gov.nih.nci.caarray.services.fileparse2.parsers.test
Class ParsingTest

java.lang.Object
  extended by junit.framework.Assert
      extended by junit.framework.TestCase
          extended by gov.nih.nci.caarray.services.fileparse2.parsers.test.ParsingTest
All Implemented Interfaces:
junit.framework.Test

public class ParsingTest
extends junit.framework.TestCase

Testing caArray's EJB by logging in the application with a test account.

For the login, you must configure on the command with:

-Djava.security.auth.login.config=[jboss-home]/client/auth.conf

Author:
tranp

Constructor Summary
ParsingTest()
           
ParsingTest(java.lang.String arg0)
           
 
Method Summary
static void main(java.lang.String[] args)
           
 void setUp()
           
static junit.framework.Test suite()
           
 void testCopyLabeledExtract()
           
 void testFileUploadManager()
           
 void testGetHyb()
           
 void testParseCELDev()
           
 void testParseCHPDev()
           
 void testParseCHPStage()
           
 void testParseGAL()
           
 void testParseGPRDev()
           
 void testParseGPRDev2()
          This test tests two cases: 1.
 void testParseGPRFromUCSFSpotDev()
           
 void testParseImaGeneDev()
           
 
Methods inherited from class junit.framework.TestCase
countTestCases, createResult, getName, run, run, runBare, runTest, setName, tearDown, toString
 
Methods inherited from class junit.framework.Assert
assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertEquals, assertFalse, assertFalse, assertNotNull, assertNotNull, assertNotSame, assertNotSame, assertNull, assertNull, assertSame, assertSame, assertTrue, assertTrue, fail, fail
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

ParsingTest

public ParsingTest()

ParsingTest

public ParsingTest(java.lang.String arg0)
Parameters:
arg0 -
Method Detail

main

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

suite

public static junit.framework.Test suite()

setUp

public void setUp()
           throws java.lang.Exception
Overrides:
setUp in class junit.framework.TestCase
Throws:
java.lang.Exception

testParseCHPDev

public void testParseCHPDev()
                     throws java.lang.Exception
Throws:
java.lang.Exception

testParseGPRFromUCSFSpotDev

public void testParseGPRFromUCSFSpotDev()
                                 throws java.lang.Exception
Throws:
java.lang.Exception

testParseImaGeneDev

public void testParseImaGeneDev()
                         throws java.lang.Exception
Throws:
java.lang.Exception

testParseGPRDev2

public void testParseGPRDev2()
                      throws java.lang.Exception
This test tests two cases: 1. Mapping of quantitation names in quantitationNames.properties. 2. Invalid column name and rollback The tests use Xiaopeng's GPR file that has column name "Rgn Rē (635/532)". For case 1, that column name is converted to "Rgn R2 635/532" as specified in quantificationName.properties and the parsing succeeded For case2, remove this mapping from quantificationName.properties and an exception is thrown with message "column name Rgn R2 (635/532) not found" and upload annotations are rolled back.

Throws:
java.lang.Exception

testParseGPRDev

public void testParseGPRDev()
                     throws java.lang.Exception
Throws:
java.lang.Exception

testGetHyb

public void testGetHyb()
                throws java.lang.Exception
Throws:
java.lang.Exception

testParseCELDev

public void testParseCELDev()
                     throws java.lang.Exception
Throws:
java.lang.Exception

testParseCHPStage

public void testParseCHPStage()
                       throws java.lang.Exception
Throws:
java.lang.Exception

testParseGAL

public void testParseGAL()
                  throws java.lang.Exception
Throws:
java.lang.Exception

testFileUploadManager

public void testFileUploadManager()
                           throws java.lang.Exception
Throws:
java.lang.Exception

testCopyLabeledExtract

public void testCopyLabeledExtract()
                            throws java.lang.Exception
Throws:
java.lang.Exception