org.emboss.jemboss.server
Class JembossAuthServer

java.lang.Object
  |
  +--org.emboss.jemboss.server.JembossAuthServer

public class JembossAuthServer
extends java.lang.Object

Jemboss Authenticated Server for SOAP


Field Summary
(package private)  java.lang.String acdDirToParse
           
(package private)  java.lang.String embossBin
           
(package private)  java.lang.String embossData
           
(package private)  java.lang.String embossPath
           
private  java.lang.String[] env
           
private  java.lang.String environ
           
private  java.lang.String errorLog
           
private  java.lang.String fs
           
(package private)  JembossParams jp
           
private  java.lang.String logFile
           
(package private)  java.lang.String plplot
           
private  java.lang.String ps
           
private  java.lang.String tmproot
           
 
Constructor Summary
JembossAuthServer()
           
 
Method Summary
 java.lang.String about()
           
 java.lang.String abouturl()
           
private  void appendToLogFile(java.lang.String logEntry, java.lang.String logFileName)
          Appends a log entry to the log file
 java.lang.String appversion()
           
 java.util.Vector call_ajax(java.lang.String fileContent, java.lang.String seqtype)
          Uses JNI to calculate sequence attributes using EMBOSS library call.
 java.util.Vector call_ajax(java.lang.String fileContent, java.lang.String seqtype, java.lang.String userName, byte[] passwd)
          Uses JNI to calculate sequence attributes using EMBOSS library call.
 java.lang.Object clone()
           
 java.util.Vector delete_saved_results(java.lang.String project, java.lang.String cl, java.lang.String userName, byte[] passwd)
          Private server Deletes a projects saved results.
 java.lang.String docurl()
           
private  java.util.Hashtable getHashtable(java.util.Vector v)
           
 java.util.Vector getWossname()
          Returns the output of the EMBOSS utility wossname
 java.lang.String helpurl()
           
 java.util.Vector list_saved_results(java.lang.String userName, byte[] passwd)
          Private Server List of the saved results on the server.
private  java.util.Vector loadFilesContent(Ajax aj, java.lang.String userName, byte[] passwd, java.io.File projectDir, java.lang.String project, java.util.Vector result, java.util.Hashtable inFiles)
          Reads in files from EMBOSS output
 java.lang.String name()
           
private  java.lang.String quoteMe(java.lang.String s)
          Quote all tokens ready for shell scripts
private  java.util.Vector returnError(Ajax aj, java.lang.String msg)
          Report the stderr and stdout to error logs
 java.util.Vector run_prog(java.lang.String embossCommand, java.lang.String options, java.util.Hashtable inFiles, java.lang.String userName, byte[] passwd)
          Private Authenticated Server Run an EMBOSS application
 java.util.Vector run_prog(java.lang.String embossCommand, java.lang.String options, java.util.Vector inFiles, java.lang.String userName, byte[] passwd)
           
private  void runAsBatch(Ajax aj, java.lang.String userName, byte[] passwd, java.lang.String project, java.lang.String embossCommand)
           
private  void runAsGNQSBatch(Ajax aj, java.lang.String userName, byte[] passwd, java.lang.String project, java.lang.String embossCommand)
          Submit to a Generic NQS batch queue.
private  void runAsPBSBatch(Ajax aj, java.lang.String userName, byte[] passwd, java.lang.String project, java.lang.String embossCommand)
          Submit to a OpenPBS batch queue.
 java.util.Vector save_project_file(java.lang.String project, java.lang.String filename, java.lang.String notes, java.lang.String userName, byte[] passwd)
          Private server Save a file to a project directory on the server.
 java.util.Hashtable servicedesc()
           
 java.util.Vector show_acd(java.lang.String appName)
          Retrieves the ACD file of an application.
 java.util.Vector show_db()
          Returns the databases held on the server
 java.util.Vector show_help(java.lang.String applName)
          Returns the help for an application as given by 'tfm'
 java.util.Vector show_saved_results(java.lang.String project, java.lang.String cl, java.lang.String userName, byte[] passwd)
          Private Server Returns the results for a saved project.
 java.util.Vector update_result_status(java.lang.String prog, java.lang.String opt, java.util.Hashtable resToQuery, java.lang.String userName, byte[] passwd)
           
 java.util.Vector update_result_status(java.lang.String prog, java.lang.String opt, java.util.Vector resToQuery, java.lang.String userName, byte[] passwd)
          Used to provide information on the batch/background processes.
private  boolean verifyUser(Ajax aj, java.lang.String userName, byte[] passwd, java.util.Vector res)
           
 java.lang.String version()
           
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

tmproot

private java.lang.String tmproot

logFile

private java.lang.String logFile

errorLog

private java.lang.String errorLog

fs

private java.lang.String fs

ps

private java.lang.String ps

jp

JembossParams jp

plplot

java.lang.String plplot

embossData

java.lang.String embossData

embossBin

java.lang.String embossBin

embossPath

java.lang.String embossPath

acdDirToParse

java.lang.String acdDirToParse

env

private java.lang.String[] env

environ

private java.lang.String environ
Constructor Detail

JembossAuthServer

public JembossAuthServer()
Method Detail

name

public java.lang.String name()

version

public java.lang.String version()

appversion

public java.lang.String appversion()

about

public java.lang.String about()

helpurl

public java.lang.String helpurl()

abouturl

public java.lang.String abouturl()

docurl

public java.lang.String docurl()

servicedesc

public java.util.Hashtable servicedesc()

show_acd

public java.util.Vector show_acd(java.lang.String appName)
Retrieves the ACD file of an application.

Returns:
Vector of containing the ACD string

getWossname

public java.util.Vector getWossname()
Returns the output of the EMBOSS utility wossname

Returns:
wossname output

show_help

public java.util.Vector show_help(java.lang.String applName)
Returns the help for an application as given by 'tfm'

Returns:
help

call_ajax

public java.util.Vector call_ajax(java.lang.String fileContent,
                                  java.lang.String seqtype,
                                  java.lang.String userName,
                                  byte[] passwd)
Uses JNI to calculate sequence attributes using EMBOSS library call.

Returns:
sequence length, weight & type (protein/nucleotide)

call_ajax

public java.util.Vector call_ajax(java.lang.String fileContent,
                                  java.lang.String seqtype)
Uses JNI to calculate sequence attributes using EMBOSS library call.

Returns:
sequence length, weight & type (protein/nucleotide)

show_db

public java.util.Vector show_db()
Returns the databases held on the server

Returns:
output from 'showdb'

run_prog

public java.util.Vector run_prog(java.lang.String embossCommand,
                                 java.lang.String options,
                                 java.util.Vector inFiles,
                                 java.lang.String userName,
                                 byte[] passwd)

getHashtable

private java.util.Hashtable getHashtable(java.util.Vector v)

run_prog

public java.util.Vector run_prog(java.lang.String embossCommand,
                                 java.lang.String options,
                                 java.util.Hashtable inFiles,
                                 java.lang.String userName,
                                 byte[] passwd)
Private Authenticated Server Run an EMBOSS application

Returns:
output files from application run

quoteMe

private java.lang.String quoteMe(java.lang.String s)
Quote all tokens ready for shell scripts


runAsPBSBatch

private void runAsPBSBatch(Ajax aj,
                           java.lang.String userName,
                           byte[] passwd,
                           java.lang.String project,
                           java.lang.String embossCommand)
Submit to a OpenPBS batch queue. This method creates a script for submission to a batch queueing system.


runAsGNQSBatch

private void runAsGNQSBatch(Ajax aj,
                            java.lang.String userName,
                            byte[] passwd,
                            java.lang.String project,
                            java.lang.String embossCommand)
Submit to a Generic NQS batch queue. This method creates a script for submission to a batch queueing system.


runAsBatch

private void runAsBatch(Ajax aj,
                        java.lang.String userName,
                        byte[] passwd,
                        java.lang.String project,
                        java.lang.String embossCommand)

show_saved_results

public java.util.Vector show_saved_results(java.lang.String project,
                                           java.lang.String cl,
                                           java.lang.String userName,
                                           byte[] passwd)
Private Server Returns the results for a saved project.

Returns:
saved results files

save_project_file

public java.util.Vector save_project_file(java.lang.String project,
                                          java.lang.String filename,
                                          java.lang.String notes,
                                          java.lang.String userName,
                                          byte[] passwd)
Private server Save a file to a project directory on the server.

Returns:
message

delete_saved_results

public java.util.Vector delete_saved_results(java.lang.String project,
                                             java.lang.String cl,
                                             java.lang.String userName,
                                             byte[] passwd)
Private server Deletes a projects saved results.

Returns:
message

list_saved_results

public java.util.Vector list_saved_results(java.lang.String userName,
                                           byte[] passwd)
Private Server List of the saved results on the server.

Returns:
list of the saved results.

appendToLogFile

private void appendToLogFile(java.lang.String logEntry,
                             java.lang.String logFileName)
Appends a log entry to the log file


loadFilesContent

private java.util.Vector loadFilesContent(Ajax aj,
                                          java.lang.String userName,
                                          byte[] passwd,
                                          java.io.File projectDir,
                                          java.lang.String project,
                                          java.util.Vector result,
                                          java.util.Hashtable inFiles)
Reads in files from EMBOSS output


update_result_status

public java.util.Vector update_result_status(java.lang.String prog,
                                             java.lang.String opt,
                                             java.util.Vector resToQuery,
                                             java.lang.String userName,
                                             byte[] passwd)
Used to provide information on the batch/background processes.


update_result_status

public java.util.Vector update_result_status(java.lang.String prog,
                                             java.lang.String opt,
                                             java.util.Hashtable resToQuery,
                                             java.lang.String userName,
                                             byte[] passwd)

verifyUser

private boolean verifyUser(Ajax aj,
                           java.lang.String userName,
                           byte[] passwd,
                           java.util.Vector res)

returnError

private java.util.Vector returnError(Ajax aj,
                                     java.lang.String msg)
Report the stderr and stdout to error logs


clone

public final java.lang.Object clone()
                             throws java.lang.CloneNotSupportedException
Overrides:
clone in class java.lang.Object
java.lang.CloneNotSupportedException