A C D E F I L M O R S U

A

AccountFileManager - class AccountFileManager.

This class takes care of file manipulations on the server, as well creating new user accounts, checking the login operation, and reading the user's directory contents.

AccountFileManager(BQUser, String) - Constructor for class AccountFileManager

Constructor needs a BQUser object and the path to the bioquery-users directory.

authenticate() - Method in class AccountFileManager

Checks the username and password of the BQUser passed in the constructor.

AutoSubmitEngine - class AutoSubmitEngine.

This class is a Singleton Thread that carries out the automatic submission of Querys.

C

copyFile(String, String) - Method in class AccountFileManager

Copies the file from oldPath to newPath.

createDirectory(String) - Method in class AccountFileManager

Creates a new directory in the user's home directory.

createNewAccount() - Method in class AccountFileManager

Creates a new user account based on the BQUser passed to the constructor.

D

deleteFile(String) - Method in class AccountFileManager

Deletes the file or directory at path.

doGet(HttpServletRequest, HttpServletResponse) - Method in class FileManagerServlet

doGet method for testing purposes only.

doGet(HttpServletRequest, HttpServletResponse) - Method in class SubmitQueryServlet

doGet method for testing purposes only.

doGet(HttpServletRequest, HttpServletResponse) - Method in class UpdateServlet

doGet method for testing purposes only.

doPost(HttpServletRequest, HttpServletResponse) - Method in class FileManagerServlet

This method handles all communication requests from the Client, which must be as POST requests.

doPost(HttpServletRequest, HttpServletResponse) - Method in class SubmitQueryServlet

Overriden doPost method accepts a serialized Query object, instantiates it, submits it to it's database, and returns the results back to the client as the Response.

doPost(HttpServletRequest, HttpServletResponse) - Method in class UpdateServlet

Handles requests from the Client.

E

endLine - Static variable in class ServerLog

F

FileManagerServlet - class FileManagerServlet.

This class handles all File communications with the Client.

FileManagerServlet() - Constructor for class FileManagerServlet

I

init() - Method in class FileManagerServlet

Loads the BioQuery users directory parameter from the web.xml file.

init() - Method in class UpdateServlet

Loads the jar file directory parameter from the web.xml file.

L

logEntry(Exception) - Static method in class ServerLog

logEntry(String) - Static method in class ServerLog

logEntry(String, Exception) - Static method in class ServerLog

M

main(String[]) - Static method in class AutoSubmitEngine

main simply calls shutDownEngine which gives an alternate way to shut down the AutoSubmitEngine Thread (by typing in the command line of the server: java AutoSubmitEngine.

moveFile(String, String) - Method in class AccountFileManager

Moves the file from oldPath to newPath.

O

openFile(String) - Method in class AccountFileManager

Opens the file for the given filePath and returns an InputStream to that file's contents.

R

renameFile(String, String) - Method in class AccountFileManager

Renames the file at oldPath to newName.

run() - Method in class AutoSubmitEngine

This Thread periodically checks the time, and just after midnight begins asking Query files if it is time to autosubmit them.

S

saveFile(InputStream, String) - Method in class AccountFileManager

Saves the contents of the given InputStream into a file with the location and name given in path.

ServerLog - class ServerLog.

Static methods log messages to a file.

ServerLog() - Constructor for class ServerLog

shutDownEngine() - Static method in class AutoSubmitEngine

Shuts down the AutoSubmitEngine and terminates the Thread.

startAutoSubmitEngine(String) - Static method in class AutoSubmitEngine

Starts the AutoSubmitEngine, which runs forever as a separate Thread.

SubmitQueryServlet - class SubmitQueryServlet.

The SubmitQueryServlet is no longer in use by the BioQuery application and does not need to be installed! This servlet received commands and Query objects from the client in order to submit Querys from the server, rather than directly from the client.

SubmitQueryServlet() - Constructor for class SubmitQueryServlet

U

updateFileList() - Method in class AccountFileManager

Returns a List containing the full path of every file and directory in this users account, relative to this users directory.

UpdateServlet - class UpdateServlet.

The UpdateServlet handles the automatic updating of the bioquery program, in collaboration with class BQUpdate on the Client side.

UpdateServlet() - Constructor for class UpdateServlet

A C D E F I L M O R S U