private String setOneBinaryInput()

in taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalToolInvocation.java [127:193]

57 lines of code
12 McCabe index (conditional complexity)


	private String setOneBinaryInput(ReferenceService referenceService,
			T2Reference t2Reference, ScriptInput input, String targetSuffix)
			throws InvocationException {

		if (input.isFile() || input.isTempFile()) {
			// Try to get it as a file
			String target = tempDir.getAbsolutePath() + "/" + targetSuffix;
			FileReference fileRef = getAsFileReference(referenceService,
					t2Reference);
			if (fileRef != null) {

				if (!input.isForceCopy()) {
					if (linkCommand != null) {
						String source = fileRef.getFile().getAbsolutePath();
						String actualLinkCommand = getActualOsCommand(
								linkCommand, source, targetSuffix, target);
						logger.info("Link command is " + actualLinkCommand);
						String[] splitCmds = actualLinkCommand.split(" ");
						ProcessBuilder builder = new ProcessBuilder(splitCmds);
						builder.directory(tempDir);
						try {
							int code = builder.start().waitFor();
							if (code == 0) {
								return target;
							} else {
								logger.error("Link command gave errorcode: "
										+ code);
							}

						} catch (InterruptedException e) {
							// go through
						} catch (IOException e) {
							// go through
						}

					}
				}
			}

			InputStream is = null;
			OutputStream os = null;
			is = getAsStream(referenceService, t2Reference);

			try {
				os = new FileOutputStream(target);
			} catch (FileNotFoundException e) {
				throw new InvocationException(e);
			}

			try {
				IOUtils.copyLarge(is, os);
			} catch (IOException e) {
				throw new InvocationException(e);
			}
			try {
				is.close();
				os.close();
			} catch (IOException e) {
				throw new InvocationException(e);
			}
			return target;
		} else {
			String value = (String) referenceService.renderIdentifier(
					t2Reference, String.class, this.getContext());
			return value;
		}
	}