public String getQueryParameterFilter(MarrsQuery mq, String key) {
String q = mq.getQueryText();
Pattern pat = Pattern.compile("\\$\\{" + key + "(\\|([\\w-]+))?\\}");
Matcher mat = pat.matcher(q);
if (mat.find()) {
return mat.group(2);
} else return null;
}
/**
* Gets a set of query substitution parameters. The resulting map contains the parameters as keys,
* and the (optional) filters as values
*/
public Map<String, String> getQueryParameters(MarrsQuery mq) {
Map<String, String> result = new HashMap<String, String>();
String q = mq.getQueryText();
Pattern pat = Pattern.compile("\\$\\{(\\w+)(\\|([\\w-]+))?\\}");
Matcher mat = pat.matcher(q);
while (mat.find()) {
String key = mat.group(1);
String filter = mat.group(3);
result.put(key, filter);
}
return result;
}
public void saveToFile(File dest) throws IOException {
File temp = File.createTempFile(dest.getName(), ".tmp", dest.getParentFile());
try {
Element root = new Element("MarrsProject");
root.setAttribute("title", title);
root.setAttribute("schemaversion", "" + CURRENT_SCHEMAVERSION);
for (MarrsQuery q : rows) {
Element queryElt = new Element("Query");
CDATA data = new CDATA(q.getQueryText());
queryElt.addContent(data);
queryElt.setAttribute("title", q.getTitle());
queryElt.setAttribute("type", "" + q.getQueryType());
if (q.getAskBefore() != null) {
Element askElt = new Element("AskBefore");
askElt.setAttribute("key", q.getAskBefore());
queryElt.addContent(askElt);
}
for (Map.Entry<String, String> context : q.getContext().entrySet()) {
Element contextElt = new Element("Context");
contextElt.setAttribute(
"key", context.getKey()); // for now, we only use "type" to filter context, so this is
// hardcoded.
contextElt.setAttribute("value", context.getValue());
queryElt.addContent(contextElt);
}
for (String var : q.getPostProcessingVars()) {
Element processElt = new Element("PostProcessing");
processElt.setAttribute(
"var", var); // for now, we only use "type" to filter context, so this is hardcoded.
processElt.setAttribute("operation", q.getPostProcessingOperation(var));
queryElt.addContent(processElt);
}
root.addContent(queryElt);
}
for (Map.Entry<String, String> param : parameters.entrySet()) {
Element paramElt = new Element("Param");
paramElt.setAttribute("key", param.getKey());
paramElt.setAttribute("val", param.getValue());
root.addContent(paramElt);
}
for (NodeAttribute attr : nodeAttributes) {
Element nodeAttr = new Element("NodeAttribute");
nodeAttr.setAttribute("key", attr.key);
nodeAttr.setAttribute("value", attr.value);
for (Map.Entry<String, String> e : attr.vizprops.entrySet()) {
Element vizprop = new Element("Vizmap");
vizprop.setAttribute("prop", e.getKey());
vizprop.setAttribute("value", e.getValue());
nodeAttr.addContent(vizprop);
}
root.addContent(nodeAttr);
}
Document doc = new Document(root);
XMLOutputter xout = new XMLOutputter();
Format format = Format.getPrettyFormat();
format.setIndent("\t");
format.setLineSeparator("\n");
format.setTextMode(TextMode.PRESERVE);
xout.setFormat(format);
xout.output(doc, new FileOutputStream(temp));
temp.renameTo(dest);
dirty = false;
} finally {
temp.delete();
}
}
public static MarrsProject createFromFile(InputSource in) throws JDOMException, IOException {
List<String> warnings = new ArrayList<String>();
SAXBuilder builder = new SAXBuilder(false); // no validation when reading the xml file
// try to read the file; if an error occurs, catch the exception and print feedback
// build JDOM tree
Document doc = builder.build(in);
// Copy the pathway information to a VPathway
Element root = doc.getRootElement();
if (!root.getName().equals("MarrsProject")) {
throw new IllegalArgumentException("Not a MarrsProject file");
}
MarrsProject project = new MarrsProject();
project.title = root.getAttributeValue("title");
Double version = StringUtils.safeParseDouble(root.getAttributeValue("schemaversion"));
if (version == null || version > CURRENT_SCHEMAVERSION) {
warnings.add(
"WARNING: project file version is higher than this plugin version. You'll have to upgrade the plugin to make full use of any new features.");
}
// if missing, may be null. String values are allowed...
project.pubVersion = root.getAttributeValue("pubversion");
for (Object o : root.getChildren("Query")) {
Element eQuery = (Element) o;
String title = eQuery.getAttributeValue("title");
String typeName = eQuery.getAttributeValue("type");
QueryType found = findQueryType(typeName);
if (found == null) {
warnings.add("WARNING: Parse error, query type " + typeName + " unknown. Skipping query");
continue;
}
String queryText = eQuery.getText();
MarrsQuery q = new MarrsQuery(title, queryText, found);
for (Object context : eQuery.getChildren("Context")) {
q.setContextQuery(true);
Element eContext = (Element) context;
String key = eContext.getAttributeValue("key");
String val = eContext.getAttributeValue("value");
if (val != null) q.putContext(key, val);
}
for (Object test : eQuery.getChildren("Test")) {
Element eTest = (Element) test;
String key = eTest.getAttributeValue("key");
String val = eTest.getAttributeValue("value");
if (val != null) {
q.setTestParam(key, val);
}
}
Object ask = eQuery.getChild("AskBefore");
if (ask != null) {
String key = ((Element) ask).getAttributeValue("key");
q.setAskBefore(key);
}
for (Object pp : eQuery.getChildren("PostProcessing")) {
String var = ((Element) pp).getAttributeValue("var");
String operation = ((Element) pp).getAttributeValue("operation");
q.setPostProcessing(var, operation);
}
project.addQuery(q);
}
for (Object o : root.getChildren("Param")) {
Element eParam = (Element) o;
String key = eParam.getAttributeValue("key");
String val = eParam.getAttributeValue("val");
project.setQueryParameter(key, val);
}
for (Object o : root.getChildren("NodeAttribute")) {
NodeAttribute attr = new NodeAttribute();
Element eNodeAttribute = (Element) o;
attr.key = eNodeAttribute.getAttributeValue("key");
attr.value = eNodeAttribute.getAttributeValue("value");
for (Object vp : eNodeAttribute.getChildren("Vizmap")) {
Element eVizmap = (Element) vp;
String prop = eVizmap.getAttributeValue("prop");
String propValue = eVizmap.getAttributeValue("value");
attr.vizprops.put(prop, propValue);
}
project.nodeAttributes.add(attr);
}
project.dirty = false;
if (warnings.size() > 0) {
// TODO: set dialog root
JOptionPane.showMessageDialog(
null, "<html><ul><li>" + StringUtils.join("<br/><li>", warnings) + "</ul></html>");
}
return project;
}
public String getSubstitutedQuery(MarrsQuery mq) throws MarrsException {
String q = mq.getQueryText();
Map<String, String> queryData = getQueryParameters(mq);
for (String key : queryData.keySet()) {
if (!parameters.containsKey(key)) {
throw new MarrsException("Missing substitution parameter: " + key);
}
String contents = parameters.get(key);
String filter = queryData.get(key);
if ("uri-list".equals(filter)) {
Pattern pat =
Pattern.compile("\\s*<[-~#_:/%.0-9a-zA-Z]+>(\\s*,\\s*<[-~#_:/%.0-9a-zA-Z]+>)*\\s*$");
Matcher mat = pat.matcher(contents);
if (!mat.matches()) {
throw new MarrsException(
"'"
+ contents
+ "' does not match pattern for parameter ${"
+ key
+ "|"
+ filter
+ "}");
}
} else if ("uri-bracketed"
.equals(
filter)) /* difference between uri and uri-bracketed is the surrounding < and > characters */ {
Pattern pat = Pattern.compile("\\s*<[-~#_:/%.0-9a-zA-Z]+>\\s*");
Matcher mat = pat.matcher(contents);
if (!mat.matches()) {
throw new MarrsException(
"'"
+ contents
+ "' does not match pattern for parameter ${"
+ key
+ "|"
+ filter
+ "}");
}
} else if ("uri".equals(filter)) {
Pattern pat = Pattern.compile("[-~#_:/%.0-9a-zA-Z]+");
Matcher mat = pat.matcher(contents);
if (!mat.matches()) {
throw new MarrsException(
"'"
+ contents
+ "' does not match pattern for parameter ${"
+ key
+ "|"
+ filter
+ "}");
}
} else if ("literal".equals(filter)) {
Pattern pat = Pattern.compile("^[^\"\\n]*$");
Matcher mat = pat.matcher(contents);
if (!mat.matches()) {
throw new MarrsException(
"'"
+ contents
+ "' does not match pattern for parameter ${"
+ key
+ "|"
+ filter
+ "}");
}
} else {
/* most restrictive base pattern */
Pattern pat = Pattern.compile("[-~#_:/%.0-9a-zA-Z]+");
Matcher mat = pat.matcher(contents);
if (!mat.matches()) {
throw new MarrsException(
"'" + contents + "' does not match pattern for parameter ${" + key + "}");
}
}
// TODO: replace & appendReplace
q = q.replaceAll("\\$\\{" + key + "(\\|([\\w-]+))?\\}", contents);
}
System.out.println(q);
return q;
}