GenBatchScripts (HTMLtools javadoc documentation)

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Class GenBatchScripts

java.lang.Object
  GenBatchScripts

public class GenBatchScripts
extends java.lang.Object
extends java.lang.Object

Class GenBatchScripts to generate a set of scripts to batch convert a set of data specified by the {test-TODO-list.txt} table. It is invoked by '-genBatchScripts:{mAdb-TestsToDo.txt,batchScripts,ParamsScripts, InputTree,Summary,Analyses,JTV}'.

It generates a set of parameter .map files in the batchDir directory. These can then be run by a converter batch file called with the same base name as the {test-TODO-list.txt} file, but with a ".doit" file extension. The operation also creates a BAT script to start the converter on this data called {test-TODO-list.bat} for use with Windows. The paths created in the used for the inputTreeDir and outputTreeDir base paths and use the "Relative directory" data in the {test-TODO-list.txt} within those directories. This will process a data set to generate a set of HTML pages and converted database .txt files defined by the {test-TODO-list.txt} database. Default is no batch script generation.

 Data in the Test-ToDo-List Table
 Column entry    Description 
 "Affy .CEL file (16)" - The Affymetrix .CEL file name in the 
                        GSP-Inventory.xls Egxxxx worksheets
 "Simple GSP ID (10)" - The Simple GSP ID sample name in the 
                        GSP-Inventory.xls Egxxxx worksheets
 "GSP ID (9)" - The default GSP ID sample name in the GSP-Inventory.xls 
                        EGxxxx worksheets
 "Class A" - The samples in class A for the test
 "Class B" - The samples in class B for the test
 "t-Test or Fold-Change Test" - A/B indicates a fold change reported
                        as A samples / B samples.
 "Test Name" - The unique name of the test  formed from the Egxxx number.
                        E.g., EG5.1-test-3
 "p-Value test thresh" -  If there are at least 2 samples for both A 
                        and B classes, this is the p-value threshold 
                        to be used. It is empty if there are not at 
                        least 2 samples/class.
 "fold-change test thresh" -  The fold-change threshold to be used. 
                        It is shown as +/-nX since we do the test for 
                        genes > nX and genes < 1/nX and report them 
                        separately.
 "HTML page label" - Converter web page content page label
 "HTML page description" - Converter web page description content page label
 "HTML tissue name" - Converter tissue name used in the Web page and in 
                        possibly in other  areas.
 "Relative directory" - Relative subdirectory entry in the directory 
                        tree used for a) mAdb tests results (.txt & .zip 
                        files) go, b) converter input data and HTML and 
                        JTV output data, and c) the Jak-Stat Prospector Web site 
                        subdirectory tree.
 
 Test name usage:  File names generated using the 'Test Name'
 tests (MRR & JTV) input:  Converter output:
 Tests for samples:     
  {testName}+FC.txt         {testName}+FC.html 
                            {testName}+FC-keep.html      
  {testName}-FC.txt         {testName}-FC.html 
                            {testName}-FC-keep.html
          
 AND of above tests for ALL samples:
  {testName}+FC-ALL.txt     {testName}+FC-ALL.html 
                            {testName}+FC-ALL-keep.html    
  {testName}-FC-ALL.txt     {testName}-FC-ALL.html 
                            {testName}-FC-ALL-keep.html
         
 JTV for test samples:      (must have >= 3 samples between both classes)
  {testName}+FC-JTV.zip     {testName}+FC-JTV/ 
                            {testName}+FC-JTV.html  
  {testName}-FC-JTV.zip     {testName}-FC-JTV/ 
                            {testName}-FC-JTV.html
                            
 JTV above for and of above test with ALL Samples:
  {testName}+FC-ALL-JTV.zip {testName}+FC-ALL-JTV/ 
                            {testName}+FC-ALL-JTV.html 
  {testName}-FC-ALL-JTV.zip {testName}-FC-ALL-JTV/ 
                            {testName}-FC-ALL-JTV.html 

Generated params .map scripts to process the data
 The -genBatchScripts function will generate the following converter scripts
 to process the data: 
   params-+FC.map 
   params--FC.map  
   params-+FC-keep.map 
   params--FC-keep.map 
   params-+FC-ALL.map 
   params--FC-ALL.map 
   params-+FC-JTV.map (must have >= 3 samples between both classes)
   params--FC-JTV.map (must have >= 3 samples between both classes)
   params-+FC-ALL-JTV.map 
   params--FC-ALL-JTV.map
 
 The converter output will be a mixture of .txt, .html files, and 
 processed JTV directories and .zip files.
 The JTV .zip files have the .zip removed and an HTML file generated 
 to start up the JTV applet from the Web page.
 
 List of variables set by switch:
 -genBatchScript:{test-TODO-list.txt,batchDir,inputTreeDir, outputTreeDir}
 cvt.genTestToDoListFile
 cvt.genBatchDir
 cvt.genInputTreeDir
 cvt.genOutputTreeDir
 cvt.genBatchScriptFlag

 List of Methods

 ===================
 GenBatchScripts() - Constructor
 initGenBatch() - initialize the input files and I/O paths
 initTblHeaderIndexes() - get TestToDo Table header idx variables
 getTestToDoRowData() - get and save the row data to class variables.
 createBatchScripts() - generate the batch scripts
 generateHTMLsummaryFile() - Generate HTML summary file parameter map file.
 generateParamMapTestFiles() - Generate an HTML test file parameter map file.
 generateJTV_HTMLfile() - Generate a JTV HTML file parameter map file 
 getAllTestDataForRelDir() - get list of test data for rel-dir in tdfrd instance.
 makeUniqueRelDirList() - generate unique list of Relative Dir. entries.
 makeBatFile() - Windows .bat string to run -batchProcess generated batch
 copySupportFiles() - copy support files to the batchScriptsDir.
 getExperGroupsInTestList() get unique list of EG groups in list of tests.
 cvtSimpleGspId2EG() - map Simple GSP ID to an EGxxxx.y
 
 Internal Class

 =================== 
 Class TestDataForRelDir contains lists of rows of data computed as side 
 effect for computing active lists when calling getAllTestDataForRelDir().

This code is available at the HTMLtools project on SourceForge at http://htmltools.sourceforge.org/ under the "Common Public License Version 1.0" http://www.opensource.org/licenses/cpl1.0.php.

It was derived and refactored from the open source MAExplorer (http://maexplorer.sourceforge.org/), and Open2Dprot (http://Open2Dprot.sourceforge.net/) Table modules.

$Date: 2009/07/15 11:45:56 $ $Revision: 1.27 $
Copyright 2008, 2009 by Peter Lemkin E-Mail: lemkin@users.sourceforge.net http://lemkingroup.com/

Nested Class Summary
`(package private) class`	`GenBatchScripts.TestDataForRelDir` Class to contain lists of rows of data computed as side effect for computing active lists when calling getAllTestDataForRelDir().

Field Summary
`private java.lang.String`	`analysesPath` The directory where save the generated Analyses files when the subsequent batch job is run.
`java.lang.String`	`batchConversionDate` Date stamp for batch conversion
`java.lang.String`	`batchDoitFile` Batch .doit file name for the created batch output file.
`java.lang.String`	`batchPath` Path batch top level directory
`HTMLtools`	`cvt`
`FileTable`	`fio` Global fileTable instance
`FileTable`	`ftCTT` FileTable created from the {CellTypeTissue.map} used to map "CellTypeTissue" data to the "Introduction" data..
`FileTable`	`ftEG` FileTable created from the {experimentGroups.map} Table that 'could' be used to get other experiment group data for the summaries if we decide we want to add it.
`FileTable`	`ftGTT` The FileTable created from the {test-ToDo-list.txt} file.
`FileTable`	`ftL2S` FileTable created from the {long2ShortHdrNamesTable.map} Table that 'could' be used to map 'Short GSP ID's to 'GSP ID's if we decide to list the members of the tests.
`private int`	`idx_pValueThr` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxAffyCELfile` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxClassA` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxClassB` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxFCcalc` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxFCthr` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxGSP_ID` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxHTMLpageDescr` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxHTMLpageLabel` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxHTMLtissueName` The index variables for the Test-ToDo ftGTT Table instance variables.
`int`	`idxParamJTV` Indexes into Parameter templates lists.
`int`	`idxParamMRR` Indexes into Parameter templates lists.
`int`	`idxParamMRRkeep` Indexes into Parameter templates lists.
`int`	`idxParamMRRsaveFile` Indexes into Parameter templates lists.
`int`	`idxParamTI` Indexes into Parameter templates lists.
`private int`	`idxRelDir` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxSimpleGSP_ID` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxTestName` The index variables for the Test-ToDo ftGTT Table instance variables.
`private java.lang.String`	`inputTreePath` The directory where the subsequent batch job gets its input data files.
`private java.lang.String`	`jtvPath` The directory where save the generated JTV files when the subsequent batch job is run.
`int`	`nParamScripts` Counter for generated parameter scripts.
`int`	`nParamTemplates` Size of list of Parameter template names and file names
`int`	`nSummaryHTMLfiles` Counter for generated Summary HTML files.
`private java.lang.String`	`paramsTestDir` The directory where save the generated params .map files.
`java.lang.String[]`	`paramTemplates` List of Parameter template strings
`java.lang.String[]`	`paramTemplatesFiles` List of default Parameter template file names.
`java.lang.String[]`	`paramTemplatesNames` List of Parameter template names
`private java.lang.String`	`s_pValueThr` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sAffyCELfile` The Test-ToDo ftGTT Table instance variables
`java.lang.String`	`sBatchDoitData` Batch Data as the file name used to create the batch output file.
`private java.lang.String`	`sClassA` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sClassB` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sFCcalc` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sFCthr` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sGSP_ID` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sHTMLpageDescr` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sHTMLpageLabel` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sHTMLtissueName` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sRelDir` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sSimpleGSP_ID` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sTestName` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`summaryPath` The directory where save the generated Summary HTML files.
`private GenBatchScripts.TestDataForRelDir`	`tdfrd` Class to contain lists of rows of data computed as side effect for computing active lists when calling getAllTestDataForRelDir().
`java.lang.String[]`	`uniqueRelDir` Unique list of Relative Directory entries.

Constructor Summary
`GenBatchScripts(HTMLtools cvt)` GenBatchScripts() - Constructor

Method Summary
`private boolean`	`copySupportFiles(java.lang.String batchScriptsDir, java.lang.String[] genSupportFilesToCopy, int nGenSupportFilesToCopy)` copySupportFiles() - copy support files to the batchScriptsDir.
`boolean`	`createBatchScripts()` createBatchScripts() - generate the batch scripts.
`private boolean`	`createWriteParamMapFile(int nMaps, java.lang.String[] keyList, java.lang.String[] toStrList, java.lang.String paramTestDir, java.lang.String paramTemplate, java.lang.String paramMapNameFile)` createAndWriteParamMapFile() - create and write a parameter map file.
`private java.lang.String`	`cvtSimpleGspId2EG(java.lang.String sgi)` cvtSimpleGspId2EG() - map Simple GSP ID to an EGxxxx.y
`private boolean`	`generateHTMLsummaryFile(java.lang.String summaryFileDir, java.lang.String tissueName, java.lang.String relativeDir, int[] rowListForTest, java.lang.String sTemplate)` generateHTMLsummaryFile() - Generate an HTML summary file parameter map file.
`private boolean`	`genParamMapTestFiles(java.lang.String paramTestPath, java.lang.String analysesPath, java.lang.String tissueName, java.lang.String relativeDir)` generateParamMapTestFiles() - Generate parameter map files for tissue.
`private boolean`	`getAllTestDataForRelDir(java.lang.String relDir)` getAllTestDataForRelDir() - get list of test data for a relative directory in tdfrd class instance.
`private boolean`	`getTestToDoRowData(int r)` getTestToDoRowData() - get and save the row data to class variables.
`boolean`	`initGenBatch(java.lang.String baseDataDir, java.lang.String genTestToDoListPath, java.lang.String cellTypeTissuePath, java.lang.String long2ShortHdrNamesTablePath, java.lang.String experimentGroupsPath)` initGenBatch() - initialize the input files and I/O paths to make sure they are well formed and exist.
`private boolean`	`initTblHeaderIndexes()` initTblHeaderIndexes() - get TestToDo Table header idx variables [REFACTOR] so that the ftGTT files are not hardwired.
`private java.lang.String`	`makeBatFileStr(java.lang.String batchScriptsDir, java.lang.String doitScriptName, java.lang.String batFileName)` makeBatFile() - Windows .bat string to run -batchProcess generated batch
`private java.lang.String[]`	`makeUniqueRelDirList()` makeUniqueRelDirList() - generate unique list of Relative Directory entries.

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

cvt

public HTMLtools cvt

fio

public FileTable fio

Global fileTable instance

tdfrd

private GenBatchScripts.TestDataForRelDir tdfrd

Class to contain lists of rows of data computed as side effect for computing active lists when calling getAllTestDataForRelDir().

paramsTestDir

private java.lang.String paramsTestDir

The directory where save the generated params .map files.

inputTreePath

private java.lang.String inputTreePath

The directory where the subsequent batch job gets its input data files.

summaryPath

private java.lang.String summaryPath

The directory where save the generated Summary HTML files.

analysesPath

private java.lang.String analysesPath

The directory where save the generated Analyses files when the subsequent batch job is run.

jtvPath

private java.lang.String jtvPath

The directory where save the generated JTV files when the subsequent batch job is run.

uniqueRelDir

public java.lang.String[] uniqueRelDir

Unique list of Relative Directory entries.

ftGTT

public FileTable ftGTT

The FileTable created from the {test-ToDo-list.txt} file. Set with '-genBatchScripts:{mAdb-TestsToDo.txt,batchScripts, ParamsScripts,InputTree,Summary,Analyses,JTV}'.

ftCTT

public FileTable ftCTT

FileTable created from the {CellTypeTissue.map} used to map "CellTypeTissue" data to the "Introduction" data..

ftL2S

public FileTable ftL2S

FileTable created from the {long2ShortHdrNamesTable.map} Table that 'could' be used to map 'Short GSP ID's to 'GSP ID's if we decide to list the members of the tests. [TODO]

ftEG

public FileTable ftEG

FileTable created from the {experimentGroups.map} Table that 'could' be used to get other experiment group data for the summaries if we decide we want to add it. [TODO]

batchPath

public java.lang.String batchPath

Path batch top level directory