/**
* Gets the name.
*
* @return the name
*/
public String getName() {
StringBuilder name = new StringBuilder();
if (!StringUtil.isNullOrEmpty(title)) {
name.append(title);
}
if (!StringUtil.isNullOrEmpty(firstname)) {
if (name.length() > 0) {
name.append(" ");
}
name.append(firstname);
}
if (!StringUtil.isNullOrEmpty(lastname)) {
if (name.length() > 0) {
name.append(" ");
}
name.append(lastname);
}
return name.toString();
}
/*.................................................................................................................*/
boolean checkUsernamePassword(boolean tellUserAboutCipres) {
if (StringUtil.blank(username) || StringUtil.blank(password)) {
MesquiteBoolean answer = new MesquiteBoolean(false);
MesquiteString usernameString = new MesquiteString();
if (username != null) usernameString.setValue(username);
MesquiteString passwordString = new MesquiteString();
if (password != null) passwordString.setValue(password);
String help =
"You will need an account on the CIPRes REST system to use this service. To register, go to https://www.phylo.org/restusers/register.action";
new UserNamePasswordDialog(
ownerModule.containerOfModule(),
"Sign in to CIPRes",
help,
"",
"Username",
"Password",
answer,
usernameString,
passwordString);
if (answer.getValue()) {
username = usernameString.getValue();
password = passwordString.getValue();
}
ownerModule.storePreferences();
}
boolean success = StringUtil.notEmpty(username) && StringUtil.notEmpty(password);
if (!success && tellUserAboutCipres) {
MesquiteMessage.discreetNotifyUser(
"Use of the CIPRes service requires an account with CIPRes's REST service. Go to https://www.phylo.org/restusers/register.action to register for an account");
}
return success;
}
/**
* this is the primary method that sends a query to the CIPRes REST service. It expects to receive
* an XML file, which it returns in Document if the root tag matc hes xmlRootTag
*/
public Document cipresQuery(HttpClient httpclient, String URL, String xmlRootTag) {
if (StringUtil.blank(URL)) return null;
try {
HttpGet httpget = new HttpGet(URL);
httpget.addHeader("cipres-appkey", CIPRESkey);
try {
HttpResponse response = httpclient.execute(httpget);
HttpEntity responseEntity = response.getEntity();
InputStream instream = responseEntity.getContent();
BufferedReader br = new BufferedReader(new InputStreamReader(instream));
String line = "";
StringBuffer sb = new StringBuffer();
while ((line = br.readLine()) != null) {
sb.append(line + StringUtil.lineEnding());
}
Document cipresResponseDoc = loadXMLFile(xmlRootTag, sb.toString());
if (cipresResponseDoc != null && verbose) {
ownerModule.logln(sb.toString());
}
if (cipresResponseDoc == null) {
Document errorDoc = loadXMLFile(sb.toString());
if (errorDoc != null) reportError(errorDoc, "Error in communicating with CIPRes", true);
}
EntityUtils.consume(response.getEntity());
return cipresResponseDoc;
} catch (IOException e) {
Debugg.printStackTrace(e);
} catch (Exception e) {
Debugg.printStackTrace(e);
}
} catch (Exception e) {
Debugg.printStackTrace(e);
}
return null;
}
/*.................................................................................................................*/
public void actionPerformed(ActionEvent e) {
if (e.getActionCommand().equalsIgnoreCase("setToDefaults")) {
setDefaultTNTCommandsSearchOptions();
searchField.setText(searchArguments);
bootstrapSearchField.setText(bootstrapSearchArguments);
harvestOnlyStrictConsensusBox.setState(harvestOnlyStrictConsensus);
resamplingAllConsensusTreesBox.setState(!resamplingAllConsensusTrees);
bootStrapRepsField.setValue(bootstrapreps);
} else if (e.getActionCommand().equalsIgnoreCase("setToDefaultsOtherOptions")) {
setDefaultTNTCommandsOtherOptions();
otherOptionsField.setText(otherOptions);
convertGapsBox.setState(convertGapsToMissing);
} else if (e.getActionCommand().equalsIgnoreCase("browseSearchScript")
&& searchScriptPathField != null) {
MesquiteString directoryName = new MesquiteString();
MesquiteString fileName = new MesquiteString();
String path =
MesquiteFile.openFileDialog("Choose Search Script File", directoryName, fileName);
if (StringUtil.notEmpty(path)) searchScriptPathField.setText(path);
} else if (e.getActionCommand().equalsIgnoreCase("browseBootSearchScript")
&& bootSearchScriptPathField != null) {
MesquiteString directoryName = new MesquiteString();
MesquiteString fileName = new MesquiteString();
String path =
MesquiteFile.openFileDialog(
"Choose Resampling Search Script File", directoryName, fileName);
if (StringUtil.notEmpty(path)) bootSearchScriptPathField.setText(path);
}
}
/*.................................................................................................................*/
public boolean downloadWorkingResults(
HttpClient httpclient,
String jobURL,
String rootDir,
String fileName,
boolean onlyNewOrModified) {
if (StringUtil.blank(fileName)) return false;
String workingUri = getWorkingDirectory(jobURL);
if (StringUtil.notEmpty(workingUri)) {
Document cipresResponseDoc = cipresQuery(httpclient, workingUri, "workingdir");
if (cipresResponseDoc != null) {
CipresJobFile[] cipresJobFiles = processFilesDocument(cipresResponseDoc);
if (cipresJobFiles == null || cipresJobFiles.length == 0) {
return false;
}
for (int job = 0; job < cipresJobFiles.length; job++) {
if (fileName.equalsIgnoreCase(cipresJobFiles[job].getFileName())
&& (!onlyNewOrModified
|| fileNewOrModified(previousCipresJobFiles, cipresJobFiles, job)))
cipresDownload(
httpclient,
cipresJobFiles[job].getDownloadURL(),
rootDir + cipresJobFiles[job].getFileName());
}
previousCipresJobFiles = cipresJobFiles.clone();
return true;
}
}
return false;
}
/** Called to alter data in all cells */
public boolean operateOnData(CharacterData data) {
if (!(data instanceof ContinuousData)) return false;
ContinuousData cData = (ContinuousData) data;
int numItems = cData.getNumItems();
String[] items = new String[numItems];
for (int i = 0; i < items.length; i++) {
if (StringUtil.blank(cData.getItemName(i))) items[i] = "(unnamed)";
else items[i] = cData.getItemName(i);
}
int d =
ListDialog.queryList(
containerOfModule(),
"Rename item",
"Rename item:",
MesquiteString.helpString,
items,
0);
if (!MesquiteInteger.isCombinable(d) || d < 0 || d >= numItems) return false;
else {
String s =
MesquiteString.queryString(
containerOfModule(), "Rename Item", "New name for " + items[d], items[d]);
if (StringUtil.blank(s)) return false;
cData.setItemReference(d, NameReference.getNameReference(s));
return true;
}
}
/** Create LockssKeystore from a config subtree */
LockssKeyStore createLockssKeyStore(Configuration config) {
log.debug2("Creating LockssKeyStore from config: " + config);
String name = config.get(KEYSTORE_PARAM_NAME);
LockssKeyStore lk = new LockssKeyStore(name);
String file = config.get(KEYSTORE_PARAM_FILE);
String resource = config.get(KEYSTORE_PARAM_RESOURCE);
String url = config.get(KEYSTORE_PARAM_URL);
if (!StringUtil.isNullString(file)) {
lk.setLocation(file, LocationType.File);
} else if (!StringUtil.isNullString(resource)) {
lk.setLocation(resource, LocationType.Resource);
} else if (!StringUtil.isNullString(url)) {
lk.setLocation(url, LocationType.Url);
}
lk.setType(config.get(KEYSTORE_PARAM_TYPE, defaultKeyStoreType));
lk.setProvider(config.get(KEYSTORE_PARAM_PROVIDER, defaultKeyStoreProvider));
lk.setPassword(config.get(KEYSTORE_PARAM_PASSWORD));
lk.setKeyPassword(config.get(KEYSTORE_PARAM_KEY_PASSWORD));
lk.setKeyPasswordFile(config.get(KEYSTORE_PARAM_KEY_PASSWORD_FILE));
lk.setMayCreate(config.getBoolean(KEYSTORE_PARAM_CREATE, DEFAULT_CREATE));
return lk;
}
/** This method simply lists the tools available */
public void listTools(HttpClient httpclient) {
Document cipresResponseDoc = cipresQuery(httpclient, baseURL + "/tool", "tools");
if (cipresResponseDoc != null) {
String elementName = "tool";
List tools = cipresResponseDoc.getRootElement().elements(elementName);
int count = 0;
for (Iterator iter = tools.iterator();
iter.hasNext(); ) { // let's get a count as to how many tools there are.
Element nextTool = (Element) iter.next();
count++;
}
String[] toolName = new String[count];
count = 0;
for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
Element nextTool = (Element) iter.next();
String name = nextTool.elementText("toolId");
if (!StringUtil.blank(name) && count < toolName.length) {
ownerModule.logln(name);
}
name = nextTool.elementText("toolName");
if (!StringUtil.blank(name) && count < toolName.length) {
ownerModule.logln(" " + name);
}
count++;
}
}
}
void setConfig(Configuration config) {
log.debug("config: " + config);
proxyHost = config.get(PARAM_PROXY_HOST);
proxyPort = config.getInt(PARAM_PROXY_PORT, DEFAULT_PROXY_PORT);
if (StringUtil.isNullString(proxyHost) || proxyPort <= 0) {
String http_proxy = System.getenv("http_proxy");
if (!StringUtil.isNullString(http_proxy)) {
try {
HostPortParser hpp = new HostPortParser(http_proxy);
proxyHost = hpp.getHost();
proxyPort = hpp.getPort();
} catch (HostPortParser.InvalidSpec e) {
log.warning("Can't parse http_proxy environment var, ignoring: " + http_proxy + ": " + e);
}
}
}
if (StringUtil.isNullString(proxyHost) || proxyPort <= 0) {
proxyHost = null;
} else {
log.info("Proxying through " + proxyHost + ":" + proxyPort);
}
userAgent = config.get(PARAM_USER_AGENT);
if (StringUtil.isNullString(userAgent)) {
userAgent = null;
} else {
log.debug("Setting User-Agent to " + userAgent);
}
}
/**
* Gets background color for cell for row ic. Override it if you want to change the color from the
* default.
*/
public Color getBackgroundColorOfCell(int it, boolean selected) {
if (observedStates == null) {
doCalcs();
if (observedStates == null) return null;
}
if (observedStates.getParentData() != null) {
captureCharacterDataFromObservedStates();
Associable tInfo = data.getTaxaInfo(false);
NameReference genBankColor = NameReference.getNameReference("genbankcolor");
Object obj = tInfo.getAssociatedObject(genBankColor, it); // not saved to file
if (obj instanceof Color) return (Color) obj;
}
if (bits == null || it < 0 || it > bits.getSize()) return null;
String note = getNote(it);
if (selected) {
if (bits.isBitOn(it)) return ColorDistribution.darkGreen;
else return ColorDistribution.darkRed;
} else if (bits.isBitOn(it)) {
if (StringUtil.blank(note)) return ColorDistribution.veryLightGreen;
if (!(note.equalsIgnoreCase("x"))) return ColorDistribution.lightGreenYellowish;
return ColorDistribution.lightGreenYellow;
} else {
if (StringUtil.blank(note)) return ColorDistribution.brown;
if (!(note.equalsIgnoreCase("x"))) {
return Color.red;
}
return ColorDistribution.lightRed;
}
}
public void processCompletedOutputFiles(String[] outputFilePaths) {
if (outputFilePaths.length > 1 && !StringUtil.blank(outputFilePaths[1])) {
ZephyrUtil.copyLogFile(this, "TNT", outputFilePaths[1]);
}
if (outputFilePaths.length > 2 && !StringUtil.blank(outputFilePaths[2])) {
ZephyrUtil.copyOutputText(this, outputFilePaths[2], commands);
}
}
// Break the line at commas, return a map of the resulting strings
// broken at equals sign. (<i>Ie</i>, name value pairs.)
Map getRow(String line) {
Map map = new HashMap();
for (Iterator iter = StringUtil.breakAt(line, ',').iterator(); iter.hasNext(); ) {
String item = (String) iter.next();
List pair = StringUtil.breakAt(item, '=');
map.put(pair.get(0), pair.get(1));
}
return map;
}
/**
* Did the client provide the minimal parameters required?
*
* @return true If so
*/
private boolean verifyMinimumParameters() {
int count = 0;
if (!StringUtil.isNullString(getParameter(AP_E_PUBLICATION))) count++;
if (!StringUtil.isNullString(getParameter(AP_E_CLASSNAME))) count++;
if (!StringUtil.isNullString(getParameter(AP_E_PLUGIN))) count++;
return (count > 0);
}
/** Concatenate params for URL string */
static String concatParams(String p1, String p2) {
if (StringUtil.isNullString(p1)) {
return p2;
}
if (StringUtil.isNullString(p2)) {
return p1;
}
return p1 + "&" + p2;
}
private void doSleep() throws IOException {
String timestr = getParameter(KEY_TIME);
try {
long time = StringUtil.parseTimeInterval(timestr);
Deadline.in(time).sleep();
statusMsg = "Slept for " + StringUtil.timeIntervalToString(time);
} catch (NumberFormatException e) {
errMsg = "Illegal duration: " + e;
} catch (InterruptedException e) {
errMsg = "Interrupted: " + e;
}
}
private StringSet getStringSet(String key, String deli) {
StringSet set = new StringSet();
String v = getValue(key);
if (v != null) {
String[] vv = StringUtil.split(v, deli);
for (String x : vv) {
x = StringUtil.trimToEmpty(x);
if (x.length() > 0) set.put(x);
}
}
return set;
}
/**
* 从一个string类型的list中移出没有实际内容（包括只含空格内容）的元素 返回一个新的list
*
* @param list
* @return
*/
public static List<String> filterBlankElements(List<String> list) {
List<String> result = new ArrayList<String>();
if (list == null || list.isEmpty()) {
return result;
}
for (String element : list) {
if (StringUtil.isEmpty(element) || StringUtil.isEmpty(element.trim())) {
continue;
}
result.add(element);
}
return result;
}
private static void appendHTML(JEditorPane editor, String html) {
try {
html = StringUtil.replaceAll(html, "\t", " ");
html = StringUtil.replaceAll(html, "\r\n", "\n");
html = StringUtil.replaceAll(html, "\r", "");
Vector vt = StringUtil.toStringVector(html, "\n");
HTMLEditorKit kit = (HTMLEditorKit) editor.getEditorKit();
HTMLDocument doc = (HTMLDocument) editor.getDocument();
for (int iIndex = 0; iIndex < vt.size(); iIndex++)
kit.insertHTML(doc, doc.getLength(), (String) vt.elementAt(iIndex), 0, 0, null);
} catch (Exception e) {
e.printStackTrace();
}
}
/** Concatenate params for URL string */
String concatParams(Properties props) {
if (props == null) {
return null;
}
java.util.List list = new ArrayList();
for (Iterator iter = props.keySet().iterator(); iter.hasNext(); ) {
String key = (String) iter.next();
String val = props.getProperty(key);
if (!StringUtil.isNullString(val)) {
list.add(key + "=" + urlEncode(val));
}
}
return StringUtil.separatedString(list, "&");
}
/*.................................................................................................................*/
public boolean monitorAndCleanUpShell(String jobURL) {
boolean stillGoing = true;
if (!checkUsernamePassword(true)) {
return false;
}
lastModified = null;
if (outputFilePaths != null) {
lastModified = new long[outputFilePaths.length];
LongArray.deassignArray(lastModified);
}
String status = "";
while (!jobCompleted(jobURL) && stillGoing) {
if (StringUtil.blank(status))
ownerModule.logln(
"CIPRes Job Status: " + getJobStatus(jobURL) + " (" + StringUtil.getDateTime() + ")");
// if (jobSubmitted(jobURL))
// processOutputFiles();
try {
Thread.sleep(minPollIntervalSeconds * 1000);
} catch (InterruptedException e) {
MesquiteMessage.notifyProgrammer("InterruptedException in CIPRes monitoring");
return false;
}
stillGoing = watcher == null || watcher.continueShellProcess(null);
String newStatus = getJobStatus(jobURL);
if (newStatus != null && !newStatus.equalsIgnoreCase(status)) {
ownerModule.logln(
"CIPRes Job Status: " + newStatus + " (" + StringUtil.getDateTime() + ")");
status = newStatus;
} else ownerModule.log(".");
if (newStatus != null && newStatus.equalsIgnoreCase("SUBMITTED")) { // job is running
processOutputFiles(jobURL);
}
}
ownerModule.logln("CIPRes job completed.");
if (outputFileProcessor != null) {
if (rootDir != null) {
ownerModule.logln("About to download results from CIPRes.");
if (downloadResults(jobURL, rootDir, false))
outputFileProcessor.processCompletedOutputFiles(outputFilePaths);
else return false;
}
}
return true;
}
protected Properties filterResponseProps(Properties props) {
Properties res = new Properties();
for (Map.Entry ent : props.entrySet()) {
String key = (String) ent.getKey();
if (StringUtil.startsWithIgnoreCase(key, "x-lockss")
|| StringUtil.startsWithIgnoreCase(key, "x_lockss")
|| key.equalsIgnoreCase("org.lockss.version.number")) {
continue;
}
// We've lost the original case - capitalize them the way most people
// expect
res.put(StringUtil.titleCase(key, '-'), (String) ent.getValue());
}
return res;
}
protected String doHandleGet(UserSession ctx, String link, Map args) {
PhotoFilter filter = ctx.getPhotoFilter();
String un = ctx.getAsString(args, PhotoFilter.USER_NAME);
if (StringUtil.isLegalUserName(un)) {
filter.setUserName(un);
}
String tags = ctx.getAsString(args, PhotoFilter.TAGS);
if (StringUtil.isLegalTagsString(tags)) {
filter.setTags(new Tags(tags));
}
return PartUtil.SHOW_PHOTO_PAGE_NAME;
}
/*.................................................................................................................*/
public boolean downloadResults(
HttpClient httpclient, String jobURL, String rootDir, boolean onlyNewOrModified) {
String resultsUri = getResultsDirectory(jobURL);
if (StringUtil.notEmpty(resultsUri)) {
Document cipresResponseDoc = cipresQuery(httpclient, resultsUri, "results");
if (cipresResponseDoc != null) {
CipresJobFile[] cipresJobFiles = processFilesDocument(cipresResponseDoc);
if (cipresJobFiles == null || cipresJobFiles.length == 0) {
ownerModule.logln(cipresResponseDoc.toString());
return false;
}
for (int job = 0; job < cipresJobFiles.length; job++) {
if (!onlyNewOrModified || fileNewOrModified(previousCipresJobFiles, cipresJobFiles, job))
cipresDownload(
httpclient,
cipresJobFiles[job].getDownloadURL(),
rootDir + cipresJobFiles[job].getFileName());
}
previousCipresJobFiles = cipresJobFiles.clone();
return true;
}
}
return false;
}
public String[] getJobURLs(Document cipresResponseDoc) {
String elementName = "jobstatus";
Element jobs = cipresResponseDoc.getRootElement().element("jobs");
if (jobs == null) return null;
List tools = jobs.elements("jobstatus");
int count = 0;
for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
Element nextTool = (Element) iter.next();
count++;
}
String[] url = new String[count];
count = 0;
for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
Element nextJob = (Element) iter.next();
if (nextJob != null) {
Element selfUriElement = nextJob.element("selfUri");
if (selfUriElement != null) {
String jobURL = selfUriElement.elementText("url");
if (!StringUtil.blank(jobURL) && count < url.length) {
url[count] = jobURL;
}
}
count++;
}
}
return url;
}
/**
* A target system is required to create an AU - was it provided?
*
* @return true If at least one target was specified
*/
private boolean verifyTarget() {
if (!isCreateCommand()) {
return true;
}
return !StringUtil.isNullString(getParameter(AP_E_TARGET));
}
/*................................................................................................*/
public boolean startJob(String arguments, Object condition, boolean hiredByName) {
addMenuItem("Directory for Sample Trees From Directory...", makeCommand("setDirPath", this));
fillerTasks = new Vector();
if (!MesquiteThread
.isScripting()) { // enclosed in conditional to avoid hiring query when opening file; should
// be handled by snapshot/doCommand when file is opened.
String directoryPath =
MesquiteFile.chooseDirectory(
"Choose directory containing tree files:",
previousDirectory); // MesquiteFile.saveFileAsDialog("Base name for files (files will
// be named <name>1.nex, <name>2.nex, etc.)", baseName);
if (StringUtil.blank(directoryPath)) { // TODO: clean this up?
return false;
} else {
directory = new File(directoryPath);
previousDirectory = directory.getParent();
if (directory.exists() && directory.isDirectory()) {
return hireFillers(directoryPath);
}
}
}
return true; // Add something to make sure directory paths are set up correctly, when not
// scripting...
}
/*................................................................................................*/
private boolean hireFillers(String directoryPath) {
String[] files = directory.list();
String treePath;
for (int i = 0; i < files.length; i++) {
if (files[i] != null) {
String fileLowerCase = files[i].toLowerCase();
if (fileLowerCase.endsWith(".nex") || fileLowerCase.endsWith(".nexus")) {
treePath = directoryPath + MesquiteFile.fileSeparator + files[i];
File treeFile = new File(treePath);
String treeFileName = treeFile.getName();
if (StringUtil.blank(treeFileName)) {
return false;
}
TreeBlockFiller newFiller;
newFiller =
(TreeBlockFiller)
hireNamedEmployee(TreeBlockFiller.class, "#SampleOneTreeFromFile"); // treePath);
if (newFiller != null) {
if (((SampleOneTreeFromFile) newFiller).setFilePath(treePath)
&& ((SampleOneTreeFromFile) newFiller).processFile()) {
fillerTasks.addElement(newFiller);
} else
Debugg.println(
"Filler "
+ i
+ " processFile = "
+ ((SampleOneTreeFromFile) newFiller).processFile());
}
}
}
}
return true;
}
/** monitors the run. */
public boolean monitorAndCleanUpShell() {
lastModified = null;
boolean stillGoing = true;
if (outputFilePaths != null) {
lastModified = new long[outputFilePaths.length];
LongArray.deassignArray(lastModified);
}
if (!StringUtil.blank(
runningFilePath)) // is file at runningFilePath; watch for its disappearance
while (MesquiteFile.fileExists(runningFilePath) && stillGoing) {
processOutputFiles();
try {
Thread.sleep(sleepTime);
} catch (InterruptedException e) {
MesquiteMessage.notifyProgrammer(
"InterruptedException in shell script executed by " + name);
return false;
}
stillGoing = watcher == null || watcher.continueShellProcess(proc);
}
if (outputFileProcessor != null)
outputFileProcessor.processCompletedOutputFiles(outputFilePaths);
return true;
}
public static ArrayList<String> getTagListFromString(String tags, char separator) {
ArrayList<String> result = new ArrayList<String>(8);
if (tags != null) {
int i = 0;
int j = 0;
for (; i < tags.length(); i = j) {
for (; ((i < tags.length()) && (tags.charAt(i) == separator)); ) {
i++;
}
for (j = i; ((j < tags.length()) && (tags.charAt(j) != separator)); ) {
j++;
}
if (i != j) {
String tag = asTag(tags.substring(i, j));
if (!result.contains(tag) && !StringUtil.isNullOrEmptyString(tag)) {
result.add(tag);
}
}
}
}
return result;
}
protected void logParams() {
Enumeration en = req.getParameterNames();
while (en.hasMoreElements()) {
String name = (String) en.nextElement();
String vals[];
String dispval;
if (StringUtil.indexOfIgnoreCase(name, "passw") >= 0) {
dispval = req.getParameter(name).length() == 0 ? "" : "********";
} else if (log.isDebug2() && (vals = req.getParameterValues(name)).length > 1) {
dispval = StringUtil.separatedString(vals, ", ");
} else {
dispval = req.getParameter(name);
}
log.debug(name + " = " + dispval);
}
}
