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Make the tool shed's install and test exclude list locally accessible rather than stored in cfengine.

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This commit is contained in:
Greg Von Kuster
2013-12-20 09:50:03 -05:00
parent 9a351e1285
commit b177363064
4 changed files with 23 additions and 63 deletions
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lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py
+10 -1
View File
@@ -197,7 +197,16 @@ def validate_repositories( app, info_only=False, verbosity=1 ):
test_environment_dict[ 'tool_shed_mercurial_version' ] = __version__.version
test_environment_dict[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() )
tool_test_results_dict[ 'test_environment' ] = test_environment_dict
repository_metadata.tool_test_results = tool_test_results_dict
# Store only the configured number of test runs.
num_tool_test_results_saved = int( app.config.num_tool_test_results_saved )
if len( tool_test_results_dicts ) >= num_tool_test_results_saved:
test_results_index = num_tool_test_results_saved - 1
new_tool_test_results_dicts = tool_test_results_dicts[ :test_results_index ]
else:
new_tool_test_results_dicts = [ d for d in tool_test_results_dicts ]
# Insert the new element into the first position in the list.
new_tool_test_results_dicts.insert( 0, tool_test_results_dict )
repository_metadata.tool_test_results = new_tool_test_results_dicts
app.sa_session.add( repository_metadata )
app.sa_session.flush()
stop = time.time()
test/install_and_test_tool_shed_repositories/base/twilltestcase.py
-10
View File
@@ -41,16 +41,6 @@ class InstallTestRepository( TwillTestCase ):
self.shed_tools_dict = {}
self.home()
def deactivate_repository( self, repository ):
"""Deactivate a repository."""
url = '/admin_toolshed/deactivate_or_uninstall_repository?id=%s' % self.security.encode_id( repository.id )
self.visit_url( url )
tc.fv ( 1, "remove_from_disk", 'false' )
tc.submit( 'deactivate_or_uninstall_repository_button' )
strings_displayed = [ 'The repository named' ]
strings_displayed.append( 'has been deactivated' )
self.check_for_strings( strings_displayed, strings_not_displayed=[] )
def initiate_installation_process( self,
install_tool_dependencies=False,
install_repository_dependencies=True,
test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py
+8 -14
View File
@@ -63,12 +63,11 @@ test_toolbox = None
# Here's the directory where everything happens. Temporary directories are created within this directory to contain
# the database, new repositories, etc.
galaxy_test_tmp_dir = os.path.join( test_home_directory, 'tmp' )
# File containing information about problematic repositories to exclude from test runs.
exclude_list_file = os.path.join( test_home_directory, 'exclude.xml' )
default_galaxy_locales = 'en'
default_galaxy_test_file_dir = "test-data"
os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir
# This file is copied to the Galaxy root directory by buildbot.
# It is managed by cfengine and is not locally available.
exclude_list_file = os.environ.get( 'GALAXY_INSTALL_TEST_EXCLUDE_REPOSITORIES', 'repositories_with_tools_exclude.xml' )
# This script can be run in such a way that no Tool Shed database records should be changed.
if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ:
@@ -138,25 +137,20 @@ def get_tool_info_from_test_id( test_id ):
return tool_id, tool_version
def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ):
# Initialize a dictionary for the summary that will be printed to stdout.
install_and_test_statistics_dict = install_and_test_base_util.initialize_install_and_test_statistics_dict( test_framework )
error_message = ''
# Initialize a dictionary for the summary that will be printed to stdout.
total_repositories_processed = install_and_test_statistics_dict[ 'total_repositories_processed' ]
repositories_to_install, error_message = \
install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url, test_framework )
if error_message:
return None, error_message
# Handle repositories not to be tested.
if os.path.exists( exclude_list_file ):
# Entries in the exclude_list look something like this.
# { 'reason': The default reason or the reason specified in this section,
# 'repositories':
# [( name, owner, changeset revision if changeset revision else None ),
# ( name, owner, changeset revision if changeset revision else None )] }
# If changeset revision is None, that means the entire repository is excluded from testing, otherwise only the specified
# revision should be skipped.
log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \
str( exclude_list_file ) )
log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % str( exclude_list_file ) )
# The following exclude_list will look something like this:
# [{ 'reason': The default reason or the reason specified in this section,
# 'repositories': [( name, owner, changeset_revision if changeset_revision else None ),
# ( name, owner, changeset_revision if changeset_revision else None )]}]
exclude_list = install_and_test_base_util.parse_exclude_list( exclude_list_file )
else:
exclude_list = []
test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py
+5 -38
View File
@@ -61,12 +61,11 @@ test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_rep
# Here's the directory where everything happens. Temporary directories are created within this directory to contain
# the database, new repositories, etc.
galaxy_test_tmp_dir = os.path.join( test_home_directory, 'tmp' )
# File containing information about problematic repositories to exclude from test runs.
exclude_list_file = os.path.join( test_home_directory, 'exclude.xml' )
default_galaxy_locales = 'en'
default_galaxy_test_file_dir = "test-data"
os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir
# This file is copied to the Galaxy root directory by buildbot.
# It is managed by cfengine and is not locally available.
exclude_list_file = os.environ.get( 'GALAXY_INSTALL_TEST_EXCLUDE_REPOSITORIES', 'tool_dependency_definition_exclude.xml' )
# This script can be run in such a way that no Tool Shed database records should be changed.
if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ:
@@ -77,29 +76,15 @@ else:
test_framework = install_and_test_base_util.TOOL_DEPENDENCY_DEFINITIONS
def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ):
# Initialize a dictionary for the summary that will be printed to stdout.
install_and_test_statistics_dict = install_and_test_base_util.initialize_install_and_test_statistics_dict( test_framework )
error_message = ''
# Initialize a dictionary for the summary that will be printed to stdout.
total_repositories_processed = install_and_test_statistics_dict[ 'total_repositories_processed' ]
repositories_to_install, error_message = \
install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url, test_framework )
if error_message:
return None, error_message
# Handle repositories not to be tested.
if os.path.exists( exclude_list_file ):
# Entries in the exclude_list look something like this.
# { 'reason': The default reason or the reason specified in this section,
# 'repositories':
# [( name, owner, changeset revision if changeset revision else None ),
# ( name, owner, changeset revision if changeset revision else None )] }
# If changeset revision is None, that means the entire repository is excluded from testing, otherwise only the specified
# revision should be skipped.
# We are testing deprecated repositories because it is possible that a deprecated repository contains valid tools that
# someone has previously installed. Deleted repositories have never been installed, so should not be tested. If they are
# undeleted, this script will then test them the next time it runs. We don't need to check if a repository has been deleted
# here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False.
log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \
str( exclude_list_file ) )
log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % str( exclude_list_file ) )
# The following exclude_list will look something like this:
# [{ 'reason': The default reason or the reason specified in this section,
# 'repositories': [( name, owner, changeset_revision if changeset_revision else None ),
@@ -201,19 +186,9 @@ def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool
install_and_test_statistics_dict[ 'total_repositories_processed' ] += 1
if error_message:
# The repository installation failed.
log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % \
( changeset_revision, name, owner ) )
log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) )
install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict )
tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message
# Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed.
log.debug( 'Attempting to uninstall revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) )
try:
repository = \
test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision )
except Exception, e:
error_message = 'Unable to find revision %s of repository %s owned by %s: %s.' % \
( changeset_revision, name, owner, str( e ) )
log.exception( error_message )
params = dict( test_install_error=True,
do_not_test=False )
# TODO: do something useful with response_dict
@@ -223,14 +198,6 @@ def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool
repository_dict,
params,
can_update_tool_shed )
try:
# We are uninstalling this repository and all of its repository dependencies.
install_and_test_base_util.uninstall_repository_and_repository_dependencies( app, repository_dict )
except Exception, e:
log.exception( 'Error attempting to uninstall revision %s of repository %s owned by %s: %s' % \
( changeset_revision, name, owner, str( e ) ) )
log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % \
( changeset_revision, name, owner ) )
else:
# The repository was successfully installed.
params, install_and_test_statistics_dict, tool_test_results_dict = \