public void downloadBAMTool(String toolName, HttpServletResponse response)
throws BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException {
try {
ServletOutputStream out = response.getOutputStream();
DataHandler downloadData = stub.downloadToolBox(toolName);
if (downloadData != null) {
String fileName = "";
if (!toolName.endsWith(".tbox")) {
fileName = toolName + ".tbox";
} else fileName = toolName;
response.setHeader("Content-Disposition", "fileName=" + fileName);
response.setContentType(downloadData.getContentType());
InputStream in = downloadData.getDataSource().getInputStream();
int nextChar;
while ((nextChar = in.read()) != -1) {
out.write((char) nextChar);
}
out.flush();
in.close();
} else {
out.write("The requested service archive was not found on the server".getBytes());
}
} catch (RemoteException e) {
log.error(e.getMessage(), e);
throw new BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException(e);
} catch (IOException e) {
log.error(e.getMessage(), e);
throw new BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException(e);
}
}
public BAMToolBoxDeployerClient(
String cookie, String backEndServerURL, ConfigurationContext configCtx) throws AxisFault {
String serviceURL = backEndServerURL + BAMToolBoxService;
stub = new BAMToolboxDepolyerServiceStub(configCtx, serviceURL);
ServiceClient client = stub._getServiceClient();
Options option = client.getOptions();
option.setManageSession(true);
option.setProperty(org.apache.axis2.transport.http.HTTPConstants.COOKIE_STRING, cookie);
}
public BasicToolBox[] getAllBasicTools()
throws BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException {
try {
return stub.getBasicToolBoxes();
} catch (RemoteException e) {
log.error(e.getMessage(), e);
throw new BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException(e);
}
}
public boolean undeployToolBox(String[] toolName)
throws RemoteException, BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException {
try {
return stub.undeployToolBox(toolName);
} catch (RemoteException e) {
log.error(e);
throw e;
} catch (BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException e) {
log.error(e.getFaultMessage().getBAMToolboxDeploymentException());
throw e;
}
}
public ToolBoxStatusDTO getToolBoxStatus(String toolType, String search)
throws BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException, RemoteException {
try {
return stub.getDeployedToolBoxes(toolType, search);
} catch (RemoteException e) {
log.error(e.getMessage(), e);
throw e;
} catch (BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException e) {
log.error(e.getFaultMessage().getBAMToolboxDeploymentException().getMessage(), e);
throw e;
}
}
public boolean uploadToolBox(DataHandler toolbox, String toolName)
throws RemoteException, BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException {
try {
return stub.uploadBAMToolBox(toolbox, toolName);
} catch (RemoteException e) {
log.error(e.getMessage(), e);
throw e;
} catch (BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException e) {
log.error(e.getFaultMessage().getBAMToolboxDeploymentException().getMessage(), e);
throw e;
}
}
public void installToolBoxFromURL(String url)
throws BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException {
try {
stub.deployToolBoxFromURL(url);
} catch (RemoteException e) {
log.error(e.getMessage(), e);
throw new BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException(e);
} catch (BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException e) {
log.error(e.getFaultMessage().getBAMToolboxDeploymentException().getMessage(), e);
throw e;
}
}
public void deploySample(String sampleId)
throws BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException {
try {
stub.deployBasicToolBox(Integer.parseInt(sampleId));
} catch (RemoteException e) {
log.error(e.getMessage(), e);
throw new BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException(e);
} catch (BAMToolboxDepolyerServiceBAMToolboxDeploymentExceptionException e) {
log.error(e.getFaultMessage().getBAMToolboxDeploymentException().getMessage(), e);
throw e;
}
}
