		while (true) {
			try {
				copy_stream(running.getInputStream(), stdout_buf);
				copy_stream(running.getErrorStream(), stderr_buf);
			} catch (IOException e1) {
				throw new InvocationException(e1);
			}
			try {
				int exitcode = running.exitValue();
				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());
					}
				}
				else
					break;
			} catch (IllegalThreadStateException e) {

				try {
					Thread.sleep(100);
				} catch (InterruptedException e1) {
					throw new InvocationException(e);
				}

			}
		}

		HashMap<String, Object> results = new HashMap<String, Object>();
			results.put("STDOUT", stdout_buf.toByteArray());
			results.put("STDERR", stderr_buf.toByteArray());

		for (Map.Entry<String, ScriptOutput> cur : usecase.getOutputs().entrySet()) {
			ScriptOutput scriptOutput = cur.getValue();
			File result = new File(tempDir.getAbsoluteFile() + "/" + cur.getValue().getPath());
			if (result.exists()) {
				AbstractExternalReference ref;
				if (isRetrieveData()) {
					FileInputStream is;
					try {
						is = new FileInputStream(result);
					} catch (FileNotFoundException e) {
						throw new InvocationException(e);
					}
					if (scriptOutput.isBinary()) {
						ref = inlineByteArrayReferenceBuilder.createReference(is, null);
					} else {
						ref = inlineStringReferenceBuilder.createReference(is, null);
					}
					try {
						is.close();
					} catch (IOException e) {
						throw new InvocationException(e);
					}
				}
				else {
					ref = new FileReference(result);
					if (scriptOutput.isBinary()) {
						((FileReference) ref)
								.setDataNature(ReferencedDataNature.BINARY);
					} else {
						((FileReference) ref)
								.setDataNature(ReferencedDataNature.TEXT);
						((FileReference) ref).setCharset("UTF-8");
					}
				}
				results.put(cur.getKey(), ref);
			} else {
				ErrorDocument ed = referenceService.getErrorDocumentService().registerError("No result for " + cur.getKey(), 0, getContext());
				results.put(cur.getKey(), ed);
			}
		}
		
		if (isRetrieveData()) {
			forgetRun();
			try {
				deleteDirectory(tempDir.getCanonicalPath());
			} catch (IOException e) {
				throw new InvocationException(e);
			}
		}

		return results;
	}