mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
More fixes for twill 0.9, the annotation profiler tests do not yet pass, but all else should work now, more tests coming soon.
This commit is contained in:
Greg Von Kuster
+74
-60
@@ -1,8 +1,7 @@
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import pkg_resources
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pkg_resources.require('twill')
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pkg_resources.require( "twill==0.9" )
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import StringIO
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import os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile
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import StringIO, os, sys, random, filecmp, time, unittest, urllib, logging, difflib, zipfile
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from itertools import *
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import twill
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@@ -18,7 +17,7 @@ tc.config('use_tidy', 0)
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# Dial ClientCookie logging down (very noisy)
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logging.getLogger( "ClientCookie.cookies" ).setLevel( logging.WARNING )
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#log = logging.getLogger( __name__ )
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log = logging.getLogger( __name__ )
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class TwillTestCase( unittest.TestCase ):
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@@ -244,8 +243,14 @@ class TwillTestCase( unittest.TestCase ):
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self.assertEqual(len(elems), 1)
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self.visit_page( "delete?id=%s" % elems[0].get('id') )
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def edit_metadata( self, hid=None, form=1, **kwd ):
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"""Edits the metadata associated with a history item. There are currently 3 forms on the edit page."""
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def edit_metadata( self, hid=None, form_no=0, **kwd ):
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"""
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Edits the metadata associated with a history item."""
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# There are currently 4 forms on the edit page:
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# 0. name="edit_attributes"
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# 1. name="auto_detect"
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# 2. name="convert_data"
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# 3. name="change_datatype"
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data_list = self.get_history()
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self.assertTrue( data_list )
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if hid is None: # take last hid
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@@ -253,12 +258,16 @@ class TwillTestCase( unittest.TestCase ):
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hid = elem.get('hid')
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self.assertTrue( hid )
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self.visit_page( 'edit?hid=%d' % hid )
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if form == 1: button = "save" #Edit Attributes form
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elif form == 2: button = "detect" #Auto-detect Metadata Attributes
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elif form == 3: button = "convert_data" #Convert to new format form
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elif form == 4: button = "change" #Change data type form
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if form_no == 0:
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button = "save" #Edit Attributes form
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elif form_no == 1:
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button = "detect" #Auto-detect Metadata Attributes
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elif form_no == 2:
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button = "convert_data" #Convert to new format form
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elif form_no == 3:
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button = "change" #Change data type form
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if kwd:
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self.submit_form(form=form, button=button, **kwd)
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self.submit_form( form_no=form_no, button=button, **kwd)
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def get_dataset_ids_in_history( self ):
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"""Returns the ids of datasets in a history"""
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@@ -406,23 +415,24 @@ class TwillTestCase( unittest.TestCase ):
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def showforms( self ):
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"""Shows form, helpful for debugging new tests"""
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return tc.browser.showforms()
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return tc.showforms()
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def submit_form( self, form=1, button="runtool_btn", **kwd ):
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"""Populates and submits a form from the keyword arguments"""
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#Check for onchange attribute, submit a change if required
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for i, f in enumerate( tc.showforms() ):
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if i == form - 1:
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def submit_form( self, form_no=0, button="runtool_btn", **kwd ):
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"""Populates and submits a form from the keyword arguments."""
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for i, f in enumerate( self.showforms() ):
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if i == form_no:
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break
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# An HTMLForm contains a sequence of Controls. Supported control classes are:
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# TextControl, FileControl, ListControl, RadioControl, CheckboxControl, SelectControl,
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# SubmitControl, ImageControl
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for i, control in enumerate( f.controls ):
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try:
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# Check for refresh_on_change attribute, submit a change if required
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if 'refresh_on_change' in control.attrs.keys():
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changed = False
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for elem in kwd[control.name]:
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"""
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For DataToolParameter, control.value is the index of the DataToolParameter select list,
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but elem is the filename. The following loop gets the filename of that index.
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"""
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# For DataToolParameter, control.value is the index of the DataToolParameter select list,
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# but elem is the filename. The following loop gets the filename of that index.
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param_text = ''
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for param in tc.show().split('<select'):
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param = ('<select' + param.split('select>')[0] + 'select>').replace('selected', 'selected="yes"')
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@@ -433,52 +443,56 @@ class TwillTestCase( unittest.TestCase ):
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param_text = option.text.strip()
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break
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break
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if elem not in control.value and param_text.find(elem) == -1 :
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changed = True
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break
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if changed:
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# Clear Control and set to proper value - the command:
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# formvalue <formnum> <fieldname> <value>
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# sets the given field in the given form to the given value.
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# For read-only form widgets/controls, the click may be recorded for use by submit,
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# but the value is not changed unless the 'config' command has changed the default behavior.
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# Clear Control and set to proper value
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control.clear()
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for elem in kwd[control.name]:
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tc.formvalue(str(form), str(i+1), str(elem) )
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#Create a new submit control, allows form to refresh, instead of going to next page
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control = ClientForm.SubmitControl('SubmitControl','___refresh_grouping___',{'name':'refresh_grouping'})
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# kwd[control.name] should be a singlelist
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for elem in kwd[ control.name ]:
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tc.fv( f.name, control.name, str( elem ) )
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# Create a new submit control, allows form to refresh, instead of going to next page
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control = ClientForm.SubmitControl( 'SubmitControl', '___refresh_grouping___', {'name':'refresh_grouping'} )
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control.add_to_form( f )
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control.fixup()
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#submit for refresh
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tc.submit('___refresh_grouping___')
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#start over submit_form()
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return self.submit_form(form, button, **kwd)
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# Submit for refresh
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tc.submit( '___refresh_grouping___' )
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return self.submit_form( form_no=form_no, button=button, **kwd )
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except Exception, e:
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# Log.debug("In submit_form, caught exception: %s" %str( e ))
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log.debug( "In submit_form, continuing, but caught exception: %s" % str( e ) )
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continue
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for key, value in kwd.items():
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# needs to be able to handle multiple values per key
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if not isinstance(value, list):
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value = [ value ]
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for i, control in enumerate( f.controls ):
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if control.name == key:
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control.clear()
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if control.is_of_kind("text"):
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# set the given field in the given form to the given value.
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tc.formvalue(str(form), str(i+1), ",".join(value) )
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else:
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try:
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for elem in value:
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tc.formvalue(str(form), str(i+1), str(elem) )
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except Exception, exc:
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errmsg = "Attempting to set field '%s' to value '%s' threw exception: '%s'\n" % ( str( key ), str( elem ), str( exc ) )
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errmsg += "control: %s\n" % str( control )
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errmsg += "If the above control is a DataToolparameter whose data type class does not include a sniff() method,\n"
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errmsg += "make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.\n"
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raise AssertionError( errmsg )
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break
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tc.submit(button)
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# No refresh_on_change attribute found in current form, so process as usual
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for control_name, control_value in kwd.items():
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if not isinstance( control_value, list ):
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control_value = [ control_value ]
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try:
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control = f.find_control( name=control_name )
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except:
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# This assumes we always want the first control of the given name,
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# which may not be ideal...
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control = f.find_control( name=control_name, nr=0 )
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control.clear()
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if control.is_of_kind( "text" ):
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tc.fv( f.name, control.name, ",".join( control_value ) )
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elif control.is_of_kind( "list" ):
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try:
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if control.is_of_kind( "multilist" ):
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for elem in control_value:
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control.get( name=elem ).selected = True
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else: # control.is_of_kind( "singlelist" )
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for elem in control_value:
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tc.fv( f.name, control.name, str( elem ) )
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except Exception, exc:
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errmsg = "Attempting to set field '%s' to value '%s' in form '%s' threw exception: %s\n" % ( control_name, str( control_value ), f.name, str( exc ) )
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errmsg += "control: %s\n" % str( control )
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errmsg += "If the above control is a DataToolparameter whose data type class does not include a sniff() method,\n"
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errmsg += "make sure to include a proper 'ftype' attribute to the tag for the control within the <test> tag set.\n"
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raise AssertionError( errmsg )
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else:
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# Add conditions for other control types here when necessary.
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pass
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tc.submit( button )
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def visit_page( self, page ):
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tc.go("./%s" % page)
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@@ -493,8 +507,8 @@ class TwillTestCase( unittest.TestCase ):
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tool_id = tool_id.replace(" ", "+")
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"""Runs the tool 'tool_id' and passes it the key/values from the *kwd"""
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self.visit_url( "%s/tool_runner/index?tool_id=%s" % (self.url, tool_id) )
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tc.find('runtool_btn')
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self.submit_form(**kwd)
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tc.find( 'runtool_btn' )
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self.submit_form( **kwd )
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def wait( self, maxiter=20 ):
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"""Waits for the tools to finish"""
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@@ -2,7 +2,7 @@ import atexit, logging, os, sys, tempfile
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import pkg_resources
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pkg_resources.require( "twill==0.8.3" )
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pkg_resources.require( "twill==0.9" )
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pkg_resources.require( "Paste" )
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pkg_resources.require( "PasteDeploy" )
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pkg_resources.require( "Cheetah" )
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@@ -9,17 +9,17 @@ class TestMetadataEdit( TwillTestCase ):
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self.check_history_for_string('\? bed')
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self.check_metadata_for_string('1.bed uploaded file unspecified (\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked', hid=1)
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"""test editing attributes"""
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self.edit_metadata(hid=1, form=1, name='Testdata', info="Uploaded my file", dbkey='hg16', startCol='6')
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self.edit_metadata(hid=1, form_no=0, name='Testdata', info="Uploaded my file", dbkey='hg16', startCol='6')
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self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected', hid=1)
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"""test Auto-detecting attributes"""
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self.edit_metadata(hid=1, form=2)
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self.edit_metadata(hid=1, form_no=1)
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self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected', hid=1)
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"""test converting formats"""
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self.edit_metadata(hid=1, form=3, target_type='gff')
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self.edit_metadata(hid=1, form_no=2, target_type='gff')
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self.check_history_for_string('hg16 Testdata Convert BED to GFF')
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self.check_metadata_for_string('"gff" selected="yes"', hid=1)
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"""test changing data type"""
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self.edit_metadata(hid=1, form=4, datatype='gff3')
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self.edit_metadata(hid=1, form_no=3, datatype='gff3')
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self.check_history_for_string('hg16 Testdata Convert BED to GFF format: gff3')
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self.delete_history_item( 1 )
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def test_9999_clean_up( self ):
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@@ -30,7 +30,7 @@
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<test>
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<param name="input1" value="3.bed" dbkey="hg18"/>
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<param name="keep_empty" value=""/>
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<param name="summary" value="-S"/>
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<param name="summary" value="Summary"/>
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<param name="table_names" value="acembly,affyGnf1h,affyHuEx1,knownAlt,knownGene,mrna,multiz17way,multiz28way,refGene,snp126"/>
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<output name="out_file1" file="annotation_profiler_2.out" />
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</test>
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@@ -33,8 +33,8 @@
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<param name="input2" value="2.bed"/>
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<param name="field1" value="2"/>
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<param name="field2" value="2"/>
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<param name="unmatched" value="-u"/>
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<param name="partial" value="-p"/>
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<param name="unmatched" value="Yes"/>
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<param name="partial" value="Yes"/>
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<output name="out_file1" file="joiner_out2.bed"/>
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</test>
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</tests>
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@@ -33,7 +33,7 @@
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<param name="input1" value="1.bed" />
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<param name="input2" value="2.bed" />
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<param name="min" value="10" />
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<param name="returntype" value="-p" />
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<param name="returntype" value="Overlapping pieces of Intervals" />
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<output name="output" file="gops_intersect_p_out.bed" />
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</test>
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<test>
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@@ -43,7 +43,7 @@
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<param name="input1" value="1.bed" />
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<param name="input2" value="2.bed" />
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<param name="min" value="10" />
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<param name="returntype" value="-p" />
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<param name="returntype" value="Non-overlapping pieces of intervals" />
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<output name="output" file="gops-subtract-p.dat" />
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</test>
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</tests>
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