org.utgenome.gwt.utgb.server
Class WebTrackBase

java.lang.Object
  javax.servlet.GenericServlet
      javax.servlet.http.HttpServlet
          org.utgenome.gwt.utgb.server.RequestHandlerBase
              org.utgenome.gwt.utgb.server.WebTrackBase

All Implemented Interfaces:

Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig, RequestHandler

Direct Known Subclasses:

ACGT, BEDViewer, BSSReadView, ChromosomeMap, CSEGViewer, DASDsn, DASViewer, DotPlot, EchoBackView, FontMetric, FontPanel, GeneViewer, KeywordSearch, LoadView, MethylViewer, ReadView, SAMViewer, ScaleBar, Sequence, SnappyVersion, Transparent, UsingTemplate

public abstract class WebTrackBase
extends RequestHandlerBase

Author:

leo

See Also:

Serialized Form

Constructor Summary

WebTrackBase()

Method Summary

String	createSQL(String sqlTemplate, Object... args) Create an SQL from a given template and variable assignments.
String	createSQLFromFile(String sqlFileName, Object... args) Create an SQL from a given file (relative to the caller class) and variable assignments.
static String	createSQLStatement(String sqlTemplate, Object... args)
String	getActionPrefix(javax.servlet.http.HttpServletRequest request) Return the action prefix of the request
String	getActionSuffix(javax.servlet.http.HttpServletRequest request) Return the action suffix attached to the request
org.xerial.db.sql.DatabaseAccess	getDatabaseAccess(String databaseID) Retrieves the database access
static String	getHTTPRequestQueryString(javax.servlet.http.HttpServletRequest request)
static String	getProjectRootPath() Returns the path to the project root folder
String	getTrackConfigProperty(String key, String defaultValue) Get the property written in the track-config.xml file
<T> List<T>	loadJSON(Reader jsonStream, Class<T> resultClass) load the json data, and converts them into a list of result class instances
<T> void	loadJSON(Reader jsonStream, Class<T> resultClass, org.xerial.util.ObjectHandler<T> resultHandler) Load JSON data from the stream and convert the JSON data into Object of the given resultClass.
BufferedReader	openAction(javax.servlet.http.HttpServletRequest request, String path) Opens a BufferedReader that reads data from another action
BufferedReader	openAction(javax.servlet.http.HttpServletRequest request, String path, boolean bypassRequestParameter)
<T> void	toJSON(String databaseID, String sql, Class<T> resultClass, javax.servlet.http.HttpServletResponse response)

Methods inherited from class org.utgenome.gwt.utgb.server.RequestHandlerBase

doGet, doPost, handle, validate

Methods inherited from class javax.servlet.http.HttpServlet

doDelete, doHead, doOptions, doPut, doTrace, getLastModified, service, service

Methods inherited from class javax.servlet.GenericServlet

destroy, getInitParameter, getInitParameterNames, getServletConfig, getServletContext, getServletInfo, getServletName, init, init, log, log

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

WebTrackBase

public WebTrackBase()

Method Detail

createSQLStatement

public static String createSQLStatement(String sqlTemplate,
                                        Object... args)
                                 throws UTGBException

Throws:

UTGBException

getDatabaseAccess

public org.xerial.db.sql.DatabaseAccess getDatabaseAccess(String databaseID)
                                                   throws UTGBException

Retrieves the database access

Parameters:

name -

Returns:

Throws:

UTGBException

getTrackConfigProperty

public String getTrackConfigProperty(String key,
                                     String defaultValue)

Get the property written in the track-config.xml file

Parameters:

key -

Returns:

toJSON

public <T> void toJSON(String databaseID,
                       String sql,
                       Class<T> resultClass,
                       javax.servlet.http.HttpServletResponse response)
            throws UTGBException,
                   IOException

Type Parameters:

T -

Parameters:

databaseID -

sql -

classType -

Throws:

UTGBException

IOException

loadJSON

public <T> void loadJSON(Reader jsonStream,
                         Class<T> resultClass,
                         org.xerial.util.ObjectHandler<T> resultHandler)
              throws UTGBException,
                     IOException

Load JSON data from the stream and convert the JSON data into Object of the given resultClass. Each object is passed to the result handler.

Type Parameters:

T -

Parameters:

jsonStream -

resultClass -

resultHandler -

Throws:

UTGBException

IOException

loadJSON

public <T> List<T> loadJSON(Reader jsonStream,
                            Class<T> resultClass)
                 throws UTGBException,
                        IOException

load the json data, and converts them into a list of result class instances

Type Parameters:

T -

Parameters:

jsonStream -

resultClass -

Returns:

Throws:

UTGBException

IOException

openAction

public BufferedReader openAction(javax.servlet.http.HttpServletRequest request,
                                 String path)
                          throws javax.servlet.ServletException,
                                 IOException

Opens a BufferedReader that reads data from another action

Parameters:

request -

path - path to the another action. e.g. "hello"

Returns:

Throws:

javax.servlet.ServletException

IOException

openAction

public BufferedReader openAction(javax.servlet.http.HttpServletRequest request,
                                 String path,
                                 boolean bypassRequestParameter)
                          throws javax.servlet.ServletException,
                                 IOException

Parameters:

request -

path -

bypassRequestParameter -

Returns:

Throws:

javax.servlet.ServletException

IOException

getHTTPRequestQueryString

public static String getHTTPRequestQueryString(javax.servlet.http.HttpServletRequest request)

createSQLFromFile

public String createSQLFromFile(String sqlFileName,
                                Object... args)
                         throws IOException,
                                UTGBException

Create an SQL from a given file (relative to the caller class) and variable assignments.

Parameters:

sqlFileName - an SQL (text) file name, which contains a single sql expression. This SQL file can contain variables $1, $2, ..., where each of them corresponds to the args of this method

args - values each of them are assigned to the corresponding variable in the SQL

Returns:

the generated SQL

Throws:

IOException - when failed to read the file

UTGBException - UTGBErrorCode.InvalidSQLSyntax

createSQL

public String createSQL(String sqlTemplate,
                        Object... args)
                 throws UTGBException

Create an SQL from a given template and variable assignments.

Parameters:

sqlTemplate - an SQL template, which can contain variables $1, $2, ..., each of them corresponds to the args of this method

args - variable assignments

Returns:

the generated SQL

Throws:

UTGBException - UTGBErrorCode.InvalidSQLSyntax

getProjectRootPath

public static String getProjectRootPath()

Returns the path to the project root folder

Returns:

getActionSuffix

public String getActionSuffix(javax.servlet.http.HttpServletRequest request)

Return the action suffix attached to the request

Parameters:

request -

Returns:

the action suffix. if no suffix is specified in the action, return "".

getActionPrefix

public String getActionPrefix(javax.servlet.http.HttpServletRequest request)

Return the action prefix of the request

Parameters:

request -

Returns: