opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00
Code Issues Packages Projects Releases Wiki Activity

Working on getting tests going again. Modified the history.xml template to

Browse Source 
only return active datasets so deletes should test correctly again.
This commit is contained in:
James Taylor
2007-03-08 18:14:50 +00:00
parent 9370ea6a48
commit ea9a819235
5 changed files with 42 additions and 63 deletions
Download Patch File Download Diff File Expand all files Collapse all files
lib/galaxy/tools/__init__.py
+6 -5
View File
@@ -8,7 +8,7 @@ from cookbook.patterns import Bunch
from galaxy import util, jobs
from elementtree import ElementTree
from parameters import *
from galaxy.tools.test import ToolTestBuilder, BadToolTest
from galaxy.tools.test import ToolTestBuilder
log = logging.getLogger( __name__ )
@@ -245,8 +245,8 @@ class Tool:
self.tests = []
for i, test_elem in enumerate( tests_elem.findall( 'test' ) ):
name = test_elem.get( 'name', 'Test-%d' % (i+1) )
test = ToolTestBuilder( self, name )
try:
test = ToolTestBuilder( self, name )
for param_elem in test_elem.findall( "param" ):
attrib = dict( param_elem.attrib )
if 'values' in attrib:
@@ -265,10 +265,11 @@ class Tool:
if file is None:
raise Exception( "Test output does not have a 'file'")
test.add_output( name, file )
self.tests.append( test )
except Exception, e:
self.tests.append( BadToolTest( self, name, e ) )
test.error = True
test.exception = e
self.tests.append( test )
def parse_page( self, input_elem, enctypes ):
param_map = odict()
for param_elem in input_elem.findall("param"):
lib/galaxy/tools/test.py
+3 -10
View File
@@ -14,18 +14,11 @@ class ToolTestBuilder( object ):
self.required_files = []
self.inputs = []
self.outputs = []
self.error = False
self.exception = None
def add_param( self, name, value, extra ):
if isinstance( self.tool.param_map[name], parameters.DataToolParameter ):
self.required_files.append( ( value, extra ) )
self.inputs.append( ( name, value, extra ) )
def add_output( self, name, file ):
self.outputs.append( ( name, file ) )
class BadToolTest( object ):
"""
Represents a tool test that failed to parse
"""
def __init__( self, tool, name, exception=None ):
self.tool = tool
self.name = name
self.exception = exception
self.outputs.append( ( name, file ) )
templates/history.xml
+1 -1
View File
@@ -1,6 +1,6 @@
<?xml version="1.0"?>
<history>
#for $data in $history.datasets
#for $data in $history.active_datasets
<data id="$data.id" hid="$data.hid" name="$data.name" state="$data.state" dbkey="$data.dbkey">
$data.blurb
</data>
test/functional/test_3A_GetData.py
+25 -25
View File
@@ -28,29 +28,29 @@ class UcscTests(TwillTestCase):
self.wait()
self.check_data('3A_GetData_ucsc_bed_range.dat', hid=1)
def test_30_Biomart_Uniprot(self):
"""3A_GetData: Connection to Biomart"""
#All this test does, is check to see if biomart is accessible through Galaxy. A dataset is never retrieved or checked.
# some button indices are hardcoded (twill limitation)
self.run_tool('biomart')
self.submit_form(form='mainform', button='get_count_button',
dataBase='default____UNIPROT PROTOTYPE 4-5 (EBI)', dataset='uniprot'
)
#self.submit_form(form='settings', button='stage_filter',
# database='UNIPROTPROTOTYPE4-5(EBI)__default', dataset='uniprot'
#)
#self.submit_form(form='settings', button=6,
# uniprot_collection_start=1, uniprot_collection_end=1,
# uniprot_component_start=1000, uniprot_component_end=2000
#)
#self.submit_form(form='settings', button=5,
# outtype='Features', outformat='tsv'
#)
#self.check_data('biomart_uniprot.dat')
# def test_30_Biomart_Uniprot(self):
# """3A_GetData: Connection to Biomart"""
# #All this test does, is check to see if biomart is accessible through Galaxy. A dataset is never retrieved or checked.
#
# # some button indices are hardcoded (twill limitation)
# self.run_tool('biomart')
#
# self.submit_form(form='mainform', button='get_count_button',
# dataBase='default____UNIPROT PROTOTYPE 4-5 (EBI)', dataset='uniprot'
# )
#
# #self.submit_form(form='settings', button='stage_filter',
# # database='UNIPROTPROTOTYPE4-5(EBI)__default', dataset='uniprot'
# #)
#
# #self.submit_form(form='settings', button=6,
# # uniprot_collection_start=1, uniprot_collection_end=1,
# # uniprot_component_start=1000, uniprot_component_end=2000
# #)
#
# #self.submit_form(form='settings', button=5,
# # outtype='Features', outformat='tsv'
# #)
#
# #self.check_data('biomart_uniprot.dat')
test/functional/test_toolbox.py
+7 -22
View File
@@ -9,6 +9,12 @@ class ToolTestCase( TwillTestCase ):
Abstract test case that runs tests based on a `galaxy.tools.test.ToolTest`
"""
def do_it( self ):
# If the test generation had an error, raise
if self.testdef.error:
if self.testdef.exception:
raise self.testdef.exception
else:
raise Exception( "Test parse failure" )
# Start with an empty history
self.clear_history()
# Upload any needed files
@@ -31,13 +37,6 @@ class ToolTestCase( TwillTestCase ):
self.check_data( file )
def shortDescription( self ):
return self.name
class BadToolTestCase( TwillTestCase ):
def do_it( self ):
if self.testdef.exception:
raise self.testdef.exception
else:
raise Exception( "Test parse failure" )
def get_testcase( testdef, name ):
"""
@@ -49,17 +48,6 @@ def get_testcase( testdef, name ):
self.do_it()
d = dict( testdef=testdef, test_tool=test_tool, name=name )
return new.classobj( n, s, d )
def get_badtestcase( testdef, name ):
"""
Dynamically generate a `BadToolTestCase` for `testdef`
"""
n = "GeneratedToolTestCase_" + testdef.tool.id.replace( ' ', '_' )
s = ( BadToolTestCase, )
def test_tool( self ):
self.do_it()
d = dict( testdef=testdef, test_tool=test_tool, name=name )
return new.classobj( n, s, d )
def setup():
"""
@@ -76,8 +64,5 @@ def setup():
if tool.tests:
for k, testdef in enumerate( tool.tests ):
name = "%s > %s > %s" % ( section.name, tool.name, testdef.name )
if isinstance( testdef, BadToolTest ):
testcase = get_badtestcase( testdef, name )
else:
testcase = get_testcase( testdef, name )
testcase = get_testcase( testdef, name )
G[ 'testcase_%d_%d_%d' % ( i, j, k ) ] = testcase