commit/galaxy-central: greg: More code cleanup and fixes for the tool shed's install and test framework. The test environment information for both the tool shed and Galaxy should now be stored correctly in the Tool test results container on the view or manage repository page in the tool shed.
1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6fc4a1141845/ Changeset: 6fc4a1141845 User: greg Date: 2013-11-26 17:40:25 Summary: More code cleanup and fixes for the tool shed's install and test framework. The test environment information for both the tool shed and Galaxy should now be stored correctly in the Tool test results container on the view or manage repository page in the tool shed. Affected #: 4 files diff -r 4cfffc6fce30b9dd89849975c473e188936318ad -r 6fc4a11418458903a35aac3fd4878ab6c4265483 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -143,7 +143,8 @@ # Example URL: http://localhost:9009/api/repository_revisions/bb125606ff9ea620 try: repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) - repository_metadata_dict = repository_metadata.to_dict( value_mapper=self.__get_value_mapper( trans, repository_metadata ) ) + repository_metadata_dict = repository_metadata.to_dict( view='element', + value_mapper=self.__get_value_mapper( trans, repository_metadata ) ) repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', action='show', id=trans.security.encode_id( repository_metadata.id ) ) @@ -180,7 +181,8 @@ log.error( message, exc_info=True ) trans.response.status = 500 return message - repository_metadata_dict = repository_metadata.to_dict( value_mapper=self.__get_value_mapper( trans, repository_metadata ) ) + repository_metadata_dict = repository_metadata.to_dict( view='element', + value_mapper=self.__get_value_mapper( trans, repository_metadata ) ) repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', action='show', id=trans.security.encode_id( repository_metadata.id ) ) diff -r 4cfffc6fce30b9dd89849975c473e188936318ad -r 6fc4a11418458903a35aac3fd4878ab6c4265483 lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -251,7 +251,7 @@ self.do_not_test = do_not_test self.test_install_error = test_install_error self.time_last_tested = time_last_tested - self.tool_test_results = tool_test_results + self.tool_test_results = tool_test_results or dict() self.has_repository_dependencies = has_repository_dependencies # We don't consider the special case has_repository_dependencies_only_if_compiling_contained_td here. self.includes_datatypes = includes_datatypes diff -r 4cfffc6fce30b9dd89849975c473e188936318ad -r 6fc4a11418458903a35aac3fd4878ab6c4265483 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -1,16 +1,10 @@ #!/usr/bin/env python -import ConfigParser -import logging + import os -import shutil import sys -import tempfile -import time -from optparse import OptionParser -from time import strftime - -new_path = [ os.path.join( os.getcwd(), "lib" ), os.path.join( os.getcwd(), "test" ) ] +new_path = [ os.path.join( os.getcwd(), "lib" ), + os.path.join( os.getcwd(), "test" ) ] new_path.extend( sys.path[ 1: ] ) sys.path = new_path @@ -18,48 +12,56 @@ eggs.require( "SQLAlchemy >= 0.4" ) eggs.require( 'mercurial' ) +import ConfigParser import galaxy.webapps.tool_shed.config as tool_shed_config import galaxy.webapps.tool_shed.model.mapping +import logging +import shutil +import tempfile +import time -from base.util import get_test_environment from base.util import get_database_version from base.util import get_repository_current_revision -from galaxy.model.orm import and_, not_, select +from galaxy.model.orm import and_ +from galaxy.model.orm import not_ +from galaxy.model.orm import select from mercurial import hg from mercurial import ui from mercurial import __version__ +from optparse import OptionParser +from time import strftime from tool_shed.util.shed_util_common import clone_repository from tool_shed.util.shed_util_common import get_configured_ui -log = logging.getLogger() -log.setLevel( 10 ) -log.addHandler( logging.StreamHandler( sys.stdout ) ) - +log = logging.getLogger( 'check_repositories_for_functional_tests' ) assert sys.version_info[ :2 ] >= ( 2, 6 ) -class FlagRepositoriesApplication( object ): - """Encapsulates the state of a Universe application""" +class RepositoryMetadataApplication( object ): + """Application that enables updating repository_metadata table records in the Tool Shed.""" + def __init__( self, config ): if config.database_connection is False: - config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % config.database + config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % str( config.database ) + log.debug( 'Using database connection: %s' % str( config.database_connection ) ) # Setup the database engine and ORM - self.model = galaxy.webapps.tool_shed.model.mapping.init( config.file_path, config.database_connection, engine_options={}, create_tables=False ) + self.model = galaxy.webapps.tool_shed.model.mapping.init( config.file_path, + config.database_connection, + engine_options={}, + create_tables=False ) self.hgweb_config_manager = self.model.hgweb_config_manager self.hgweb_config_manager.hgweb_config_dir = config.hgweb_config_dir - print "# Using configured hgweb.config file: ", self.hgweb_config_manager.hgweb_config + log.debug( 'Using hgweb.config file: %s' % str( self.hgweb_config_manager.hgweb_config ) ) + @property def sa_session( self ): - """ - Returns a SQLAlchemy session -- currently just gets the current - session from the threadlocal session context, but this is provided - to allow migration toward a more SQLAlchemy 0.4 style of use. - """ + """Returns a SQLAlchemy session.""" return self.model.context.current + def shutdown( self ): pass -def check_and_flag_repositories( app, info_only=False, verbosity=1 ): +def check_and_update_repository_metadata( app, info_only=False, verbosity=1 ): """ This method will iterate through all records in the repository_metadata table, checking each one for tool metadata, then checking the tool metadata for tests. Each tool's metadata should look something like: @@ -352,12 +354,12 @@ print "# %s - Checking repositories for tools with functional tests." % now print "# This tool shed is configured to listen on %s:%s." % ( config_parser.get( config_section, 'host' ), config_parser.get( config_section, 'port' ) ) - app = FlagRepositoriesApplication( config ) + app = RepositoryMetadataApplication( config ) if options.info_only: print "# Displaying info only ( --info_only )" if options.verbosity: print "# Displaying extra information ( --verbosity = %d )" % options.verbosity - check_and_flag_repositories( app, info_only=options.info_only, verbosity=options.verbosity ) + check_and_update_repository_metadata( app, info_only=options.info_only, verbosity=options.verbosity ) def should_set_do_not_test_flag( app, repository, changeset_revision ): ''' diff -r 4cfffc6fce30b9dd89849975c473e188936318ad -r 6fc4a11418458903a35aac3fd4878ab6c4265483 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -1,32 +1,70 @@ #!/usr/bin/env python +""" +This script cannot be run directly, because it needs to have test/functional/test_toolbox.py in sys.argv in +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 os +import sys +# Assume we are run from the galaxy root directory, add lib to the python path +cwd = os.getcwd() +sys.path.append( cwd ) +new_path = [ os.path.join( cwd, "scripts" ), + os.path.join( cwd, "lib" ), + os.path.join( cwd, 'test' ), + os.path.join( cwd, 'scripts', 'api' ) ] +new_path.extend( sys.path ) +sys.path = new_path -# NOTE: This script cannot be run directly, because it needs to have test/functional/test_toolbox.py in sys.argv in -# 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. +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 atexit +import functional.test_toolbox as test_toolbox 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 os -import os.path -import platform +import nose import random import re import shutil import socket import string -import sys import tempfile import time import threading -import unittest +import tool_shed.util.shed_util_common as suc import urllib + +from base.util import get_database_version +from base.util import get_repository_current_revision +from base.util import get_test_environment +from base.util import parse_tool_panel_config +from common import update +from datetime import datetime +from galaxy.app import UniverseApplication +from galaxy.util import asbool +from galaxy.util import unicodify +from galaxy.util.json import from_json_string +from galaxy.util.json import to_json_string +from galaxy.web import buildapp +from galaxy.web.framework.helpers import time_ago +from functional_tests import generate_config_file +from mercurial import __version__ +from nose.plugins import Plugin +from paste import httpserver from time import strftime +from tool_shed.util import tool_dependency_util +from tool_shed.util.xml_util import parse_xml -# Assume we are run from the galaxy root directory, add lib to the python path -cwd = os.getcwd() -sys.path.append( cwd ) +log = logging.getLogger( 'install_and_test_repositories' ) +assert sys.version_info[ :2 ] >= ( 2, 6 ) test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_repositories' ) default_test_file_dir = os.path.join( test_home_directory, 'test_data' ) @@ -36,134 +74,15 @@ default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir -new_path = [ os.path.join( cwd, "scripts" ), os.path.join( cwd, "lib" ), os.path.join( cwd, 'test' ), os.path.join( cwd, 'scripts', 'api' ) ] -new_path.extend( sys.path ) -sys.path = new_path - -from functional_tests import generate_config_file - -from galaxy import eggs - -eggs.require( "nose" ) -eggs.require( "NoseHTML" ) -eggs.require( "NoseTestDiff" ) -eggs.require( "twill==0.9" ) -eggs.require( "Paste" ) -eggs.require( "PasteDeploy" ) -eggs.require( "Cheetah" ) -eggs.require( "simplejson" ) -eggs.require( 'mercurial' ) - -import simplejson -import twill - -from datetime import datetime -from mercurial import __version__ - -# 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 install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories -import install_and_test_tool_shed_repositories.base.test_db_util as test_db_util -import functional.test_toolbox as test_toolbox - -from paste import httpserver - -# This is for the galaxy application. -import galaxy.app -from galaxy.app import UniverseApplication -from galaxy.web import buildapp -from galaxy.util import parse_xml, asbool -from galaxy.util.json import from_json_string, to_json_string - -import tool_shed.util.shed_util_common as suc -from tool_shed.util import tool_dependency_util - -from galaxy.web.framework.helpers import time_ago - -import nose.core -import nose.config -import nose.loader -import nose.plugins.manager -from nose.plugins import Plugin - -from base.util import get_database_version -from base.util import get_repository_current_revision -from base.util import get_test_environment -from base.util import parse_tool_panel_config - -from galaxy.util import unicodify - -from common import update - -log = logging.getLogger( 'install_and_test_repositories' ) default_galaxy_test_port_min = 10000 default_galaxy_test_port_max = 10999 default_galaxy_test_host = '127.0.0.1' default_galaxy_master_api_key = None -# should this serve static resources (scripts, images, styles, etc.) +# Should this serve static resources (scripts, images, styles, etc.)? STATIC_ENABLED = True -def get_static_settings(): - """Returns dictionary of the settings necessary for a galaxy App - to be wrapped in the static middleware. - - This mainly consists of the filesystem locations of url-mapped - static resources. - """ - cwd = os.getcwd() - static_dir = os.path.join( cwd, 'static' ) - #TODO: these should be copied from universe_wsgi.ini - return dict( - #TODO: static_enabled needed here? - 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_webapp_global_conf(): - """Get the global_conf dictionary sent as the first argument to app_factory. - """ - # (was originally sent '{}') - nothing here for now except static settings - global_conf = {} - if STATIC_ENABLED: - global_conf.update( get_static_settings() ) - return global_conf - -# Optionally, set the environment variable GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF -# to the location of a tool sheds configuration file that includes the tool shed -# that repositories will be installed from. - -tool_sheds_conf_xml = '''<?xml version="1.0"?> -<tool_sheds> - <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/> - <tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/> -</tool_sheds> -''' - -# Create a blank shed_tool_conf.xml to hold the installed repositories. -shed_tool_conf_xml_template = '''<?xml version="1.0"?> -<toolbox tool_path="${shed_tool_path}"> -</toolbox> -''' - -# Since we will be running functional tests, we'll need the upload tool, but the rest can be omitted. -tool_conf_xml = '''<?xml version="1.0"?> -<toolbox> - <section name="Get Data" id="getext"> - <tool file="data_source/upload.xml"/> - </section> -</toolbox> -''' - - job_conf_xml = '''<?xml version="1.0"?><!-- A test job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --><job_conf> @@ -182,17 +101,48 @@ </job_conf> ''' +# Create a blank shed_tool_conf.xml to define the installed repositories. +shed_tool_conf_xml_template = '''<?xml version="1.0"?> +<toolbox tool_path="${shed_tool_path}"> +</toolbox> +''' + +# Since we will be running functional tests we'll need the upload tool, but the rest can be omitted. +tool_conf_xml = '''<?xml version="1.0"?> +<toolbox> + <section name="Get Data" id="getext"> + <tool file="data_source/upload.xml"/> + </section> +</toolbox> +''' + +# Set up an empty shed_tool_data_table_conf.xml. +tool_data_table_conf_xml_template = '''<?xml version="1.0"?> +<tables> +</tables> +''' + +# Optionally set the environment variable GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF to the location of a +# tool shed's configuration file that includes the tool shed from which repositories will be installed. +tool_sheds_conf_xml = '''<?xml version="1.0"?> +<tool_sheds> + <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/> + <tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/> +</tool_sheds> +''' + # If we have a tool_data_table_conf.test.xml, set it up to be loaded when the UniverseApplication is started. # This allows one to specify a set of tool data that is used exclusively for testing, and not loaded into any # Galaxy instance. By default, this will be in the test-data-repo/location directory generated by buildbot_setup.sh. if os.path.exists( 'tool_data_table_conf.test.xml' ): additional_tool_data_tables = 'tool_data_table_conf.test.xml' - additional_tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_EXTRA_TOOL_DATA_PATH', os.path.join( 'test-data-repo', 'location' ) ) + additional_tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_EXTRA_TOOL_DATA_PATH', + os.path.join( 'test-data-repo', 'location' ) ) else: additional_tool_data_tables = None additional_tool_data_path = None -# Also set up default tool data tables. +# Set up default tool data tables. if os.path.exists( 'tool_data_table_conf.xml' ): tool_data_table_conf = 'tool_data_table_conf.xml' elif os.path.exists( 'tool_data_table_conf.xml.sample' ): @@ -200,28 +150,14 @@ else: tool_data_table_conf = None -# And set up a blank shed_tool_data_table_conf.xml. -tool_data_table_conf_xml_template = '''<?xml version="1.0"?> -<tables> -</tables> -''' - -# The tool shed url and api key must be set for this script to work correctly. Additionally, if the tool shed url does not -# point to one of the defaults, the GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF needs to point to a tool sheds configuration file -# that contains a definition for that tool shed. - +# The GALAXY_INSTALL_TEST_TOOL_SHED_URL and GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variables must be +# set for this script to work correctly. If the value of GALAXY_INSTALL_TEST_TOOL_SHED_URL does not refer to one +# of the defaults, the GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must refer to a tool shed configuration file that contains +# a definition for that tool shed. galaxy_tool_shed_url = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_URL', None ) tool_shed_api_key = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY', None ) exclude_list_file = os.environ.get( 'GALAXY_INSTALL_TEST_EXCLUDE_REPOSITORIES', 'install_test_exclude.xml' ) -if tool_shed_api_key is None: - print "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variable to be set and non-empty." - exit( 1 ) - -if galaxy_tool_shed_url is None: - print "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_URL environment variable to be set and non-empty." - exit( 1 ) - if 'GALAXY_INSTALL_TEST_SECRET' not in os.environ: galaxy_encode_secret = 'changethisinproductiontoo' os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] = galaxy_encode_secret @@ -237,6 +173,7 @@ else: testing_single_repository[ 'changeset_revision' ] = None + class ReportResults( Plugin ): '''Simple Nose plugin to record the IDs of all tests run, regardless of success.''' name = "reportresults" @@ -481,6 +418,24 @@ str( repository_dict.get( 'owner', None ) ) ) ) return repository_dicts, error_message +def get_static_settings(): + """ + Return a dictionary of the settings necessary for a Galaxy application to be wrapped in the static + middleware. This mainly consists of the file system locations of url-mapped static resources. + """ + cwd = os.getcwd() + static_dir = os.path.join( cwd, 'static' ) + #TODO: these should be copied from universe_wsgi.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_tool_info_from_test_id( test_id ): """ Test IDs come in the form test_tool_number @@ -500,8 +455,17 @@ if error_message: return None, error_message tool_test_results = repository_metadata.get( 'tool_test_results', {} ) + if tool_test_results is None: + return None, error_message return tool_test_results, error_message +def get_webapp_global_conf(): + """Return the global_conf dictionary sent as the first argument to app_factory.""" + global_conf = {} + if STATIC_ENABLED: + global_conf.update( get_static_settings() ) + return global_conf + def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, tool_test_results_dict, results_dict ): """Handle missing repository or tool dependencies for an installed repository.""" # If a tool dependency fails to install correctly, this should be considered an installation error, @@ -671,7 +635,7 @@ # that are missing test components. We need to be careful to not lose this information. For all other repositories, # no changes will have been made to this dictionary by the preparation script, and tool_test_results_dict will be None. # Initialize the tool_test_results_dict dictionary with the information about the current test environment. - test_environment_dict = tool_test_results_dict.get( 'test_environent', None ) + test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) test_environment_dict = get_test_environment( test_environment_dict ) test_environment_dict[ 'galaxy_database_version' ] = get_database_version( app ) test_environment_dict[ 'galaxy_revision' ] = get_repository_current_revision( os.getcwd() ) @@ -772,261 +736,21 @@ return None, error_message return parsed_json, error_message -def parse_exclude_list( xml_filename ): - """Return a list of repositories to exclude from testing.""" - # This method should return a list with the following structure: - # [{ '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 = [] - exclude_verbose = [] - xml_tree = parse_xml( xml_filename ) - tool_sheds = xml_tree.findall( 'repositories' ) - xml_element = [] - exclude_count = 0 - for tool_shed in tool_sheds: - if galaxy_tool_shed_url != tool_shed.attrib[ 'tool_shed' ]: - continue - else: - xml_element = tool_shed - for reason_section in xml_element: - reason_text = reason_section.find( 'text' ).text - repositories = reason_section.findall( 'repository' ) - exclude_dict = dict( reason=reason_text, repositories=[] ) - for repository in repositories: - repository_tuple = get_repository_tuple_from_elem( repository ) - if repository_tuple not in exclude_dict[ 'repositories' ]: - exclude_verbose.append( repository_tuple ) - exclude_count += 1 - exclude_dict[ 'repositories' ].append( repository_tuple ) - exclude_list.append( exclude_dict ) - log.debug( '%s repositories excluded from testing...' % str( exclude_count ) ) - if '-list_repositories' in sys.argv: - for name, owner, changeset_revision in exclude_verbose: - if changeset_revision: - log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) ) - else: - log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) - return exclude_list - -def register_test_result( url, test_results_dict, repository_dict, params ): - """ - Update the repository metadata tool_test_results and appropriate flags using the Tool SHed API. This method - updates tool_test_results with the relevant data, sets the do_not_test and tools_functionally correct flags - to the appropriate values and updates the time_last_tested field to the value of the received time_tested. - """ - if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: - return {} - else: - metadata_revision_id = repository_dict.get( 'id', None ) - log.debug("RRR In register_test_result, metadata_revision_id: %s" % str( metadata_revision_id )) - if metadata_revision_id is not None: - # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. - time_tested = datetime.utcnow() - test_results_dict[ 'time_last_tested' ] = time_ago( time_tested ) - params[ 'tool_test_results' ] = test_results_dict - url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) - try: - return update( tool_shed_api_key, url, params, return_formatted=False ) - except Exception, e: - log.exception( 'Error attempting to register test results: %s' % str( e ) ) - return {} - -def remove_generated_tests( app ): - """ - Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them - and try to re-run the tests after uninstalling the repository, which will cause false failure reports, - since the test data has been deleted from disk by now. - """ - tests_to_delete = [] - tools_to_delete = [] - global test_toolbox - for key in test_toolbox.__dict__: - if key.startswith( 'TestForTool_' ): - log.debug( 'Tool test found in test_toolbox, deleting: %s' % str( key ) ) - # We can't delete this test just yet, we're still iterating over __dict__. - tests_to_delete.append( key ) - tool_id = key.replace( 'TestForTool_', '' ) - for tool in app.toolbox.tools_by_id: - if tool.replace( '_', ' ' ) == tool_id.replace( '_', ' ' ): - tools_to_delete.append( tool ) - for key in tests_to_delete: - # Now delete the tests found in the previous loop. - del test_toolbox.__dict__[ key ] - for tool in tools_to_delete: - del app.toolbox.tools_by_id[ tool ] - -def remove_install_tests(): - """ - Delete any configured repository installation tests from the test_toolbox.__dict__, otherwise nose will find them - and try to install the repository again while running tool functional tests. - """ - tests_to_delete = [] - global test_toolbox - # Push all the toolbox tests to module level - for key in test_install_repositories.__dict__: - if key.startswith( 'TestInstallRepository_' ): - log.debug( 'Repository installation process found, deleting: %s' % str( key ) ) - # We can't delete this test just yet, we're still iterating over __dict__. - tests_to_delete.append( key ) - for key in tests_to_delete: - # Now delete the tests found in the previous loop. - del test_install_repositories.__dict__[ key ] - -def run_tests( test_config ): - loader = nose.loader.TestLoader( config=test_config ) - test_config.plugins.addPlugin( ReportResults() ) - plug_loader = test_config.plugins.prepareTestLoader( loader ) - if plug_loader is not None: - loader = plug_loader - tests = loader.loadTestsFromNames( test_config.testNames ) - test_runner = nose.core.TextTestRunner( stream=test_config.stream, - verbosity=test_config.verbosity, - config=test_config ) - plug_runner = test_config.plugins.prepareTestRunner( test_runner ) - if plug_runner is not None: - test_runner = plug_runner - result = test_runner.run( tests ) - return result, test_config.plugins._plugins - -def show_summary_output( repository_dicts ): - repositories_by_owner = {} - for repository in repository_dicts: - if repository[ 'owner' ] not in repositories_by_owner: - repositories_by_owner[ repository[ 'owner' ] ] = [] - repositories_by_owner[ repository[ 'owner' ] ].append( repository ) - for owner in repositories_by_owner: - print "# " - for repository in repositories_by_owner[ owner ]: - print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) - -def test_repository_tools( app, repository, repository_dict, tool_test_results_dict, results_dict ): - """Test tools contained in the received repository.""" - name = str( repository.name ) - owner = str( repository.owner ) - changeset_revision = str( repository.changeset_revision ) - # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the appropriate test methods. - test_toolbox.toolbox = app.toolbox - # Generate the test methods for this installed repository. We need to pass in True here, or it will look - # in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test files. - test_toolbox.build_tests( testing_shed_tools=True, master_api_key=default_galaxy_master_api_key ) - # Set up nose to run the generated functional tests. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the configured tests. - result, test_plugins = run_tests( test_config ) - success = result.wasSuccessful() - # Use the ReportResults nose plugin to get a list of tests that passed. - for plugin in test_plugins: - if hasattr( plugin, 'getTestStatus' ): - test_identifier = '%s/%s' % ( owner, name ) - passed_tests = plugin.getTestStatus( test_identifier ) - break - tool_test_results_dict[ 'passed_tests' ] = [] - for test_id in passed_tests: - # Normalize the tool ID and version display. - tool_id, tool_version = get_tool_info_from_test_id( test_id ) - test_result = dict( test_id=test_id, tool_id=tool_id, tool_version=tool_version ) - tool_test_results_dict[ 'passed_tests' ].append( test_result ) - if success: - # This repository's tools passed all functional tests. Update the repository_metadata table in the tool shed's database - # to reflect that. Call the register_test_result method, which executes a PUT request to the repository_revisions API - # controller with the status of the test. This also sets the do_not_test and tools_functionally correct flags, and - # updates the time_last_tested field to today's date. - results_dict[ 'repositories_passed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - params = dict( tools_functionally_correct=True, - do_not_test=False, - test_install_error=False ) - register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) - log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( str( changeset_revision ), str( name ) ) ) - else: - tool_test_results_dict[ 'failed_tests' ].append( extract_log_data( result, from_tool_test=True ) ) - results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_dict ) - params = dict( tools_functionally_correct=False, - test_install_error=False, - do_not_test=str( set_do_not_test ) ) - register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) - log.debug( 'Revision %s of repository %s installed successfully but did not pass functional tests.' % \ - ( str( changeset_revision ), str( name ) ) ) - # Run the uninstall method. This removes tool functional test methods from the test_toolbox module and uninstalls the - # repository using Twill. - deactivate = asbool( os.environ.get( 'GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES', False ) ) - if deactivate: - log.debug( 'Deactivating changeset revision %s of repository %s' % ( str( changeset_revision ), str( name ) ) ) - # We are deactivating this repository and all of its repository dependencies. - deactivate_repository( app, repository_dict ) - else: - log.debug( 'Uninstalling changeset revision %s of repository %s' % ( str( changeset_revision ), str( name ) ) ) - # We are uninstalling this repository and all of its repository dependencies. - uninstall_repository( app, repository_dict ) - - # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. - test_toolbox.toolbox = app.toolbox - return results_dict - -def uninstall_repository( app, repository_dict ): - """Attempt to uninstall a repository.""" - sa_session = app.model.context.current - # Clean out any generated tests. This is necessary for Twill. - remove_generated_tests( app ) - # The dict contains the only repository the app should have installed at this point. - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - # We have to do this through Twill, in order to maintain app.toolbox and shed_tool_conf.xml in a state that is valid for future tests. - for required_repository in repository.repository_dependencies: - repository_dict = dict( name=str( required_repository.name ), - owner=str( required_repository.owner ), - changeset_revision=str( required_repository.changeset_revision ) ) - # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. - test_install_repositories.generate_deactivate_or_uninstall_method( repository_dict, deactivate=False ) - log.debug( 'Changeset revision %s of %s repository %s selected for uninstallation.' % \ - ( str( required_repository.changeset_revision ), str( required_repository.status ), str( required_repository.name ) ) ) - repository_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) - test_install_repositories.generate_deactivate_or_uninstall_method( repository_dict, deactivate=False ) - log.debug( 'Changeset revision %s of %s repository %s selected for uninstallation.' % ( changeset_revision, str( repository.status ), name ) ) - # Set up nose to run the generated uninstall method as a functional test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed - # repository and delete it from disk. - result, _ = run_tests( test_config ) - success = result.wasSuccessful() - if not success: - log.debug( 'Repository %s failed to uninstall.' % str( name ) ) - -def uninstall_tool_dependency( app, tool_dependency ): - """Attempt to uninstall a tool dependency.""" - sa_session = app.model.context.current - # Clean out any generated tests. This is necessary for Twill. - tool_dependency_install_path = tool_dependency.installation_directory( app ) - uninstalled, error_message = tool_dependency_util.remove_tool_dependency( app, tool_dependency ) - if error_message: - log.debug( 'There was an error attempting to remove directory: %s' % str( tool_dependency_install_path ) ) - log.debug( error_message ) - else: - log.debug( 'Successfully removed tool dependency installation directory: %s' % str( tool_dependency_install_path ) ) - if not uninstalled or tool_dependency.status != app.model.ToolDependency.installation_status.UNINSTALLED: - tool_dependency.status = app.model.ToolDependency.installation_status.UNINSTALLED - sa_session.add( tool_dependency ) - sa_session.flush() - if os.path.exists( tool_dependency_install_path ): - log.debug( 'Uninstallation of tool dependency succeeded, but the installation path still exists on the filesystem. It is now being explicitly deleted.') - suc.remove_dir( tool_dependency_install_path ) - def main(): if tool_shed_api_key is None: # If the tool shed URL specified in any dict is not present in the tool_sheds_conf.xml, the installation will fail. log.debug( 'Cannot proceed without a valid tool shed API key set in the enviroment variable GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY.' ) return 1 + if galaxy_tool_shed_url is None: + log.debug( 'Cannot proceed without a valid Tool Shed base URL set in the environment variable GALAXY_INSTALL_TEST_TOOL_SHED_URL.' ) + return 1 # ---- Configuration ------------------------------------------------------ galaxy_test_host = os.environ.get( 'GALAXY_INSTALL_TEST_HOST', default_galaxy_test_host ) - # Set the GALAXY_INSTALL_TEST_HOST variable so that Twill will have the Galaxy url to install repositories into. + # Set the GALAXY_INSTALL_TEST_HOST variable so that Twill will have the Galaxy url to which to + # install repositories. os.environ[ 'GALAXY_INSTALL_TEST_HOST' ] = galaxy_test_host - # Set the GALAXY_TEST_HOST environment variable so that the toolbox tests will have the Galaxy url to run tool functional - # tests on. + # Set the GALAXY_TEST_HOST environment variable so that the toolbox tests will have the Galaxy url + # on which to to run tool functional tests. os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host galaxy_test_port = os.environ.get( 'GALAXY_INSTALL_TEST_PORT', str( default_galaxy_test_port_max ) ) os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port @@ -1040,17 +764,25 @@ if not os.path.isdir( galaxy_test_tmp_dir ): os.mkdir( galaxy_test_tmp_dir ) # Set up the configuration files for the Galaxy instance. - shed_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF', os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_data_table_conf.xml' ) ) - galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_TABLE_CONF', tool_data_table_conf ) - galaxy_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_conf.xml' ) ) - galaxy_job_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_JOB_CONF', os.path.join( galaxy_test_tmp_dir, 'test_job_conf.xml' ) ) - galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_conf.xml' ) ) - galaxy_migrated_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_MIGRATED_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_migrated_tool_conf.xml' ) ) - galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_sheds_conf.xml' ) ) - galaxy_shed_tools_dict = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DICT_FILE', os.path.join( galaxy_test_tmp_dir, 'shed_tool_dict' ) ) + shed_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF', + os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_data_table_conf.xml' ) ) + galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_TABLE_CONF', + tool_data_table_conf ) + galaxy_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_CONF', + os.path.join( galaxy_test_tmp_dir, 'test_tool_conf.xml' ) ) + galaxy_job_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_JOB_CONF', + os.path.join( galaxy_test_tmp_dir, 'test_job_conf.xml' ) ) + galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF', + os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_conf.xml' ) ) + galaxy_migrated_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_MIGRATED_TOOL_CONF', + os.path.join( galaxy_test_tmp_dir, 'test_migrated_tool_conf.xml' ) ) + galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF', + os.path.join( galaxy_test_tmp_dir, 'test_tool_sheds_conf.xml' ) ) + galaxy_shed_tools_dict = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DICT_FILE', + os.path.join( galaxy_test_tmp_dir, 'shed_tool_dict' ) ) file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) - # Set the GALAXY_TOOL_SHED_TEST_FILE environment variable to the path of the shed_tools_dict file, so that test.base.twilltestcase.setUp - # will find and parse it properly. + # Set the GALAXY_TOOL_SHED_TEST_FILE environment variable to the path of the shed_tools_dict file so that + # test.base.twilltestcase.setUp will find and parse it properly. os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict if 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' in os.environ: tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' ) @@ -1261,20 +993,267 @@ if os.path.exists( dir ): try: shutil.rmtree( dir ) - log.debug( "Cleaned up temporary files in %s", dir ) + log.debug( "Cleaned up temporary files in %s", str( dir ) ) except: pass else: log.debug( 'GALAXY_INSTALL_TEST_NO_CLEANUP set, not cleaning up.' ) - # Normally, the value of 'success' would determine whether this test suite is marked as passed or failed - # in the automated buildbot framework. However, due to the procedure used here, we only want to report - # failure if a repository fails to install correctly. Therefore, we have overriden the value of 'success' - # here based on what actions the script has executed. + # Normally the value of 'success' would determine whether this test suite is marked as passed or failed + # in the automated buildbot framework. However, due to the procedure used here we only want to report + # failure if a repository fails to install correctly, so we have overriden the value of 'success' here + # based on what actions the script has executed. if success: return 0 else: return 1 +def parse_exclude_list( xml_filename ): + """Return a list of repositories to exclude from testing.""" + # This method should return a list with the following structure: + # [{ '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 = [] + exclude_verbose = [] + xml_tree, error_message = parse_xml( xml_filename ) + if error_message: + log.debug( 'The xml document %s defining the exclude list is invalid, so no repositories will be excluded from testing: %s' % \ + ( str( xml_filename ), str( error_message ) ) ) + return exclude_list + tool_sheds = xml_tree.findall( 'repositories' ) + xml_element = [] + exclude_count = 0 + for tool_shed in tool_sheds: + if galaxy_tool_shed_url != tool_shed.attrib[ 'tool_shed' ]: + continue + else: + xml_element = tool_shed + for reason_section in xml_element: + reason_text = reason_section.find( 'text' ).text + repositories = reason_section.findall( 'repository' ) + exclude_dict = dict( reason=reason_text, repositories=[] ) + for repository in repositories: + repository_tuple = get_repository_tuple_from_elem( repository ) + if repository_tuple not in exclude_dict[ 'repositories' ]: + exclude_verbose.append( repository_tuple ) + exclude_count += 1 + exclude_dict[ 'repositories' ].append( repository_tuple ) + exclude_list.append( exclude_dict ) + log.debug( '%s repositories will be excluded from testing...' % str( exclude_count ) ) + if '-list_repositories' in sys.argv: + for name, owner, changeset_revision in exclude_verbose: + if changeset_revision: + log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) ) + else: + log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) + return exclude_list + +def register_test_result( url, test_results_dict, repository_dict, params ): + """ + Update the repository metadata tool_test_results and appropriate flags using the Tool SHed API. This method + updates tool_test_results with the relevant data, sets the do_not_test and tools_functionally correct flags + to the appropriate values and updates the time_last_tested field to the value of the received time_tested. + """ + if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: + return {} + else: + metadata_revision_id = repository_dict.get( 'id', None ) + if metadata_revision_id is not None: + # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. + time_tested = datetime.utcnow() + test_results_dict[ 'time_last_tested' ] = time_ago( time_tested ) + params[ 'tool_test_results' ] = test_results_dict + url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) + try: + return update( tool_shed_api_key, url, params, return_formatted=False ) + except Exception, e: + log.exception( 'Error attempting to register test results: %s' % str( e ) ) + return {} + +def remove_generated_tests( app ): + """ + Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them + and try to re-run the tests after uninstalling the repository, which will cause false failure reports, + since the test data has been deleted from disk by now. + """ + tests_to_delete = [] + tools_to_delete = [] + global test_toolbox + for key in test_toolbox.__dict__: + if key.startswith( 'TestForTool_' ): + log.debug( 'Tool test found in test_toolbox, deleting: %s' % str( key ) ) + # We can't delete this test just yet, we're still iterating over __dict__. + tests_to_delete.append( key ) + tool_id = key.replace( 'TestForTool_', '' ) + for tool in app.toolbox.tools_by_id: + if tool.replace( '_', ' ' ) == tool_id.replace( '_', ' ' ): + tools_to_delete.append( tool ) + for key in tests_to_delete: + # Now delete the tests found in the previous loop. + del test_toolbox.__dict__[ key ] + for tool in tools_to_delete: + del app.toolbox.tools_by_id[ tool ] + +def remove_install_tests(): + """ + Delete any configured repository installation tests from the test_toolbox.__dict__, otherwise nose will find them + and try to install the repository again while running tool functional tests. + """ + tests_to_delete = [] + global test_toolbox + # Push all the toolbox tests to module level + for key in test_install_repositories.__dict__: + if key.startswith( 'TestInstallRepository_' ): + log.debug( 'Repository installation process found, deleting: %s' % str( key ) ) + # We can't delete this test just yet, we're still iterating over __dict__. + tests_to_delete.append( key ) + for key in tests_to_delete: + # Now delete the tests found in the previous loop. + del test_install_repositories.__dict__[ key ] + +def run_tests( test_config ): + loader = nose.loader.TestLoader( config=test_config ) + test_config.plugins.addPlugin( ReportResults() ) + plug_loader = test_config.plugins.prepareTestLoader( loader ) + if plug_loader is not None: + loader = plug_loader + tests = loader.loadTestsFromNames( test_config.testNames ) + test_runner = nose.core.TextTestRunner( stream=test_config.stream, + verbosity=test_config.verbosity, + config=test_config ) + plug_runner = test_config.plugins.prepareTestRunner( test_runner ) + if plug_runner is not None: + test_runner = plug_runner + result = test_runner.run( tests ) + return result, test_config.plugins._plugins + +def show_summary_output( repository_dicts ): + repositories_by_owner = {} + for repository in repository_dicts: + if repository[ 'owner' ] not in repositories_by_owner: + repositories_by_owner[ repository[ 'owner' ] ] = [] + repositories_by_owner[ repository[ 'owner' ] ].append( repository ) + for owner in repositories_by_owner: + print "# " + for repository in repositories_by_owner[ owner ]: + print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) + +def test_repository_tools( app, repository, repository_dict, tool_test_results_dict, results_dict ): + """Test tools contained in the received repository.""" + name = str( repository.name ) + owner = str( repository.owner ) + changeset_revision = str( repository.changeset_revision ) + # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the appropriate test methods. + test_toolbox.toolbox = app.toolbox + # Generate the test methods for this installed repository. We need to pass in True here, or it will look + # in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test files. + test_toolbox.build_tests( testing_shed_tools=True, master_api_key=default_galaxy_master_api_key ) + # Set up nose to run the generated functional tests. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the configured tests. + result, test_plugins = run_tests( test_config ) + success = result.wasSuccessful() + # Use the ReportResults nose plugin to get a list of tests that passed. + for plugin in test_plugins: + if hasattr( plugin, 'getTestStatus' ): + test_identifier = '%s/%s' % ( owner, name ) + passed_tests = plugin.getTestStatus( test_identifier ) + break + tool_test_results_dict[ 'passed_tests' ] = [] + for test_id in passed_tests: + # Normalize the tool ID and version display. + tool_id, tool_version = get_tool_info_from_test_id( test_id ) + test_result = dict( test_id=test_id, tool_id=tool_id, tool_version=tool_version ) + tool_test_results_dict[ 'passed_tests' ].append( test_result ) + if success: + # This repository's tools passed all functional tests. Update the repository_metadata table in the tool shed's database + # to reflect that. Call the register_test_result method, which executes a PUT request to the repository_revisions API + # controller with the status of the test. This also sets the do_not_test and tools_functionally correct flags, and + # updates the time_last_tested field to today's date. + results_dict[ 'repositories_passed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) + params = dict( tools_functionally_correct=True, + do_not_test=False, + test_install_error=False ) + register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) + log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( str( changeset_revision ), str( name ) ) ) + else: + tool_test_results_dict[ 'failed_tests' ].append( extract_log_data( result, from_tool_test=True ) ) + results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) + set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_dict ) + params = dict( tools_functionally_correct=False, + test_install_error=False, + do_not_test=str( set_do_not_test ) ) + register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) + log.debug( 'Revision %s of repository %s installed successfully but did not pass functional tests.' % \ + ( str( changeset_revision ), str( name ) ) ) + # Run the uninstall method. This removes tool functional test methods from the test_toolbox module and uninstalls the + # repository using Twill. + deactivate = asbool( os.environ.get( 'GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES', False ) ) + if deactivate: + log.debug( 'Deactivating changeset revision %s of repository %s' % ( str( changeset_revision ), str( name ) ) ) + # We are deactivating this repository and all of its repository dependencies. + deactivate_repository( app, repository_dict ) + else: + log.debug( 'Uninstalling changeset revision %s of repository %s' % ( str( changeset_revision ), str( name ) ) ) + # We are uninstalling this repository and all of its repository dependencies. + uninstall_repository( app, repository_dict ) + + # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. + test_toolbox.toolbox = app.toolbox + return results_dict + +def uninstall_repository( app, repository_dict ): + """Attempt to uninstall a repository.""" + sa_session = app.model.context.current + # Clean out any generated tests. This is necessary for Twill. + remove_generated_tests( app ) + # The dict contains the only repository the app should have installed at this point. + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + # We have to do this through Twill, in order to maintain app.toolbox and shed_tool_conf.xml in a state that is valid for future tests. + for required_repository in repository.repository_dependencies: + repository_dict = dict( name=str( required_repository.name ), + owner=str( required_repository.owner ), + changeset_revision=str( required_repository.changeset_revision ) ) + # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. + test_install_repositories.generate_deactivate_or_uninstall_method( repository_dict, deactivate=False ) + log.debug( 'Changeset revision %s of %s repository %s selected for uninstallation.' % \ + ( str( required_repository.changeset_revision ), str( required_repository.status ), str( required_repository.name ) ) ) + repository_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + test_install_repositories.generate_deactivate_or_uninstall_method( repository_dict, deactivate=False ) + log.debug( 'Changeset revision %s of %s repository %s selected for uninstallation.' % ( changeset_revision, str( repository.status ), name ) ) + # Set up nose to run the generated uninstall method as a functional test. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed + # repository and delete it from disk. + result, _ = run_tests( test_config ) + success = result.wasSuccessful() + if not success: + log.debug( 'Repository %s failed to uninstall.' % str( name ) ) + +def uninstall_tool_dependency( app, tool_dependency ): + """Attempt to uninstall a tool dependency.""" + sa_session = app.model.context.current + # Clean out any generated tests. This is necessary for Twill. + tool_dependency_install_path = tool_dependency.installation_directory( app ) + uninstalled, error_message = tool_dependency_util.remove_tool_dependency( app, tool_dependency ) + if error_message: + log.debug( 'There was an error attempting to remove directory: %s' % str( tool_dependency_install_path ) ) + log.debug( error_message ) + else: + log.debug( 'Successfully removed tool dependency installation directory: %s' % str( tool_dependency_install_path ) ) + if not uninstalled or tool_dependency.status != app.model.ToolDependency.installation_status.UNINSTALLED: + tool_dependency.status = app.model.ToolDependency.installation_status.UNINSTALLED + sa_session.add( tool_dependency ) + sa_session.flush() + if os.path.exists( tool_dependency_install_path ): + log.debug( 'Uninstallation of tool dependency succeeded, but the installation path still exists on the filesystem. It is now being explicitly deleted.') + suc.remove_dir( tool_dependency_install_path ) + if __name__ == "__main__": # The tool_test_results_dict should always have the following structure: # { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.
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