edu.mssm.crover.ims.tasks.tools
Class TIWebUpdateScheduler

java.lang.Object
  |
  +--edu.mssm.crover.ims.tasks.tools.TIWebUpdateScheduler

public class TIWebUpdateScheduler

extends java.lang.Object

Demonstrates how to schedule a pipeline of tasks for future execution, where each task depends on the successful completion of the previous one. This tool schedules a task which performs a masking operation on the FASTA sequences, performs a MegaBLAST operation on the resulting sequence file, then runs a timegablast operation on the result, then runs a tiquery operation on the timegablast output file, and finally puts the result from the tiquery operation into an ORACLE table.

Field Summary

static Task	task_gct
static Task	task_mb
static Task	task_ms
static Task	task_tim
static Task	task_tiq
static Task	task_tiweb
static TaskManager	tm

Constructor Summary

TIWebUpdateScheduler()

Method Summary

static int	getChunkSize(java.lang.String[] args)
static java.lang.String	getDatabase(java.lang.String[] args)
static java.lang.String	getOrganism(java.lang.String[] args)
static java.lang.String	getSeqfile(java.lang.String[] args)
static void	main(java.lang.String[] args)
static boolean	putIntoDatabase(java.lang.String[] args)
static java.lang.String	runFillTIWebTable(java.util.Vector taskid_tiq, java.lang.String organism)
static java.lang.String	runGetTissueList(java.lang.String organism)
static java.lang.String	runMaskSequence(AnnotatedBioSequence[] seq_ms)
static java.lang.String	runMegablast(java.lang.String taskid_ms, java.lang.String database)
static java.lang.String	runTIMegablast(java.lang.String taskid_mb)
static java.lang.String	runTIQuery(java.lang.String taskid_tim, java.lang.String[] tiq_args, java.lang.String taskid_gct)
static java.lang.String	submit(AnnotatedBioSequence[] abs, java.lang.String organism, java.lang.String taskid_gct, java.lang.String database)

Methods inherited from class java.lang.Object

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

Field Detail

tm

public static TaskManager tm

task_ms

public static Task task_ms

task_mb

public static Task task_mb

task_tim

public static Task task_tim

task_gct

public static Task task_gct

task_tiq

public static Task task_tiq

task_tiweb

public static Task task_tiweb

Constructor Detail

TIWebUpdateScheduler

public TIWebUpdateScheduler()

Method Detail

main

public static void main(java.lang.String[] args)

submit

public static java.lang.String submit(AnnotatedBioSequence[] abs,
                                      java.lang.String organism,
                                      java.lang.String taskid_gct,
                                      java.lang.String database)
                               throws java.io.FileNotFoundException,
                                      java.io.IOException,
                                      TaskNotFoundException

java.io.FileNotFoundException

java.io.IOException

TaskNotFoundException

runMaskSequence

public static java.lang.String runMaskSequence(AnnotatedBioSequence[] seq_ms)
                                        throws java.io.FileNotFoundException

java.io.FileNotFoundException

runMegablast

public static java.lang.String runMegablast(java.lang.String taskid_ms,
                                            java.lang.String database)
                                     throws TaskNotFoundException,
                                            java.io.IOException

TaskNotFoundException

java.io.IOException

runTIMegablast

public static java.lang.String runTIMegablast(java.lang.String taskid_mb)

runGetTissueList

public static java.lang.String runGetTissueList(java.lang.String organism)

runTIQuery

public static java.lang.String runTIQuery(java.lang.String taskid_tim,
                                          java.lang.String[] tiq_args,
                                          java.lang.String taskid_gct)

runFillTIWebTable

public static java.lang.String runFillTIWebTable(java.util.Vector taskid_tiq,
                                                 java.lang.String organism)

getSeqfile

public static java.lang.String getSeqfile(java.lang.String[] args)

getOrganism

public static java.lang.String getOrganism(java.lang.String[] args)

getDatabase

public static java.lang.String getDatabase(java.lang.String[] args)

getChunkSize

public static int getChunkSize(java.lang.String[] args)

putIntoDatabase

public static boolean putIntoDatabase(java.lang.String[] args)