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;
}
/** 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 jobStatusFromResponse(Document cipresResponseDoc) {
String status = "Status not available";
Element element = cipresResponseDoc.getRootElement().element("terminalStage");
if (element != null) {
status = element.getText();
if ("true".equalsIgnoreCase(status)) return JOBCOMPLETED;
}
element = cipresResponseDoc.getRootElement().element("messages");
if (element == null) return status;
List entries = element.elements("message");
String reportedJobID = "";
for (Iterator iter = entries.iterator(); iter.hasNext(); ) {
Element nextEntry = (Element) iter.next();
if (nextEntry != null) status = nextEntry.elementText("stage");
}
element = cipresResponseDoc.getRootElement().element("minPollIntervalSeconds");
if (element != null) {
minPollIntervalSeconds = MesquiteInteger.fromString(element.getText());
if (!MesquiteInteger.isCombinable(minPollIntervalSeconds) || minPollIntervalSeconds <= 0)
minPollIntervalSeconds = defaultMinPollIntervalSeconds;
}
if (JOBCOMPLETED.equalsIgnoreCase(status)) return JOBCOMPLETED;
return status;
}
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");
}
}
}
/**
* 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 void processJobSubmissionResponse(Document cipresResponseDoc, MesquiteString jobURL) {
Element element = cipresResponseDoc.getRootElement().element("selfUri");
Element subelement = null;
if (element != null) subelement = element.element("url");
if ("false".equals(cipresResponseDoc.getRootElement().elementText("failed"))) {
element = cipresResponseDoc.getRootElement().element("metadata");
List entries = element.elements("entry");
String reportedJobID = "";
for (Iterator iter = entries.iterator(); iter.hasNext(); ) {
Element nextEntry = (Element) iter.next();
if ("clientJobId".equals(nextEntry.elementText("key")))
reportedJobID = nextEntry.elementText("value");
}
ownerModule.logln("\nJob successfully submitted to CIPRes.");
ownerModule.logln(" Job URL: " + subelement.getText());
ownerModule.logln(" Job ID: " + reportedJobID + "\n");
if (jobURL != null) jobURL.setValue(subelement.getText());
}
}