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More tool shed functional test enhancements.

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This commit is contained in:
Dave Bouvier
2012-12-14 16:20:22 -05:00
parent 8e2a484a0b
commit de45c8e7ad
13 changed files with 139 additions and 13 deletions
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lib/galaxy/visualization/genomes.py
+15 -8
View File
@@ -1,9 +1,11 @@
import os, re, sys, glob
import os, re, sys, glob, logging
from bx.seq.twobit import TwoBitFile
from galaxy.util.json import from_json_string
from galaxy import model
from galaxy.util.bunch import Bunch
log = logging.getLogger( __name__ )
# FIXME: copied from tracks.py
# Message strings returned to browser
messages = Bunch(
@@ -166,13 +168,18 @@ class Genomes( object ):
self.genomes[ key ] = Genome( key, len_file=f )
# Add genome data (twobit files) to genomes.
for line in open( os.path.join( app.config.tool_data_path, "twobit.loc" ) ):
if line.startswith("#"): continue
val = line.split()
if len( val ) == 2:
key, path = val
if key in self.genomes:
self.genomes[ key ].twobit_file = path
# FIXME: If a galaxy instance does not have ~/tool-data/twobit.loc file, the following error is thrown:
# IOError: [Errno 2] No such file or directory: '~/tool-data/twobit.loc'
try:
for line in open( os.path.join( app.config.tool_data_path, "twobit.loc" ) ):
if line.startswith("#"): continue
val = line.split()
if len( val ) == 2:
key, path = val
if key in self.genomes:
self.genomes[ key ].twobit_file = path
except IOError, e:
log.exception( str( e ) )
def get_build( self, dbkey ):
""" Returns build for the given key. """
test/tool_shed/base/twilltestcase.py
+50 -1
View File
@@ -1,6 +1,7 @@
import galaxy.webapps.community.util.hgweb_config
import galaxy.model as galaxy_model
import common, string, os, re, test_db_util
import common, string, os, re, test_db_util, simplejson
import galaxy.util as util
from base.twilltestcase import tc, from_json_string, TwillTestCase, security, urllib
from galaxy.tool_shed.encoding_util import tool_shed_encode
@@ -23,8 +24,10 @@ class ShedTwillTestCase( TwillTestCase ):
self.galaxy_host = os.environ.get( 'GALAXY_TEST_HOST' )
self.galaxy_port = os.environ.get( 'GALAXY_TEST_PORT' )
self.galaxy_url = "http://%s:%s" % ( self.galaxy_host, self.galaxy_port )
self.shed_tool_data_table_conf = os.environ.get( 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF' )
self.file_dir = os.environ.get( 'TOOL_SHED_TEST_FILE_DIR', None )
self.tool_shed_test_file = None
self.tool_data_path = os.environ.get( 'GALAXY_TEST_TOOL_DATA_PATH' )
self.shed_tools_dict = {}
self.home()
def browse_category( self, category, strings_displayed=[], strings_not_displayed=[] ):
@@ -439,9 +442,14 @@ class ShedTwillTestCase( TwillTestCase ):
repo = hg.repository( ui.ui(), self.get_repo_path( repository ) )
tip_ctx = repo.changectx( repo.changelog.tip() )
return tip_ctx.rev() < 0
def reset_installed_repository_metadata( self, repository ):
url = '/admin_toolshed/reset_repository_metadata?id=%s' % self.security.encode_id( repository.id )
self.visit_galaxy_url( url )
self.check_for_strings( [ 'Metadata has been reset' ] )
def reset_repository_metadata( self, repository ):
url = '/repository/reset_all_metadata?id=%s' % self.security.encode_id( repository.id )
self.visit_url( url )
self.check_for_strings( [ 'All repository metadata has been reset.' ] )
def revoke_write_access( self, repository, username ):
url = '/repository/manage_repository?user_access_button=Remove&id=%s&remove_auth=%s' % \
( self.security.encode_id( repository.id ), username )
@@ -466,6 +474,10 @@ class ShedTwillTestCase( TwillTestCase ):
def tip_has_metadata( self, repository ):
tip = self.get_repository_tip( repository )
return test_db_util.get_repository_metadata_by_repository_id_changeset_revision( repository.id, tip )
def update_installed_repository( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ):
url = '/admin_toolshed/check_for_updates?id=%s' % self.security.encode_id( installed_repository.id )
self.visit_galaxy_url( url )
self.check_for_strings( strings_displayed, strings_not_displayed )
def upload_file( self,
repository,
filename,
@@ -482,6 +494,27 @@ class ShedTwillTestCase( TwillTestCase ):
tc.formfile( "1", "file_data", self.get_filename( filename, filepath ) )
tc.submit( "upload_button" )
self.check_for_strings( strings_displayed, strings_not_displayed )
def verify_installed_repository_metadata_unchanged( self, name, owner ):
installed_repository = test_db_util.get_installed_repository_by_name_owner( name, owner )
differs = False
metadata = installed_repository.metadata
self.reset_installed_repository_metadata( installed_repository )
new_metadata = installed_repository.metadata
# This test assumes that the different metadata components will always appear in the same order. If this is ever not
# the case, this test must be updated.
for metadata_key in [ 'datatypes', 'tools', 'tool_dependencies', 'repository_dependencies', 'workflows' ]:
if ( metadata_key in metadata and metadata_key not in new_metadata ) or \
( metadata_key not in metadata and metadata_key in new_metadata ):
differs = True
break
elif metadata_key not in metadata and metadata_key not in new_metadata:
continue
else:
if metadata[ metadata_key ] != new_metadata[ metadata_key ]:
differs = True
break
if differs:
raise AssertionError( 'Metadata for installed repository %s differs after metadata reset.' % name )
def verify_installed_repository_on_browse_page( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ):
url = '/admin_toolshed/browse_repositories'
self.visit_galaxy_url( url )
@@ -491,6 +524,17 @@ class ShedTwillTestCase( TwillTestCase ):
installed_repository.tool_shed,
installed_repository.installed_changeset_revision ] )
self.check_for_strings( strings_displayed, strings_not_displayed )
def verify_installed_repository_data_table_entries( self, data_tables=[] ):
data_table = util.parse_xml( self.shed_tool_data_table_conf )
found = False
for table_elem in data_table.findall( 'table' ):
for data_table in data_tables:
if 'name' in table_elem.attrib and table_elem.attrib[ 'name' ] == data_table:
file_elem = table_elem.find( 'file' )
assert os.path.exists( file_elem.attrib[ 'path' ] ), 'Tool data table file %s not found.' % file_elem.path
found = True
break
assert found, 'No entry for %s in %s.' % ( data_table, self.shed_tool_data_table_conf )
def verify_tool_metadata_for_installed_repository( self, installed_repository, strings_displayed=[], strings_not_displayed=[] ):
repository_id = self.security.encode_id( installed_repository.id )
for tool in installed_repository.metadata[ 'tools' ]:
@@ -499,6 +543,11 @@ class ShedTwillTestCase( TwillTestCase ):
url = '/admin_toolshed/view_tool_metadata?repository_id=%s&tool_id=%s' % ( repository_id, urllib.quote_plus( tool[ 'id' ] ) )
self.visit_galaxy_url( url )
self.check_for_strings( strings, strings_not_displayed )
def verify_unchanged_repository_metadata( self, repository ):
self.check_repository_changelog( repository )
html = self.last_page()
self.reset_repository_metadata( repository )
self.check_repository_changelog( repository, strings_displayed=[ html ] )
def visit_galaxy_url( self, url ):
url = '%s%s' % ( self.galaxy_url, url )
self.visit_url( url )
test/tool_shed/functional/test_0000_basic_repository_features.py
+4
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@@ -155,3 +155,7 @@ class TestBasicRepositoryFeatures( ShedTwillTestCase ):
tip_changeset = self.get_repository_tip( repository )
search_fields = dict( tool_id='Filter1', tool_name='filter', tool_version='2.2.0' )
self.search_for_valid_tools( search_fields=search_fields, strings_displayed=[ tip_changeset ], strings_not_displayed=[] )
def test_0085_verify_repository_metadata( self ):
'''Verify that resetting the metadata does not change it.'''
repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
self.verify_unchanged_repository_metadata( repository )
test/tool_shed/functional/test_0020_basic_repository_dependencies.py
+6
View File
@@ -68,3 +68,9 @@ class TestBasicRepositoryDependencies( ShedTwillTestCase ):
changeset_revision = self.get_repository_tip( datatypes_repository )
strings_displayed = [ datatypes_repository_name, common.test_user_1_name, changeset_revision, 'Repository dependencies' ]
self.display_manage_repository_page( repository, strings_displayed=strings_displayed )
def test_0040_verify_repository_metadata( self ):
'''Verify that resetting the metadata does not change it.'''
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
self.verify_unchanged_repository_metadata( emboss_repository )
self.verify_unchanged_repository_metadata( datatypes_repository )
test/tool_shed/functional/test_0030_repository_dependency_revisions.py
+8
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@@ -131,3 +131,11 @@ class TestRepositoryDependencyRevisions( ShedTwillTestCase ):
self.display_manage_repository_page( repository,
changeset_revision=changeset_revision,
strings_displayed=[ str( metadata ) for metadata in repository_dependency_metadata ] )
def test_0040_verify_repository_metadata( self ):
'''Verify that resetting the metadata does not change it.'''
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
emboss_5_repository = test_db_util.get_repository_by_name_and_owner( emboss_5_repository_name, common.test_user_1_name )
emboss_6_repository = test_db_util.get_repository_by_name_and_owner( emboss_6_repository_name, common.test_user_1_name )
datatypes_repository = test_db_util.get_repository_by_name_and_owner( datatypes_repository_name, common.test_user_1_name )
for repository in [ emboss_repository, emboss_5_repository, emboss_6_repository, datatypes_repository ]:
self.verify_unchanged_repository_metadata( repository )
test/tool_shed/functional/test_0040_repository_circular_dependencies.py
+6
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@@ -97,3 +97,9 @@ class TestRepositoryCircularDependencies( ShedTwillTestCase ):
# In this case, the displayed dependency will specify the tip revision, but this will not always be the case.
self.check_repository_dependency( filtering_repository, freebayes_repository, self.get_repository_tip( freebayes_repository ) )
self.check_repository_dependency( freebayes_repository, filtering_repository, self.get_repository_tip( filtering_repository ) )
def test_0035_verify_repository_metadata( self ):
'''Verify that resetting the metadata does not change it.'''
freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
for repository in [ freebayes_repository, filtering_repository ]:
self.verify_unchanged_repository_metadata( repository )
test/tool_shed/functional/test_0050_circular_n_levels.py
+8
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@@ -147,3 +147,11 @@ class TestRepositoryCircularDependenciesToNLevels( ShedTwillTestCase ):
for changeset_revision in self.get_repository_metadata_revisions( emboss_repository ):
self.check_repository_dependency( freebayes_repository, emboss_repository, changeset_revision )
self.display_manage_repository_page( freebayes_repository, strings_displayed=[ 'Freebayes depends on the filtering repository.' ] )
def test_0035_verify_repository_metadata( self ):
'''Verify that resetting the metadata does not change it.'''
emboss_datatypes_repository = test_db_util.get_repository_by_name_and_owner( emboss_datatypes_repository_name, common.test_user_1_name )
emboss_repository = test_db_util.get_repository_by_name_and_owner( emboss_repository_name, common.test_user_1_name )
filtering_repository = test_db_util.get_repository_by_name_and_owner( filtering_repository_name, common.test_user_1_name )
freebayes_repository = test_db_util.get_repository_by_name_and_owner( freebayes_repository_name, common.test_user_1_name )
for repository in [ emboss_datatypes_repository, emboss_repository, freebayes_repository, filtering_repository ]:
self.verify_unchanged_repository_metadata( repository )
test/tool_shed/functional/test_0060_workflows.py
+4
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@@ -54,3 +54,7 @@ class TestToolShedWorkflowFeatures( ShedTwillTestCase ):
commit_message="Uploaded filtering 2.2.0",
remove_repo_files_not_in_tar='No' )
self.load_workflow_image( repository, workflow_name, strings_not_displayed=[ '#EBBCB2' ] )
def test_0025_verify_repository_metadata( self ):
'''Verify that resetting the metadata does not change it.'''
repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )
self.verify_unchanged_repository_metadata( repository )
test/tool_shed/functional/test_1000_install_basic_repository.py
+4 -1
View File
@@ -28,4 +28,7 @@ class BasicToolShedFeatures( ShedTwillTestCase ):
self.verify_installed_repository_on_browse_page( installed_repository )
self.display_installed_repository_manage_page( installed_repository,
strings_displayed=[ 'Installed tool shed repository', 'Tools', 'Filter1' ] )
self.verify_tool_metadata_for_installed_repository( installed_repository )
self.verify_tool_metadata_for_installed_repository( installed_repository )
def test_0025_verify_installed_repository_metadata( self ):
'''Verify that resetting the metadata on an installed repository does not change the metadata.'''
self.verify_installed_repository_metadata_unchanged( 'filtering_0000', common.test_user_1_name )
test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py
+7
View File
@@ -25,3 +25,10 @@ class ToolWithToolDependencies( ShedTwillTestCase ):
strings_displayed=[ 'Installed tool shed repository', 'Tools', 'FreeBayes' ] )
self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False )
self.verify_tool_metadata_for_installed_repository( installed_repository )
def test_0020_verify_installed_repository_metadata( self ):
'''Verify that resetting the metadata on an installed repository does not change the metadata.'''
self.verify_installed_repository_metadata_unchanged( 'freebayes_0010', common.test_user_1_name )
def test_0025_verify_sample_files( self ):
'''Verify that the installed repository populated shed_tool_data_table.xml and the sample files.'''
self.verify_installed_repository_data_table_entries( data_tables=[ 'sam_fa_indexes' ] )
test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py
+3
View File
@@ -25,3 +25,6 @@ class ToolWithRepositoryDependencies( ShedTwillTestCase ):
strings_displayed=[ 'Installed tool shed repository', 'Tools', 'antigenic' ] )
self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False )
self.verify_tool_metadata_for_installed_repository( installed_repository )
def test_0020_verify_installed_repository_metadata( self ):
'''Verify that resetting the metadata on an installed repository does not change the metadata.'''
self.verify_installed_repository_metadata_unchanged( 'emboss_0020', common.test_user_1_name )
test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py
+4
View File
@@ -27,3 +27,7 @@ class RepositoryWithDependencyRevisions( ShedTwillTestCase ):
strings_displayed=[ 'Installed tool shed repository', 'Tools', 'antigenic' ] )
self.check_installed_repository_tool_dependencies( installed_repository, dependencies_installed=False )
self.verify_tool_metadata_for_installed_repository( installed_repository )
self.update_installed_repository( installed_repository, strings_displayed=[ "there are no updates available" ] )
def test_0025_verify_installed_repository_metadata( self ):
'''Verify that resetting the metadata on an installed repository does not change the metadata.'''
self.verify_installed_repository_metadata_unchanged( 'emboss_0030', common.test_user_1_name )
test/tool_shed/functional_tests.py
+20 -3
View File
@@ -68,6 +68,14 @@ shed_tool_conf_xml_template = '''<?xml version="1.0"?>
</toolbox>
'''
tool_conf_xml = '''<?xml version="1.0"?>
<toolbox>
<section name="Get Data" id="getext">
<tool file="data_source/upload.xml"/>
</section>
</toolbox>
'''
tool_data_table_conf_xml_template = '''<?xml version="1.0"?>
<tables>
</tables>
@@ -113,8 +121,14 @@ def main():
shed_db_path = os.path.join( tempdir, 'database' )
shed_tool_data_table_conf_file = os.environ.get( 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF', os.path.join( tool_shed_test_tmp_dir, 'shed_tool_data_table_conf.xml' ) )
galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_DATA_TABLE_CONF', os.path.join( tool_shed_test_tmp_dir, 'tool_data_table_conf.xml' ) )
galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_tool_conf.xml' ) )
galaxy_tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_tool_conf.xml' ) )
galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_TEST_SHED_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_shed_tool_conf.xml' ) )
galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_TEST_SHED_TOOLS_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_sheds_conf.xml' ) )
if 'GALAXY_TEST_TOOL_DATA_PATH' in os.environ:
tool_data_path = os.environ.get( 'GALAXY_TEST_TOOL_DATA_PATH' )
else:
tool_data_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir )
os.environ[ 'GALAXY_TEST_TOOL_DATA_PATH' ] = tool_data_path
if 'GALAXY_TEST_DBPATH' in os.environ:
galaxy_db_path = os.environ[ 'GALAXY_TEST_DBPATH' ]
else:
@@ -153,7 +167,7 @@ def main():
file( galaxy_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template )
# Generate the shed_tool_data_table_conf.xml file.
file( shed_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template )
os.environ[ 'TOOL_SHED_TEST_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file
# ---- Build Tool Shed Application --------------------------------------------------
toolshedapp = None
global_conf = { '__file__' : 'community_wsgi.ini.sample' }
@@ -231,6 +245,8 @@ def main():
# ---- Optionally start up a Galaxy instance ------------------------------------------------------
if 'TOOL_SHED_TEST_OMIT_GALAXY' not in os.environ:
# Generate the tool_conf.xml file.
file( galaxy_tool_conf_file, 'w' ).write( tool_conf_xml )
# Generate the shed_tool_conf.xml file.
tool_sheds_conf_template_parser = string.Template( tool_sheds_conf_xml_template )
tool_sheds_conf_xml = tool_sheds_conf_template_parser.safe_substitute( shed_url=tool_shed_test_host, shed_port=tool_shed_test_port )
@@ -251,10 +267,11 @@ def main():
database_engine_option_pool_size = '10',
file_path = galaxy_file_path,
tool_path = tool_path,
tool_data_path = tool_data_path,
tool_dependency_dir=galaxy_tool_dependency_dir,
shed_tool_path=galaxy_shed_tool_path,
update_integrated_tool_panel = False,
tool_config_file = galaxy_shed_tool_conf_file,
tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ],
tool_sheds_config_file = galaxy_tool_sheds_conf_file,
datatype_converters_config_file = "datatype_converters_conf.xml.sample",
tool_parse_help = False,