private void readFromXmlElement()

in taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ToolDescription.java [316:454]
125 lines of code
44 McCabe index (conditional complexity)

	private void readFromXmlElement(Element programNode) throws DeserializationException {
		if (programNode.getName().compareToIgnoreCase("program") != 0)
			throw new DeserializationException("Expected <program>, read '" + programNode.getName() + "'");

		setUsecaseid(programNode.getAttributeValue("name"));
		setDescription(programNode.getAttributeValue("description"));
		setCommand(programNode.getAttributeValue("command"));
		String timeoutStr = programNode.getAttributeValue("timeout");
		if (timeoutStr != null)
			setExecutionTimeoutInSeconds(Integer.parseInt(timeoutStr));
		timeoutStr = programNode.getAttributeValue("preparing_timeout");
		if (timeoutStr != null)
			setPreparingTimeoutInSeconds(Integer.parseInt(timeoutStr));

		String includeStdInStr = programNode.getAttributeValue("includeStdIn");
		if (includeStdInStr != null && !includeStdInStr.isEmpty()) {
			setIncludeStdIn(includeStdInStr.equals("true"));
		}

		String includeStdOutStr = programNode.getAttributeValue("includeStdOut");
		if (includeStdOutStr != null && !includeStdOutStr.isEmpty()) {
			setIncludeStdOut(includeStdOutStr.equals("true"));
		}

		String includeStdErrStr = programNode.getAttributeValue("includeStdErr");
		if (includeStdErrStr != null && !includeStdErrStr.isEmpty()) {
			setIncludeStdErr(includeStdErrStr.equals("true"));
		}

		for (Object cur_ob : programNode.getChildren()) {
			Element cur = (Element) cur_ob;

			String name = cur.getAttributeValue("name");

			String type = cur.getName();
			boolean binary = false;
			if (null != cur.getAttributeValue("binary") && cur.getAttributeValue("binary").equalsIgnoreCase("true")) {
				binary = true;
			}
			boolean list = false;
			if (null != cur.getAttributeValue("list") && cur.getAttributeValue("list").equalsIgnoreCase("true")) {
				list = true;
			}
			boolean concatenate = false;
			if (null != cur.getAttributeValue("concatenate") && cur.getAttributeValue("concatenate").equalsIgnoreCase("true")) {
				concatenate = true;
			}
			boolean forceCopy = false;
			if (null != cur.getAttributeValue("forceCopy") && cur.getAttributeValue("forceCopy").equalsIgnoreCase("true")) {
				forceCopy = true;
			}

			Element inner = null;
			String innerType = null, tag = null, path = null;
			if (cur.getChildren().size() > 0) {
				inner = (Element) cur.getChildren().get(0);
				innerType = inner.getName();
				tag = inner.getAttributeValue("tag");
				path = inner.getAttributeValue("path");
			}
			// build mime type declaration list
			ArrayList<String> mime = new ArrayList<String>();
			for (Object child : cur.getChildren()) {
				Element curChild = (Element) child;
				if (curChild.getName().equalsIgnoreCase("mime")) {
					mime.add(curChild.getAttributeValue("type"));
				}
			}
			if (type.equalsIgnoreCase("static")) {
				ScriptInputStatic si = new ScriptInputStatic();
				Element content = cur.getChild("content");
				if (content == null)
					throw new DeserializationException("FIXME: script tag without embedded content tag");
				si.setUrl(content.getAttributeValue("url"));
				if (si.getUrl() == null)
					si.setContent(content.getText());
				fillInputDescription(si, binary, forceCopy, innerType, tag, path);
				getStatic_inputs().add(si);
			} else if (type.equalsIgnoreCase("input")) {
				ScriptInputUser indesc = new ScriptInputUser();
				indesc.setList(list);
				indesc.setMime(mime);
				indesc.setConcatenate(concatenate);
				fillInputDescription(indesc, binary, forceCopy, innerType, tag, path);
				getInputs().put(Tools.sanitiseName(name), indesc);
			} else if (type.equalsIgnoreCase("output")) {
				ScriptOutput outdesc = new ScriptOutput();
				outdesc.setMime(mime);

				boolean ok = true;
				if (null == innerType) {
					// don't know what to do
					throw new DeserializationException("FIXME: Found null == innerType for output, is this the bug?");
				} else if (innerType.equalsIgnoreCase("fromfile")) {
					outdesc.setPath(path);
					outdesc.setBinary(binary);
				} else {
					throw new DeserializationException("Problem reading output port: unknown innerType '" + innerType + "'");
				}
				if (ok) {
					getOutputs().put(Tools.sanitiseName(name), outdesc);
				}
			} else if (type.equalsIgnoreCase("rte") || type.equalsIgnoreCase("re")) {
				getREs().add(new RuntimeEnvironmentConstraint(name, cur.getAttributeValue("relation")));
			} else if (type.equalsIgnoreCase("group")) {
				group = name;
			} else if (type.equalsIgnoreCase("test")) {
				test_local = cur.getAttributeValue("local");
			} else if (type.equalsIgnoreCase("icon")) {
				icon_url = cur.getAttributeValue("url");
			} else if (type.equalsIgnoreCase("queue")) {
				for (Object child_ob : cur.getChildren()) {
					Element child = (Element) child_ob;
					if (child.getName().equalsIgnoreCase("prefer"))
						getQueue_preferred().add(child.getAttributeValue("url"));
					else if (child.getName().equalsIgnoreCase("deny"))
						getQueue_deny().add(child.getAttributeValue("url"));
					else
						throw new DeserializationException("Error while reading usecase " + this.getUsecaseid() + ": invalid queue entry");
				}
			} else if (type.equalsIgnoreCase("command")) {
				// i like to have the ability to inject complete shell script
				// fragments into the use case,
				// so this should be replace and should allow multiple lines
				if ((getCommand() != null) && !getCommand().isEmpty()) {
					throw new DeserializationException("You have specified both command attribute and command tag.");
				}
				setCommand(cur.getText());
			} else if (type.equalsIgnoreCase("validReturnCodes")) {
					String codeString = cur.getAttributeValue("codes");
					if (codeString != null) {
						setReturnCodesAsText(codeString);
					}
			}
			else {
				throw new DeserializationException("Unexpected and uninterpreted attribute " + type);
			}
		}
	}