Changes to allow all test outputs generated by twill to be saved to a folder pointed to by

an environment variable "GALAXY_TEST_SAVE" if defined before running functional tests
If the environment variable is empty, all tests procede as usual and test outputs are deleted
without saving

scripts/functional_tests.py

@@ -47,6 +47,8 @@ def main():
     
     galaxy_test_host = os.environ.get( 'GALAXY_TEST_HOST', default_galaxy_test_host )
     galaxy_test_port = os.environ.get( 'GALAXY_TEST_PORT', None )
+    galaxy_test_save = os.environ.get( 'GALAXY_TEST_SAVE', None)
+
     if 'HTTP_ACCEPT_LANGUAGE' not in os.environ:
         os.environ['HTTP_ACCEPT_LANGUAGE'] = default_galaxy_locales
     galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', default_galaxy_test_file_dir )
@@ -126,10 +128,14 @@ def main():
             
     print "Database connection:", database_connection
     
-    # What requires these?        
+    # What requires these?
+    # handy for (eg) functional tests to save outputs?        
+    if galaxy_test_save:
+    	os.environ['GALAXY_TEST_SAVE'] = galaxy_test_save
+    # pass in through script setenv
+    # will leave a copy of ALL test validate files        
     os.environ['GALAXY_TEST_HOST'] = galaxy_test_host
     os.environ['GALAXY_TEST_FILE_DIR'] = galaxy_test_file_dir
-            
     # ---- Build Application --------------------------------------------------
        
     app = None

test/base/twilltestcase.py

@@ -32,7 +32,14 @@ class TwillTestCase( unittest.TestCase ):
         self.port = os.environ.get( 'GALAXY_TEST_PORT' )
         self.url = "http://%s:%s" % ( self.host, self.port )
         self.file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR' )
+        self.keepOutdir = os.environ.get( 'GALAXY_TEST_SAVE', '' )
+        if self.keepOutdir > '':
+           try:
+               os.makedirs(self.keepOutdir)
+           except:
+               pass
         self.home()
+
         #self.set_history()
 
     # Functions associated with files
@@ -632,6 +639,10 @@ class TwillTestCase( unittest.TestCase ):
             self.visit_page( "display?hid=" + hid )
             data = self.last_page()
             file( temp_name, 'wb' ).write(data)
+            if self.keepOutdir > '':
+                ofn = os.path.join(self.keepOutdir,os.path.basename(local_name))
+                shutil.copy(temp_name,ofn)
+                log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % (self.keepOutdir,ofn))
             try:
                 # have to nest try-except in try-finally to handle 2.4
                 try:

tools/rgenetics/rgQC.xml

@@ -28,6 +28,7 @@
     </param>
     <param name='title' value='rgQCtest1' />
     <output name='html_file' file='rgtestouts/rgQC/rgQCtest1.html' ftype='html' lines_diff='300'>
+    <param name="dbkey" value="hg18" />
     <extra_files type="file" name='tinywga_All_Paged.pdf' value="rgtestouts/rgQC/tinywga_All_Paged.pdf" compare="sim_size" delta = "100000"/>
     <extra_files type="file" name='tinywga.log' value="rgtestouts/rgQC/tinywga.log" compare="diff" lines_diff="15"/>
     <extra_files type="file" name='tinywga.frq' value="rgtestouts/rgQC/tinywga.frq" compare="diff" />