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

Finish flake8 of test/ .

Browse Source
This commit is contained in:
Nicola Soranzo
2015-08-26 20:08:09 +01:00
parent b0f2eaec03
commit 2fccd0c11f
12 changed files with 226 additions and 228 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.ci/flake8_blacklist.txt
-3
View File
@@ -19,7 +19,4 @@ scripts/scramble/
scripts/tool_shed/
scripts/tools/
scripts/transfer.py
test/base/
test/casperjs/
test/install_and_test_tool_shed_repositories/
tools/
.ci/flake8_wrapper.sh
+1 -1
View File
@@ -5,4 +5,4 @@ set -e
flake8 --exclude `paste -sd, .ci/flake8_blacklist.txt` .
# Look for obviously broken stuff lots more places.
flake8 --select=E901,E902,F821,F822,F823,F831 --exclude lib/galaxy/util/pastescript/serve.py,lib/pkg_resources.py lib/ test/{api,unit}
flake8 --select=E901,E902,F821,F822,F823,F831 --exclude lib/pkg_resources.py contrib/ lib/
test/base/asserts/__init__.py
+4 -3
View File
@@ -1,6 +1,7 @@
import inspect
import logging
import sys
log = logging.getLogger( __name__ )
assertion_module_names = ['text', 'tabular', 'xml']
@@ -14,7 +15,7 @@ for assertion_module_name in assertion_module_names:
full_assertion_module_name = 'base.asserts.' + assertion_module_name
log.debug(full_assertion_module_name)
try:
#Dynamically import module
# Dynamically import module
__import__(full_assertion_module_name)
assertion_module = sys.modules[full_assertion_module_name]
assertion_modules.append(assertion_module)
@@ -40,7 +41,7 @@ def verify_assertion(data, assertion_description):
if assert_function is None:
errmsg = "Unable to find test function associated with XML tag '%s'. Check your tool file syntax." % tag
raise AssertionError(errmsg)
assert_function_args = inspect.getargspec(assert_function).args
args = {}
for attribute, value in assertion_description["attributes"].iteritems():
@@ -72,6 +73,6 @@ def verify_assertion(data, assertion_description):
if "children" in assert_function_args:
args["children"] = assertion_description["children"]
# TODO: Verify all needed function arguments are specified.
assert_function(**args)
test/base/interactor.py
+16 -15
View File
@@ -1,17 +1,18 @@
import os
import re
from json import dumps
from logging import getLogger
from StringIO import StringIO
from galaxy.tools.parser.interface import TestCollectionDef
from galaxy import eggs
eggs.require( "requests" )
from requests import get, post
from galaxy import util
from galaxy.tools.parser.interface import TestCollectionDef
from galaxy.util.bunch import Bunch
from galaxy.util.odict import odict
from galaxy.util.bunch import Bunch
from requests import get
from requests import post
from json import dumps
from logging import getLogger
log = getLogger( __name__ )
# Off by default because it can pound the database pretty heavily
@@ -57,7 +58,7 @@ class GalaxyInteractorApi( object ):
name = output_testdef.name
self.wait_for_jobs( history_id, jobs, maxseconds )
hid = self.__output_id( output_data )
## TODO: Twill version verifys dataset is 'ok' in here.
# TODO: Twill version verifys dataset is 'ok' in here.
self.verify_output_dataset( history_id=history_id, hda_id=hid, outfile=outfile, attributes=attributes, shed_tool_id=shed_tool_id )
primary_datasets = attributes.get( 'primary_datasets', {} )
@@ -155,10 +156,10 @@ class GalaxyInteractorApi( object ):
file_name = self.twill_test_case.get_filename( composite_file.get( 'value' ), shed_tool_id=shed_tool_id )
files["files_%s|file_data" % i] = open( file_name, 'rb' )
tool_input.update({
#"files_%d|NAME" % i: name,
# "files_%d|NAME" % i: name,
"files_%d|type" % i: "upload_dataset",
## TODO:
#"files_%d|space_to_tab" % i: composite_file.get( 'space_to_tab', False )
# TODO:
# "files_%d|space_to_tab" % i: composite_file.get( 'space_to_tab', False )
})
name = test_data[ 'name' ]
else:
@@ -180,7 +181,7 @@ class GalaxyInteractorApi( object ):
dataset = submit_response["outputs"][0]
except KeyError:
raise Exception(submit_response)
#raise Exception(str(dataset))
# raise Exception(str(dataset))
hid = dataset['id']
self.uploads[ os.path.basename(fname) ] = self.uploads[ fname ] = self.uploads[ name ] = {"src": "hda", "id": hid}
return self.__wait_for_history( history_id )
@@ -203,7 +204,7 @@ class GalaxyInteractorApi( object ):
new_values.append( value )
inputs_tree[ key ] = new_values
# # HACK: Flatten single-value lists. Required when using expand_grouping
# HACK: Flatten single-value lists. Required when using expand_grouping
for key, value in inputs_tree.iteritems():
if isinstance(value, list) and len(value) == 1:
inputs_tree[key] = value[0]
@@ -255,9 +256,9 @@ class GalaxyInteractorApi( object ):
return output_collections_dict
def __dictify_outputs( self, datasets_object ):
## Convert outputs list to a dictionary that can be accessed by
## output_name so can be more flexiable about ordering of outputs
## but also allows fallback to legacy access as list mode.
# Convert outputs list to a dictionary that can be accessed by
# output_name so can be more flexiable about ordering of outputs
# but also allows fallback to legacy access as list mode.
outputs_dict = odict()
index = 0
for output in datasets_object[ 'outputs' ]:
test/base/twilltestcase.py
+45 -48
View File
@@ -1,4 +1,3 @@
import StringIO
import difflib
import filecmp
import logging
@@ -6,6 +5,7 @@ import os
import pprint
import re
import shutil
import StringIO
import subprocess
import tarfile
import tempfile
@@ -13,9 +13,10 @@ import time
import unittest
import urllib
import zipfile
from json import loads
from urlparse import urlparse
from xml.etree import ElementTree
from galaxy import eggs
eggs.require( "MarkupSafe" )
from markupsafe import escape
@@ -24,14 +25,13 @@ import twill
import twill.commands as tc
from twill.other_packages._mechanize_dist import ClientForm
from base.asserts import verify_assertions
from base.test_data import TestDataResolver
from galaxy.util import asbool
from galaxy.util.json import loads
from galaxy.web import security
from galaxy.web.framework.helpers import iff
#Force twill to log to a buffer -- FIXME: Should this go to stdout and be captured by nose?
from base.asserts import verify_assertions
from base.test_data import TestDataResolver
# Force twill to log to a buffer -- FIXME: Should this go to stdout and be captured by nose?
buffer = StringIO.StringIO()
twill.set_output( buffer )
tc.config( 'use_tidy', 0 )
@@ -69,8 +69,8 @@ class TwillTestCase( unittest.TestCase ):
def act_on_multiple_datasets( self, cntrller, library_id, do_action, ldda_ids='', strings_displayed=[] ):
# Can't use the ~/library_admin/libraries form as twill barfs on it so we'll simulate the form submission
# by going directly to the form action
self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=%s&library_id=%s&ldda_ids=%s&do_action=%s' \
% ( self.url, cntrller, library_id, ldda_ids, do_action ) )
self.visit_url( '%s/library_common/act_on_multiple_datasets?cntrller=%s&library_id=%s&ldda_ids=%s&do_action=%s' %
( self.url, cntrller, library_id, ldda_ids, do_action ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
@@ -139,7 +139,7 @@ class TwillTestCase( unittest.TestCase ):
self.check_page_for_string( check_str )
def add_tag( self, item_id, item_class, context, new_tag ):
self.visit_url( "%s/tag/add_tag_async?item_id=%s&item_class=%s&context=%s&new_tag=%s" % \
self.visit_url( "%s/tag/add_tag_async?item_id=%s&item_class=%s&context=%s&new_tag=%s" %
( self.url, item_id, item_class, context, new_tag ) )
def add_template( self, cntrller, item_type, form_type, form_id, form_name,
@@ -156,7 +156,7 @@ class TwillTestCase( unittest.TestCase ):
elif item_type == 'ldda':
params[ 'ldda_id' ] = ldda_id
self.visit_url( url, params )
self.check_page_for_string ( "Select a template for the" )
self.check_page_for_string( "Select a template for the" )
self.refresh_form( "form_id", form_id )
# For some unknown reason, twill barfs if the form number ( 1 ) is used in the following
# rather than the form anme ( select_template ), so we have to use the form name.
@@ -308,6 +308,7 @@ class TwillTestCase( unittest.TestCase ):
parent_folder = parent_folder.parent
path += ldda.name
return path
def mkdir( file ):
dir = os.path.join( tmpd, os.path.dirname( file ) )
if not os.path.exists( dir ):
@@ -361,7 +362,7 @@ class TwillTestCase( unittest.TestCase ):
(3) The contents of that key match the provided value.
If use_string_contains=True, this will perform a substring match, otherwise an exact match.
"""
#TODO: multi key, value
# TODO: multi key, value
hda = dict()
for history_item in self.get_history_from_api():
if history_item[ 'id' ] == hda_id:
@@ -458,7 +459,7 @@ class TwillTestCase( unittest.TestCase ):
def check_request_grid( self, cntrller, state, deleted=False, strings_displayed=[] ):
params = { 'f-state': state, 'f-deleted': deleted, 'sort': 'create_time' }
self.visit_url( '/%s/browse_requests' % cntrller )
self.visit_url( '/%s/browse_requests' % cntrller, params )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
@@ -603,7 +604,7 @@ class TwillTestCase( unittest.TestCase ):
url = "/admin/groups"
params = dict( operation='create', create_group_button='Save', name=name )
if in_user_ids:
params [ 'in_users' ] = ','.join( in_user_ids )
params[ 'in_users' ] = ','.join( in_user_ids )
if in_role_ids:
params[ 'in_roles' ] = ','.join( in_role_ids )
if create_role_for_group:
@@ -743,7 +744,6 @@ class TwillTestCase( unittest.TestCase ):
tc.fv( "1", "name", name )
tc.fv( "1", "desc", desc )
for index, field_value_tuple in enumerate( field_value_tuples ):
field_index = index + 1
field_name, field_value, refresh_on_change = field_value_tuple
if refresh_on_change:
# Only the AddressField type has a refresh on change setup on selecting an option
@@ -754,7 +754,7 @@ class TwillTestCase( unittest.TestCase ):
# handle new address
self.check_page_for_string( 'Short address description' )
for address_field, value in address_value.items():
tc.fv( "1", field_name+'_'+address_field, value )
tc.fv( "1", field_name + '_' + address_field, value )
else:
# existing address
tc.fv( "1", field_name, address_value )
@@ -783,7 +783,7 @@ class TwillTestCase( unittest.TestCase ):
url_params[ 'create_group_for_role' ] = [ 'yes', 'yes' ]
doseq = True
else:
doseq=False
doseq = False
self.visit_url( url, params=url_params, doseq=doseq )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
@@ -869,11 +869,11 @@ class TwillTestCase( unittest.TestCase ):
# page from an external URL. By "barfs", I mean that twill somehow loses hod on the
# cntrller param. We'll just simulate the form submission by building the URL manually.
# Here's the old, better approach...
#self.visit_url( "%s/library_common/browse_library?cntrller=%s&id=%s" % ( self.url, cntrller, library_id ) )
#for ldda_id in ldda_ids:
# self.visit_url( "%s/library_common/browse_library?cntrller=%s&id=%s" % ( self.url, cntrller, library_id ) )
# for ldda_id in ldda_ids:
# tc.fv( "1", "ldda_ids", ldda_id )
#tc.fv( "1", "do_action", format )
#tc.submit( "action_on_datasets_button" )
# tc.fv( "1", "do_action", format )
# tc.submit( "action_on_datasets_button" )
# Here's the new approach...
params = dict( cntrller=cntrller, library_id=library_id, do_action=format, ldda_ids=ldda_ids )
url = "/library_common/act_on_multiple_datasets"
@@ -893,7 +893,6 @@ class TwillTestCase( unittest.TestCase ):
if new_desc:
tc.fv( "1", "desc", new_desc )
for index, ( field_name, field_value ) in enumerate( new_fields ):
field_name_index = index + 1
tc.fv( "1", field_name, field_value )
tc.submit( "edit_basic_request_info_button" )
for check_str in strings_displayed_after_submit:
@@ -1071,7 +1070,7 @@ class TwillTestCase( unittest.TestCase ):
attributes = {}
if attributes.get( 'sort', False ):
history_data.sort()
##Why even bother with the check loop below, why not just use the diff output? This seems wasteful.
# Why even bother with the check loop below, why not just use the diff output? This seems wasteful.
if len( local_file ) == len( history_data ):
for i in range( len( history_data ) ):
if local_file[i].rstrip( '\r\n' ) != history_data[i].rstrip( '\r\n' ):
@@ -1091,11 +1090,11 @@ class TwillTestCase( unittest.TestCase ):
diff_slice = diff[0:40]
else:
diff_slice = diff[:25] + ["********\n", "*SNIP *\n", "********\n"] + diff[-25:]
#FIXME: This pdf stuff is rather special cased and has not been updated to consider lines_diff
#due to unknown desired behavior when used in conjunction with a non-zero lines_diff
#PDF forgiveness can probably be handled better by not special casing by __extension__ here
#and instead using lines_diff or a regular expression matching
#or by creating and using a specialized pdf comparison function
# FIXME: This pdf stuff is rather special cased and has not been updated to consider lines_diff
# due to unknown desired behavior when used in conjunction with a non-zero lines_diff
# PDF forgiveness can probably be handled better by not special casing by __extension__ here
# and instead using lines_diff or a regular expression matching
# or by creating and using a specialized pdf comparison function
if file1.endswith( '.pdf' ) or file2.endswith( '.pdf' ):
# PDF files contain creation dates, modification dates, ids and descriptions that change with each
# new file, so we need to handle these differences. As long as the rest of the PDF file does
@@ -1145,7 +1144,7 @@ class TwillTestCase( unittest.TestCase ):
for i in range( len( history_data ) ):
if not re.match( local_file[i].rstrip( '\r\n' ), history_data[i].rstrip( '\r\n' ) ):
line_diff_count += 1
diffs.append( 'Regular Expression: %s\nData file : %s' % ( local_file[i].rstrip( '\r\n' ), history_data[i].rstrip( '\r\n' ) ) )
diffs.append( 'Regular Expression: %s\nData file : %s' % ( local_file[i].rstrip( '\r\n' ), history_data[i].rstrip( '\r\n' ) ) )
if line_diff_count > lines_diff:
raise AssertionError( "Regular expression did not match data file (allowed variants=%i):\n%s" % ( lines_diff, "".join( diffs ) ) )
@@ -1160,13 +1159,13 @@ class TwillTestCase( unittest.TestCase ):
history_data = ''.join( history_data )
else:
history_data = open( file2, 'U' ).read()
#lines_diff not applicable to multiline matching
# lines_diff not applicable to multiline matching
assert re.match( local_file, history_data, re.MULTILINE ), "Multiline Regular expression did not match data file"
def files_contains( self, file1, file2, attributes=None ):
"""Checks the contents of file2 for substrings found in file1, on a per-line basis"""
local_file = open( file1, 'U' ).readlines() # regex file
#TODO: allow forcing ordering of contains
# TODO: allow forcing ordering of contains
history_data = open( file2, 'U' ).read()
lines_diff = int( attributes.get( 'lines_diff', 0 ) )
line_diff_count = 0
@@ -1188,7 +1187,7 @@ class TwillTestCase( unittest.TestCase ):
template_refresh_field_contents='', template_fields=[], strings_displayed=[], strings_not_displayed=[],
strings_displayed_after_submit=[], strings_not_displayed_after_submit=[] ):
"""Add information to a library using an existing template with 2 elements"""
self.visit_url( "%s/library_common/folder_info?cntrller=%s&id=%s&library_id=%s" % \
self.visit_url( "%s/library_common/folder_info?cntrller=%s&id=%s&library_id=%s" %
( self.url, cntrller, folder_id, library_id ) )
if name and new_name and description:
tc.fv( '1', "name", new_name )
@@ -1300,7 +1299,7 @@ class TwillTestCase( unittest.TestCase ):
return jsondata[ 'state' ] in [ 'queued', 'running' ]
def get_tags( self, item_id, item_class ):
self.visit_url( "%s/tag/get_tagging_elt_async?item_id=%s&item_class=%s" % \
self.visit_url( "%s/tag/get_tagging_elt_async?item_id=%s&item_class=%s" %
( self.url, item_id, item_class ) )
def history_as_xml_tree( self, show_deleted=False ):
@@ -1353,8 +1352,8 @@ class TwillTestCase( unittest.TestCase ):
def import_datasets_to_histories( self, cntrller, library_id, ldda_ids='', new_history_name='Unnamed history', strings_displayed=[] ):
# Can't use the ~/library_admin/libraries form as twill barfs on it so we'll simulate the form submission
# by going directly to the form action
self.visit_url( '%s/library_common/import_datasets_to_histories?cntrller=%s&library_id=%s&ldda_ids=%s&new_history_name=%s&import_datasets_to_histories_button=Import+library+datasets' \
% ( self.url, cntrller, library_id, ldda_ids, new_history_name ) )
self.visit_url( '%s/library_common/import_datasets_to_histories?cntrller=%s&library_id=%s&ldda_ids=%s&new_history_name=%s&import_datasets_to_histories_button=Import+library+datasets' %
( self.url, cntrller, library_id, ldda_ids, new_history_name ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
@@ -1417,7 +1416,7 @@ class TwillTestCase( unittest.TestCase ):
def ldda_info( self, cntrller, library_id, folder_id, ldda_id, strings_displayed=[], strings_not_displayed=[] ):
"""View library_dataset_dataset_association information"""
self.visit_url( "%s/library_common/ldda_info?cntrller=%s&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_common/ldda_info?cntrller=%s&library_id=%s&folder_id=%s&id=%s" %
( self.url, cntrller, library_id, folder_id, ldda_id ) )
for check_str in strings_displayed:
self.check_page_for_string( check_str )
@@ -1431,7 +1430,7 @@ class TwillTestCase( unittest.TestCase ):
def ldda_edit_info( self, cntrller, library_id, folder_id, ldda_id, ldda_name, new_ldda_name='', template_refresh_field_name='1_field_name',
template_refresh_field_contents='', template_fields=[], strings_displayed=[], strings_not_displayed=[] ):
"""Edit library_dataset_dataset_association information, optionally template element information"""
self.visit_url( "%s/library_common/ldda_edit_info?cntrller=%s&library_id=%s&folder_id=%s&id=%s" % \
self.visit_url( "%s/library_common/ldda_edit_info?cntrller=%s&library_id=%s&folder_id=%s&id=%s" %
( self.url, cntrller, library_id, folder_id, ldda_id ) )
check_str = 'Edit attributes of %s' % ldda_name
self.check_page_for_string( check_str )
@@ -1554,13 +1553,13 @@ class TwillTestCase( unittest.TestCase ):
# If inheritable is True, the item is currently inheritable.
if item_type == 'library':
url = "%s/library_common/manage_template_inheritance?cntrller=%s&item_type=%s&library_id=%s" % \
( self.url, cntrller, item_type, library_id )
( self.url, cntrller, item_type, library_id )
elif item_type == 'folder':
url = "%s/library_common/manage_template_inheritance?cntrller=%s&item_type=%s&library_id=%s&folder_id=%s" % \
( self.url, cntrller, item_type, library_id, folder_id )
( self.url, cntrller, item_type, library_id, folder_id )
elif item_type == 'ldda':
url = "%s/library_common/manage_template_inheritance?cntrller=%s&item_type=%s&library_id=%s&folder_id=%s&ldda_id=%s" % \
( self.url, cntrller, item_type, library_id, folder_id, ldda_id )
( self.url, cntrller, item_type, library_id, folder_id, ldda_id )
self.visit_url( url )
if inheritable:
self.check_page_for_string = 'will no longer be inherited to contained folders and datasets'
@@ -1868,12 +1867,12 @@ class TwillTestCase( unittest.TestCase ):
formcontrols = self.get_form_controls( f )
hc_prefix = '<HiddenControl('
for i, control in enumerate( f.controls ):
if not hc_prefix in str( control ):
if hc_prefix not in str( control ):
try:
#check if a repeat element needs to be added
# check if a repeat element needs to be added
if control.name is not None:
if control.name not in kwd and control.name.endswith( '_add' ):
#control name doesn't exist, could be repeat
# control name doesn't exist, could be repeat
repeat_startswith = control.name[0:-4]
if repeat_startswith and not [ c_name for c_name in controls.keys() if c_name.startswith( repeat_startswith ) ] and [ c_name for c_name in kwd.keys() if c_name.startswith( repeat_startswith ) ]:
tc.browser.clicked( f, control )
@@ -2148,7 +2147,7 @@ class TwillTestCase( unittest.TestCase ):
"""Pasted data in the upload utility"""
self.visit_url( "/tool_runner/index?tool_id=upload1" )
try:
self.refresh_form( "file_type", ftype ) #Refresh, to support composite files
self.refresh_form( "file_type", ftype ) # Refresh, to support composite files
tc.fv( "tool_form", "dbkey", dbkey )
tc.fv( "tool_form", "url_paste", url_paste )
tc.submit( "runtool_btn" )
@@ -2344,8 +2343,6 @@ class TwillTestCase( unittest.TestCase ):
message = template % (actual_md5, expected_md5)
assert False, message
def view_external_service( self, external_service_id, strings_displayed=[] ):
self.visit_url( '%s/external_service/view_external_service?id=%s' % ( self.url, external_service_id ) )
for check_str in strings_displayed:
@@ -2354,9 +2351,9 @@ class TwillTestCase( unittest.TestCase ):
def view_form( self, id, form_type='', form_name='', form_desc='', form_layout_name='', field_dicts=[] ):
'''View form details'''
self.visit_url( "%s/forms/view_latest_form_definition?id=%s" % ( self.url, id ) )
#self.check_page_for_string( form_type )
# self.check_page_for_string( form_type )
self.check_page_for_string( form_name )
#self.check_page_for_string( form_desc )
# self.check_page_for_string( form_desc )
self.check_page_for_string( form_layout_name )
for i, field_dict in enumerate( field_dicts ):
self.check_page_for_string( field_dict[ 'label' ] )
test/casperjs/casperjs_runner.py
+39 -37
View File
@@ -16,7 +16,7 @@ Note: that you can enable (lots of) debugging info using cli options:
(see casperjs.org for more information)
Note: This works with CasperJS 1.1 and PhantomJS 1.9.2 and these libraries seem to break backward
compatbility a lot.
compatibility a lot.
Note: You can pass in extra data using --data='<some JSON object>'
and it will be available in your script as spaceghost.fixtureData.
@@ -33,8 +33,20 @@ Note: You can pass in extra data using --data='<some JSON object>'
casperjs test api-configuration-tests.js --url="http://localhost:8080" \
--admin='{"email": "foo@example.com", "password": "123456" }' \
"""
# -------------------------------------------------------------------- can't do 2.5
import errno
import json
import logging
import os
import re
import subprocess
import sys
import unittest
from server_env import TestEnvironment
# -------------------------------------------------------------------- can't do 2.5
( major, minor, micro, releaselevel, serial ) = sys.version_info
if minor < 6:
msg = 'casperjs requires python 2.6 or newer. Using: %s' % ( sys.version )
@@ -46,16 +58,7 @@ if minor < 6:
raise AssertionError( msg )
# --------------------------------------------------------------------
import os
import subprocess
import json
import errno
import re
import unittest
from server_env import TestEnvironment
import logging
logging.basicConfig( stream=sys.stderr, name=__name__ )
log = logging.getLogger( __name__ )
@@ -90,7 +93,7 @@ class CasperJSTestCase( unittest.TestCase ):
"""
# debugging flag - set to true to have casperjs tests output with --verbose=true and --logLevel=debug
#debug = True
# debug = True
debug = False
# bit of a hack - this is the beginning of the last string when capserjs --verbose=true --logLevel=debug
# use this to get subprocess to stop waiting for output
@@ -113,7 +116,7 @@ class CasperJSTestCase( unittest.TestCase ):
stdout=subprocess.PIPE, stderr=subprocess.PIPE )
# output from the browser (stderr only) immediately
while process.poll() == None:
while process.poll() is None:
stderr_msg = process.stderr.readline()
stderr_msg = self.strip_escape_codes( stderr_msg.strip() )
if stderr_msg:
@@ -125,17 +128,17 @@ class CasperJSTestCase( unittest.TestCase ):
# stdout is assumed to have the json test data/results
( stdout_output, stderr_output ) = process.communicate()
#log.debug( '%s stdout output:\n%s', rel_script_path, stdout_output )
#log.debug( '%s stderr output:\n%s', rel_script_path, stderr_output )
# log.debug( '%s stdout output:\n%s', rel_script_path, stdout_output )
# log.debug( '%s stderr output:\n%s', rel_script_path, stderr_output )
log.debug( 'process.returncode: %d', process.returncode )
# 1.1 has an annoying info bar that happens before it gets to our stuff, so...
stdout_output = '\n'.join( stdout_output.split( '\n' )[1:] )
#log.debug( 'stdout_output:\n' + stdout_output )
# log.debug( 'stdout_output:\n' + stdout_output )
if process.returncode == 1:
#TODO: this is a fail on first effect
# TODO: this is a fail on first effect
raise self.browser_error_to_exception( rel_script_path, stdout_output )
# couldn't find the headless browser,
@@ -170,13 +173,12 @@ class CasperJSTestCase( unittest.TestCase ):
command_line_list.append( '--return-json' )
# check flag to output (very) verbose debugging messages from casperjs and tests
#NOTE: this can be set in the class or by using the debug_these_tests flag in server_env
if( ( self.debug )
or ( rel_script_path in self.env.debug_these_tests ) ):
# NOTE: this can be set in the class or by using the debug_these_tests flag in server_env
if self.debug or ( rel_script_path in self.env.debug_these_tests ):
command_line_list.extend([ '--verbose=true', '--logLevel=debug' ])
#TODO: add capture, html output flags
# TODO: add capture, html output flags
#TODO: allow casperjs cli options ('--includes='), ?in args, kwargs?
# TODO: allow casperjs cli options ('--includes='), ?in args, kwargs?
command_line_list.extend( args )
# send extra data - encode kwargs as json to pass to casper for decoding
@@ -259,7 +261,7 @@ class CasperJSTestCase( unittest.TestCase ):
def run( self, result=None ):
# wrap this in order to save ref to result
#TODO: gotta be a better way
# TODO: gotta be a better way
self.result = result
unittest.TestCase.run( self, result=result )
@@ -268,7 +270,7 @@ class CasperJSTestCase( unittest.TestCase ):
class CasperJsonToUnittestResultsConverter( object ):
"""Convert casper failures, success to individual unittest.TestResults
"""
#TODO: So far I can add result instances - but each has the id, shortDescription
# TODO: So far I can add result instances - but each has the id, shortDescription
# of the TestCase.testMethod that called it. Can't find out how to change these.
def convert( self, json_results, test ):
@@ -286,11 +288,11 @@ class CasperJsonToUnittestResultsConverter( object ):
def add_json_failures_to_results( self, failures, test ):
"""Converts JSON test failures.
"""
#precondition: result should be an attr of test (a TestResult)
#TODO: no way to change test.desc, name in output?
# precondition: result should be an attr of test (a TestResult)
# TODO: no way to change test.desc, name in output?
for failure in failures:
#TODO: doesn't change shortDescription
#if 'standard' in failure:
# TODO: doesn't change shortDescription
# if 'standard' in failure:
# self.__doc__ = failure[ 'standard' ]
test.result.addFailure( test, self.casper_failure_to_unittest_failure( failure ) )
test.result.testsRun += 1
@@ -301,29 +303,29 @@ class CasperJsonToUnittestResultsConverter( object ):
Used to add failures to a casperjs TestCase.
"""
#TODO: this is all too elaborate
# TODO: this is all too elaborate
fail_type = casper_failure[ 'type' ]
values = json.dumps( casper_failure[ 'values' ] )
desc = casper_failure[ 'standard' ]
if 'messgae' in casper_failure:
desc = casper_failure[ 'message' ]
failure_msg = "(%s) %s: %s" % ( fail_type, desc, values )
#TODO: tb is empty ([]) - can we get file info from casper, covert to py trace?
# TODO: tb is empty ([]) - can we get file info from casper, covert to py trace?
return ( failure_class, failure_msg, [] )
def add_json_successes_to_results( self, successes, test ):
"""Converts JSON test successes.
"""
for success in successes:
## attempt to re-write test result description - doesn't work
#if 'standard' in success:
# attempt to re-write test result description - doesn't work
# if 'standard' in success:
# self.__doc__ = success[ 'standard' ]
test.result.addSuccess( test )
test.result.testsRun += 1
# ==================================================================== MODULE FIXTURE
#NOTE: nose will run these automatically
# NOTE: nose will run these automatically
def setup_module():
log.debug( '\n--------------- setting up module' )
@@ -349,15 +351,15 @@ class Test_01_User( CasperJSTestCase ):
register new user, logout, attempt bad registrations.
"""
# all keywords will be compiled into a single JSON obj and passed to the server
#self.run_js_script( 'registration-tests.js',
# self.run_js_script( 'registration-tests.js',
# testUser=test_user )
# # this causes a time out in history-panel-tests: why?
# # also: I can't seem to bump the timeout to an error (using a handler) - causes script to hang
# # removing for the sake of bbot
self.run_js_script( 'registration-tests.js' )
#TODO:?? could theoretically do db cleanup, checks here with SQLALX
#TODO: have run_js_script return other persistent fixture data (uploaded files, etc.)
# TODO:?? could theoretically do db cleanup, checks here with SQLALX
# TODO: have run_js_script return other persistent fixture data (uploaded files, etc.)
def test_20_login( self ):
"""User log in tests.
@@ -462,6 +464,6 @@ if __name__ == '__main__':
from server_env import log as server_env_log
server_env_log.setLevel( logging.DEBUG )
setup_module()
#TODO: server_env config doesn't work with unittest's lame main fn
# TODO: server_env config doesn't work with unittest's lame main fn
unittest.main()
# teardown_module() isn't called when unittest.main is used
test/casperjs/server_env.py
+19 -16
View File
@@ -3,10 +3,13 @@ Classes to handle fetching the proper environment and urls for the selenium
tests to run against.
"""
import os
import logging
import os
from json import loads
log = logging.getLogger( __name__ )
class TestEnvironment( object ):
"""Provides basic information on the server being tested.
@@ -15,18 +18,18 @@ class TestEnvironment( object ):
"""
_instance = None
ENV_PROTOCOL = None
ENV_HOST = 'GALAXY_TEST_HOST'
ENV_PORT = 'GALAXY_TEST_PORT'
ENV_HISTORY_ID = 'GALAXY_TEST_HISTORY_ID'
ENV_FILE_DIR = 'GALAXY_TEST_FILE_DIR'
ENV_PROTOCOL = None
ENV_HOST = 'GALAXY_TEST_HOST'
ENV_PORT = 'GALAXY_TEST_PORT'
ENV_HISTORY_ID = 'GALAXY_TEST_HISTORY_ID'
ENV_FILE_DIR = 'GALAXY_TEST_FILE_DIR'
ENV_TOOL_SHED_TEST_FILE = 'GALAXY_TOOL_SHED_TEST_FILE'
ENV_SAVED_FILES_DIR = 'GALAXY_TEST_SAVE' # AKA: twilltestcase.keepOutdir
ENV_SAVED_FILES_DIR = 'GALAXY_TEST_SAVE' # AKA: twilltestcase.keepOutdir
ENV_DEBUG_THESE_TESTS = 'GALAXY_DEBUG_THESE_TESTS'
DEFAULT_PROTOCOL = 'http'
DEFAULT_HOST = 'localhost'
DEFAULT_PORT = '8080'
DEFAULT_HOST = 'localhost'
DEFAULT_PORT = '8080'
@classmethod
def instance( cls, config=None ):
@@ -43,13 +46,13 @@ class TestEnvironment( object ):
self.config = env_config_dict or {}
self.protocol = self._get_setting_from_config_or_env(
'protocol', self.ENV_PROTOCOL, self.DEFAULT_PROTOCOL ) #TODO: required=True )
'protocol', self.ENV_PROTOCOL, self.DEFAULT_PROTOCOL ) # TODO: required=True )
self.host = self._get_setting_from_config_or_env(
'host', self.ENV_HOST, self.DEFAULT_HOST ) #TODO: required=True )
'host', self.ENV_HOST, self.DEFAULT_HOST ) # TODO: required=True )
self.port = self._get_setting_from_config_or_env(
'port', self.ENV_PORT, self.DEFAULT_PORT ) #TODO: required=True )
'port', self.ENV_PORT, self.DEFAULT_PORT ) # TODO: required=True )
#TODO: move these setters/init'rs into a parser dict
# TODO: move these setters/init'rs into a parser dict
self.history_id = self._get_setting_from_config_or_env(
'history_id', self.ENV_HISTORY_ID )
self.file_dir = self._get_setting_from_config_or_env(
@@ -73,7 +76,7 @@ class TestEnvironment( object ):
def as_dict( self, attributes=None ):
if not attributes:
#TODO:?? raise to class scope?
# TODO:?? raise to class scope?
attributes = [ 'protocol', 'host', 'port', 'history_id', 'file_dir',
'tool_shed_test_file', 'shed_tools_dict', 'saved_output_dir', 'debug_these_tests' ]
this_dict = {}
@@ -134,7 +137,7 @@ class TestEnvironment( object ):
def url( self ):
"""Builds and returns the url of the test server.
"""
url = '%s://%s' %( self.protocol, self.host )
url = '%s://%s' % ( self.protocol, self.host )
if self.port and self.port != 80:
url += ':%s' %( str( self.port ) )
url += ':%s' % ( str( self.port ) )
return url
test/install_and_test_tool_shed_repositories/base/twilltestcase.py
+11 -15
View File
@@ -1,21 +1,19 @@
import logging
import os
import re
import test_db_util
import time
import galaxy.model as model
from galaxy import eggs
eggs.require( 'twill' )
import twill.commands as tc
import galaxy.model.tool_shed_install as install_model
import galaxy.util
from galaxy.web import security
from base.twilltestcase import TwillTestCase
from base.tool_shed_util import repository_installation_timeout
from galaxy import eggs
eggs.require( 'twill' )
import twill.commands as tc
from . import test_db_util
log = logging.getLogger( __name__ )
@@ -65,8 +63,6 @@ class InstallTestRepository( TwillTestCase ):
def install_repository( self, repository_info_dict, install_tool_dependencies=True, install_repository_dependencies=True,
strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[],
post_submit_strings_displayed=[], new_tool_panel_section_label=None, **kwd ):
name = repository_info_dict[ 'name' ]
owner = repository_info_dict[ 'owner' ]
changeset_revision = repository_info_dict[ 'changeset_revision' ]
encoded_repository_id = repository_info_dict[ 'repository_id' ]
tool_shed_url = repository_info_dict[ 'tool_shed_url' ]
@@ -120,7 +116,7 @@ class InstallTestRepository( TwillTestCase ):
else:
if field_name in kwd:
log.debug( 'No field %s in form %s, discarding from return value.' % ( str( control ), str( form_id ) ) )
del( kwd[ field_name ] )
del kwd[ field_name ]
return kwd
def wait_for_repository_installation( self, repository_ids ):
@@ -131,20 +127,20 @@ class InstallTestRepository( TwillTestCase ):
if repository_ids:
for repository_id in repository_ids:
galaxy_repository = test_db_util.get_repository( self.security.decode_id( repository_id ) )
log.debug( 'Repository %s with ID %s has initial state %s.' % \
log.debug( 'Repository %s with ID %s has initial state %s.' %
( str( galaxy_repository.name ), str( repository_id ), str( galaxy_repository.status ) ) )
timeout_counter = 0
while galaxy_repository.status not in final_states:
test_db_util.refresh( galaxy_repository )
log.debug( 'Repository %s with ID %s is in state %s, continuing to wait.' % \
log.debug( 'Repository %s with ID %s is in state %s, continuing to wait.' %
( str( galaxy_repository.name ), str( repository_id ), str( galaxy_repository.status ) ) )
timeout_counter = timeout_counter + 1
if timeout_counter % 10 == 0:
log.debug( 'Waited %d seconds for repository %s.' % ( timeout_counter, str( galaxy_repository.name ) ) )
# This timeout currently defaults to 10 minutes.
if timeout_counter > repository_installation_timeout:
raise AssertionError( 'Repository installation timed out after %d seconds, repository state is %s.' % \
( timeout_counter, repository.status ) )
raise AssertionError( 'Repository installation timed out after %d seconds, repository state is %s.' %
( timeout_counter, galaxy_repository.status ) )
break
time.sleep( 1 )
# Set all metadata on each installed repository.
@@ -162,7 +158,7 @@ class InstallTestRepository( TwillTestCase ):
log.debug( 'Waited %d seconds for repository %s.' % ( timeout_counter, str( galaxy_repository.name ) ) )
# This timeout currently defaults to 10 minutes.
if timeout_counter > repository_installation_timeout:
raise AssertionError( 'Repository installation timed out after %d seconds, repository state is %s.' % \
raise AssertionError( 'Repository installation timed out after %d seconds, repository state is %s.' %
( timeout_counter, galaxy_repository.status ) )
break
time.sleep( 1 )
test/install_and_test_tool_shed_repositories/base/util.py
+60 -51
View File
@@ -1,5 +1,12 @@
import json
import logging
import os
import platform
import string
import subprocess
import sys
import time
from datetime import datetime, timedelta
cwd = os.getcwd()
sys.path.append( cwd )
@@ -12,45 +19,22 @@ sys.path = new_path
from galaxy import eggs
eggs.require( 'mercurial' )
eggs.require( "nose" )
import nose
from mercurial import hg, ui
from nose.plugins import Plugin
import json
import logging
import galaxy.webapps.tool_shed.model.mapping
import install_and_test_tool_shed_repositories.base.test_db_util as test_db_util
import install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories
import nose
import platform
import string
import subprocess
import time
import tool_shed.repository_types.util as rt_util
import tool_shed.util.shed_util_common as suc
import urllib
from datetime import datetime
from datetime import timedelta
from common import get_api_url
from common import get_latest_downloadable_changeset_revision_via_api
from common import get_repository_dict
from common import json_from_url
from common import submit
from common import update
from galaxy.util import asbool
from galaxy.util import listify
from galaxy.util import unicodify
import galaxy.webapps.tool_shed.model.mapping
from nose.plugins import Plugin
from tool_shed.util import common_util
from tool_shed.util import hg_util
from tool_shed.util import tool_dependency_util
from common import get_repository_dict, json_from_url, submit, update
from galaxy.util import asbool, listify, unicodify
from tool_shed.util import common_util, hg_util
from tool_shed.util.xml_util import parse_xml
from mercurial import hg
from mercurial import ui
log = logging.getLogger(__name__)
# Set up a job_conf.xml that explicitly limits jobs to 10 minutes.
@@ -307,6 +291,7 @@ def get_missing_repository_dependencies( repository, all_missing_repository_depe
all_missing_repository_dependencies ) )
return all_missing_repository_dependencies
def get_missing_tool_dependencies( repository, all_missing_tool_dependencies=None ):
"""
Return the entire list of missing tool dependencies for the received repository. The entire
@@ -326,6 +311,7 @@ def get_missing_tool_dependencies( repository, all_missing_tool_dependencies=Non
all_missing_tool_dependencies ) )
return all_missing_tool_dependencies
def get_repositories_to_install( tool_shed_url, test_framework ):
"""
Get a list of repository info dicts to install. This method expects a json list of dicts with the following structure:
@@ -374,7 +360,7 @@ def get_repositories_to_install( tool_shed_url, test_framework ):
if changeset_revision != hg_util.INITIAL_CHANGELOG_HASH:
# If testing repositories of type tool_dependency_definition, filter accordingly.
if test_framework == TOOL_DEPENDENCY_DEFINITIONS and \
repository_dict.get( 'type', None ) != rt_util.TOOL_DEPENDENCY_DEFINITION:
repository_dict.get( 'type', None ) != rt_util.TOOL_DEPENDENCY_DEFINITION:
continue
# Merge the dictionary returned from /api/repository_revisions with the detailed repository_dict and
# append it to the list of repository_dicts to install and test.
@@ -415,6 +401,7 @@ def get_repositories_to_install( tool_shed_url, test_framework ):
( changeset_revision, name, owner, repository_id, repository_metadata_id )
return repository_dicts, error_message
def get_repository( name, owner, changeset_revision ):
"""Return a repository record associated with the received name, owner, changeset_revision if one exists."""
repository = None
@@ -425,6 +412,7 @@ def get_repository( name, owner, changeset_revision ):
pass
return repository
def get_repository_current_revision( repo_path ):
"""This method uses the python mercurial API to get the current working directory's mercurial changeset hash."""
# Initialize a mercurial repo object from the provided path.
@@ -439,6 +427,7 @@ def get_repository_current_revision( repo_path ):
hg_id = '%d:%s' % ( ctx_rev, str( changectx ) )
return hg_id
def get_repository_dependencies_dicts( tool_shed_url, encoded_repository_metadata_id ):
"""
Return the list of dictionaries that define all repository dependencies of the repository_metadata
@@ -452,6 +441,7 @@ def get_repository_dependencies_dicts( tool_shed_url, encoded_repository_metadat
return None, error_message
return repository_dependencies_dicts, error_message
def get_repository_tuple_from_elem( elem ):
attributes = elem.attrib
name = attributes.get( 'name', None )
@@ -459,6 +449,7 @@ def get_repository_tuple_from_elem( elem ):
changeset_revision = attributes.get( 'changeset_revision', None )
return ( name, owner, changeset_revision )
def get_static_settings():
"""
Return a dictionary of the settings necessary for a Galaxy application to be wrapped in the static
@@ -466,16 +457,17 @@ def get_static_settings():
"""
cwd = os.getcwd()
static_dir = os.path.join( cwd, 'static' )
#TODO: these should be copied from galaxy.ini
#TODO: static_enabled needed here?
return dict( static_enabled = True,
static_cache_time = 360,
static_dir = static_dir,
static_images_dir = os.path.join( static_dir, 'images', '' ),
static_favicon_dir = os.path.join( static_dir, 'favicon.ico' ),
static_scripts_dir = os.path.join( static_dir, 'scripts', '' ),
static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ),
static_robots_txt = os.path.join( static_dir, 'robots.txt' ) )
# TODO: these should be copied from galaxy.ini
# TODO: static_enabled needed here?
return dict( static_enabled=True,
static_cache_time=360,
static_dir=static_dir,
static_images_dir=os.path.join( static_dir, 'images', '' ),
static_favicon_dir=os.path.join( static_dir, 'favicon.ico' ),
static_scripts_dir=os.path.join( static_dir, 'scripts', '' ),
static_style_dir=os.path.join( static_dir, 'june_2007_style', 'blue' ),
static_robots_txt=os.path.join( static_dir, 'robots.txt' ) )
def get_time_last_tested( tool_shed_url, encoded_repository_metadata_id ):
"""
@@ -497,6 +489,7 @@ def get_time_last_tested( tool_shed_url, encoded_repository_metadata_id ):
error_message = 'The url %s returned the invalid repository_metadata_dict %s' % ( str( api_url ), str( repository_metadata_dict ) )
return None, error_message
def get_tool_test_results_dict( tool_test_results_dicts ):
if tool_test_results_dicts:
# Inspect the tool_test_results_dict for the last test run to make sure it contains only a test_environment
@@ -509,7 +502,7 @@ def get_tool_test_results_dict( tool_test_results_dicts ):
# since it will be re-inserted later.
tool_test_results_dict = tool_test_results_dicts.pop( 0 )
elif len( tool_test_results_dict ) == 2 and \
'test_environment' in tool_test_results_dict and 'missing_test_components' in tool_test_results_dict:
'test_environment' in tool_test_results_dict and 'missing_test_components' in tool_test_results_dict:
# We can re-use tool_test_results_dict if its only entries are "test_environment" and "missing_test_components".
# In this case, some tools are missing tests components while others are not.
tool_test_results_dict = tool_test_results_dicts.pop( 0 )
@@ -517,10 +510,11 @@ def get_tool_test_results_dict( tool_test_results_dicts ):
# The latest tool_test_results_dict has been populated with the results of a test run, so it cannot be used.
tool_test_results_dict = {}
else:
# Create a new dictionary for this test test run,
# Create a new dictionary for this test test run,
tool_test_results_dict = {}
return tool_test_results_dict
def get_tool_test_results_dicts( tool_shed_url, encoded_repository_metadata_id ):
"""
Return the list of dictionaries contained in the Tool Shed's repository_metadata.tool_test_results
@@ -541,6 +535,7 @@ def get_tool_test_results_dicts( tool_shed_url, encoded_repository_metadata_id )
error_message = 'The url %s returned the invalid repository_metadata_dict %s' % ( str( api_url ), str( repository_metadata_dict ) )
return None, error_message
def get_webapp_global_conf():
"""Return the global_conf dictionary sent as the first argument to app_factory."""
global_conf = {}
@@ -548,6 +543,7 @@ def get_webapp_global_conf():
global_conf.update( get_static_settings() )
return global_conf
def initialize_install_and_test_statistics_dict():
# Initialize a dictionary for the summary that will be printed to stdout.
install_and_test_statistics_dict = {}
@@ -560,6 +556,7 @@ def initialize_install_and_test_statistics_dict():
install_and_test_statistics_dict[ 'at_least_one_test_failed' ] = []
return install_and_test_statistics_dict
def initialize_tool_tests_results_dict( app, tool_test_results_dict ):
test_environment_dict = tool_test_results_dict.get( 'test_environment', {} )
if len( test_environment_dict ) == 0:
@@ -593,6 +590,7 @@ def initialize_tool_tests_results_dict( app, tool_test_results_dict ):
tool_dependencies=[] )
return tool_test_results_dict
def install_repository( app, repository_dict ):
"""Install a repository defined by the received repository_dict from the tool shed into Galaxy."""
name = str( repository_dict.get( 'name', None ) )
@@ -617,6 +615,7 @@ def install_repository( app, repository_dict ):
log.error( error_message )
return repository, error_message
def is_excluded( exclude_list_dicts, name, owner, changeset_revision, encoded_repository_metadata_id ):
"""
Return True if the repository defined by the received name, owner, changeset_revision should
@@ -645,7 +644,7 @@ def is_excluded( exclude_list_dicts, name, owner, changeset_revision, encoded_re
rd_owner = repository_dependency_dict.get( 'owner', '' )
rd_changeset_revision = repository_dependency_dict.get( 'changeset_revision', '' )
if ( rd_name, rd_owner, rd_changeset_revision ) in exclude_repositories or \
( rd_name, rd_owner, None ) in exclude_repositories:
( rd_name, rd_owner, None ) in exclude_repositories:
print 'Revision %s of repository %s owned by %s is excluded from testing because ' % \
( changeset_revision, name, owner, reason )
print 'it requires revision %s of repository %s owned by %s (which is excluded from testing).' % \
@@ -656,6 +655,7 @@ def is_excluded( exclude_list_dicts, name, owner, changeset_revision, encoded_re
break
return False, None
def is_latest_downloadable_revision( url, repository_dict ):
"""
Return True if the changeset_revision defined in the received repository_dict is the latest
@@ -675,6 +675,7 @@ def is_latest_downloadable_revision( url, repository_dict ):
is_latest_downloadable = changeset_revision == str( latest_revision )
return is_latest_downloadable, error_message
def parse_exclude_list( xml_filename ):
"""Return a list of repositories to exclude from testing."""
# This method expects an xml document that looks something like this:
@@ -731,6 +732,7 @@ def parse_exclude_list( xml_filename ):
print 'The exclude file %s defines no repositories to be excluded from testing.' % xml_filename
return exclude_list
def populate_dependency_install_containers( app, repository, repository_identifier_tup, install_and_test_statistics_dict,
tool_test_results_dict ):
"""
@@ -839,6 +841,7 @@ def populate_dependency_install_containers( app, repository, repository_identifi
tool_test_results_dict[ 'successful_installations' ][ 'tool_dependencies' ].append( tool_dependency_info_dict )
return params, install_and_test_statistics_dict, tool_test_results_dict
def populate_install_containers_for_repository_dependencies( app, repository, repository_metadata_id, install_and_test_statistics_dict,
can_update_tool_shed ):
"""
@@ -905,7 +908,7 @@ def populate_install_containers_for_repository_dependencies( app, repository, re
# This is counter intuitive because the following check is on strings like this: '2014-01-21T19:46:06.953741',
# so if "time_last_tested > twenty_hours_ago" is True, then it implies that the time_last_tested column
# was actually updated less than 20 hours ago, and should not be updated again because we're likely processing
# another dependent repository, many of which can have the same repository dependency.
# another dependent repository, many of which can have the same repository dependency.
try:
# Be very conservative here. Our default behavior will be to assume containers have not been populated
# during the current test run.
@@ -930,8 +933,8 @@ def populate_install_containers_for_repository_dependencies( app, repository, re
if len( tool_test_results_dict ) <= 1:
tool_test_results_dict = tool_test_results_dicts.pop( 0 )
elif len( tool_test_results_dict ) == 2 and \
'test_environment' in tool_test_results_dict and \
'missing_test_components' in tool_test_results_dict:
'test_environment' in tool_test_results_dict and \
'missing_test_components' in tool_test_results_dict:
tool_test_results_dict = tool_test_results_dicts.pop( 0 )
else:
tool_test_results_dict = {}
@@ -986,6 +989,7 @@ def populate_install_containers_for_repository_dependencies( app, repository, re
print 'tool_shed: %s name: %s owner: %s changeset_revision: %s' % \
( cleaned_tool_shed_url, name, owner, changeset_revision )
def populate_shed_conf_file( shed_conf_file, tool_path, xml_elems=None ):
"""Populate the file defined by shed_conf_file with xml_elems or initialize it with a template string."""
if xml_elems is None:
@@ -993,6 +997,7 @@ def populate_shed_conf_file( shed_conf_file, tool_path, xml_elems=None ):
xml_elems = tool_conf_template_parser.safe_substitute( shed_tool_path=tool_path )
file( shed_conf_file, 'w' ).write( xml_elems )
def populate_galaxy_shed_tools_dict_file( galaxy_shed_tools_dict_file, shed_tools_dict=None ):
"""
Populate the file defined by galaxy_shed_tools_dict_file with the contents of the shed_tools_dict
@@ -1002,12 +1007,13 @@ def populate_galaxy_shed_tools_dict_file( galaxy_shed_tools_dict_file, shed_tool
shed_tools_dict = {}
file( galaxy_shed_tools_dict_file, 'w' ).write( json.dumps( shed_tools_dict ) )
def print_install_and_test_results( install_stage_type, install_and_test_statistics_dict, error_message ):
"Print statistics for the current test run."
if error_message:
print "Error returned from install_and_test_repositories:"
print error_message
elif isinstance ( install_and_test_statistics_dict, dict ):
elif isinstance( install_and_test_statistics_dict, dict ):
all_tests_passed = install_and_test_statistics_dict.get( 'all_tests_passed', None )
at_least_one_test_failed = install_and_test_statistics_dict.get( 'at_least_one_test_failed', None )
repositories_with_installation_error = \
@@ -1049,6 +1055,7 @@ def print_install_and_test_results( install_stage_type, install_and_test_statist
display_repositories_by_owner( at_least_one_test_failed )
print "####################################################################################"
def remove_protocol_from_tool_shed_url( base_url ):
"""Eliminate the protocol from the received base_url and return the possibly altered url."""
# The tool_shed value stored in the tool_shed_repository record does not include the protocol, but does
@@ -1057,7 +1064,7 @@ def remove_protocol_from_tool_shed_url( base_url ):
if base_url.find( '://' ) > -1:
try:
protocol, base = base_url.split( '://' )
except ValueError, e:
except ValueError:
# The received base_url must be an invalid url.
log.debug( "Returning unchanged invalid base_url from remove_protocol_from_tool_shed_url: %s" % str( base_url ) )
return base_url
@@ -1066,8 +1073,9 @@ def remove_protocol_from_tool_shed_url( base_url ):
log.debug( "Returning base_url from remove_protocol_from_tool_shed_url: %s" % str( base_url ) )
return base_url
def run_tests( test_config ):
## TODO: replace whole method with...
# TODO: replace whole method with...
# from base import nose_util
# result = nose_util.run( test_config, plugins=[ new ReportResults() ] )
# return result, test_config.plugins._plugins
@@ -1086,6 +1094,7 @@ def run_tests( test_config ):
result = test_runner.run( tests )
return result, test_config.plugins._plugins
def save_test_results_for_changeset_revision( url, tool_test_results_dicts, tool_test_results_dict, repository_dict,
params, can_update_tool_shed ):
"""
@@ -1145,5 +1154,5 @@ def save_test_results_for_changeset_revision( url, tool_test_results_dicts, tool
( changeset_revision, name, owner, str( response_from_update ) )
print '\n=============================================================\n'
except Exception, e:
log.exception( 'Error updating tool_test_results for repository_metadata id %s:\n%s' % \
log.exception( 'Error updating tool_test_results for repository_metadata id %s:\n%s' %
( str( metadata_revision_id ), str( e ) ) )
test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py
+4 -2
View File
@@ -1,5 +1,6 @@
import logging
import new
import install_and_test_tool_shed_repositories.base.test_db_util as test_db_util
from install_and_test_tool_shed_repositories.base.twilltestcase import InstallTestRepository
@@ -16,11 +17,12 @@ class InstallTestRepositories( InstallTestRepository ):
self.login( email=admin_email, username=admin_username )
admin_user = test_db_util.get_user( admin_email )
assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email
admin_user_private_role = test_db_util.get_private_role( admin_user )
# Install the repository through the web interface using twill. The install_repository() method may
test_db_util.get_private_role( admin_user )
# Install the repository through the web interface using twill. The install_repository() method may
# actually install more than this singe repository because repository dependencies can be installed.
self.install_repository( repository_dict )
def generate_install_method( repository_dict=None ):
"""Generate abstract test cases for the defined list of repositories."""
test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
+15 -19
View File
@@ -4,8 +4,18 @@ This script cannot be run directly, because it needs to have test/functional/tes
order to run functional tests on repository tools after installation. The install_and_test_tool_shed_repositories.sh
will execute this script with the appropriate parameters.
"""
import httplib
import logging
import os
import random
import re
import shutil
import socket
import sys
import tempfile
import threading
import time
# Assume we are run from the galaxy root directory, add lib to the python path
cwd = os.getcwd()
sys.path.append( cwd )
@@ -23,32 +33,17 @@ eggs.require( 'mercurial' )
# This should not be required, but it is under certain conditions thanks to this bug:
# http://code.google.com/p/python-nose/issues/detail?id=284
eggs.require( "pysqlite" )
import httplib
import install_and_test_tool_shed_repositories.base.test_db_util as test_db_util
import install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories
import logging
import nose
import random
import re
import shutil
import socket
import tempfile
import time
import threading
from paste import httpserver
import install_and_test_tool_shed_repositories.base.util as install_and_test_base_util
from base.tool_shed_util import parse_tool_panel_config
from functional import database_contexts
from functional_tests import generate_config_file
from galaxy.app import UniverseApplication
from galaxy.util.json import loads
from galaxy.util import asbool
from galaxy.web import buildapp
from functional_tests import generate_config_file
from paste import httpserver
from functional import database_contexts
log = logging.getLogger( 'install_and_test_repositories_with_tools' )
@@ -75,6 +70,7 @@ else:
can_update_tool_shed = True
test_framework = install_and_test_base_util.REPOSITORIES_WITH_TOOLS
test_toolbox = None
def get_failed_test_dicts( test_result, from_tool_test=True ):
@@ -407,7 +403,7 @@ def main():
else:
tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir )
galaxy_db_path = os.path.join( tempdir, 'database' )
# Checks if galaxy_db_path exists, if not create it.
# Checks if galaxy_db_path exists, if not create it.
if not os.path.exists(galaxy_db_path):
os.makedirs(galaxy_db_path)
# Configure the paths Galaxy needs to install and test tools.
test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
+12 -18
View File
@@ -4,8 +4,17 @@ This script cannot be run directly, because it needs to have test/functional/tes
order to run functional tests on repository tools after installation. The install_and_test_tool_shed_repositories.sh
will execute this script with the appropriate parameters.
"""
import httplib
import logging
import os
import random
import shutil
import socket
import sys
import tempfile
import threading
import time
# Assume we are run from the galaxy root directory, add lib to the python path
cwd = os.getcwd()
sys.path.append( cwd )
@@ -17,34 +26,19 @@ new_path.extend( sys.path )
sys.path = new_path
from galaxy import eggs
eggs.require( "nose" )
eggs.require( "Paste" )
eggs.require( 'mercurial' )
# This should not be required, but it is under certain conditions thanks to this bug:
# http://code.google.com/p/python-nose/issues/detail?id=284
eggs.require( "pysqlite" )
import httplib
import install_and_test_tool_shed_repositories.base.test_db_util as test_db_util
import install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories
import logging
import nose
import random
import shutil
import socket
import tempfile
import time
import threading
from paste import httpserver
import install_and_test_tool_shed_repositories.base.util as install_and_test_base_util
from functional import database_contexts
from functional_tests import generate_config_file
from galaxy.app import UniverseApplication
from galaxy.util import asbool
from galaxy.web import buildapp
from functional_tests import generate_config_file
from paste import httpserver
from functional import database_contexts
log = logging.getLogger( 'install_and_test_tool_dependency_definitions' )