/*.................................................................................................................*/
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 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++;
}
}
}
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;
}
/*.................................................................................................................*/
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;
}
/**
* 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;
}
/**
* This method returns a Document from the contents of the XML file as contained in the String
* xmlFile, with no restriction as to the root element.
*/
public Document loadXMLFile(String xmlFile) {
if (!StringUtil.blank(xmlFile)) {
Document CipresDoc = XMLUtil.getDocumentFromString(xmlFile);
return CipresDoc;
}
return null;
}
/**
* This processes information about the files contained in either the results or working directory
* of a job.
*/
public CipresJobFile[] processFilesDocument(Document cipresResponseDoc) {
Element jobfiles = cipresResponseDoc.getRootElement().element("jobfiles");
if (jobfiles == null) return null;
List tools = jobfiles.elements("jobfile");
int count = 0;
for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
Element nextTool = (Element) iter.next();
count++;
}
if (count == 0) return null;
CipresJobFile[] cipresJobFile = new CipresJobFile[count];
count = 0;
for (Iterator iter = tools.iterator(); iter.hasNext(); ) {
Element nextJob = (Element) iter.next();
if (nextJob != null) {
if (cipresJobFile[count] == null) cipresJobFile[count] = new CipresJobFile();
Element jobFileElement = nextJob.element("downloadUri");
String fileInfo = null;
if (jobFileElement != null) {
fileInfo = jobFileElement.elementText("url");
if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
cipresJobFile[count].setDownloadURL(fileInfo);
}
fileInfo = jobFileElement.elementText("title");
if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
cipresJobFile[count].setDownloadTitle(fileInfo);
}
}
fileInfo = nextJob.elementText("dateModified");
if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
cipresJobFile[count].setLastModified(fileInfo);
}
fileInfo = nextJob.elementText("filename");
if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
cipresJobFile[count].setFileName(fileInfo);
}
fileInfo = nextJob.elementText("length");
if (!StringUtil.blank(fileInfo) && count < cipresJobFile.length) {
cipresJobFile[count].setLength(MesquiteLong.fromString(fileInfo));
}
count++;
}
}
return cipresJobFile;
}
/*.................................................................................................................*/
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;
}