public String setOneInput()

in taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalToolInvocation.java [196:293]
88 lines of code
19 McCabe index (conditional complexity)

	public String setOneInput(ReferenceService referenceService,
			T2Reference t2Reference, ScriptInput input)
			throws InvocationException {

		if (input.getCharsetName() == null) {
			input.setCharsetName(Charset.defaultCharset().name());
		}
		String target = null;
		String targetSuffix = null;
		if (input.isFile()) {
			targetSuffix = input.getTag();
		} else if (input.isTempFile()) {
			targetSuffix = "tempfile." + (nTempFiles++) + ".tmp";
		}

		if (input.isBinary()) {
			return setOneBinaryInput(referenceService, t2Reference, input,
					targetSuffix);
		}

		logger.info("Target is " + target);
		if (input.isFile() || input.isTempFile()) {
			target = tempDir.getAbsolutePath() + "/" + targetSuffix;
			// Try to get it as a file
			Reader r;
			Writer w;
			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
						}

					}
				}

				if (fileRef.getDataNature().equals(ReferencedDataNature.TEXT)) {
					r = new InputStreamReader(fileRef.openStream(this
							.getContext()), Charset.forName(fileRef
							.getCharset()));
				} else {
					try {
						r = new FileReader(fileRef.getFile());
					} catch (FileNotFoundException e) {
						throw new InvocationException(e);
					}
				}
			} else {
				r = new InputStreamReader(getAsStream(referenceService,
						t2Reference));
			}
			try {
				w = new OutputStreamWriter(new FileOutputStream(target), input
						.getCharsetName());
			} catch (UnsupportedEncodingException e) {
				throw new InvocationException(e);
			} catch (FileNotFoundException e) {
				throw new InvocationException(e);
			}
			try {
				IOUtils.copyLarge(r, w);
			} catch (IOException e) {
				throw new InvocationException(e);
			}
			try {
				r.close();
				w.close();
			} catch (IOException e) {
				throw new InvocationException(e);
			}
			return target;
		} else {
			String value = (String) referenceService.renderIdentifier(
					t2Reference, String.class, this.getContext());
			return value;
		}
	}