/*.................................................................................................................*/
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;
}
/*.................................................................................................................*/
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;
}
/*.................................................................................................................*/
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 void reportError(Document doc, String noteToUser, boolean resetPassword) {
if (doc == null) return;
String displayMessage = doc.getRootElement().elementText("displayMessage");
String message = doc.getRootElement().elementText("message");
if (StringUtil.notEmpty(message)) {
if ("Authentication Error".equalsIgnoreCase(displayMessage)) {
if (resetPassword) password = "";
} else {
ownerModule.logln("\n******************");
ownerModule.logln(noteToUser);
ownerModule.logln(displayMessage);
ownerModule.logln(message);
List paramErrors = doc.getRootElement().elements("paramError");
if (paramErrors != null)
for (Iterator iter = paramErrors.iterator(); iter.hasNext(); ) {
Element nextEntry = (Element) iter.next();
String param = nextEntry.elementText("param");
String error = nextEntry.elementText("error");
ownerModule.logln(" " + param + ": " + error);
}
ownerModule.logln("\n******************\n");
}
}
}
/*.................................................................................................................*/
public void prepareBuilder(MultipartEntityBuilder builder, String cipresTool, String jobID) {
if (builder != null) {
builder.setMode(HttpMultipartMode.BROWSER_COMPATIBLE);
builder.addTextBody("tool", cipresTool);
if (StringUtil.notEmpty(jobID)) builder.addTextBody("metadata.clientJobId", jobID);
builder.addTextBody("metadata.statusEmail", "true");
builder.addTextBody("vparam.runtime_", "0.50", ContentType.TEXT_PLAIN);
}
}
/*.................................................................................................................*/
boolean fileNewOrModified(
CipresJobFile[] previousJobFiles, CipresJobFile[] jobFiles, int fileNumber) {
if (previousJobFiles != null && jobFiles != null && fileNumber < jobFiles.length) {
String fileName = jobFiles[fileNumber].getFileName();
if (StringUtil.notEmpty(fileName)) {
for (int i = 0; i < previousJobFiles.length; i++) {
if (fileName.equalsIgnoreCase(
previousJobFiles[i].getFileName())) { // we've found the file
String lastMod = jobFiles[fileNumber].getLastModified();
if (StringUtil.notEmpty(lastMod))
return !lastMod.equals(
previousJobFiles[i].getLastModified()); // return true if the strings don't match
else return true;
}
}
}
}
return true;
}
/*.................................................................................................................*/
public void getResults(HttpClient httpclient, String jobURL) {
String resultsUri = getResultsDirectory(jobURL);
if (StringUtil.notEmpty(resultsUri)) {
Document cipresResponseDoc = cipresQuery(httpclient, resultsUri, "results");
if (cipresResponseDoc != null) {
CipresJobFile[] cipresJobFiles = processFilesDocument(cipresResponseDoc);
for (int job = 0; job < cipresJobFiles.length; job++) {
Debugg.println("fileName: " + cipresJobFiles[job].getFileName());
Debugg.println(" downloadURL: " + cipresJobFiles[job].getDownloadURL());
Debugg.println(" downloadTitle: " + cipresJobFiles[job].getDownloadTitle());
Debugg.println(" length: " + cipresJobFiles[job].getLength());
}
previousCipresJobFiles = cipresJobFiles.clone();
}
}
}
/** The core method that initiates a job on CIPRes. */
public boolean postJob(
HttpClient httpclient, MultipartEntityBuilder builder, MesquiteString jobURL) {
if (builder == null) return false;
String URL = baseURL + "/job/" + username;
HttpPost httppost = new HttpPost(URL);
httppost.addHeader("cipres-appkey", CIPRESkey);
// some of this from
// http://stackoverflow.com/questions/18964288/upload-a-file-through-an-http-form-via-multipartentitybuilder-with-a-progress
HttpEntity cipresEntity = builder.build();
httppost.setEntity(cipresEntity);
try {
HttpResponse response = httpclient.execute(httppost);
HttpEntity responseEntity = response.getEntity();
InputStream instream = responseEntity.getContent();
BufferedReader br = new BufferedReader(new InputStreamReader(instream));
StringBuffer sb = new StringBuffer();
String line = "";
while ((line = br.readLine()) != null) {
sb.append(line + StringUtil.lineEnding());
}
Document cipresResponseDoc = loadXMLFile("jobstatus", sb.toString()); // let's see how it went
boolean success = false;
if (cipresResponseDoc != null) {
processJobSubmissionResponse(cipresResponseDoc, jobURL);
if (verbose) ownerModule.logln(sb.toString());
if (jobURL != null) success = StringUtil.notEmpty(jobURL.getValue());
else success = true;
} else {
cipresResponseDoc = loadXMLFile(sb.toString());
reportError(cipresResponseDoc, "Error with CIPRes run", false);
}
EntityUtils.consume(response.getEntity());
return success;
} catch (IOException e) {
Debugg.printStackTrace(e);
}
return false;
}