galaxy-commits December 2013

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commit/galaxy-central: greg: Enhance the tool shed's install and test framework to handle repositories of type tool_dependency_definition.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/356e0b061fb4/ Changeset: 356e0b061fb4 User: greg Date: 2013-12-18 18:29:01 Summary: Enhance the tool shed's install and test framework to handle repositories of type tool_dependency_definition. Affected #: 4 files diff -r 0a6f8a07b0c3ca8d58302cb3714ed01d132e52ec -r 356e0b061fb4c0500db7faf11de8bf5edb2f9c41 install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -40,10 +40,13 @@ fi # Test installation of repositories of type tool_dependency_definition. -# ...coming soon! +python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \ + test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \ + test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ + test/functional/test_toolbox.py # Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files. -python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ - test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ - test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ - test/functional/test_toolbox.py +#python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ +# test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ +# test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ +# test/functional/test_toolbox.py diff -r 0a6f8a07b0c3ca8d58302cb3714ed01d132e52ec -r 356e0b061fb4c0500db7faf11de8bf5edb2f9c41 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -20,6 +20,7 @@ import nose import platform import time +import tool_shed.repository_types.util as rt_util import tool_shed.util.shed_util_common as suc import urllib @@ -142,6 +143,9 @@ else: testing_single_repository_dict[ 'changeset_revision' ] = None +# Test frameworks that use this utility module. +REPOSITORIES_WITH_TOOLS = 'repositories_with_tools' +TOOL_DEPENDENCY_DEFINITIONS = 'tool_dependency_definitions' class ReportResults( Plugin ): '''Simple Nose plugin to record the IDs of all tests run, regardless of success.''' @@ -230,7 +234,7 @@ missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency ) ) return missing_tool_dependencies -def get_repositories_to_install( tool_shed_url ): +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: [{ "changeset_revision": <revision>, @@ -247,12 +251,18 @@ parts = [ 'repository_revisions' ] # We'll filter out deprecated repositories from testing since testing them is necessary only if reproducibility # is guaranteed and we currently do not guarantee reproducibility. - params = dict( do_not_test='false', - downloadable='true', - includes_tools='true', - malicious='false', - missing_test_components='false', - skip_tool_test='false' ) + if test_framework == REPOSITORIES_WITH_TOOLS: + params = dict( do_not_test='false', + downloadable='true', + includes_tools='true', + malicious='false', + missing_test_components='false', + skip_tool_test='false' ) + elif test_framework == TOOL_DEPENDENCY_DEFINITIONS: + params = dict( do_not_test='false', + downloadable='true', + malicious='false', + skip_tool_test='false' ) api_url = get_api_url( base=tool_shed_url, parts=parts, params=params ) baseline_repository_dicts, error_message = json_from_url( api_url ) if error_message: @@ -272,6 +282,9 @@ # Don't test empty repositories. changeset_revision = baseline_repository_dict[ 'changeset_revision' ] if changeset_revision != suc.INITIAL_CHANGELOG_HASH: + # If testing repositories of type tool_dependency_definition, filter accordingly. + if test_framework == TOOL_DEPENDENCY_DEFINITIONS and repository_dict[ 'type' ] != 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. if latest_revision_only: @@ -299,7 +312,7 @@ # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL # environment variable. log.debug( "The Tool Shed's API url...\n%s" % str( api_url ) ) - log.debug( "...retrieved %d repository revisions for testing." % len( repository_dicts ) ) + log.debug( "...retrieved %d repository revisions for installation and possible testing." % len( repository_dicts ) ) log.debug( "Repository revisions for testing:" ) for repository_dict in repository_dicts: name = str( repository_dict.get( 'name', None ) ) @@ -309,15 +322,13 @@ return repository_dicts, error_message def get_repository_current_revision( repo_path ): - ''' - This method uses the python mercurial API to get the current working directory's mercurial changeset hash. Note that if the author of mercurial - changes the API, this method will have to be updated or replaced. - ''' + """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. repo = hg.repository( ui.ui(), repo_path ) # Get the working directory's change context. ctx = repo[ None ] - # Extract the changeset hash of the first parent of that change context (the most recent changeset to which the working directory was updated). + # Extract the changeset hash of the first parent of that change context (the most recent changeset to which the + # working directory was updated). changectx = ctx.parents()[ 0 ] # Also get the numeric revision, so we can return the customary id:hash changeset identifiers. ctx_rev = changectx.rev() @@ -461,13 +472,18 @@ changeset_revision=str( repository.changeset_revision ) ) ) return results_dict -def initialize_results_dict(): +def initialize_results_dict( test_framework ): # Initialize a dictionary for the summary that will be printed to stdout. results_dict = {} - results_dict[ 'total_repositories_tested' ] = 0 - results_dict[ 'all_tests_passed' ] = [] - results_dict[ 'at_least_one_test_failed' ] = [] - results_dict[ 'repositories_failed_install' ] = [] + if test_framework == REPOSITORIES_WITH_TOOLS: + results_dict[ 'total_repositories_tested' ] = 0 + results_dict[ 'all_tests_passed' ] = [] + results_dict[ 'at_least_one_test_failed' ] = [] + results_dict[ 'repositories_failed_install' ] = [] + elif test_framework == TOOL_DEPENDENCY_DEFINITIONS: + results_dict[ 'total_repositories_installed' ] = 0 + results_dict[ 'repositories_with_installation_error' ] = 0 + results_dict[ 'tool_dependencies_with_installation_error' ] = 0 return results_dict def initialize_tool_tests_results_dict( app, tool_test_results_dict ): diff -r 0a6f8a07b0c3ca8d58302cb3714ed01d132e52ec -r 356e0b061fb4c0500db7faf11de8bf5edb2f9c41 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -52,7 +52,7 @@ from functional import database_contexts -log = logging.getLogger( 'install_and_test_repositories' ) +log = logging.getLogger( 'install_and_test_repositories_with_tools' ) assert sys.version_info[ :2 ] >= ( 2, 6 ) test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_repositories', 'repositories_with_tools' ) @@ -72,6 +72,8 @@ else: can_update_tool_shed = True +test_framework = install_and_test_base_util.REPOSITORIES_WITH_TOOLS + def get_failed_test_dicts( test_result, from_tool_test=True ): """Extract any useful data from the test_result.failures and test_result.errors attributes.""" failed_test_dicts = [] @@ -132,12 +134,12 @@ return tool_id, tool_version def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): - results_dict = install_and_test_base_util.initialize_results_dict() + results_dict = install_and_test_base_util.initialize_results_dict( test_framework ) error_message = '' # Initialize a dictionary for the summary that will be printed to stdout. total_repositories_tested = results_dict[ 'total_repositories_tested' ] repositories_to_install, error_message = \ - install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url ) + 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. @@ -153,7 +155,8 @@ # 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...', install_and_test_base_util.exclude_list_file ) + log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \ + str( install_and_test_base_util.exclude_list_file ) ) exclude_list = install_and_test_base_util.parse_exclude_list( install_and_test_base_util.exclude_list_file ) else: exclude_list = [] diff -r 0a6f8a07b0c3ca8d58302cb3714ed01d132e52ec -r 356e0b061fb4c0500db7faf11de8bf5edb2f9c41 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- /dev/null +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -0,0 +1,525 @@ +#!/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 + +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 re +import shutil +import socket +import string +import tempfile +import time +import threading + +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 galaxy.app import UniverseApplication +from galaxy.util.json import from_json_string +from galaxy.util.json import to_json_string +from galaxy.web import buildapp +from functional_tests import generate_config_file +from nose.plugins import Plugin +from paste import httpserver + +from functional import database_contexts + +log = logging.getLogger( 'install_and_test_tool_dependency_definitions' ) + +assert sys.version_info[ :2 ] >= ( 2, 6 ) +test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_repositories', 'tool_dependency_definitions' ) + +# 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' ) +default_galaxy_locales = 'en' +default_galaxy_test_file_dir = "test-data" +os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir + +# 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: + can_update_tool_shed = False +else: + can_update_tool_shed = True + +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 ): + results_dict = install_and_test_base_util.initialize_results_dict( test_framework ) + error_message = '' + # Initialize a dictionary for the summary that will be printed to stdout. + total_repositories_installed = results_dict[ 'total_repositories_installed' ] + 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( install_and_test_base_util.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( install_and_test_base_util.exclude_list_file ) ) + exclude_list = install_and_test_base_util.parse_exclude_list( install_and_test_base_util.exclude_list_file ) + else: + exclude_list = [] + # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was + # started up, installing repository and tool dependencies. Upon successful installation, generate a test case for each + # functional test defined for each tool in the repository and execute the test cases. Record the result of the tests. + # The traceback and captured output of the tool that was run will be recored for test failures. After all tests have + # completed, the repository is uninstalled, so test cases don't interfere with the next repository's functional tests. + for repository_dict in repositories_to_install: + # Each repository_dict looks something like: + # { "changeset_revision": "13fa22a258b5", + # "contents_url": "/api/repositories/529fd61ab1c6cc36/contents", + # "deleted": false, + # "deprecated": false, + # "description": "Convert column case.", + # "downloadable": true, + # "id": "529fd61ab1c6cc36", + # "long_description": "This tool takes the specified columns and converts them to uppercase or lowercase.", + # "malicious": false, + # "name": "change_case", + # "owner": "test", + # "private": false, + # "repository_id": "529fd61ab1c6cc36", + # "times_downloaded": 0, + # "tool_shed_url": "http://toolshed.local:10001", + # "url": "/api/repository_revisions/529fd61ab1c6cc36", + # "user_id": "529fd61ab1c6cc36" } + encoded_repository_metadata_id = repository_dict.get( 'id', None ) + # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. + repository_dict[ 'tool_shed_url' ] = install_and_test_base_util.galaxy_tool_shed_url + # Get the name and owner out of the repository info dict. + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + log.debug( "Processing revision %s of repository %s owned by %s..." % ( changeset_revision, name, owner ) ) + repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + # Retrieve the stored list of tool_test_results_dicts. + tool_test_results_dicts, error_message = \ + install_and_test_base_util.get_tool_test_results_dicts( install_and_test_base_util.galaxy_tool_shed_url, + encoded_repository_metadata_id ) + if error_message: + log.debug( error_message ) + else: + tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) + # See if this repository should be skipped for any reason. + this_repository_is_in_the_exclude_list = False + skip_reason = None + for exclude_dict in exclude_list: + reason = exclude_dict[ 'reason' ] + exclude_repositories = exclude_dict[ 'repositories' ] + if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: + this_repository_is_in_the_exclude_list = True + skip_reason = reason + break + if this_repository_is_in_the_exclude_list: + tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) + params = dict( do_not_test=False ) + # TODO: do something useful with response_dict + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) + log.debug( "Not testing revision %s of repository %s owned by %s because it is in the exclude list for this test run." % \ + ( changeset_revision, name, owner ) ) + else: + tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) + repository, error_message = install_and_test_base_util.install_repository( app, repository_dict ) + if error_message: + 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 repository %s owned by %s.' % ( 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 installed repository %s owned by %s: %s.' % ( name, owner, str( e ) ) + log.exception( error_message ) + test_result = dict( tool_shed=install_and_test_base_util.galaxy_tool_shed_url, + name=name, + owner=owner, + changeset_revision=changeset_revision, + error_message=error_message ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) + params = dict( tools_functionally_correct=False, + test_install_error=True, + do_not_test=False ) + # TODO: do something useful with response_dict + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + 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 ) ) ) + results_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) + log.debug( 'Repository %s failed to install correctly.' % str( name ) ) + else: + log.debug( 'Installation of %s succeeded.' % str( repository.name ) ) + missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) + if missing_tool_dependencies or repository.missing_repository_dependencies: + results_dict = install_and_test_base_util.handle_missing_dependencies( app, + repository, + missing_tool_dependencies, + repository_dict, + tool_test_results_dicts, + tool_test_results_dict, + results_dict, + can_update_tool_shed ) + results_dict[ 'total_repositories_installed' ] = total_repositories_installed + return results_dict, error_message + +def main(): + if install_and_test_base_util.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 install_and_test_base_util.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', install_and_test_base_util.default_galaxy_test_host ) + # 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 + # 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( install_and_test_base_util.default_galaxy_test_port_max ) ) + os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port + tool_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_PATH', 'tools' ) + if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: + os.environ[ 'HTTP_ACCEPT_LANGUAGE' ] = default_galaxy_locales + galaxy_test_file_dir = os.environ.get( 'GALAXY_INSTALL_TEST_FILE_DIR', default_galaxy_test_file_dir ) + if not os.path.isabs( galaxy_test_file_dir ): + galaxy_test_file_dir = os.path.abspath( galaxy_test_file_dir ) + use_distributed_object_store = os.environ.get( 'GALAXY_INSTALL_TEST_USE_DISTRIBUTED_OBJECT_STORE', False ) + 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', + install_and_test_base_util.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. + 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' ) + else: + tool_data_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + os.environ[ 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' ] = tool_data_path + # Configure the database connection and path. + if 'GALAXY_INSTALL_TEST_DBPATH' in os.environ: + galaxy_db_path = os.environ[ 'GALAXY_INSTALL_TEST_DBPATH' ] + else: + tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + galaxy_db_path = os.path.join( tempdir, 'database' ) + # Configure the paths Galaxy needs to install and test tools. + galaxy_file_path = os.path.join( galaxy_db_path, 'files' ) + new_repos_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + galaxy_tempfiles = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + galaxy_shed_tool_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir, prefix='shed_tools' ) + galaxy_migrated_tool_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + # Set up the tool dependency path for the Galaxy instance. + tool_dependency_dir = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR', None ) + if tool_dependency_dir is None: + tool_dependency_dir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + os.environ[ 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR' ] = tool_dependency_dir + os.environ[ 'GALAXY_TOOL_DEPENDENCY_DIR' ] = tool_dependency_dir + if 'GALAXY_INSTALL_TEST_DBURI' in os.environ: + database_connection = os.environ[ 'GALAXY_INSTALL_TEST_DBURI' ] + else: + database_connection = 'sqlite:///' + os.path.join( galaxy_db_path, 'install_and_test_repositories.sqlite' ) + kwargs = {} + for dir in [ galaxy_test_tmp_dir ]: + try: + os.makedirs( dir ) + except OSError: + pass + print "Database connection: ", database_connection + # Generate the shed_tool_data_table_conf.xml file. + file( shed_tool_data_table_conf_file, 'w' ).write( install_and_test_base_util.tool_data_table_conf_xml_template ) + os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file + # ---- Start up a Galaxy instance ------------------------------------------------------ + # Generate the tool_conf.xml file. + file( galaxy_tool_conf_file, 'w' ).write( install_and_test_base_util.tool_conf_xml ) + # Generate the job_conf.xml file. + file( galaxy_job_conf_file, 'w' ).write( install_and_test_base_util.job_conf_xml ) + # Generate the tool_sheds_conf.xml file, but only if a the user has not specified an existing one in the environment. + if 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF' not in os.environ: + file( galaxy_tool_sheds_conf_file, 'w' ).write( install_and_test_base_util.tool_sheds_conf_xml ) + # Generate the shed_tool_conf.xml file. + tool_conf_template_parser = string.Template( install_and_test_base_util.shed_tool_conf_xml_template ) + shed_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_shed_tool_path ) + file( galaxy_shed_tool_conf_file, 'w' ).write( shed_tool_conf_xml ) + os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file + # Generate the migrated_tool_conf.xml file. + migrated_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_migrated_tool_path ) + file( galaxy_migrated_tool_conf_file, 'w' ).write( migrated_tool_conf_xml ) + # Write the embedded web application's specific configuration to a temporary file. This is necessary in order for + # the external metadata script to find the right datasets. + kwargs = dict( admin_users = 'test(a)bx.psu.edu', + master_api_key = install_and_test_base_util.default_galaxy_master_api_key, + allow_user_creation = True, + allow_user_deletion = True, + allow_library_path_paste = True, + database_connection = database_connection, + datatype_converters_config_file = "datatype_converters_conf.xml.sample", + file_path = galaxy_file_path, + id_secret = install_and_test_base_util.galaxy_encode_secret, + job_config_file = galaxy_job_conf_file, + job_queue_workers = 5, + log_destination = "stdout", + migrated_tools_config = galaxy_migrated_tool_conf_file, + new_file_path = galaxy_tempfiles, + running_functional_tests = True, + shed_tool_data_table_config = shed_tool_data_table_conf_file, + shed_tool_path = galaxy_shed_tool_path, + template_path = "templates", + tool_config_file = ','.join( [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] ), + tool_data_path = tool_data_path, + tool_data_table_config_path = galaxy_tool_data_table_conf_file, + tool_dependency_dir = tool_dependency_dir, + tool_path = tool_path, + tool_parse_help = False, + tool_sheds_config_file = galaxy_tool_sheds_conf_file, + update_integrated_tool_panel = False, + use_heartbeat = False ) + galaxy_config_file = os.environ.get( 'GALAXY_INSTALL_TEST_INI_FILE', None ) + # If the user has passed in a path for the .ini file, do not overwrite it. + if not galaxy_config_file: + galaxy_config_file = os.path.join( galaxy_test_tmp_dir, 'install_test_tool_shed_repositories_wsgi.ini' ) + config_items = [] + for label in kwargs: + config_tuple = label, kwargs[ label ] + config_items.append( config_tuple ) + # Write a temporary file, based on universe_wsgi.ini.sample, using the configuration options defined above. + generate_config_file( 'universe_wsgi.ini.sample', galaxy_config_file, config_items ) + kwargs[ 'tool_config_file' ] = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] + # Set the global_conf[ '__file__' ] option to the location of the temporary .ini file, which gets passed to set_metadata.sh. + kwargs[ 'global_conf' ] = install_and_test_base_util.get_webapp_global_conf() + kwargs[ 'global_conf' ][ '__file__' ] = galaxy_config_file + # ---- Build Galaxy Application -------------------------------------------------- + if not database_connection.startswith( 'sqlite://' ): + kwargs[ 'database_engine_option_max_overflow' ] = '20' + kwargs[ 'database_engine_option_pool_size' ] = '10' + kwargs[ 'config_file' ] = galaxy_config_file + app = UniverseApplication( **kwargs ) + database_contexts.galaxy_context = app.model.context + database_contexts.install_context = app.install_model.context + + log.debug( "Embedded Galaxy application started..." ) + # ---- Run galaxy webserver ------------------------------------------------------ + server = None + global_conf = install_and_test_base_util.get_webapp_global_conf() + global_conf[ 'database_file' ] = database_connection + webapp = buildapp.app_factory( global_conf, + use_translogger=False, + static_enabled=install_and_test_base_util.STATIC_ENABLED, + app=app ) + # Serve the app on a specified or random port. + if galaxy_test_port is not None: + server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) + else: + random.seed() + for i in range( 0, 9 ): + try: + galaxy_test_port = str( random.randint( install_and_test_base_util.default_galaxy_test_port_min, + install_and_test_base_util.default_galaxy_test_port_max ) ) + log.debug( "Attempting to serve app on randomly chosen port: %s", galaxy_test_port ) + server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) + break + except socket.error, e: + if e[0] == 98: + continue + raise + else: + raise Exception( "Unable to open a port between %s and %s to start Galaxy server" % \ + ( install_and_test_base_util.default_galaxy_test_port_min, install_and_test_base_util.default_galaxy_test_port_max ) ) + os.environ[ 'GALAXY_INSTALL_TEST_PORT' ] = galaxy_test_port + # Start the server. + t = threading.Thread( target=server.serve_forever ) + t.start() + # Test if the server is up. + for i in range( 10 ): + # Directly test the app, not the proxy. + conn = httplib.HTTPConnection( galaxy_test_host, galaxy_test_port ) + conn.request( "GET", "/" ) + if conn.getresponse().status == 200: + break + time.sleep( 0.1 ) + else: + raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" ) + log.debug( "Embedded galaxy web server started..." ) + log.debug( "The embedded Galaxy application is running on %s:%s" % ( str( galaxy_test_host ), str( galaxy_test_port ) ) ) + log.debug( "Repositories will be installed from the tool shed at %s" % str( install_and_test_base_util.galaxy_tool_shed_url ) ) + # If a tool_data_table_conf.test.xml file was found, add the entries from it into the app's tool data tables. + if install_and_test_base_util.additional_tool_data_tables: + app.tool_data_tables.add_new_entries_from_config_file( config_filename=install_and_test_base_util.additional_tool_data_tables, + tool_data_path=install_and_test_base_util.additional_tool_data_path, + shed_tool_data_table_config=None, + persist=False ) + now = time.strftime( "%Y-%m-%d %H:%M:%S" ) + print "####################################################################################" + print "# %s - running repository installation and testing script." % now + print "####################################################################################" + results_dict, error_message = install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ) + if error_message: + log.debug( error_message ) + else: + total_repositories_installed = results_dict[ 'total_repositories_installed' ] + repositories_with_installation_error = results_dict[ 'repositories_with_installation_error' ] + tool_dependencies_with_installation_error = results_dict[ 'tool_dependencies_with_installation_error' ] + now = time.strftime( "%Y-%m-%d %H:%M:%S" ) + print "####################################################################################" + print "# %s - repository installation and testing script completed." % now + print "# Repository revisions tested: %s" % str( total_repositories_installed ) + if not can_update_tool_shed: + print "# This run will not update the Tool Shed database." + if repositories_with_installation_error: + print '# ----------------------------------------------------------------------------------' + print "# %d repositories have installation errors:" % len( repositories_with_installation_error ) + install_and_test_base_util.show_summary_output( repositories_with_installation_error ) + if tool_dependencies_with_installation_error: + print '# ----------------------------------------------------------------------------------' + print "# %d tool dependencies have installation errors:" % len( tool_dependencies_with_installation_error ) + install_and_test_base_util.show_summary_output( tool_dependencies_with_installation_error ) + print "####################################################################################" + log.debug( "Shutting down..." ) + # Gracefully shut down the embedded web server and UniverseApplication. + if server: + log.debug( "Shutting down embedded galaxy web server..." ) + server.server_close() + server = None + log.debug( "Embedded galaxy server stopped..." ) + if app: + log.debug( "Shutting down galaxy application..." ) + app.shutdown() + app = None + log.debug( "Embedded galaxy application stopped..." ) + # Clean up test files unless otherwise specified. + if 'GALAXY_INSTALL_TEST_NO_CLEANUP' not in os.environ: + for dir in [ galaxy_test_tmp_dir ]: + if os.path.exists( dir ): + try: + shutil.rmtree( 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.' ) + # Return a "successful" response to buildbot. + return 0 + +if __name__ == "__main__": + # The tool_test_results_dict should always have the following structure: + # { + # "test_environment": + # { + # "galaxy_revision": "9001:abcd1234", + # "galaxy_database_version": "114", + # "tool_shed_revision": "9001:abcd1234", + # "tool_shed_mercurial_version": "2.3.1", + # "tool_shed_database_version": "17", + # "python_version": "2.7.2", + # "architecture": "x86_64", + # "system": "Darwin 12.2.0" + # }, + # "installation_errors": + # { + # 'tool_dependencies': + # [ + # { + # 'type': 'Type of tool dependency, e.g. package, set_environment, etc.', + # 'name': 'Name of the tool dependency.', + # 'version': 'Version if this is a package, otherwise blank.', + # 'error_message': 'The error message returned when installation was attempted.', + # }, + # ], + # 'repository_dependencies': + # [ + # { + # 'tool_shed': 'The tool shed that this repository was installed from.', + # 'name': 'The name of the repository that failed to install.', + # 'owner': 'Owner of the failed repository.', + # 'changeset_revision': 'Changeset revision of the failed repository.', + # 'error_message': 'The error message that was returned when the repository failed to install.', + # }, + # ], + # 'current_repository': + # [ + # { + # 'tool_shed': 'The tool shed that this repository was installed from.', + # 'name': 'The name of the repository that failed to install.', + # 'owner': 'Owner of the failed repository.', + # 'changeset_revision': 'Changeset revision of the failed repository.', + # 'error_message': 'The error message that was returned when the repository failed to install.', + # }, + # ], + # { + # "name": "The name of the repository.", + # "owner": "The owner of the repository.", + # "changeset_revision": "The changeset revision of the repository.", + # "error_message": "The message stored in tool_dependency.error_message." + # }, + # } + # } + sys.exit( main() ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Refactor the tool shed's install and test framework in preparation for enhancements to test repositories of type tool_dependency_definition.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0a6f8a07b0c3/ Changeset: 0a6f8a07b0c3 User: greg Date: 2013-12-18 17:16:09 Summary: Refactor the tool shed's install and test framework in preparation for enhancements to test repositories of type tool_dependency_definition. Affected #: 2 files diff -r ce186eb5fefcb7ff332c73bd0869b9e222293d0b -r 0a6f8a07b0c3ca8d58302cb3714ed01d132e52ec test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -1,25 +1,195 @@ -import logging import os import sys cwd = os.getcwd() -if cwd not in sys.path: - sys.path.append( cwd ) - -new_path = [ os.path.join( cwd, "lib" ) ] -if new_path not in sys.path: - new_path.extend( sys.path ) - sys.path = new_path +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 from galaxy import eggs +eggs.require( 'mercurial' ) +eggs.require( "nose" ) -eggs.require( 'mercurial' ) +import logging +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 time +import tool_shed.util.shed_util_common as suc +import urllib + +from base.tool_shed_util import log_reason_repository_cannot_be_uninstalled + +from common import update + +from galaxy.util import asbool +from galaxy.util import listify +from galaxy.util import unicodify +from galaxy.util.json import from_json_string +from nose.plugins import Plugin +from tool_shed.util import tool_dependency_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. +job_conf_xml = '''<?xml version="1.0"?> + +<job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + </plugins> + <handlers> + <handler id="main"/> + </handlers> + <destinations> + <destination id="local" runner="local"/> + </destinations> + <limits> + <limit type="walltime">00:10:00</limit> + </limits> +</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> +''' + +# Should this serve static resources (scripts, images, styles, etc.)? +STATIC_ENABLED = True + +# 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' ) ) +else: + additional_tool_data_tables = None + additional_tool_data_path = None + +# 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' ): + tool_data_table_conf = 'tool_data_table_conf.xml.sample' +else: + tool_data_table_conf = None + +# 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 'GALAXY_INSTALL_TEST_SECRET' not in os.environ: + galaxy_encode_secret = 'changethisinproductiontoo' + os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] = galaxy_encode_secret +else: + galaxy_encode_secret = os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] + +default_galaxy_test_port_min = 10000 +default_galaxy_test_port_max = 10999 +default_galaxy_test_host = '127.0.0.1' +# The following should be an actual value (not None). If developers manually specify their +# tests to use the API it will not work unless a master API key is specified. +default_galaxy_master_api_key = 123456 + +testing_single_repository_dict = {} +if 'repository_name' in os.environ and 'repository_owner' in os.environ: + testing_single_repository_dict[ 'name' ] = str( os.environ[ 'repository_name' ] ) + testing_single_repository_dict[ 'owner' ] = str( os.environ[ 'repository_owner' ] ) + if 'repository_revision' in os.environ: + testing_single_repository_dict[ 'changeset_revision' ] = str( os.environ[ 'repository_revision' ] ) + else: + testing_single_repository_dict[ 'changeset_revision' ] = None + + +class ReportResults( Plugin ): + '''Simple Nose plugin to record the IDs of all tests run, regardless of success.''' + name = "reportresults" + passed = {} + + def options( self, parser, env=os.environ ): + super( ReportResults, self ).options( parser, env=env ) + + def configure(self, options, conf): + super( ReportResults, self ).configure( options, conf ) + if not self.enabled: + return + + def addSuccess( self, test ): + '''Only record test IDs that correspond to tool functional tests.''' + if 'TestForTool' in test.id(): + test_id = test.id() + # Rearrange the test ID to match the format that is produced in test_results.failures + test_id_parts = test_id.split( '.' ) + fixed_test_id = '%s (%s)' % ( test_id_parts[ -1 ], '.'.join( test_id_parts[ :-1 ] ) ) + test_parts = fixed_test_id.split( '/' ) + owner = test_parts[ -4 ] + name = test_parts[ -3 ] + test_identifier = '%s/%s' % ( owner, name ) + if test_identifier not in self.passed: + self.passed[ test_identifier ] = [] + self.passed[ test_identifier ].append( fixed_test_id ) + + def getTestStatus( self, test_identifier ): + if test_identifier in self.passed: + passed_tests = self.passed[ test_identifier ] + del self.passed[ test_identifier ] + return passed_tests + return [] + +def get_api_url( base, parts=[], params=None ): + if 'api' in parts and parts.index( 'api' ) != 0: + parts.pop( parts.index( 'api' ) ) + parts.insert( 0, 'api' ) + elif 'api' not in parts: + parts.insert( 0, 'api' ) + url = suc.url_join( base, *parts ) + if params is not None: + query_string = urllib.urlencode( params ) + url += '?%s' % query_string + return url + def get_database_version( app ): ''' This method returns the value of the version column from the migrate_version table, using the provided app's SQLAlchemy session to determine @@ -37,6 +207,107 @@ break return version +def get_latest_downloadable_changeset_revision( url, name, owner ): + error_message = '' + parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] + params = dict( name=name, owner=owner ) + api_url = get_api_url( base=url, parts=parts, params=params ) + changeset_revisions, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + if changeset_revisions: + return changeset_revisions[ -1 ], error_message + else: + return suc.INITIAL_CHANGELOG_HASH, error_message + +def get_missing_tool_dependencies( repository ): + log.debug( 'Checking %s repository %s for missing tool dependencies.' % ( repository.status, repository.name ) ) + missing_tool_dependencies = repository.missing_tool_dependencies + for tool_dependency in repository.tool_dependencies: + log.debug( 'Tool dependency %s version %s has status %s.' % ( tool_dependency.name, tool_dependency.version, tool_dependency.status ) ) + for repository_dependency in repository.repository_dependencies: + if repository_dependency.includes_tool_dependencies: + missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency ) ) + return missing_tool_dependencies + +def get_repositories_to_install( tool_shed_url ): + """ + Get a list of repository info dicts to install. This method expects a json list of dicts with the following structure: + [{ "changeset_revision": <revision>, + "encoded_repository_id": <encoded repository id from the tool shed>, + "name": <name>, + "owner": <owner>, + "tool_shed_url": <url> }] + """ + error_message = '' + latest_revision_only = '-check_all_revisions' not in sys.argv + if latest_revision_only: + log.debug( 'Testing is restricted to the latest downloadable revision in this test run.' ) + repository_dicts = [] + parts = [ 'repository_revisions' ] + # We'll filter out deprecated repositories from testing since testing them is necessary only if reproducibility + # is guaranteed and we currently do not guarantee reproducibility. + params = dict( do_not_test='false', + downloadable='true', + includes_tools='true', + malicious='false', + missing_test_components='false', + skip_tool_test='false' ) + api_url = get_api_url( base=tool_shed_url, parts=parts, params=params ) + baseline_repository_dicts, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + for baseline_repository_dict in baseline_repository_dicts: + # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the + # module that will generate the install methods. + repository_dict, error_message = \ + get_repository_dict( galaxy_tool_shed_url, baseline_repository_dict ) + if error_message: + log.debug( 'Error getting additional details from the API: %s' % str( error_message ) ) + else: + # Don't test deprecated repositories since testing them is necessary only if reproducibility is guaranteed + # and we are not currently guaranteeing reproducibility. + deprecated = asbool( repository_dict.get( 'deprecated', False ) ) + if not deprecated: + # Don't test empty repositories. + changeset_revision = baseline_repository_dict[ 'changeset_revision' ] + if changeset_revision != suc.INITIAL_CHANGELOG_HASH: + # 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. + if latest_revision_only: + latest_revision = repository_dict[ 'latest_revision' ] + if changeset_revision == latest_revision: + repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) + else: + repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) + if testing_single_repository_dict: + tsr_name = testing_single_repository_dict[ 'name' ] + tsr_owner = testing_single_repository_dict[ 'owner' ] + tsr_changeset_revision = testing_single_repository_dict[ 'changeset_revision' ] + log.debug( 'Testing single repository with name %s and owner %s.' % ( str( tsr_name ), str( tsr_owner ) ) ) + for repository_to_install in repository_dicts: + rti_name = repository_to_install[ 'name' ] + rti_owner = repository_to_install[ 'owner' ] + rti_changeset_revision = repository_to_install[ 'changeset_revision' ] + if rti_name == tsr_name and rti_owner == tsr_owner: + if tsr_changeset_revision is None: + return [ repository_to_install ], error_message + else: + if tsr_changeset_revision == rti_changeset_revision: + return repository_dicts, error_message + return repository_dicts, error_message + # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL + # environment variable. + log.debug( "The Tool Shed's API url...\n%s" % str( api_url ) ) + log.debug( "...retrieved %d repository revisions for testing." % len( repository_dicts ) ) + log.debug( "Repository revisions for testing:" ) + for repository_dict in repository_dicts: + name = str( repository_dict.get( 'name', None ) ) + owner = str( repository_dict.get( 'owner', None ) ) + changeset_revision = str( repository_dict.get( 'changeset_revision', None ) ) + log.debug( "Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) ) + return repository_dicts, error_message + def get_repository_current_revision( repo_path ): ''' This method uses the python mercurial API to get the current working directory's mercurial changeset hash. Note that if the author of mercurial @@ -52,3 +323,415 @@ ctx_rev = changectx.rev() hg_id = '%d:%s' % ( ctx_rev, str( changectx ) ) return hg_id + +def get_repository_dict( url, repository_dict ): + error_message = '' + parts = [ 'api', 'repositories', repository_dict[ 'repository_id' ] ] + api_url = get_api_url( base=url, parts=parts ) + extended_dict, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + name = str( extended_dict[ 'name' ] ) + owner = str( extended_dict[ 'owner' ] ) + latest_changeset_revision, error_message = get_latest_downloadable_changeset_revision( url, name, owner ) + if error_message: + return None, error_message + extended_dict[ 'latest_revision' ] = str( latest_changeset_revision ) + return extended_dict, error_message + +def get_repository_tuple_from_elem( elem ): + attributes = elem.attrib + name = attributes.get( 'name', None ) + owner = attributes.get( 'owner', None ) + 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 + 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_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 + # entry. If it contains more entries, then the script ~/tool_shed/api/check_repositories_for_functional_tests.py + # was not executed in preparation for this script's execution, so we'll just create an empty dictionary. + tool_test_results_dict = tool_test_results_dicts[ 0 ] + if len( tool_test_results_dict ) <= 1: + # We can re-use the mostly empty tool_test_results_dict for this run because it is either empty or it contains only + # a test_environment entry. If we use it we need to temporarily eliminate it from the list of 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: + # 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 ) + else: + # 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, + 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 + column via the Tool Shed API. + """ + error_message = '' + parts = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] + api_url = get_api_url( base=tool_shed_url, parts=parts ) + repository_metadata, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + # The tool_test_results used to be stored as a single dictionary rather than a list, but we currently + # return a list. + tool_test_results = listify( repository_metadata.get( 'tool_test_results', [] ) ) + 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_dicts, + tool_test_results_dict, results_dict, can_update_tool_shed ): + """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, + # and functional tests should be skipped, since the tool dependency needs to be correctly installed + # for the test to be considered reliable. + log.debug( 'The following dependencies of this repository are missing, so skipping functional tests.' ) + # In keeping with the standard display layout, add the error message to the dict for each tool individually. + for dependency in repository.missing_tool_dependencies: + name = str( dependency.name ) + type = str( dependency.type ) + version = str( dependency.version ) + error_message = unicodify( dependency.error_message ) + log.debug( 'Missing tool dependency %s of type %s version %s: %s' % ( name, type, version, error_message ) ) + test_result = dict( type=dependency.type, + name=dependency.name, + version=dependency.version, + error_message=dependency.error_message ) + tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) + for dependency in repository.missing_repository_dependencies: + name = str( dependency.name ) + owner = str( dependency.owner ) + changeset_revision = str( dependency.changeset_revision ) + error_message = unicodify( dependency.error_message ) + log.debug( 'Missing repository dependency %s changeset revision %s owned by %s: %s' % \ + ( name, changeset_revision, owner, error_message ) ) + test_result = dict( tool_shed=dependency.tool_shed, + name=dependency.name, + owner=dependency.owner, + changeset_revision=dependency.changeset_revision, + error_message=dependency.error_message ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) + # Record the status of this repository in the tool shed. + params = dict( tools_functionally_correct=False, + do_not_test=False, + test_install_error=True ) + # TODO: do something useful with response_dict + response_dict = register_test_result( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) + # Since this repository is missing components we do not want to test it, uninstall it. + uninstall_repository_and_repository_dependencies( app, repository_dict ) + results_dict[ 'repositories_failed_install' ].append( dict( name=str( repository.name ), + owner=str( repository.owner ), + changeset_revision=str( repository.changeset_revision ) ) ) + return results_dict + +def initialize_results_dict(): + # Initialize a dictionary for the summary that will be printed to stdout. + results_dict = {} + results_dict[ 'total_repositories_tested' ] = 0 + results_dict[ 'all_tests_passed' ] = [] + results_dict[ 'at_least_one_test_failed' ] = [] + results_dict[ 'repositories_failed_install' ] = [] + return results_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: + # Set information about the tool shed to nothing since we cannot currently determine it from here. + # We could eventually add an API method... + test_environment_dict = dict( tool_shed_database_version='', + tool_shed_mercurial_version='', + tool_shed_revision='' ) + # Add the current time as the approximate time that this test run occurs. A similar value will also be + # set to the repository_metadata.time_last_tested column, but we also store it here because the Tool Shed + # may be configured to store multiple test run results, so each must be associated with a time stamp. + now = time.strftime( "%Y-%m-%d %H:%M:%S" ) + # Add information about the current platform. + test_environment_dict[ 'time_tested' ] = now + test_environment_dict[ 'python_version' ] = platform.python_version() + test_environment_dict[ 'architecture' ] = platform.machine() + operating_system, hostname, operating_system_version, uname, arch, processor = platform.uname() + test_environment_dict[ 'system' ] = '%s %s' % ( operating_system, operating_system_version ) + # Add information about the current Galaxy environment. + test_environment_dict[ 'galaxy_database_version' ] = get_database_version( app ) + test_environment_dict[ 'galaxy_revision' ] = get_repository_current_revision( os.getcwd() ) + # Initialize and populate the tool_test_results_dict. + tool_test_results_dict[ 'test_environment' ] = test_environment_dict + tool_test_results_dict[ 'passed_tests' ] = [] + tool_test_results_dict[ 'failed_tests' ] = [] + tool_test_results_dict[ 'installation_errors' ] = dict( current_repository=[], + repository_dependencies=[], + 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[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + error_message = '' + repository = None + log.debug( "Installing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) ) + # Use the repository information dictionary to generate an install method that will install the repository into the + # embedded Galaxy application, with tool dependencies and repository dependencies, if any. + test_install_repositories.generate_install_method( repository_dict ) + # Configure nose to run the install method as a test. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the configured install method as a test. This method uses the embedded Galaxy application's web interface to + # install the specified repository with tool and repository dependencies also selected for installation. + result, _ = run_tests( test_config ) + try: + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + except Exception, e: + error_message = 'Error getting revision %s of repository %s owned by %s: %s' % ( changeset_revision, name, owner, str( e ) ) + log.exception( error_message ) + return repository, error_message + +def is_latest_downloadable_revision( url, repository_dict ): + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + latest_revision = get_latest_downloadable_changeset_revision( url, name=name, owner=owner ) + return changeset_revision == str( latest_revision ) + +def json_from_url( url ): + error_message = '' + url_handle = urllib.urlopen( url ) + url_contents = url_handle.read() + try: + parsed_json = from_json_string( url_contents ) + except Exception, e: + error_message = str( url_contents ) + log.exception( 'Error parsing JSON data in json_from_url(): %s.' % str( e ) ) + 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, 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( 'The xml document %s containing the exclude list defines the following %s repositories to be excluded from testing...' % \ + ( str( xml_filename ), 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, tool_test_results_dicts, tool_test_results_dict, repository_dict, params, can_update_tool_shed ): + """ + 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 can_update_tool_shed: + metadata_revision_id = repository_dict.get( 'id', None ) + if metadata_revision_id is not None: + tool_test_results_dicts.insert( 0, tool_test_results_dict ) + params[ 'tool_test_results' ] = tool_test_results_dicts + # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. + params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' + 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 {} + else: + return {} + +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 ): + # Group summary display by repository owner. + repository_dicts_by_owner = {} + for repository_dict in repository_dicts: + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + if owner in repository_dicts_by_owner: + repository_dicts_by_owner[ owner ].append( repository_dict ) + else: + repository_dicts_by_owner[ owner ] = [ repository_dict ] + # Display grouped summary. + for owner, grouped_repository_dicts in repository_dicts_by_owner.items(): + print "# " + for repository_dict in grouped_repository_dicts: + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + print "# Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) + +def uninstall_repository_and_repository_dependencies( app, repository_dict ): + """Uninstall a repository and all of its repository dependencies.""" + # This method assumes that the repositor defined by the received repository_dict is not a repository + # dependency of another repository. + sa_session = app.install_model.context + # 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' ] ) + # Since this install and test framework uninstalls repositories immediately after installing and testing + # them, the values of repository.installed_changeset_revision and repository.changeset_revision should be + # the same. + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + if repository.can_uninstall( app ): + # A repository can be uninstalled only if no dependent repositories are installed. So uninstallation order + # id critical. A repository is always uninstalled first, and the each of its dependencies is checked to see + # if it can be uninstalled. + uninstall_repository_dict = dict( name=name, + owner=owner, + changeset_revision=changeset_revision ) + log.debug( 'Revision %s of repository %s owned by %s selected for uninstallation.' % ( changeset_revision, name, owner ) ) + try: + test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) + # 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 all of its repository dependencies, deleting each of them from disk. + result, _ = run_tests( test_config ) + repository_uninstall_successful = result.wasSuccessful() + except Exception, e: + repository_uninstall_successful = False + log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ + ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) + if repository_uninstall_successful: + # Now that the repository is uninstalled we can attempt to uninstall each of its repository dependencies. + # 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. Since some of the repository's repository dependencies may require other of + # the repository's repository dependencies, we'll keep track of the repositories we've been able to unistall. + processed_repository_dependency_ids = [] + while len( processed_repository_dependency_ids ) < len( repository.repository_dependencies ): + for repository_dependency in repository.repository_dependencies: + if repository_dependency.id not in processed_repository_dependency_ids and repository_dependency.can_uninstall( app ): + processed_repository_dependency_ids.append( repository_dependency.id ) + rd_name = str( repository_dependency.name ) + rd_owner = str( repository_dependency.owner ) + rd_changeset_revision = str( repository_dependency.changeset_revision ) + uninstall_repository_dict = dict( name=rd_name, + owner=rd_owner, + changeset_revision=rd_changeset_revision ) + log.debug( 'Revision %s of repository dependency %s owned by %s selected for uninstallation.' % \ + ( rd_changeset_revision, rd_name, rd_owner ) ) + # Generate a test method to uninstall the repository dependency through the embedded Galaxy application's + # web interface. + try: + test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) + # 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. + result, _ = run_tests( test_config ) + if not result.wasSuccessful(): + # We won't set ok here because we'll continue to uninstall whatever we can. + log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % \ + ( rd_changeset_revision, rd_name, rd_owner ) ) + except Exception, e: + log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ + ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) + else: + log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % ( changeset_revision, name, owner ) ) + else: + log_reason_repository_cannot_be_uninstalled( app, repository ) + +def uninstall_tool_dependency( app, tool_dependency ): + """Attempt to uninstall a tool dependency.""" + sa_session = app.install_model.context + # 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 ) + diff -r ce186eb5fefcb7ff332c73bd0869b9e222293d0b -r 0a6f8a07b0c3ca8d58302cb3714ed01d132e52ec test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -24,13 +24,11 @@ # http://code.google.com/p/python-nose/issues/detail?id=284 eggs.require( "pysqlite" ) -test_toolbox = None 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 platform import random import re import shutil @@ -39,37 +37,27 @@ import tempfile import time import threading -import tool_shed.util.shed_util_common as suc -import urllib -from base.tool_shed_util import log_reason_repository_cannot_be_uninstalled +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 install_and_test_tool_shed_repositories.base.util import get_database_version -from install_and_test_tool_shed_repositories.base.util import get_repository_current_revision -from common import update -from datetime import datetime + from galaxy.app import UniverseApplication -from galaxy.util import asbool -from galaxy.util import listify -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 tool_shed.util import tool_dependency_util -from tool_shed.util.xml_util import parse_xml from functional import database_contexts 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' ) +test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_repositories', 'repositories_with_tools' ) + +test_toolbox = None # Here's the directory where everything happens. Temporary directories are created within this directory to contain # the database, new repositories, etc. @@ -78,184 +66,12 @@ default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir -default_galaxy_test_port_min = 10000 -default_galaxy_test_port_max = 10999 -default_galaxy_test_host = '127.0.0.1' -# The following should be an actual value (not None). If developers manually specify their -# tests to use the API it will not work unless a master API key is specified. -default_galaxy_master_api_key = 123456 - # 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: can_update_tool_shed = False else: can_update_tool_shed = True -# Should this serve static resources (scripts, images, styles, etc.)? -STATIC_ENABLED = True - -# Set up a job_conf.xml that explicitly limits jobs to 10 minutes. -job_conf_xml = '''<?xml version="1.0"?> - -<job_conf> - <plugins> - <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> - </plugins> - <handlers> - <handler id="main"/> - </handlers> - <destinations> - <destination id="local" runner="local"/> - </destinations> - <limits> - <limit type="walltime">00:10:00</limit> - </limits> -</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' ) ) -else: - additional_tool_data_tables = None - additional_tool_data_path = None - -# 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' ): - tool_data_table_conf = 'tool_data_table_conf.xml.sample' -else: - tool_data_table_conf = None - -# 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 'GALAXY_INSTALL_TEST_SECRET' not in os.environ: - galaxy_encode_secret = 'changethisinproductiontoo' - os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] = galaxy_encode_secret -else: - galaxy_encode_secret = os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] - -testing_single_repository_dict = {} -if 'repository_name' in os.environ and 'repository_owner' in os.environ: - testing_single_repository_dict[ 'name' ] = str( os.environ[ 'repository_name' ] ) - testing_single_repository_dict[ 'owner' ] = str( os.environ[ 'repository_owner' ] ) - if 'repository_revision' in os.environ: - testing_single_repository_dict[ 'changeset_revision' ] = str( os.environ[ 'repository_revision' ] ) - else: - testing_single_repository_dict[ 'changeset_revision' ] = None - - -class ReportResults( Plugin ): - '''Simple Nose plugin to record the IDs of all tests run, regardless of success.''' - name = "reportresults" - passed = {} - - def options( self, parser, env=os.environ ): - super( ReportResults, self ).options( parser, env=env ) - - def configure(self, options, conf): - super( ReportResults, self ).configure( options, conf ) - if not self.enabled: - return - - def addSuccess( self, test ): - '''Only record test IDs that correspond to tool functional tests.''' - if 'TestForTool' in test.id(): - test_id = test.id() - # Rearrange the test ID to match the format that is produced in test_results.failures - test_id_parts = test_id.split( '.' ) - fixed_test_id = '%s (%s)' % ( test_id_parts[ -1 ], '.'.join( test_id_parts[ :-1 ] ) ) - test_parts = fixed_test_id.split( '/' ) - owner = test_parts[ -4 ] - name = test_parts[ -3 ] - test_identifier = '%s/%s' % ( owner, name ) - if test_identifier not in self.passed: - self.passed[ test_identifier ] = [] - self.passed[ test_identifier ].append( fixed_test_id ) - - def getTestStatus( self, test_identifier ): - if test_identifier in self.passed: - passed_tests = self.passed[ test_identifier ] - del self.passed[ test_identifier ] - return passed_tests - return [] - -def deactivate_repository( app, repository_dict ): - sa_session = app.install_model.context - # 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 ) - repository_dict_for_deactivation = dict( name=name, - owner=owner, - changeset_revision=changeset_revision ) - log.debug( 'Changeset revision %s of repository %s owned by %s selected for deactivation.' % ( changeset_revision, name, owner ) ) - test_install_repositories.generate_deactivate_method( repository_dict_for_deactivation ) - # 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 deactivate method which uses the Galaxy web interface to deactivate the repository. - result, _ = run_tests( test_config ) - success = result.wasSuccessful() - if not success: - log.debug( 'Deactivation of revision %s repository %s owned by %s failed.' % ( changeset_revision, name, owner ) ) - -def get_api_url( base, parts=[], params=None ): - if 'api' in parts and parts.index( 'api' ) != 0: - parts.pop( parts.index( 'api' ) ) - parts.insert( 0, 'api' ) - elif 'api' not in parts: - parts.insert( 0, 'api' ) - url = suc.url_join( base, *parts ) - if params is not None: - query_string = urllib.urlencode( params ) - url += '?%s' % query_string - return url - def get_failed_test_dicts( test_result, from_tool_test=True ): """Extract any useful data from the test_result.failures and test_result.errors attributes.""" failed_test_dicts = [] @@ -304,146 +120,6 @@ failed_test_dicts.append( test_status_dict ) return failed_test_dicts -def get_latest_downloadable_changeset_revision( url, name, owner ): - error_message = '' - parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] - params = dict( name=name, owner=owner ) - api_url = get_api_url( base=url, parts=parts, params=params ) - changeset_revisions, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - if changeset_revisions: - return changeset_revisions[ -1 ], error_message - else: - return suc.INITIAL_CHANGELOG_HASH, error_message - -def get_missing_tool_dependencies( repository ): - log.debug( 'Checking %s repository %s for missing tool dependencies.' % ( repository.status, repository.name ) ) - missing_tool_dependencies = repository.missing_tool_dependencies - for tool_dependency in repository.tool_dependencies: - log.debug( 'Tool dependency %s version %s has status %s.' % ( tool_dependency.name, tool_dependency.version, tool_dependency.status ) ) - for repository_dependency in repository.repository_dependencies: - if repository_dependency.includes_tool_dependencies: - missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency ) ) - return missing_tool_dependencies - -def get_repository_dict( url, repository_dict ): - error_message = '' - parts = [ 'api', 'repositories', repository_dict[ 'repository_id' ] ] - api_url = get_api_url( base=url, parts=parts ) - extended_dict, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - name = str( extended_dict[ 'name' ] ) - owner = str( extended_dict[ 'owner' ] ) - latest_changeset_revision, error_message = get_latest_downloadable_changeset_revision( url, name, owner ) - if error_message: - return None, error_message - extended_dict[ 'latest_revision' ] = str( latest_changeset_revision ) - return extended_dict, error_message - -def get_repository_tuple_from_elem( elem ): - attributes = elem.attrib - name = attributes.get( 'name', None ) - owner = attributes.get( 'owner', None ) - changeset_revision = attributes.get( 'changeset_revision', None ) - return ( name, owner, changeset_revision ) - -def get_repositories_to_install( tool_shed_url ): - """ - Get a list of repository info dicts to install. This method expects a json list of dicts with the following structure: - [{ "changeset_revision": <revision>, - "encoded_repository_id": <encoded repository id from the tool shed>, - "name": <name>, - "owner": <owner>, - "tool_shed_url": <url> }] - """ - error_message = '' - latest_revision_only = '-check_all_revisions' not in sys.argv - if latest_revision_only: - log.debug( 'Testing is restricted to the latest downloadable revision in this test run.' ) - repository_dicts = [] - parts = [ 'repository_revisions' ] - # We'll filter out deprecated repositories from testing since testing them is necessary only if reproducibility - # is guaranteed and we currently do not guarantee reproducibility. - params = dict( do_not_test='false', - downloadable='true', - includes_tools='true', - malicious='false', - missing_test_components='false', - skip_tool_test='false' ) - api_url = get_api_url( base=tool_shed_url, parts=parts, params=params ) - baseline_repository_dicts, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - for baseline_repository_dict in baseline_repository_dicts: - # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the - # module that will generate the install methods. - repository_dict, error_message = get_repository_dict( galaxy_tool_shed_url, baseline_repository_dict ) - if error_message: - log.debug( 'Error getting additional details from the API: %s' % str( error_message ) ) - else: - # Don't test deprecated repositories since testing them is necessary only if reproducibility is guaranteed - # and we are not currently guaranteeing reproducibility. - deprecated = asbool( repository_dict.get( 'deprecated', False ) ) - if not deprecated: - # Don't test empty repositories. - changeset_revision = baseline_repository_dict[ 'changeset_revision' ] - if changeset_revision != suc.INITIAL_CHANGELOG_HASH: - # 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. - if latest_revision_only: - latest_revision = repository_dict[ 'latest_revision' ] - if changeset_revision == latest_revision: - repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - else: - repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - if testing_single_repository_dict: - tsr_name = testing_single_repository_dict[ 'name' ] - tsr_owner = testing_single_repository_dict[ 'owner' ] - tsr_changeset_revision = testing_single_repository_dict[ 'changeset_revision' ] - log.debug( 'Testing single repository with name %s and owner %s.' % ( str( tsr_name ), str( tsr_owner ) ) ) - for repository_to_install in repository_dicts: - rti_name = repository_to_install[ 'name' ] - rti_owner = repository_to_install[ 'owner' ] - rti_changeset_revision = repository_to_install[ 'changeset_revision' ] - if rti_name == tsr_name and rti_owner == tsr_owner: - if tsr_changeset_revision is None: - return [ repository_to_install ], error_message - else: - if tsr_changeset_revision == rti_changeset_revision: - return repository_dicts, error_message - return repository_dicts, error_message - # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL - # environment variable. - log.debug( "The Tool Shed's API url...\n%s" % str( api_url ) ) - log.debug( "...retrieved %d repository revisions for testing." % len( repository_dicts ) ) - log.debug( "Repository revisions for testing:" ) - for repository_dict in repository_dicts: - name = str( repository_dict.get( 'name', None ) ) - owner = str( repository_dict.get( 'owner', None ) ) - changeset_revision = str( repository_dict.get( 'changeset_revision', None ) ) - log.debug( "Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) ) - 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 @@ -455,137 +131,17 @@ tool_id = parts[ -2 ] return tool_id, tool_version -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 - column via the Tool Shed API. - """ +def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): + results_dict = install_and_test_base_util.initialize_results_dict() error_message = '' - parts = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] - api_url = get_api_url( base=tool_shed_url, parts=parts ) - repository_metadata, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - # The tool_test_results used to be stored as a single dictionary rather than a list, but we currently - # return a list. - tool_test_results = listify( repository_metadata.get( 'tool_test_results', [] ) ) - 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_dicts, 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, - # and functional tests should be skipped, since the tool dependency needs to be correctly installed - # for the test to be considered reliable. - log.debug( 'The following dependencies of this repository are missing, so skipping functional tests.' ) - # In keeping with the standard display layout, add the error message to the dict for each tool individually. - for dependency in repository.missing_tool_dependencies: - name = str( dependency.name ) - type = str( dependency.type ) - version = str( dependency.version ) - error_message = unicodify( dependency.error_message ) - log.debug( 'Missing tool dependency %s of type %s version %s: %s' % ( name, type, version, error_message ) ) - test_result = dict( type=dependency.type, - name=dependency.name, - version=dependency.version, - error_message=dependency.error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) - for dependency in repository.missing_repository_dependencies: - name = str( dependency.name ) - owner = str( dependency.owner ) - changeset_revision = str( dependency.changeset_revision ) - error_message = unicodify( dependency.error_message ) - log.debug( 'Missing repository dependency %s changeset revision %s owned by %s: %s' % \ - ( name, changeset_revision, owner, error_message ) ) - test_result = dict( tool_shed=dependency.tool_shed, - name=dependency.name, - owner=dependency.owner, - changeset_revision=dependency.changeset_revision, - error_message=dependency.error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) - # Record the status of this repository in the tool shed. - params = dict( tools_functionally_correct=False, - do_not_test=False, - test_install_error=True ) - # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) - # Since this repository is missing components, we do not want to test it, so deactivate it or uninstall it. - # The deactivate flag is set to True if the environment variable GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES - # is set to 'true'. - deactivate = asbool( os.environ.get( 'GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES', False ) ) - if deactivate: - for missing_tool_dependency in missing_tool_dependencies: - uninstall_tool_dependency( app, missing_tool_dependency ) - # We are deactivating this repository and all of its repository dependencies. - deactivate_repository( app, repository_dict ) - else: - # We are uninstalling this repository and all of its repository dependencies. - uninstall_repository_and_repository_dependencies( app, repository_dict ) - results_dict[ 'repositories_failed_install' ].append( dict( name=str( repository.name ), - owner=str( repository.owner ), - changeset_revision=str( repository.changeset_revision ) ) ) - # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. - test_toolbox.toolbox = app.toolbox - return results_dict - -def initialize_results_dict(): - # Initialize a dictionary for the summary that will be printed to stdout. - results_dict = {} - results_dict[ 'total_repositories_tested' ] = 0 - results_dict[ 'all_tests_passed' ] = [] - results_dict[ 'at_least_one_test_failed' ] = [] - results_dict[ 'repositories_failed_install' ] = [] - return 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[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - error_message = '' - repository = None - log.debug( "Installing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) ) - # Explicitly clear tests from twill's test environment. - remove_generated_tests( app ) - # Use the repository information dictionary to generate an install method that will install the repository into the - # embedded Galaxy application, with tool dependencies and repository dependencies, if any. - test_install_repositories.generate_install_method( repository_dict ) - # Configure nose to run the install method as a test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the configured install method as a test. This method uses the embedded Galaxy application's web interface to - # install the specified repository with tool and repository dependencies also selected for installation. - result, _ = run_tests( test_config ) - try: - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - except Exception, e: - error_message = 'Error getting revision %s of repository %s owned by %s: %s' % ( changeset_revision, name, owner, str( e ) ) - log.exception( error_message ) - return repository, error_message - -def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): - results_dict = initialize_results_dict() - error_message = '' - # Allow the option to keep or delete tool dependencies when a repository has been tested. - deactivate = asbool( os.environ.get( 'GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES', False ) ) # Initialize a dictionary for the summary that will be printed to stdout. total_repositories_tested = results_dict[ 'total_repositories_tested' ] - repositories_to_install, error_message = get_repositories_to_install( galaxy_tool_shed_url ) + repositories_to_install, error_message = \ + install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url ) if error_message: return None, error_message # Handle repositories not to be tested. - if os.path.exists( exclude_list_file ): + if os.path.exists( install_and_test_base_util.exclude_list_file ): # Entries in the exclude_list look something like this. # { 'reason': The default reason or the reason specified in this section, # 'repositories': @@ -597,8 +153,8 @@ # 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...', exclude_list_file ) - exclude_list = parse_exclude_list( exclude_list_file ) + log.debug( 'Loading the list of repositories excluded from testing from the file %s...', install_and_test_base_util.exclude_list_file ) + exclude_list = install_and_test_base_util.parse_exclude_list( install_and_test_base_util.exclude_list_file ) else: exclude_list = [] # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was @@ -627,7 +183,7 @@ # "user_id": "529fd61ab1c6cc36" } encoded_repository_metadata_id = repository_dict.get( 'id', None ) # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. - repository_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url + repository_dict[ 'tool_shed_url' ] = install_and_test_base_util.galaxy_tool_shed_url # Get the name and owner out of the repository info dict. name = str( repository_dict[ 'name' ] ) owner = str( repository_dict[ 'owner' ] ) @@ -635,31 +191,13 @@ log.debug( "Processing revision %s of repository %s owned by %s..." % ( changeset_revision, name, owner ) ) repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) # Retrieve the stored list of tool_test_results_dicts. - tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, encoded_repository_metadata_id ) + tool_test_results_dicts, error_message = \ + install_and_test_base_util.get_tool_test_results_dicts( install_and_test_base_util.galaxy_tool_shed_url, + encoded_repository_metadata_id ) if error_message: log.debug( error_message ) else: - 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 - # entry. If it contains more entries, then the script ~/tool_shed/api/check_repositories_for_functional_tests.py - # was not executed in preparation for this script's execution, so we'll just create an empty dictionary. - tool_test_results_dict = tool_test_results_dicts[ 0 ] - if len( tool_test_results_dict ) <= 1: - # We can re-use the mostly empty tool_test_results_dict for this run because it is either empty or it contains only - # a test_environment entry. If we use it we need to temporarily eliminate it from the list of 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: - # 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 ) - else: - # 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, - tool_test_results_dict = {} + tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) # See if this repository should be skipped for any reason. this_repository_is_in_the_exclude_list = False skip_reason = None @@ -675,37 +213,20 @@ params = dict( tools_functionally_correct=False, do_not_test=False ) # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( "Not testing revision %s of repository %s owned by %s because it is in the exclude list for this test run." % \ ( changeset_revision, name, owner ) ) else: - test_environment_dict = tool_test_results_dict.get( 'test_environment', {} ) - if len( test_environment_dict ) == 0: - # Set information about the tool shed to nothing since we cannot currently determine it from here. - # We could eventually add an API method... - test_environment_dict = dict( tool_shed_database_version='', - tool_shed_mercurial_version='', - tool_shed_revision='' ) - # Add the current time as the approximate time that this test run occurs. A similar value will also be - # set to the repository_metadata.time_last_tested column, but we also store it here because the Tool Shed - # may be configured to store multiple test run results, so each must be associated with a time stamp. - now = time.strftime( "%Y-%m-%d %H:%M:%S" ) - # Add information about the current platform. - test_environment_dict[ 'time_tested' ] = now - test_environment_dict[ 'python_version' ] = platform.python_version() - test_environment_dict[ 'architecture' ] = platform.machine() - operating_system, hostname, operating_system_version, uname, arch, processor = platform.uname() - test_environment_dict[ 'system' ] = '%s %s' % ( operating_system, operating_system_version ) - # Add information about the current Galaxy environment. - test_environment_dict[ 'galaxy_database_version' ] = get_database_version( app ) - test_environment_dict[ 'galaxy_revision' ] = get_repository_current_revision( os.getcwd() ) - # Initialize and populate the tool_test_results_dict. - tool_test_results_dict[ 'test_environment' ] = test_environment_dict - tool_test_results_dict[ 'passed_tests' ] = [] - tool_test_results_dict[ 'failed_tests' ] = [] - tool_test_results_dict[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) + tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) + # Explicitly clear tests from twill's test environment. + remove_generated_tests( app ) # Proceed with installing repositories and testing contained tools. - repository, error_message = install_repository( app, repository_dict ) + repository, error_message = install_and_test_base_util.install_repository( app, repository_dict ) if error_message: 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. @@ -715,7 +236,7 @@ except Exception, e: error_message = 'Unable to find installed repository %s owned by %s: %s.' % ( name, owner, str( e ) ) log.exception( error_message ) - test_result = dict( tool_shed=galaxy_tool_shed_url, + test_result = dict( tool_shed=install_and_test_base_util.galaxy_tool_shed_url, name=name, owner=owner, changeset_revision=changeset_revision, @@ -725,20 +246,20 @@ test_install_error=True, do_not_test=False ) # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) try: - if deactivate: - # We are deactivating this repository and all of its repository dependencies. - deactivate_repository( app, repository_dict ) - else: - # We are uninstalling this repository and all of its repository dependencies. - uninstall_repository_and_repository_dependencies( app, repository_dict ) - except: - log.exception( 'Encountered error attempting to deactivate or uninstall %s.', str( repository_dict[ 'name' ] ) ) + # 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 ) ) ) + # Clean out any generated tests. This is necessary for Twill. + remove_generated_tests( app ) results_dict[ 'repositories_failed_install' ].append( repository_identifier_dict ) log.debug( 'Repository %s failed to install correctly.' % str( name ) ) else: @@ -757,15 +278,18 @@ # missing test components. if 'missing_test_components' not in tool_test_results_dict: tool_test_results_dict[ 'missing_test_components' ] = [] - missing_tool_dependencies = get_missing_tool_dependencies( repository ) + missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) if missing_tool_dependencies or repository.missing_repository_dependencies: - results_dict = handle_missing_dependencies( app, - repository, - missing_tool_dependencies, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - results_dict ) + results_dict = install_and_test_base_util.handle_missing_dependencies( app, + repository, + missing_tool_dependencies, + repository_dict, + tool_test_results_dicts, + tool_test_results_dict, + results_dict, + can_update_tool_shed ) + # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. + test_toolbox.toolbox = app.toolbox else: # If the repository has a test-data directory we write the generated shed_tools_dict to a file, so the functional # test framework can find it. @@ -787,49 +311,35 @@ do_not_test=False, test_install_error=False ) # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) + response_dict = \ + install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) results_dict[ 'at_least_one_test_failed' ].append( repository_identifier_dict ) total_repositories_tested += 1 results_dict[ 'total_repositories_tested' ] = total_repositories_tested return results_dict, error_message -def is_latest_downloadable_revision( url, repository_dict ): - latest_revision = get_latest_downloadable_changeset_revision( url, name=repository_dict[ 'name' ], owner=repository_dict[ 'owner' ] ) - return str( repository_dict[ 'changeset_revision' ] ) == str( latest_revision ) - -def json_from_url( url ): - error_message = '' - url_handle = urllib.urlopen( url ) - url_contents = url_handle.read() - try: - parsed_json = from_json_string( url_contents ) - except Exception, e: - error_message = str( url_contents ) - log.exception( 'Error parsing JSON data in json_from_url(): %s.' % str( e ) ) - return None, error_message - return parsed_json, error_message - def main(): - if tool_shed_api_key is None: + if install_and_test_base_util.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: + if install_and_test_base_util.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 ) + galaxy_test_host = os.environ.get( 'GALAXY_INSTALL_TEST_HOST', install_and_test_base_util.default_galaxy_test_host ) # 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 # 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 ) ) + galaxy_test_port = os.environ.get( 'GALAXY_INSTALL_TEST_PORT', str( install_and_test_base_util.default_galaxy_test_port_max ) ) os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port tool_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_PATH', 'tools' ) if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: @@ -844,7 +354,7 @@ 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 ) + install_and_test_base_util.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', @@ -896,18 +406,18 @@ pass print "Database connection: ", database_connection # Generate the shed_tool_data_table_conf.xml file. - file( shed_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template ) + file( shed_tool_data_table_conf_file, 'w' ).write( install_and_test_base_util.tool_data_table_conf_xml_template ) os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file # ---- Start up a Galaxy instance ------------------------------------------------------ # Generate the tool_conf.xml file. - file( galaxy_tool_conf_file, 'w' ).write( tool_conf_xml ) + file( galaxy_tool_conf_file, 'w' ).write( install_and_test_base_util.tool_conf_xml ) # Generate the job_conf.xml file. - file( galaxy_job_conf_file, 'w' ).write( job_conf_xml ) + file( galaxy_job_conf_file, 'w' ).write( install_and_test_base_util.job_conf_xml ) # Generate the tool_sheds_conf.xml file, but only if a the user has not specified an existing one in the environment. if 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF' not in os.environ: - file( galaxy_tool_sheds_conf_file, 'w' ).write( tool_sheds_conf_xml ) + file( galaxy_tool_sheds_conf_file, 'w' ).write( install_and_test_base_util.tool_sheds_conf_xml ) # Generate the shed_tool_conf.xml file. - tool_conf_template_parser = string.Template( shed_tool_conf_xml_template ) + tool_conf_template_parser = string.Template( install_and_test_base_util.shed_tool_conf_xml_template ) shed_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_shed_tool_path ) file( galaxy_shed_tool_conf_file, 'w' ).write( shed_tool_conf_xml ) os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file @@ -917,14 +427,14 @@ # Write the embedded web application's specific configuration to a temporary file. This is necessary in order for # the external metadata script to find the right datasets. kwargs = dict( admin_users = 'test(a)bx.psu.edu', - master_api_key = default_galaxy_master_api_key, + master_api_key = install_and_test_base_util.default_galaxy_master_api_key, allow_user_creation = True, allow_user_deletion = True, allow_library_path_paste = True, database_connection = database_connection, datatype_converters_config_file = "datatype_converters_conf.xml.sample", file_path = galaxy_file_path, - id_secret = galaxy_encode_secret, + id_secret = install_and_test_base_util.galaxy_encode_secret, job_config_file = galaxy_job_conf_file, job_queue_workers = 5, log_destination = "stdout", @@ -955,7 +465,7 @@ generate_config_file( 'universe_wsgi.ini.sample', galaxy_config_file, config_items ) kwargs[ 'tool_config_file' ] = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] # Set the global_conf[ '__file__' ] option to the location of the temporary .ini file, which gets passed to set_metadata.sh. - kwargs[ 'global_conf' ] = get_webapp_global_conf() + kwargs[ 'global_conf' ] = install_and_test_base_util.get_webapp_global_conf() kwargs[ 'global_conf' ][ '__file__' ] = galaxy_config_file # ---- Build Galaxy Application -------------------------------------------------- if not database_connection.startswith( 'sqlite://' ): @@ -972,11 +482,11 @@ log.debug( "Embedded Galaxy application started..." ) # ---- Run galaxy webserver ------------------------------------------------------ server = None - global_conf = get_webapp_global_conf() + global_conf = install_and_test_base_util.get_webapp_global_conf() global_conf[ 'database_file' ] = database_connection webapp = buildapp.app_factory( global_conf, use_translogger=False, - static_enabled=STATIC_ENABLED, + static_enabled=install_and_test_base_util.STATIC_ENABLED, app=app ) # Serve the app on a specified or random port. if galaxy_test_port is not None: @@ -985,7 +495,8 @@ random.seed() for i in range( 0, 9 ): try: - galaxy_test_port = str( random.randint( default_galaxy_test_port_min, default_galaxy_test_port_max ) ) + galaxy_test_port = str( random.randint( install_and_test_base_util.default_galaxy_test_port_min, + install_and_test_base_util.default_galaxy_test_port_max ) ) log.debug( "Attempting to serve app on randomly chosen port: %s", galaxy_test_port ) server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) break @@ -995,7 +506,7 @@ raise else: raise Exception( "Unable to open a port between %s and %s to start Galaxy server" % \ - ( default_galaxy_test_port_min, default_galaxy_test_port_max ) ) + ( install_and_test_base_util.default_galaxy_test_port_min, install_and_test_base_util.default_galaxy_test_port_max ) ) os.environ[ 'GALAXY_INSTALL_TEST_PORT' ] = galaxy_test_port # Start the server. t = threading.Thread( target=server.serve_forever ) @@ -1012,12 +523,11 @@ raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" ) log.debug( "Embedded galaxy web server started..." ) log.debug( "The embedded Galaxy application is running on %s:%s" % ( str( galaxy_test_host ), str( galaxy_test_port ) ) ) - log.debug( "Repositories will be installed from the tool shed at %s" % str( galaxy_tool_shed_url ) ) - success = False + log.debug( "Repositories will be installed from the tool shed at %s" % str( install_and_test_base_util.galaxy_tool_shed_url ) ) # If a tool_data_table_conf.test.xml file was found, add the entries from it into the app's tool data tables. - if additional_tool_data_tables: - app.tool_data_tables.add_new_entries_from_config_file( config_filename=additional_tool_data_tables, - tool_data_path=additional_tool_data_path, + if install_and_test_base_util.additional_tool_data_tables: + app.tool_data_tables.add_new_entries_from_config_file( config_filename=install_and_test_base_util.additional_tool_data_tables, + tool_data_path=install_and_test_base_util.additional_tool_data_path, shed_tool_data_table_config=None, persist=False ) now = time.strftime( "%Y-%m-%d %H:%M:%S" ) @@ -1042,21 +552,15 @@ if all_tests_passed: print '# ----------------------------------------------------------------------------------' print "# %d repositories successfully passed all functional tests:" % len( all_tests_passed ) - show_summary_output( all_tests_passed ) + install_and_test_base_util.show_summary_output( all_tests_passed ) if at_least_one_test_failed: print '# ----------------------------------------------------------------------------------' print "# %d repositories failed at least 1 functional test:" % len( at_least_one_test_failed ) - show_summary_output( at_least_one_test_failed ) + install_and_test_base_util.show_summary_output( at_least_one_test_failed ) if repositories_failed_install: - # Set success to False so that the return code will not be 0. - success = False print '# ----------------------------------------------------------------------------------' print "# %d repositories have installation errors:" % len( repositories_failed_install ) - show_summary_output( repositories_failed_install ) - else: - success = True - else: - success = True + install_and_test_base_util.show_summary_output( repositories_failed_install ) print "####################################################################################" log.debug( "Shutting down..." ) # Gracefully shut down the embedded web server and UniverseApplication. @@ -1081,78 +585,8 @@ 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, 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( 'The xml document %s containing the exclude list defines the following %s repositories to be excluded from testing...' % \ - ( str( xml_filename ), 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, tool_test_results_dicts, tool_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 can_update_tool_shed: - metadata_revision_id = repository_dict.get( 'id', None ) - if metadata_revision_id is not None: - tool_test_results_dicts.insert( 0, tool_test_results_dict ) - params[ 'tool_test_results' ] = tool_test_results_dicts - # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. - params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' - 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 {} - else: - return {} + # Return a "successful" response to buildbot. + return 0 def remove_generated_tests( app ): """ @@ -1195,42 +629,6 @@ # 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 ): - # Group summary display by repository owner. - repository_dicts_by_owner = {} - for repository_dict in repository_dicts: - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - if owner in repository_dicts_by_owner: - repository_dicts_by_owner[ owner ].append( repository_dict ) - else: - repository_dicts_by_owner[ owner ] = [ repository_dict ] - # Display grouped summary. - for owner, grouped_repository_dicts in repository_dicts_by_owner.items(): - print "# " - for repository_dict in grouped_repository_dicts: - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - print "# Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) - def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, results_dict ): """Test tools contained in the received repository.""" name = str( repository.name ) @@ -1241,12 +639,12 @@ 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 ) + test_toolbox.build_tests( testing_shed_tools=True, master_api_key=install_and_test_base_util.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 ) + result, test_plugins = install_and_test_base_util.run_tests( test_config ) if result.wasSuccessful(): # This repository's tools passed all functional tests. Use the ReportResults nose plugin to get a list # of tests that passed. @@ -1271,11 +669,12 @@ # 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. # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( 'Revision %s of repository %s owned by %s installed and passed functional tests.' % \ ( changeset_revision, name, owner ) ) else: @@ -1284,127 +683,30 @@ tool_test_results_dict[ 'failed_tests' ] = failed_test_dicts failed_repository_dict = repository_identifier_dict results_dict[ 'at_least_one_test_failed' ].append( failed_repository_dict ) - set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_dict ) + set_do_not_test = not is_latest_downloadable_revision( install_and_test_base_util.galaxy_tool_shed_url, repository_dict ) params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=str( set_do_not_test ) ) # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( 'Revision %s of repository %s owned by %s installed successfully but did not pass functional tests.' % \ ( changeset_revision, name, owner ) ) # 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_and_repository_dependencies( app, repository_dict ) + 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. + install_and_test_base_util.uninstall_repository_and_repository_dependencies( app, repository_dict ) + # Clean out any generated tests. This is necessary for Twill. + remove_generated_tests( app ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox return results_dict -def uninstall_repository_and_repository_dependencies( app, repository_dict ): - """Uninstall a repository and all of its repository dependencies.""" - # This method assumes that the repositor defined by the received repository_dict is not a repository - # dependency of another repository. - sa_session = app.install_model.context - # 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' ] ) - # Since this install and test framework uninstalls repositories immediately after installing and testing - # them, the values of repository.installed_changeset_revision and repository.changeset_revision should be - # the same. - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - if repository.can_uninstall( app ): - # A repository can be uninstalled only if no dependent repositories are installed. So uninstallation order - # id critical. A repository is always uninstalled first, and the each of its dependencies is checked to see - # if it can be uninstalled. - uninstall_repository_dict = dict( name=name, - owner=owner, - changeset_revision=changeset_revision ) - log.debug( 'Revision %s of repository %s owned by %s selected for uninstallation.' % ( changeset_revision, name, owner ) ) - try: - test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) - # 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 all of its repository dependencies, deleting each of them from disk. - result, _ = run_tests( test_config ) - repository_uninstall_successful = result.wasSuccessful() - except Exception, e: - repository_uninstall_successful = False - log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ - ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) - if repository_uninstall_successful: - # Now that the repository is uninstalled we can attempt to uninstall each of its repository dependencies. - # 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. Since some of the repository's repository dependencies may require other of - # the repository's repository dependencies, we'll keep track of the repositories we've been able to unistall. - processed_repository_dependency_ids = [] - while len( processed_repository_dependency_ids ) < len( repository.repository_dependencies ): - for repository_dependency in repository.repository_dependencies: - if repository_dependency.id not in processed_repository_dependency_ids and repository_dependency.can_uninstall( app ): - processed_repository_dependency_ids.append( repository_dependency.id ) - rd_name = str( repository_dependency.name ) - rd_owner = str( repository_dependency.owner ) - rd_changeset_revision = str( repository_dependency.changeset_revision ) - uninstall_repository_dict = dict( name=rd_name, - owner=rd_owner, - changeset_revision=rd_changeset_revision ) - log.debug( 'Revision %s of repository dependency %s owned by %s selected for uninstallation.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) ) - # Generate a test method to uninstall the repository dependency through the embedded Galaxy application's - # web interface. - try: - test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) - # 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. - result, _ = run_tests( test_config ) - if not result.wasSuccessful(): - # We won't set ok here because we'll continue to uninstall whatever we can. - log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) ) - except Exception, e: - log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ - ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) - else: - log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % ( changeset_revision, name, owner ) ) - else: - log_reason_repository_cannot_be_uninstalled( app, repository ) - -def uninstall_tool_dependency( app, tool_dependency ): - """Attempt to uninstall a tool dependency.""" - sa_session = app.install_model.context - # 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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commit/galaxy-central: jmchilton: In upload tool sort FTP files by default.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce186eb5fefc/ Changeset: ce186eb5fefc User: jmchilton Date: 2013-12-18 15:19:58 Summary: In upload tool sort FTP files by default. Not doing enough... but it is a step forward. http://dev.list.galaxyproject.org/sort-list-of-ftp-uploaded-files-tp4662859… Affected #: 1 file diff -r c5c4deabb7316f2ef45ff8fb2718d167d91d09c0 -r ce186eb5fefcb7ff332c73bd0869b9e222293d0b lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -3,6 +3,8 @@ """ import logging, sys, os, time + +from operator import itemgetter from cgi import escape from galaxy.util import restore_text, relpath, nice_size, unicodify from galaxy.web import url_for @@ -212,6 +214,7 @@ ctime=time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) if not uploads: rval += '<tr><td colspan="4"><em>Your FTP upload directory contains no files.</em></td></tr>' + uploads = sorted(uploads, key=itemgetter("path")) for upload in uploads: rval += FTPFileField.trow % ( prefix, self.name, upload['path'], upload['path'], upload['size'], upload['ctime'] ) rval += FTPFileField.tfoot 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.

1 0

commit/galaxy-central: jmchilton: Backout of 714f5b1 for now.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c5c4deabb731/ Changeset: c5c4deabb731 User: jmchilton Date: 2013-12-18 08:23:27 Summary: Backout of 714f5b1 for now. jgoecks_: jmchilto1: 714f5b1 seems to have broken HDA ordering in history panel Affected #: 3 files diff -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 -r c5c4deabb7316f2ef45ff8fb2718d167d91d09c0 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -19,7 +19,6 @@ import socket import time from string import Template -from itertools import ifilter import galaxy.datatypes import galaxy.datatypes.registry @@ -44,11 +43,6 @@ # Default Value Required for unit tests datatypes_registry.load_datatypes() -# When constructing filters with in for a fixed set of ids, maximum -# number of items to place in the IN statement. Different databases -# are going to have different limits so it is likely best to not let -# this be unlimited - filter in Python if over this limit. -MAX_IN_FILTER_LENGTH = 100 class NoConverterException(Exception): def __init__(self, value): @@ -899,32 +893,6 @@ rval = galaxy.datatypes.data.nice_size( rval ) return rval - def contents_iter( self, **kwds ): - """ - Fetch filtered list of contents of history. - """ - python_filter = None - db_session = object_session( self ) - assert db_session != None - query = db_session.query( HistoryDatasetAssociation ).filter( HistoryDatasetAssociation.table.c.history_id == self.id ) - deleted = galaxy.util.string_as_bool_or_none( kwds.get( 'deleted', None ) ) - if deleted is not None: - query = query.filter( HistoryDatasetAssociation.deleted == bool( kwds['deleted'] ) ) - visible = galaxy.util.string_as_bool_or_none( kwds.get( 'visible', None ) ) - if visible is not None: - query = query.filter( HistoryDatasetAssociation.visible == bool( kwds['visible'] ) ) - if 'ids' in kwds: - ids = kwds['ids'] - max_in_filter_length = kwds.get('max_in_filter_length', MAX_IN_FILTER_LENGTH) - if len(ids) < max_in_filter_length: - query = query.filter( HistoryDatasetAssociation.id.in_(ids) ) - else: - python_filter = lambda hda: hda.id in ids - if python_filter: - return ifilter(python_filter, query) - else: - return query - def copy_tags_from(self,target_user,source_history): for src_shta in source_history.tags: new_shta = src_shta.copy() diff -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 -r c5c4deabb7316f2ef45ff8fb2718d167d91d09c0 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -51,28 +51,47 @@ else: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) - contents_kwds = {} + # if ids, return _FULL_ data (as show) for each id passed if ids: - ids = map( lambda id: trans.security.decode_id( id ), ids.split( ',' ) ) - contents_kwds[ 'ids' ] = ids - # If explicit ids given, always used detailed result. - details = 'all' + ids = ids.split( ',' ) + for index, hda in enumerate( history.datasets ): + encoded_hda_id = trans.security.encode_id( hda.id ) + if encoded_hda_id in ids: + #TODO: share code with show + rval.append( self._detailed_hda_dict( trans, hda ) ) + + # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history else: - contents_kwds[ 'deleted' ] = kwd.get( 'deleted', None ) - contents_kwds[ 'visible' ] = kwd.get( 'visible', None ) # details param allows a mixed set of summary and detailed hdas #TODO: this is getting convoluted due to backwards compat details = kwd.get( 'details', None ) or [] if details and details != 'all': details = util.listify( details ) - for hda in history.contents_iter( **contents_kwds ): - encoded_hda_id = trans.security.encode_id( hda.id ) - detailed = details == 'all' or ( encoded_hda_id in details ) - if detailed: - rval.append( self._detailed_hda_dict( trans, hda ) ) - else: - rval.append( self._summary_hda_dict( trans, history_id, hda ) ) + # by default return all datasets - even if deleted or hidden (defaulting the next switches to None) + # if specified return those datasets that match the setting + # backwards compat + return_deleted = util.string_as_bool_or_none( kwd.get( 'deleted', None ) ) + return_visible = util.string_as_bool_or_none( kwd.get( 'visible', None ) ) + + for hda in history.datasets: + # if either return_ setting has been requested (!= None), skip hdas that don't match the request + if return_deleted is not None: + if( ( return_deleted and not hda.deleted ) + or ( not return_deleted and hda.deleted ) ): + continue + if return_visible is not None: + if( ( return_visible and not hda.visible ) + or ( not return_visible and hda.visible ) ): + continue + + encoded_hda_id = trans.security.encode_id( hda.id ) + if( ( encoded_hda_id in details ) + or ( details == 'all' ) ): + rval.append( self._detailed_hda_dict( trans, hda ) ) + else: + rval.append( self._summary_hda_dict( trans, history_id, hda ) ) + except Exception, e: # for errors that are not specific to one hda (history lookup or summary list) rval = "Error in history API at listing contents: " + str( e ) diff -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 -r c5c4deabb7316f2ef45ff8fb2718d167d91d09c0 test/unit/test_galaxy_mapping.py --- a/test/unit/test_galaxy_mapping.py +++ b/test/unit/test_galaxy_mapping.py @@ -180,39 +180,6 @@ assert hist1.name == "History 2b" # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like. - def test_history_contents( self ): - model = self.model - u = model.User( email="contents(a)foo.bar.baz", password="password" ) - # gs = model.GalaxySession() - h1 = model.History( name="HistoryContentsHistory1", user=u) - - self.persist( u, h1, expunge=True ) - - d1 = self.new_hda( h1, name="1" ) - d2 = self.new_hda( h1, name="2", visible=False ) - d3 = self.new_hda( h1, name="3", deleted=True ) - d4 = self.new_hda( h1, name="4", visible=False, deleted=True ) - - def contents_iter_names(**kwds): - history = model.context.query( model.History ).filter( - model.History.name == "HistoryContentsHistory1" - ).first() - return set( map( lambda hda: hda.name, history.contents_iter( **kwds ) ) ) - - assert contents_iter_names() == set( [ "1", "2", "3", "4" ] ) - assert contents_iter_names( deleted=False ) == set( [ "1", "2" ] ) - assert contents_iter_names( visible=True ) == set( [ "1", "3" ] ) - assert contents_iter_names( visible=False ) == set( [ "2", "4" ] ) - assert contents_iter_names( deleted=True, visible=False ) == set( [ "4" ] ) - - assert contents_iter_names( ids=[ d1.id, d2.id, d3.id, d4.id ] ) == set( [ "1", "2", "3", "4" ] ) - assert contents_iter_names( ids=[ d1.id, d2.id, d3.id, d4.id ], max_in_filter_length=1 ) == set( [ "1", "2", "3", "4" ] ) - - assert contents_iter_names( ids=[ d1.id, d3.id ] ) == set( [ "1", "3" ] ) - - def new_hda( self, history, **kwds ): - return self.persist( self.model.HistoryDatasetAssociation( history=history, create_dataset=True, sa_session=self.model.session, **kwds ), flush=True ) - @classmethod def setUpClass(cls): # Start the database and connect the mapping @@ -224,16 +191,10 @@ return cls.model.session.query( type ) @classmethod - def persist(cls, *args, **kwargs): - session = cls.model.session - flush = kwargs.get('flush', True) + def persist(cls, *args): for arg in args: - session.add( arg ) - if flush: - session.flush() - if kwargs.get('expunge', not flush): - cls.expunge() - return arg # Return last or only arg. + cls.model.session.add( arg ) + cls.expunge() @classmethod def expunge(cls): 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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commit/galaxy-central: inithello: Fixes for test scripts 1010, 1080, 1400, and 1460.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/41c6ee05c8ac/ Changeset: 41c6ee05c8ac User: inithello Date: 2013-12-17 21:54:55 Summary: Fixes for test scripts 1010, 1080, 1400, and 1460. Affected #: 5 files diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1338,7 +1338,7 @@ def verify_installed_repository_data_table_entries( self, required_data_table_entries ): # The value of the received required_data_table_entries will be something like: [ 'sam_fa_indexes' ] - data_tables = xml_util.parse_xml( self.shed_tool_data_table_conf ) + data_tables, error_message = xml_util.parse_xml( self.shed_tool_data_table_conf ) found = False # With the tool shed, the "path" attribute that is hard-coded into the tool_data_tble_conf.xml # file is ignored. This is because the tool shed requires the directory location to which this diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py --- a/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py +++ b/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py @@ -285,6 +285,7 @@ 'Uninstalled' ] self.display_installed_repository_manage_page( installed_convert_repository, strings_displayed=strings_displayed ) + self.test_db_util.install_session.refresh( installed_column_repository ) self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'column_maker' ) def test_0065_reinstall_column_repository( self ): @@ -330,6 +331,7 @@ 'Deactivated' ] self.display_installed_repository_manage_page( installed_column_repository, strings_displayed=strings_displayed ) + self.test_db_util.install_session.refresh( installed_convert_repository ) self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'convert_chars' ) def test_0075_uninstall_column_repository( self ): @@ -387,8 +389,8 @@ common.test_user_1_name ) self.uninstall_repository( installed_column_repository, remove_from_disk=False ) self.uninstall_repository( installed_convert_repository, remove_from_disk=False ) - self.test_db_util.ga_refresh( installed_column_repository ) - self.test_db_util.ga_refresh( installed_convert_repository ) + self.test_db_util.install_session.refresh( installed_column_repository ) + self.test_db_util.install_session.refresh( installed_convert_repository ) self.check_galaxy_repository_tool_panel_section( installed_column_repository, '' ) self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'convert_chars' ) diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/functional/test_1160_circular_prior_installation_required.py --- a/test/tool_shed/functional/test_1160_circular_prior_installation_required.py +++ b/test/tool_shed/functional/test_1160_circular_prior_installation_required.py @@ -247,7 +247,7 @@ convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) # Filtering was selected for reinstallation, so convert chars and column maker should have been installed first. for repo in [ convert_repository, column_repository, filter_repository ]: - self.test_db_util.ga_session.refresh( repo ) + self.test_db_util.install_session.refresh( repo ) assert filter_repository.update_time > convert_repository.update_time, 'Prior installed convert_chars_0160 shows a later update time than filtering_0160' assert filter_repository.update_time > column_repository.update_time, 'Prior installed column_maker_0160 shows a later update time than filtering_0160' diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/functional/test_1400_review_migration_stages.py --- a/test/tool_shed/functional/test_1400_review_migration_stages.py +++ b/test/tool_shed/functional/test_1400_review_migration_stages.py @@ -34,8 +34,8 @@ migrated_tool_dependencies = [ 'emboss', '5.0.0', 'freebayes', '0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8', 'samtools', '0.1.18', 'blast+', '2.2.26+', 'bwa', '0.5.9', 'picard', '1.56.0', 'lastz', '1.02.00', 'bowtie', '0.12.7', 'FreeBayes requires g++', 'ncurses', 'zlib', - 'zlib and libpthread', 'blast.ncbi.nlm.nih.gov', 'fastx_toolkit', '0.0.13', - 'samtools', '0.1.16', 'cufflinks', '2.1.1', 'R', '2.11.0' ] + 'blast.ncbi.nlm.nih.gov', 'fastx_toolkit', '0.0.13', 'samtools', '0.1.16', 'cufflinks', + '2.1.1', 'R', '2.11.0' ] migration_scripts = [ '0002_tools.sh', '0003_tools.sh', '0004_tools.sh', '0005_tools.sh', '0006_tools.sh', '0007_tools.sh', '0008_tools.sh' ] stages.extend( migration_scripts + migrated_tool_dependencies + migrated_repository_names ) diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -391,7 +391,7 @@ use_heartbeat = False ) # ---- Build Galaxy Application -------------------------------------------------- - if not galaxy_database_connection.startswith( 'sqlite://' ): + if not galaxy_database_connection.startswith( 'sqlite://' ) and not install_galaxy_database_connection.startswith( 'sqlite://' ): kwargs[ 'database_engine_option_pool_size' ] = '10' kwargs[ 'database_engine_option_max_overflow' ] = '20' galaxyapp = GalaxyUniverseApplication( **kwargs ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Tool shed install and test framework changes to enable soon coming testing of repositories of type tool_dependency_definition.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/43b23f550399/ Changeset: 43b23f550399 User: greg Date: 2013-12-17 20:59:47 Summary: Tool shed install and test framework changes to enable soon coming testing of repositories of type tool_dependency_definition. Affected #: 5 files diff -r b1e82182414d359f6f43e117e92ec6d6638878fe -r 43b23f5503997727debf8232239434974491e55e install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -2,14 +2,16 @@ # A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/ -# The test/install_and_test_tool_shed_repositories/functional_tests.py can not be executed directly, because it must have certain functional test definitions -# in sys.argv. Running it through this shell script is the best way to ensure that it has the required definitions. +# The test/install_and_test_tool_shed_repositories/functional_tests.py cannot be executed directly because it must +# have certain functional test definitions in sys.argv. Running it through this shell script is the best way to +# ensure that it has the required definitions. -# This script requires the following environment variables: +# This script requires setting of the following environment variables: # GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY - must be set to the API key for the tool shed that is being checked. # GALAXY_INSTALL_TEST_TOOL_SHED_URL - must be set to a URL that the tool shed is listening on. -# If the tool shed url is not specified in tool_sheds_conf.xml, GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must be set to a tool sheds configuration file -# that does specify that url, otherwise repository installation will fail. + +# If the tool shed url is not specified in tool_sheds_conf.xml, GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must be set to +# a tool sheds configuration file that does specify that url or repository installation will fail. if [ -z $GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY ] ; then echo "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variable to be set and non-empty." @@ -37,7 +39,11 @@ fi fi -python test/install_and_test_tool_shed_repositories/functional_tests.py $* -v --with-nosehtml --html-report-file \ - test/install_and_test_tool_shed_repositories/run_functional_tests.html \ +# Test installation of repositories of type tool_dependency_definition. +# ...coming soon! + +# Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files. +python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ + test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ test/functional/test_toolbox.py diff -r b1e82182414d359f6f43e117e92ec6d6638878fe -r 43b23f5503997727debf8232239434974491e55e test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ /dev/null @@ -1,1492 +0,0 @@ -#!/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 - -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" ) - -test_toolbox = None -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 platform -import random -import re -import shutil -import socket -import string -import tempfile -import time -import threading -import tool_shed.util.shed_util_common as suc -import urllib - -from base.tool_shed_util import log_reason_repository_cannot_be_uninstalled -from base.tool_shed_util import parse_tool_panel_config -from install_and_test_tool_shed_repositories.base.util import get_database_version -from install_and_test_tool_shed_repositories.base.util import get_repository_current_revision -from common import update -from datetime import datetime -from galaxy.app import UniverseApplication -from galaxy.util import asbool -from galaxy.util import listify -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 tool_shed.util import tool_dependency_util -from tool_shed.util.xml_util import parse_xml - -from functional import database_contexts - -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' ) - -# 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' ) -default_galaxy_locales = 'en' -default_galaxy_test_file_dir = "test-data" -os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir - -default_galaxy_test_port_min = 10000 -default_galaxy_test_port_max = 10999 -default_galaxy_test_host = '127.0.0.1' -# The following should be an actual value (not None). If developers manually specify their -# tests to use the API it will not work unless a master API key is specified. -default_galaxy_master_api_key = 123456 - -# 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: - can_update_tool_shed = False -else: - can_update_tool_shed = True - -# Should this serve static resources (scripts, images, styles, etc.)? -STATIC_ENABLED = True - -# Set up a job_conf.xml that explicitly limits jobs to 10 minutes. -job_conf_xml = '''<?xml version="1.0"?> - -<job_conf> - <plugins> - <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> - </plugins> - <handlers> - <handler id="main"/> - </handlers> - <destinations> - <destination id="local" runner="local"/> - </destinations> - <limits> - <limit type="walltime">00:10:00</limit> - </limits> -</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' ) ) -else: - additional_tool_data_tables = None - additional_tool_data_path = None - -# 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' ): - tool_data_table_conf = 'tool_data_table_conf.xml.sample' -else: - tool_data_table_conf = None - -# 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 'GALAXY_INSTALL_TEST_SECRET' not in os.environ: - galaxy_encode_secret = 'changethisinproductiontoo' - os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] = galaxy_encode_secret -else: - galaxy_encode_secret = os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] - -testing_single_repository_dict = {} -if 'repository_name' in os.environ and 'repository_owner' in os.environ: - testing_single_repository_dict[ 'name' ] = str( os.environ[ 'repository_name' ] ) - testing_single_repository_dict[ 'owner' ] = str( os.environ[ 'repository_owner' ] ) - if 'repository_revision' in os.environ: - testing_single_repository_dict[ 'changeset_revision' ] = str( os.environ[ 'repository_revision' ] ) - else: - testing_single_repository_dict[ 'changeset_revision' ] = None - - -class ReportResults( Plugin ): - '''Simple Nose plugin to record the IDs of all tests run, regardless of success.''' - name = "reportresults" - passed = {} - - def options( self, parser, env=os.environ ): - super( ReportResults, self ).options( parser, env=env ) - - def configure(self, options, conf): - super( ReportResults, self ).configure( options, conf ) - if not self.enabled: - return - - def addSuccess( self, test ): - '''Only record test IDs that correspond to tool functional tests.''' - if 'TestForTool' in test.id(): - test_id = test.id() - # Rearrange the test ID to match the format that is produced in test_results.failures - test_id_parts = test_id.split( '.' ) - fixed_test_id = '%s (%s)' % ( test_id_parts[ -1 ], '.'.join( test_id_parts[ :-1 ] ) ) - test_parts = fixed_test_id.split( '/' ) - owner = test_parts[ -4 ] - name = test_parts[ -3 ] - test_identifier = '%s/%s' % ( owner, name ) - if test_identifier not in self.passed: - self.passed[ test_identifier ] = [] - self.passed[ test_identifier ].append( fixed_test_id ) - - def getTestStatus( self, test_identifier ): - if test_identifier in self.passed: - passed_tests = self.passed[ test_identifier ] - del self.passed[ test_identifier ] - return passed_tests - return [] - -def deactivate_repository( app, repository_dict ): - sa_session = app.install_model.context - # 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 ) - repository_dict_for_deactivation = dict( name=name, - owner=owner, - changeset_revision=changeset_revision ) - log.debug( 'Changeset revision %s of repository %s owned by %s selected for deactivation.' % ( changeset_revision, name, owner ) ) - test_install_repositories.generate_deactivate_method( repository_dict_for_deactivation ) - # 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 deactivate method which uses the Galaxy web interface to deactivate the repository. - result, _ = run_tests( test_config ) - success = result.wasSuccessful() - if not success: - log.debug( 'Deactivation of revision %s repository %s owned by %s failed.' % ( changeset_revision, name, owner ) ) - -def get_api_url( base, parts=[], params=None ): - if 'api' in parts and parts.index( 'api' ) != 0: - parts.pop( parts.index( 'api' ) ) - parts.insert( 0, 'api' ) - elif 'api' not in parts: - parts.insert( 0, 'api' ) - url = suc.url_join( base, *parts ) - if params is not None: - query_string = urllib.urlencode( params ) - url += '?%s' % query_string - return url - -def get_failed_test_dicts( test_result, from_tool_test=True ): - """Extract any useful data from the test_result.failures and test_result.errors attributes.""" - failed_test_dicts = [] - for failure in test_result.failures + test_result.errors: - # Record the twill test identifier and information about the tool so the repository owner - # can discover which test is failing. - test_id = str( failure[ 0 ] ) - if not from_tool_test: - tool_id = None - tool_version = None - else: - tool_id, tool_version = get_tool_info_from_test_id( test_id ) - test_status_dict = dict( test_id=test_id, tool_id=tool_id, tool_version=tool_version ) - log_output = failure[ 1 ].replace( '\\n', '\n' ) - # Remove debug output. - log_output = re.sub( r'control \d+:.+', r'', log_output ) - log_output = re.sub( r'\n+', r'\n', log_output ) - appending_to = 'output' - tmp_output = {} - output = {} - # Iterate through the functional test output and extract only the important data. Captured - # logging and stdout are not recorded. - for line in log_output.split( '\n' ): - if line.startswith( 'Traceback' ): - appending_to = 'traceback' - elif '>> end captured' in line or '>> end tool' in line: - continue - elif 'request returned None from get_history' in line: - continue - elif '>> begin captured logging <<' in line: - appending_to = 'logging' - continue - elif '>> begin captured stdout <<' in line: - appending_to = 'stdout' - continue - elif '>> begin captured stderr <<' in line or '>> begin tool stderr <<' in line: - appending_to = 'stderr' - continue - if appending_to in tmp_output: - tmp_output[ appending_to ].append( line ) - else: - tmp_output[ appending_to ] = [ line ] - for output_type in [ 'stderr', 'traceback' ]: - if output_type in tmp_output: - test_status_dict[ output_type ] = '\n'.join( tmp_output[ output_type ] ) - failed_test_dicts.append( test_status_dict ) - return failed_test_dicts - -def get_latest_downloadable_changeset_revision( url, name, owner ): - error_message = '' - parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] - params = dict( name=name, owner=owner ) - api_url = get_api_url( base=url, parts=parts, params=params ) - changeset_revisions, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - if changeset_revisions: - return changeset_revisions[ -1 ], error_message - else: - return suc.INITIAL_CHANGELOG_HASH, error_message - -def get_missing_tool_dependencies( repository ): - log.debug( 'Checking %s repository %s for missing tool dependencies.' % ( repository.status, repository.name ) ) - missing_tool_dependencies = repository.missing_tool_dependencies - for tool_dependency in repository.tool_dependencies: - log.debug( 'Tool dependency %s version %s has status %s.' % ( tool_dependency.name, tool_dependency.version, tool_dependency.status ) ) - for repository_dependency in repository.repository_dependencies: - if repository_dependency.includes_tool_dependencies: - missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency ) ) - return missing_tool_dependencies - -def get_repository_dict( url, repository_dict ): - error_message = '' - parts = [ 'api', 'repositories', repository_dict[ 'repository_id' ] ] - api_url = get_api_url( base=url, parts=parts ) - extended_dict, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - name = str( extended_dict[ 'name' ] ) - owner = str( extended_dict[ 'owner' ] ) - latest_changeset_revision, error_message = get_latest_downloadable_changeset_revision( url, name, owner ) - if error_message: - return None, error_message - extended_dict[ 'latest_revision' ] = str( latest_changeset_revision ) - return extended_dict, error_message - -def get_repository_tuple_from_elem( elem ): - attributes = elem.attrib - name = attributes.get( 'name', None ) - owner = attributes.get( 'owner', None ) - changeset_revision = attributes.get( 'changeset_revision', None ) - return ( name, owner, changeset_revision ) - -def get_repositories_to_install( tool_shed_url ): - """ - Get a list of repository info dicts to install. This method expects a json list of dicts with the following structure: - [{ "changeset_revision": <revision>, - "encoded_repository_id": <encoded repository id from the tool shed>, - "name": <name>, - "owner": <owner>, - "tool_shed_url": <url> }] - """ - error_message = '' - latest_revision_only = '-check_all_revisions' not in sys.argv - if latest_revision_only: - log.debug( 'Testing is restricted to the latest downloadable revision in this test run.' ) - repository_dicts = [] - parts = [ 'repository_revisions' ] - # We'll filter out deprecated repositories from testing since testing them is necessary only if reproducibility - # is guaranteed and we currently do not guarantee reproducibility. - params = dict( do_not_test='false', - downloadable='true', - includes_tools='true', - malicious='false', - missing_test_components='false', - skip_tool_test='false' ) - api_url = get_api_url( base=tool_shed_url, parts=parts, params=params ) - baseline_repository_dicts, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - for baseline_repository_dict in baseline_repository_dicts: - # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the - # module that will generate the install methods. - repository_dict, error_message = get_repository_dict( galaxy_tool_shed_url, baseline_repository_dict ) - if error_message: - log.debug( 'Error getting additional details from the API: %s' % str( error_message ) ) - else: - # Don't test deprecated repositories since testing them is necessary only if reproducibility is guaranteed - # and we are not currently guaranteeing reproducibility. - deprecated = asbool( repository_dict.get( 'deprecated', False ) ) - if not deprecated: - # Don't test empty repositories. - changeset_revision = baseline_repository_dict[ 'changeset_revision' ] - if changeset_revision != suc.INITIAL_CHANGELOG_HASH: - # 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. - if latest_revision_only: - latest_revision = repository_dict[ 'latest_revision' ] - if changeset_revision == latest_revision: - repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - else: - repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - if testing_single_repository_dict: - tsr_name = testing_single_repository_dict[ 'name' ] - tsr_owner = testing_single_repository_dict[ 'owner' ] - tsr_changeset_revision = testing_single_repository_dict[ 'changeset_revision' ] - log.debug( 'Testing single repository with name %s and owner %s.' % ( str( tsr_name ), str( tsr_owner ) ) ) - for repository_to_install in repository_dicts: - rti_name = repository_to_install[ 'name' ] - rti_owner = repository_to_install[ 'owner' ] - rti_changeset_revision = repository_to_install[ 'changeset_revision' ] - if rti_name == tsr_name and rti_owner == tsr_owner: - if tsr_changeset_revision is None: - return [ repository_to_install ], error_message - else: - if tsr_changeset_revision == rti_changeset_revision: - return repository_dicts, error_message - return repository_dicts, error_message - # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL - # environment variable. - log.debug( "The Tool Shed's API url...\n%s" % str( api_url ) ) - log.debug( "...retrieved %d repository revisions for testing." % len( repository_dicts ) ) - log.debug( "Repository revisions for testing:" ) - for repository_dict in repository_dicts: - name = str( repository_dict.get( 'name', None ) ) - owner = str( repository_dict.get( 'owner', None ) ) - changeset_revision = str( repository_dict.get( 'changeset_revision', None ) ) - log.debug( "Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) ) - 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 - (functional.test_toolbox.TestForTool_toolshed_url/repos/owner/repository_name/tool_id/tool_version) - We want the tool ID and tool version. - """ - parts = test_id.replace( ')', '' ).split( '/' ) - tool_version = parts[ -1 ] - tool_id = parts[ -2 ] - return tool_id, tool_version - -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 - column via the Tool Shed API. - """ - error_message = '' - parts = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] - api_url = get_api_url( base=tool_shed_url, parts=parts ) - repository_metadata, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - # The tool_test_results used to be stored as a single dictionary rather than a list, but we currently - # return a list. - tool_test_results = listify( repository_metadata.get( 'tool_test_results', [] ) ) - 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_dicts, 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, - # and functional tests should be skipped, since the tool dependency needs to be correctly installed - # for the test to be considered reliable. - log.debug( 'The following dependencies of this repository are missing, so skipping functional tests.' ) - # In keeping with the standard display layout, add the error message to the dict for each tool individually. - for dependency in repository.missing_tool_dependencies: - name = str( dependency.name ) - type = str( dependency.type ) - version = str( dependency.version ) - error_message = unicodify( dependency.error_message ) - log.debug( 'Missing tool dependency %s of type %s version %s: %s' % ( name, type, version, error_message ) ) - test_result = dict( type=dependency.type, - name=dependency.name, - version=dependency.version, - error_message=dependency.error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) - for dependency in repository.missing_repository_dependencies: - name = str( dependency.name ) - owner = str( dependency.owner ) - changeset_revision = str( dependency.changeset_revision ) - error_message = unicodify( dependency.error_message ) - log.debug( 'Missing repository dependency %s changeset revision %s owned by %s: %s' % \ - ( name, changeset_revision, owner, error_message ) ) - test_result = dict( tool_shed=dependency.tool_shed, - name=dependency.name, - owner=dependency.owner, - changeset_revision=dependency.changeset_revision, - error_message=dependency.error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) - # Record the status of this repository in the tool shed. - params = dict( tools_functionally_correct=False, - do_not_test=False, - test_install_error=True ) - # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) - # Since this repository is missing components, we do not want to test it, so deactivate it or uninstall it. - # The deactivate flag is set to True if the environment variable GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES - # is set to 'true'. - deactivate = asbool( os.environ.get( 'GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES', False ) ) - if deactivate: - for missing_tool_dependency in missing_tool_dependencies: - uninstall_tool_dependency( app, missing_tool_dependency ) - # We are deactivating this repository and all of its repository dependencies. - deactivate_repository( app, repository_dict ) - else: - # We are uninstalling this repository and all of its repository dependencies. - uninstall_repository_and_repository_dependencies( app, repository_dict ) - results_dict[ 'repositories_failed_install' ].append( dict( name=str( repository.name ), - owner=str( repository.owner ), - changeset_revision=str( repository.changeset_revision ) ) ) - # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. - test_toolbox.toolbox = app.toolbox - return results_dict - -def initialize_results_dict(): - # Initialize a dictionary for the summary that will be printed to stdout. - results_dict = {} - results_dict[ 'total_repositories_tested' ] = 0 - results_dict[ 'all_tests_passed' ] = [] - results_dict[ 'at_least_one_test_failed' ] = [] - results_dict[ 'repositories_failed_install' ] = [] - return 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[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - error_message = '' - repository = None - log.debug( "Installing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) ) - # Explicitly clear tests from twill's test environment. - remove_generated_tests( app ) - # Use the repository information dictionary to generate an install method that will install the repository into the - # embedded Galaxy application, with tool dependencies and repository dependencies, if any. - test_install_repositories.generate_install_method( repository_dict ) - # Configure nose to run the install method as a test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the configured install method as a test. This method uses the embedded Galaxy application's web interface to - # install the specified repository with tool and repository dependencies also selected for installation. - result, _ = run_tests( test_config ) - try: - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - except Exception, e: - error_message = 'Error getting revision %s of repository %s owned by %s: %s' % ( changeset_revision, name, owner, str( e ) ) - log.exception( error_message ) - return repository, error_message - -def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): - results_dict = initialize_results_dict() - error_message = '' - # Allow the option to keep or delete tool dependencies when a repository has been tested. - deactivate = asbool( os.environ.get( 'GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES', False ) ) - # Initialize a dictionary for the summary that will be printed to stdout. - total_repositories_tested = results_dict[ 'total_repositories_tested' ] - repositories_to_install, error_message = get_repositories_to_install( galaxy_tool_shed_url ) - 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...', exclude_list_file ) - exclude_list = parse_exclude_list( exclude_list_file ) - else: - exclude_list = [] - # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was - # started up, installing repository and tool dependencies. Upon successful installation, generate a test case for each - # functional test defined for each tool in the repository and execute the test cases. Record the result of the tests. - # The traceback and captured output of the tool that was run will be recored for test failures. After all tests have - # completed, the repository is uninstalled, so test cases don't interfere with the next repository's functional tests. - for repository_dict in repositories_to_install: - # Each repository_dict looks something like: - # { "changeset_revision": "13fa22a258b5", - # "contents_url": "/api/repositories/529fd61ab1c6cc36/contents", - # "deleted": false, - # "deprecated": false, - # "description": "Convert column case.", - # "downloadable": true, - # "id": "529fd61ab1c6cc36", - # "long_description": "This tool takes the specified columns and converts them to uppercase or lowercase.", - # "malicious": false, - # "name": "change_case", - # "owner": "test", - # "private": false, - # "repository_id": "529fd61ab1c6cc36", - # "times_downloaded": 0, - # "tool_shed_url": "http://toolshed.local:10001", - # "url": "/api/repository_revisions/529fd61ab1c6cc36", - # "user_id": "529fd61ab1c6cc36" } - encoded_repository_metadata_id = repository_dict.get( 'id', None ) - # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. - repository_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url - # Get the name and owner out of the repository info dict. - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - log.debug( "Processing revision %s of repository %s owned by %s..." % ( changeset_revision, name, owner ) ) - repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) - # Retrieve the stored list of tool_test_results_dicts. - tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, encoded_repository_metadata_id ) - if error_message: - log.debug( error_message ) - else: - 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 - # entry. If it contains more entries, then the script ~/tool_shed/api/check_repositories_for_functional_tests.py - # was not executed in preparation for this script's execution, so we'll just create an empty dictionary. - tool_test_results_dict = tool_test_results_dicts[ 0 ] - if len( tool_test_results_dict ) <= 1: - # We can re-use the mostly empty tool_test_results_dict for this run because it is either empty or it contains only - # a test_environment entry. If we use it we need to temporarily eliminate it from the list of 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: - # 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 ) - else: - # 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, - tool_test_results_dict = {} - # See if this repository should be skipped for any reason. - this_repository_is_in_the_exclude_list = False - skip_reason = None - for exclude_dict in exclude_list: - reason = exclude_dict[ 'reason' ] - exclude_repositories = exclude_dict[ 'repositories' ] - if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: - this_repository_is_in_the_exclude_list = True - skip_reason = reason - break - if this_repository_is_in_the_exclude_list: - tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) - params = dict( tools_functionally_correct=False, - do_not_test=False ) - # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) - log.debug( "Not testing revision %s of repository %s owned by %s because it is in the exclude list for this test run." % \ - ( changeset_revision, name, owner ) ) - else: - test_environment_dict = tool_test_results_dict.get( 'test_environment', {} ) - if len( test_environment_dict ) == 0: - # Set information about the tool shed to nothing since we cannot currently determine it from here. - # We could eventually add an API method... - test_environment_dict = dict( tool_shed_database_version='', - tool_shed_mercurial_version='', - tool_shed_revision='' ) - # Add the current time as the approximate time that this test run occurs. A similar value will also be - # set to the repository_metadata.time_last_tested column, but we also store it here because the Tool Shed - # may be configured to store multiple test run results, so each must be associated with a time stamp. - now = time.strftime( "%Y-%m-%d %H:%M:%S" ) - # Add information about the current platform. - test_environment_dict[ 'time_tested' ] = now - test_environment_dict[ 'python_version' ] = platform.python_version() - test_environment_dict[ 'architecture' ] = platform.machine() - operating_system, hostname, operating_system_version, uname, arch, processor = platform.uname() - test_environment_dict[ 'system' ] = '%s %s' % ( operating_system, operating_system_version ) - # Add information about the current Galaxy environment. - test_environment_dict[ 'galaxy_database_version' ] = get_database_version( app ) - test_environment_dict[ 'galaxy_revision' ] = get_repository_current_revision( os.getcwd() ) - # Initialize and populate the tool_test_results_dict. - tool_test_results_dict[ 'test_environment' ] = test_environment_dict - tool_test_results_dict[ 'passed_tests' ] = [] - tool_test_results_dict[ 'failed_tests' ] = [] - tool_test_results_dict[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) - # Proceed with installing repositories and testing contained tools. - repository, error_message = install_repository( app, repository_dict ) - if error_message: - 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 repository %s owned by %s.' % ( 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 installed repository %s owned by %s: %s.' % ( name, owner, str( e ) ) - log.exception( error_message ) - test_result = dict( tool_shed=galaxy_tool_shed_url, - name=name, - owner=owner, - changeset_revision=changeset_revision, - error_message=error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) - params = dict( tools_functionally_correct=False, - test_install_error=True, - do_not_test=False ) - # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) - try: - if deactivate: - # We are deactivating this repository and all of its repository dependencies. - deactivate_repository( app, repository_dict ) - else: - # We are uninstalling this repository and all of its repository dependencies. - uninstall_repository_and_repository_dependencies( app, repository_dict ) - except: - log.exception( 'Encountered error attempting to deactivate or uninstall %s.', str( repository_dict[ 'name' ] ) ) - results_dict[ 'repositories_failed_install' ].append( repository_identifier_dict ) - log.debug( 'Repository %s failed to install correctly.' % str( name ) ) - else: - # Configure and run functional tests for this repository. This is equivalent to sh run_functional_tests.sh -installed - remove_install_tests() - log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) - # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository - # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, - # and the tools_functionally_correct flag to False, as well as updating tool_test_results. - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) - has_test_data, shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, - from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) - # Add an empty 'missing_test_results' entry if it is missing from the tool_test_results_dict. The - # ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered information in the - # 'missing_test_components' entry of the tool_test_results_dict dictionary for repositories that are - # missing test components. - if 'missing_test_components' not in tool_test_results_dict: - tool_test_results_dict[ 'missing_test_components' ] = [] - missing_tool_dependencies = get_missing_tool_dependencies( repository ) - if missing_tool_dependencies or repository.missing_repository_dependencies: - results_dict = handle_missing_dependencies( app, - repository, - missing_tool_dependencies, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - results_dict ) - else: - # If the repository has a test-data directory we write the generated shed_tools_dict to a file, so the functional - # test framework can find it. - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) - log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), str( shed_tools_dict ) ) ) - try: - results_dict = test_repository_tools( app, - repository, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - results_dict ) - except Exception, e: - exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) - log.exception( exception_message ) - tool_test_results_dict[ 'failed_tests' ].append( exception_message ) - # Record the status of this repository in the tool shed. - params = dict( tools_functionally_correct=False, - do_not_test=False, - test_install_error=False ) - # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) - results_dict[ 'at_least_one_test_failed' ].append( repository_identifier_dict ) - total_repositories_tested += 1 - results_dict[ 'total_repositories_tested' ] = total_repositories_tested - return results_dict, error_message - -def is_latest_downloadable_revision( url, repository_dict ): - latest_revision = get_latest_downloadable_changeset_revision( url, name=repository_dict[ 'name' ], owner=repository_dict[ 'owner' ] ) - return str( repository_dict[ 'changeset_revision' ] ) == str( latest_revision ) - -def json_from_url( url ): - error_message = '' - url_handle = urllib.urlopen( url ) - url_contents = url_handle.read() - try: - parsed_json = from_json_string( url_contents ) - except Exception, e: - error_message = str( url_contents ) - log.exception( 'Error parsing JSON data in json_from_url(): %s.' % str( e ) ) - return None, error_message - return parsed_json, error_message - -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 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 - # 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 - tool_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_PATH', 'tools' ) - if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: - os.environ[ 'HTTP_ACCEPT_LANGUAGE' ] = default_galaxy_locales - galaxy_test_file_dir = os.environ.get( 'GALAXY_INSTALL_TEST_FILE_DIR', default_galaxy_test_file_dir ) - if not os.path.isabs( galaxy_test_file_dir ): - galaxy_test_file_dir = os.path.abspath( galaxy_test_file_dir ) - use_distributed_object_store = os.environ.get( 'GALAXY_INSTALL_TEST_USE_DISTRIBUTED_OBJECT_STORE', False ) - 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' ) ) - 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. - 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' ) - else: - tool_data_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) - os.environ[ 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' ] = tool_data_path - # Configure the database connection and path. - if 'GALAXY_INSTALL_TEST_DBPATH' in os.environ: - galaxy_db_path = os.environ[ 'GALAXY_INSTALL_TEST_DBPATH' ] - else: - tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) - galaxy_db_path = os.path.join( tempdir, 'database' ) - # Configure the paths Galaxy needs to install and test tools. - galaxy_file_path = os.path.join( galaxy_db_path, 'files' ) - new_repos_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) - galaxy_tempfiles = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) - galaxy_shed_tool_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir, prefix='shed_tools' ) - galaxy_migrated_tool_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) - # Set up the tool dependency path for the Galaxy instance. - tool_dependency_dir = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR', None ) - if tool_dependency_dir is None: - tool_dependency_dir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) - os.environ[ 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR' ] = tool_dependency_dir - os.environ[ 'GALAXY_TOOL_DEPENDENCY_DIR' ] = tool_dependency_dir - if 'GALAXY_INSTALL_TEST_DBURI' in os.environ: - database_connection = os.environ[ 'GALAXY_INSTALL_TEST_DBURI' ] - else: - database_connection = 'sqlite:///' + os.path.join( galaxy_db_path, 'install_and_test_repositories.sqlite' ) - kwargs = {} - for dir in [ galaxy_test_tmp_dir ]: - try: - os.makedirs( dir ) - except OSError: - pass - print "Database connection: ", database_connection - # 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[ 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file - # ---- Start up a Galaxy instance ------------------------------------------------------ - # Generate the tool_conf.xml file. - file( galaxy_tool_conf_file, 'w' ).write( tool_conf_xml ) - # Generate the job_conf.xml file. - file( galaxy_job_conf_file, 'w' ).write( job_conf_xml ) - # Generate the tool_sheds_conf.xml file, but only if a the user has not specified an existing one in the environment. - if 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF' not in os.environ: - file( galaxy_tool_sheds_conf_file, 'w' ).write( tool_sheds_conf_xml ) - # Generate the shed_tool_conf.xml file. - tool_conf_template_parser = string.Template( shed_tool_conf_xml_template ) - shed_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_shed_tool_path ) - file( galaxy_shed_tool_conf_file, 'w' ).write( shed_tool_conf_xml ) - os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file - # Generate the migrated_tool_conf.xml file. - migrated_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_migrated_tool_path ) - file( galaxy_migrated_tool_conf_file, 'w' ).write( migrated_tool_conf_xml ) - # Write the embedded web application's specific configuration to a temporary file. This is necessary in order for - # the external metadata script to find the right datasets. - kwargs = dict( admin_users = 'test(a)bx.psu.edu', - master_api_key = default_galaxy_master_api_key, - allow_user_creation = True, - allow_user_deletion = True, - allow_library_path_paste = True, - database_connection = database_connection, - datatype_converters_config_file = "datatype_converters_conf.xml.sample", - file_path = galaxy_file_path, - id_secret = galaxy_encode_secret, - job_config_file = galaxy_job_conf_file, - job_queue_workers = 5, - log_destination = "stdout", - migrated_tools_config = galaxy_migrated_tool_conf_file, - new_file_path = galaxy_tempfiles, - running_functional_tests = True, - shed_tool_data_table_config = shed_tool_data_table_conf_file, - shed_tool_path = galaxy_shed_tool_path, - template_path = "templates", - tool_config_file = ','.join( [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] ), - tool_data_path = tool_data_path, - tool_data_table_config_path = galaxy_tool_data_table_conf_file, - tool_dependency_dir = tool_dependency_dir, - tool_path = tool_path, - tool_parse_help = False, - tool_sheds_config_file = galaxy_tool_sheds_conf_file, - update_integrated_tool_panel = False, - use_heartbeat = False ) - galaxy_config_file = os.environ.get( 'GALAXY_INSTALL_TEST_INI_FILE', None ) - # If the user has passed in a path for the .ini file, do not overwrite it. - if not galaxy_config_file: - galaxy_config_file = os.path.join( galaxy_test_tmp_dir, 'install_test_tool_shed_repositories_wsgi.ini' ) - config_items = [] - for label in kwargs: - config_tuple = label, kwargs[ label ] - config_items.append( config_tuple ) - # Write a temporary file, based on universe_wsgi.ini.sample, using the configuration options defined above. - generate_config_file( 'universe_wsgi.ini.sample', galaxy_config_file, config_items ) - kwargs[ 'tool_config_file' ] = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] - # Set the global_conf[ '__file__' ] option to the location of the temporary .ini file, which gets passed to set_metadata.sh. - kwargs[ 'global_conf' ] = get_webapp_global_conf() - kwargs[ 'global_conf' ][ '__file__' ] = galaxy_config_file - # ---- Build Galaxy Application -------------------------------------------------- - if not database_connection.startswith( 'sqlite://' ): - kwargs[ 'database_engine_option_max_overflow' ] = '20' - kwargs[ 'database_engine_option_pool_size' ] = '10' - kwargs[ 'config_file' ] = galaxy_config_file - app = UniverseApplication( **kwargs ) - database_contexts.galaxy_context = app.model.context - database_contexts.install_context = app.install_model.context - global test_toolbox - import functional.test_toolbox as imported_test_toolbox - test_toolbox = imported_test_toolbox - - log.debug( "Embedded Galaxy application started..." ) - # ---- Run galaxy webserver ------------------------------------------------------ - server = None - global_conf = get_webapp_global_conf() - global_conf[ 'database_file' ] = database_connection - webapp = buildapp.app_factory( global_conf, - use_translogger=False, - static_enabled=STATIC_ENABLED, - app=app ) - # Serve the app on a specified or random port. - if galaxy_test_port is not None: - server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) - else: - random.seed() - for i in range( 0, 9 ): - try: - galaxy_test_port = str( random.randint( default_galaxy_test_port_min, default_galaxy_test_port_max ) ) - log.debug( "Attempting to serve app on randomly chosen port: %s", galaxy_test_port ) - server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) - break - except socket.error, e: - if e[0] == 98: - continue - raise - else: - raise Exception( "Unable to open a port between %s and %s to start Galaxy server" % \ - ( default_galaxy_test_port_min, default_galaxy_test_port_max ) ) - os.environ[ 'GALAXY_INSTALL_TEST_PORT' ] = galaxy_test_port - # Start the server. - t = threading.Thread( target=server.serve_forever ) - t.start() - # Test if the server is up. - for i in range( 10 ): - # Directly test the app, not the proxy. - conn = httplib.HTTPConnection( galaxy_test_host, galaxy_test_port ) - conn.request( "GET", "/" ) - if conn.getresponse().status == 200: - break - time.sleep( 0.1 ) - else: - raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" ) - log.debug( "Embedded galaxy web server started..." ) - log.debug( "The embedded Galaxy application is running on %s:%s" % ( str( galaxy_test_host ), str( galaxy_test_port ) ) ) - log.debug( "Repositories will be installed from the tool shed at %s" % str( galaxy_tool_shed_url ) ) - success = False - # If a tool_data_table_conf.test.xml file was found, add the entries from it into the app's tool data tables. - if additional_tool_data_tables: - app.tool_data_tables.add_new_entries_from_config_file( config_filename=additional_tool_data_tables, - tool_data_path=additional_tool_data_path, - shed_tool_data_table_config=None, - persist=False ) - now = time.strftime( "%Y-%m-%d %H:%M:%S" ) - print "####################################################################################" - print "# %s - running repository installation and testing script." % now - print "####################################################################################" - results_dict, error_message = install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ) - if error_message: - log.debug( error_message ) - else: - total_repositories_tested = results_dict[ 'total_repositories_tested' ] - all_tests_passed = results_dict[ 'all_tests_passed' ] - at_least_one_test_failed = results_dict[ 'at_least_one_test_failed' ] - repositories_failed_install = results_dict[ 'repositories_failed_install' ] - now = time.strftime( "%Y-%m-%d %H:%M:%S" ) - print "####################################################################################" - print "# %s - repository installation and testing script completed." % now - print "# Repository revisions tested: %s" % str( total_repositories_tested ) - if not can_update_tool_shed: - print "# This run will not update the Tool Shed database." - if total_repositories_tested > 0: - if all_tests_passed: - print '# ----------------------------------------------------------------------------------' - print "# %d repositories successfully passed all functional tests:" % len( all_tests_passed ) - show_summary_output( all_tests_passed ) - if at_least_one_test_failed: - print '# ----------------------------------------------------------------------------------' - print "# %d repositories failed at least 1 functional test:" % len( at_least_one_test_failed ) - show_summary_output( at_least_one_test_failed ) - if repositories_failed_install: - # Set success to False so that the return code will not be 0. - success = False - print '# ----------------------------------------------------------------------------------' - print "# %d repositories have installation errors:" % len( repositories_failed_install ) - show_summary_output( repositories_failed_install ) - else: - success = True - else: - success = True - print "####################################################################################" - log.debug( "Shutting down..." ) - # Gracefully shut down the embedded web server and UniverseApplication. - if server: - log.debug( "Shutting down embedded galaxy web server..." ) - server.server_close() - server = None - log.debug( "Embedded galaxy server stopped..." ) - if app: - log.debug( "Shutting down galaxy application..." ) - app.shutdown() - app = None - log.debug( "Embedded galaxy application stopped..." ) - # Clean up test files unless otherwise specified. - if 'GALAXY_INSTALL_TEST_NO_CLEANUP' not in os.environ: - for dir in [ galaxy_test_tmp_dir ]: - if os.path.exists( dir ): - try: - shutil.rmtree( 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, 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( 'The xml document %s containing the exclude list defines the following %s repositories to be excluded from testing...' % \ - ( str( xml_filename ), 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, tool_test_results_dicts, tool_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 can_update_tool_shed: - metadata_revision_id = repository_dict.get( 'id', None ) - if metadata_revision_id is not None: - tool_test_results_dicts.insert( 0, tool_test_results_dict ) - params[ 'tool_test_results' ] = tool_test_results_dicts - # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. - params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' - 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 {} - else: - 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 ): - # Group summary display by repository owner. - repository_dicts_by_owner = {} - for repository_dict in repository_dicts: - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - if owner in repository_dicts_by_owner: - repository_dicts_by_owner[ owner ].append( repository_dict ) - else: - repository_dicts_by_owner[ owner ] = [ repository_dict ] - # Display grouped summary. - for owner, grouped_repository_dicts in repository_dicts_by_owner.items(): - print "# " - for repository_dict in grouped_repository_dicts: - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - print "# Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) - -def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, 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 ) - repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=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 ) - if result.wasSuccessful(): - # This repository's tools passed all functional tests. 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 ) - # Update the repository_metadata table in the tool shed's database to include the passed tests. - passed_repository_dict = repository_identifier_dict - results_dict[ 'all_tests_passed' ].append( passed_repository_dict ) - params = dict( tools_functionally_correct=True, - do_not_test=False, - test_install_error=False ) - # Call the register_test_result() method to execute 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. - # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) - log.debug( 'Revision %s of repository %s owned by %s installed and passed functional tests.' % \ - ( changeset_revision, name, owner ) ) - else: - # The get_failed_test_dicts() method returns a list. - failed_test_dicts = get_failed_test_dicts( result, from_tool_test=True ) - tool_test_results_dict[ 'failed_tests' ] = failed_test_dicts - failed_repository_dict = repository_identifier_dict - results_dict[ 'at_least_one_test_failed' ].append( failed_repository_dict ) - 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 ) ) - # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) - log.debug( 'Revision %s of repository %s owned by %s installed successfully but did not pass functional tests.' % \ - ( changeset_revision, name, owner ) ) - # 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_and_repository_dependencies( 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_and_repository_dependencies( app, repository_dict ): - """Uninstall a repository and all of its repository dependencies.""" - # This method assumes that the repositor defined by the received repository_dict is not a repository - # dependency of another repository. - sa_session = app.install_model.context - # 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' ] ) - # Since this install and test framework uninstalls repositories immediately after installing and testing - # them, the values of repository.installed_changeset_revision and repository.changeset_revision should be - # the same. - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - if repository.can_uninstall( app ): - # A repository can be uninstalled only if no dependent repositories are installed. So uninstallation order - # id critical. A repository is always uninstalled first, and the each of its dependencies is checked to see - # if it can be uninstalled. - uninstall_repository_dict = dict( name=name, - owner=owner, - changeset_revision=changeset_revision ) - log.debug( 'Revision %s of repository %s owned by %s selected for uninstallation.' % ( changeset_revision, name, owner ) ) - try: - test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) - # 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 all of its repository dependencies, deleting each of them from disk. - result, _ = run_tests( test_config ) - repository_uninstall_successful = result.wasSuccessful() - except Exception, e: - repository_uninstall_successful = False - log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ - ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) - if repository_uninstall_successful: - # Now that the repository is uninstalled we can attempt to uninstall each of its repository dependencies. - # 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. Since some of the repository's repository dependencies may require other of - # the repository's repository dependencies, we'll keep track of the repositories we've been able to unistall. - processed_repository_dependency_ids = [] - while len( processed_repository_dependency_ids ) < len( repository.repository_dependencies ): - for repository_dependency in repository.repository_dependencies: - if repository_dependency.id not in processed_repository_dependency_ids and repository_dependency.can_uninstall( app ): - processed_repository_dependency_ids.append( repository_dependency.id ) - rd_name = str( repository_dependency.name ) - rd_owner = str( repository_dependency.owner ) - rd_changeset_revision = str( repository_dependency.changeset_revision ) - uninstall_repository_dict = dict( name=rd_name, - owner=rd_owner, - changeset_revision=rd_changeset_revision ) - log.debug( 'Revision %s of repository dependency %s owned by %s selected for uninstallation.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) ) - # Generate a test method to uninstall the repository dependency through the embedded Galaxy application's - # web interface. - try: - test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) - # 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. - result, _ = run_tests( test_config ) - if not result.wasSuccessful(): - # We won't set ok here because we'll continue to uninstall whatever we can. - log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) ) - except Exception, e: - log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ - ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) - else: - log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % ( changeset_revision, name, owner ) ) - else: - log_reason_repository_cannot_be_uninstalled( app, repository ) - -def uninstall_tool_dependency( app, tool_dependency ): - """Attempt to uninstall a tool dependency.""" - sa_session = app.install_model.context - # 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: - # { - # "test_environment": - # { - # "galaxy_revision": "9001:abcd1234", - # "galaxy_database_version": "114", - # "tool_shed_revision": "9001:abcd1234", - # "tool_shed_mercurial_version": "2.3.1", - # "tool_shed_database_version": "17", - # "python_version": "2.7.2", - # "architecture": "x86_64", - # "system": "Darwin 12.2.0" - # }, - # "passed_tests": - # [ - # { - # "test_id": "The test ID, generated by twill", - # "tool_id": "The tool ID that was tested", - # "tool_version": "The tool version that was tested", - # }, - # ] - # "failed_tests": - # [ - # { - # "test_id": "The test ID, generated by twill", - # "tool_id": "The tool ID that was tested", - # "tool_version": "The tool version that was tested", - # "stderr": "The output of the test, or a more detailed description of what was tested and what the outcome was." - # "traceback": "The captured traceback." - # }, - # ] - # "installation_errors": - # { - # 'tool_dependencies': - # [ - # { - # 'type': 'Type of tool dependency, e.g. package, set_environment, etc.', - # 'name': 'Name of the tool dependency.', - # 'version': 'Version if this is a package, otherwise blank.', - # 'error_message': 'The error message returned when installation was attempted.', - # }, - # ], - # 'repository_dependencies': - # [ - # { - # 'tool_shed': 'The tool shed that this repository was installed from.', - # 'name': 'The name of the repository that failed to install.', - # 'owner': 'Owner of the failed repository.', - # 'changeset_revision': 'Changeset revision of the failed repository.', - # 'error_message': 'The error message that was returned when the repository failed to install.', - # }, - # ], - # 'current_repository': - # [ - # { - # 'tool_shed': 'The tool shed that this repository was installed from.', - # 'name': 'The name of the repository that failed to install.', - # 'owner': 'Owner of the failed repository.', - # 'changeset_revision': 'Changeset revision of the failed repository.', - # 'error_message': 'The error message that was returned when the repository failed to install.', - # }, - # ], - # { - # "name": "The name of the repository.", - # "owner": "The owner of the repository.", - # "changeset_revision": "The changeset revision of the repository.", - # "error_message": "The message stored in tool_dependency.error_message." - # }, - # } - # "missing_test_components": - # [ - # { - # "tool_id": "The tool ID that missing components.", - # "tool_version": "The version of the tool." - # "tool_guid": "The guid of the tool." - # "missing_components": "Which components are missing, e.g. the test data filename, or the test-data directory." - # }, - # ] - # "not_tested": - # { - # "reason": "The Galaxy development team has determined that this repository should not be installed and tested by the automated framework." - # } - # } - sys.exit( main() ) diff -r b1e82182414d359f6f43e117e92ec6d6638878fe -r 43b23f5503997727debf8232239434974491e55e test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py --- /dev/null +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/__init__.py @@ -0,0 +1,1 @@ +"""Install and test tool shed repositories that contain tools and tool test components.""" \ No newline at end of file This diff is so big that we needed to truncate the remainder. 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.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8eaabf513c44/ Changeset: 8eaabf513c44 User: jmchilton Date: 2013-12-17 18:19:41 Summary: Reuse code between scripts/manage_tools.py and lib/galaxy/model/orm/scripts.py Affected #: 2 files diff -r a2bad69f03f4786309ba80ff305ebdd7b68f93fa -r 8eaabf513c4494a3990ab93bebc7d16ad9276e3d lib/galaxy/model/orm/scripts.py --- a/lib/galaxy/model/orm/scripts.py +++ b/lib/galaxy/model/orm/scripts.py @@ -43,6 +43,31 @@ } +def require_dialect_egg( db_url ): + dialect = ( db_url.split( ':', 1 ) )[0] + try: + egg = dialect_to_egg[dialect] + try: + pkg_resources.require( egg ) + log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) ) + except: + # If the module is in the path elsewhere (i.e. non-egg), it'll still load. + log.warning( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) ) + except KeyError: + # Let this go, it could possibly work with db's we don't support + log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect ) + + +def read_config_file_arg( argv, default ): + if '-c' in argv: + pos = argv.index( '-c' ) + argv.pop(pos) + config_file = argv.pop( pos ) + else: + config_file = default + return config_file + + def get_config( argv, cwd=None ): """ Read sys.argv and parse out repository of migrations and database url. @@ -73,12 +98,7 @@ database = 'galaxy' database_defaults = DATABASE[ database ] - if '-c' in argv: - pos = argv.index( '-c' ) - argv.pop(pos) - config_file = argv.pop( pos ) - else: - config_file = database_defaults.get( 'config_file', DEFAULT_CONFIG_FILE ) + config_file = read_config_file_arg( argv, database_defaults.get( 'config_file', DEFAULT_CONFIG_FILE ) ) repo = database_defaults[ 'repo' ] config_prefix = database_defaults.get( 'config_prefix', DEFAULT_CONFIG_PREFIX ) default_sqlite_file = database_defaults[ 'default_sqlite_file' ] @@ -95,16 +115,5 @@ else: db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % default_sqlite_file - dialect = ( db_url.split( ':', 1 ) )[0] - try: - egg = dialect_to_egg[dialect] - try: - pkg_resources.require( egg ) - log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) ) - except: - # If the module is in the path elsewhere (i.e. non-egg), it'll still load. - log.warning( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) ) - except KeyError: - # Let this go, it could possibly work with db's we don't support - log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect ) + require_dialect_egg( db_url ) return dict(db_url=db_url, repo=repo, config_file=config_file, database=database) diff -r a2bad69f03f4786309ba80ff305ebdd7b68f93fa -r 8eaabf513c4494a3990ab93bebc7d16ad9276e3d scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -1,7 +1,9 @@ -import sys, os.path, logging +import sys +import os.path +import logging new_path = [ os.path.join( os.getcwd(), "lib" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path +new_path.extend( sys.path[1:] ) # remove scripts/ from the path sys.path = new_path from galaxy import eggs @@ -15,15 +17,12 @@ from migrate.versioning.shell import main from ConfigParser import SafeConfigParser -from galaxy.model.orm import dialect_to_egg +from galaxy.model.orm.scripts import require_dialect_egg +from galaxy.model.orm.scripts import read_config_file_arg log = logging.getLogger( __name__ ) -config_file = 'universe_wsgi.ini' -if '-c' in sys.argv: - pos = sys.argv.index( '-c' ) - sys.argv.pop( pos ) - config_file = sys.argv.pop( pos ) +config_file = read_config_file_arg( sys.argv, 'universe_wsgi.ini' ) if not os.path.exists( config_file ): print "Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file sys.exit( 1 ) @@ -42,17 +41,6 @@ else: db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE" -dialect = ( db_url.split( ':', 1 ) )[0] -try: - egg = dialect_to_egg[dialect] - try: - pkg_resources.require( egg ) - log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) ) - except: - # If the module is in the path elsewhere (i.e. non-egg), it'll still load. - log.warning( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) ) -except KeyError: - # Let this go, it could possibly work with db's we don't support - log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect ) +require_dialect_egg( db_url ) main( repository=repo, url=db_url ) https://bitbucket.org/galaxy/galaxy-central/commits/723431aa61fb/ Changeset: 723431aa61fb User: jmchilton Date: 2013-12-17 18:19:41 Summary: Tools now properly migrated into install_database_connection database... ... this second database is specified. Affected #: 1 file diff -r 8eaabf513c4494a3990ab93bebc7d16ad9276e3d -r 723431aa61fb4c7d5cd1f73fe34e16af29368ef4 scripts/manage_tools.py --- a/scripts/manage_tools.py +++ b/scripts/manage_tools.py @@ -34,6 +34,8 @@ if config_file == 'universe_wsgi.ini.sample' and 'GALAXY_TEST_DBURI' in os.environ: # Running functional tests. db_url = os.environ[ 'GALAXY_TEST_DBURI' ] +elif cp.has_option( "app:main", "install_database_connection" ): + db_url = cp.get( "app:main", "install_database_connection" ) elif cp.has_option( "app:main", "database_connection" ): db_url = cp.get( "app:main", "database_connection" ) elif cp.has_option( "app:main", "database_file" ): https://bitbucket.org/galaxy/galaxy-central/commits/b1e82182414d/ Changeset: b1e82182414d User: jmchilton Date: 2013-12-17 18:47:48 Summary: Merge latest galaxy-central. Affected #: 7 files diff -r 723431aa61fb4c7d5cd1f73fe34e16af29368ef4 -r b1e82182414d359f6f43e117e92ec6d6638878fe lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -69,7 +69,7 @@ default_sort_key = "-update_time" columns = [ HistoryListNameColumn( "Name", key="name", attach_popup=True, filterable="advanced" ), - DatasetsByStateColumn( "Datasets", key="datasets_by_state", sortable=False ), + DatasetsByStateColumn( "Datasets", key="datasets_by_state", sortable=False, nowrap=True), grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, \ filterable="advanced", grid_name="HistoryListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), diff -r 723431aa61fb4c7d5cd1f73fe34e16af29368ef4 -r b1e82182414d359f6f43e117e92ec6d6638878fe lib/tool_shed/scripts/clean_up_tool_dependency_directory.py --- /dev/null +++ b/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py @@ -0,0 +1,58 @@ +import argparse +import os +import sys +import shutil + +def main( args ): + if not os.path.exists( args.basepath ): + print 'Tool dependency path %s does not exist.' % str( args.basepath ) + return 1 + if args.delete: + print 'Deleting contents of tool dependency path %s.' % args.basepath + for node in os.listdir( args.basepath ): + path = os.path.join( args.basepath, node ) + if os.path.isdir( path ): + try: + shutil.rmtree( path ) + print 'Deleted directory %s and all its contents.' % path + except Exception, e: + print 'Error deleting directory %s: %s' % ( path, str( e ) ) + pass + elif os.path.isfile( path ): + try: + os.remove( path ) + print 'Deleted file %s.' % path + except Exception, e: + print 'Error deleting file %s: %s' % ( path, str( e ) ) + pass + elif os.path.islink( path ): + print 'Deleting symlink %s with target %s.' % ( path, os.path.realpath( path ) ) + try: + os.remove( path ) + except Exception, e: + print 'Error deleting symlink %s: %s' % ( path, str( e ) ) + pass + else: + print 'Tool dependency path %s contains the following files and directories:' % args.basepath + for element in os.listdir( args.basepath ): + print element + return 0 + +if __name__ == '__main__': + description = 'Clean out or list the contents of the provided tool dependency path. Remove if ' + description += 'the --delete command line argument is provided.' + parser = argparse.ArgumentParser( description=description ) + parser.add_argument( '--delete', + dest='delete', + required=False, + action='store_true', + default=False, + help='Whether to delete all folders and files or list them on exit.' ) + parser.add_argument( '--basepath', + dest='basepath', + required=True, + action='store', + metavar='name', + help='The base path where tool dependencies are installed.' ) + args = parser.parse_args() + sys.exit( main( args ) ) diff -r 723431aa61fb4c7d5cd1f73fe34e16af29368ef4 -r b1e82182414d359f6f43e117e92ec6d6638878fe test/base/tool_shed_util.py --- a/test/base/tool_shed_util.py +++ b/test/base/tool_shed_util.py @@ -15,6 +15,9 @@ log = logging.getLogger(__name__) +# Set a 10 minute timeout for repository installation. +repository_installation_timeout = 600 + def get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision, tool_path ): """ Return the GALAXY_TEST_FILE_DIR, the containing repository name and the change set revision for the tool elem. diff -r 723431aa61fb4c7d5cd1f73fe34e16af29368ef4 -r b1e82182414d359f6f43e117e92ec6d6638878fe test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1,39 +1,38 @@ -import pkg_resources -pkg_resources.require( "twill==0.9" ) - +import difflib +import filecmp +import logging +import os +import re +import pprint +import shutil import StringIO -import os -import filecmp +import subprocess +import tarfile +import tempfile import time import unittest import urllib -import logging -import difflib -import tarfile import zipfile -import tempfile -import re -import shutil -import subprocess -import pprint -import twill -import twill.commands as tc -from twill.other_packages._mechanize_dist import ClientForm -pkg_resources.require( "elementtree" ) -pkg_resources.require( "MarkupSafe" ) -from markupsafe import escape -from elementtree import ElementTree from galaxy.web import security from galaxy.web.framework.helpers import iff from galaxy.util.json import from_json_string from base.asserts import verify_assertions -buffer = StringIO.StringIO() +from galaxy import eggs +eggs.require( "elementtree" ) +eggs.require( 'twill' ) + +from elementtree import ElementTree + +import twill +import twill.commands as tc +from twill.other_packages._mechanize_dist import ClientForm #Force twill to log to a buffer -- FIXME: Should this go to stdout and be captured by nose? -twill.set_output(buffer) -tc.config('use_tidy', 0) +buffer = StringIO.StringIO() +twill.set_output( buffer ) +tc.config( 'use_tidy', 0 ) # Dial ClientCookie logging down (very noisy) logging.getLogger( "ClientCookie.cookies" ).setLevel( logging.WARNING ) diff -r 723431aa61fb4c7d5cd1f73fe34e16af29368ef4 -r b1e82182414d359f6f43e117e92ec6d6638878fe test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -1,9 +1,22 @@ +import logging +import os +import re +import test_db_util +import time +import urllib + import galaxy.model as model import galaxy.model.tool_shed_install as install_model -import common, string, os, re, test_db_util, simplejson, logging, time, sys -import galaxy.util as util -from base.twilltestcase import tc, from_json_string, TwillTestCase, security, urllib -from tool_shed.util.encoding_util import tool_shed_encode, tool_shed_decode +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 log = logging.getLogger( __name__ ) @@ -52,7 +65,7 @@ if install_parameters: iri_ids = install_parameters.group(1) # In some cases, the returned iri_ids are of the form: "[u'<encoded id>', u'<encoded id>']" - # This regex ensures that non-hex characters are stripped out of the list, so that util.listify/decode_id + # This regex ensures that non-hex characters are stripped out of the list, so that galaxy.util.listify/decode_id # will handle them correctly. It's safe to pass the cleaned list to manage_repositories, because it can parse # comma-separated values. repository_ids = str( iri_ids ) @@ -60,9 +73,9 @@ encoded_kwd = install_parameters.group(2) reinstalling = install_parameters.group(3) url = '/admin_toolshed/manage_repositories?operation=install&tool_shed_repository_ids=%s&encoded_kwd=%s&reinstalling=%s' % \ - ( ','.join( util.listify( repository_ids ) ), encoded_kwd, reinstalling ) + ( ','.join( galaxy.util.listify( repository_ids ) ), encoded_kwd, reinstalling ) self.visit_url( url ) - return util.listify( repository_ids ) + return galaxy.util.listify( repository_ids ) def install_repository( self, repository_info_dict, install_tool_dependencies=True, install_repository_dependencies=True, strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[], @@ -161,9 +174,9 @@ 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 180 seconds, or 3 minutes. - if timeout_counter > common.repository_installation_timeout: - raise AssertionError( 'Repository installation timed out, %d seconds elapsed, repository state is %s.' % \ - ( timeout_counter, repository.status ) ) + # 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 ) ) break time.sleep( 1 ) diff -r 723431aa61fb4c7d5cd1f73fe34e16af29368ef4 -r b1e82182414d359f6f43e117e92ec6d6638878fe test/tool_shed/base/common.py --- a/test/tool_shed/base/common.py +++ b/test/tool_shed/base/common.py @@ -33,6 +33,3 @@ ''' new_repository_dependencies_line = ''' <repository toolshed="${toolshed_url}" name="${repository_name}" owner="${owner}" changeset_revision="${changeset_revision}"${prior_installation_required} />''' - -# Set a 3 minute timeout for repository installation. This should be sufficient, since we're not installing tool dependencies. -repository_installation_timeout = 180 \ No newline at end of file diff -r 723431aa61fb4c7d5cd1f73fe34e16af29368ef4 -r b1e82182414d359f6f43e117e92ec6d6638878fe test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -12,16 +12,27 @@ import urllib import galaxy.webapps.tool_shed.util.hgweb_config import galaxy.model.tool_shed_install as galaxy_model -import galaxy.util as util +import galaxy.util + +from base.tool_shed_util import repository_installation_timeout +from base.twilltestcase import TwillTestCase +from galaxy.util.json import from_json_string +from galaxy.web import security +from tool_shed.util.encoding_util import tool_shed_encode from tool_shed.util import shed_util_common as suc from tool_shed.util import xml_util -from base.twilltestcase import tc, from_json_string, TwillTestCase, security, urllib -from tool_shed.util.encoding_util import tool_shed_encode, tool_shed_decode from galaxy import eggs -eggs.require('mercurial') -from mercurial import hg, ui, commands +eggs.require( 'mercurial' ) +eggs.require( 'twill' ) + from mercurial.util import Abort +from mercurial import commands +from mercurial import hg +from mercurial import ui + +import twill.commands as tc + log = logging.getLogger( __name__ ) @@ -848,7 +859,7 @@ if install_parameters: iri_ids = install_parameters.group(1) # In some cases, the returned iri_ids are of the form: "[u'<encoded id>', u'<encoded id>']" - # This regex ensures that non-hex characters are stripped out of the list, so that util.listify/decode_id + # This regex ensures that non-hex characters are stripped out of the list, so that galaxy.util.listify/decode_id # will handle them correctly. It's safe to pass the cleaned list to manage_repositories, because it can parse # comma-separated values. repository_ids = str( iri_ids ) @@ -856,9 +867,9 @@ encoded_kwd = install_parameters.group(2) reinstalling = install_parameters.group(3) url = '/admin_toolshed/manage_repositories?operation=install&tool_shed_repository_ids=%s&encoded_kwd=%s&reinstalling=%s' % \ - ( ','.join( util.listify( repository_ids ) ), encoded_kwd, reinstalling ) + ( ','.join( galaxy.util.listify( repository_ids ) ), encoded_kwd, reinstalling ) self.visit_galaxy_url( url ) - return util.listify( repository_ids ) + return galaxy.util.listify( repository_ids ) def install_repositories_from_search_results( self, repositories, install_tool_dependencies=False, strings_displayed=[], strings_not_displayed=[], **kwd ): @@ -1327,7 +1338,7 @@ def verify_installed_repository_data_table_entries( self, required_data_table_entries ): # The value of the received required_data_table_entries will be something like: [ 'sam_fa_indexes' ] - data_tables = util.parse_xml( self.shed_tool_data_table_conf ) + data_tables = xml_util.parse_xml( self.shed_tool_data_table_conf ) found = False # With the tool shed, the "path" attribute that is hard-coded into the tool_data_tble_conf.xml # file is ignored. This is because the tool shed requires the directory location to which this @@ -1445,8 +1456,8 @@ while galaxy_repository.status not in final_states: test_db_util.ga_refresh( galaxy_repository ) timeout_counter = timeout_counter + 1 - # This timeout currently defaults to 180 seconds, or 3 minutes. - if timeout_counter > common.repository_installation_timeout: + # This timeout currently defaults to 10 minutes. + if timeout_counter > repository_installation_timeout: raise AssertionError( 'Repository installation timed out, %d seconds elapsed, repository state is %s.' % \ ( timeout_counter, galaxy_repository.status ) ) break 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.

1 0

commit/galaxy-central: guerler: Grids: Fix dataset state viewer in saved histories
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/62ed22bb4360/ Changeset: 62ed22bb4360 User: guerler Date: 2013-12-17 18:44:33 Summary: Grids: Fix dataset state viewer in saved histories Affected #: 1 file diff -r 270931cae37f2efaac24f6c22236e5fa0b87ce23 -r 62ed22bb4360d11fcfedcce09c961741186a3b88 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -69,7 +69,7 @@ default_sort_key = "-update_time" columns = [ HistoryListNameColumn( "Name", key="name", attach_popup=True, filterable="advanced" ), - DatasetsByStateColumn( "Datasets", key="datasets_by_state", sortable=False ), + DatasetsByStateColumn( "Datasets", key="datasets_by_state", sortable=False, nowrap=True), grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, \ filterable="advanced", grid_name="HistoryListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), 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.

1 0

commit/galaxy-central: inithello: Add script to clean up or display the contents of a tool dependency path.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/270931cae37f/ Changeset: 270931cae37f User: inithello Date: 2013-12-17 18:20:08 Summary: Add script to clean up or display the contents of a tool dependency path. Affected #: 1 file diff -r 786c58661b6429a7bcdb0978df1da74dddbd656d -r 270931cae37f2efaac24f6c22236e5fa0b87ce23 lib/tool_shed/scripts/clean_up_tool_dependency_directory.py --- /dev/null +++ b/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py @@ -0,0 +1,58 @@ +import argparse +import os +import sys +import shutil + +def main( args ): + if not os.path.exists( args.basepath ): + print 'Tool dependency path %s does not exist.' % str( args.basepath ) + return 1 + if args.delete: + print 'Deleting contents of tool dependency path %s.' % args.basepath + for node in os.listdir( args.basepath ): + path = os.path.join( args.basepath, node ) + if os.path.isdir( path ): + try: + shutil.rmtree( path ) + print 'Deleted directory %s and all its contents.' % path + except Exception, e: + print 'Error deleting directory %s: %s' % ( path, str( e ) ) + pass + elif os.path.isfile( path ): + try: + os.remove( path ) + print 'Deleted file %s.' % path + except Exception, e: + print 'Error deleting file %s: %s' % ( path, str( e ) ) + pass + elif os.path.islink( path ): + print 'Deleting symlink %s with target %s.' % ( path, os.path.realpath( path ) ) + try: + os.remove( path ) + except Exception, e: + print 'Error deleting symlink %s: %s' % ( path, str( e ) ) + pass + else: + print 'Tool dependency path %s contains the following files and directories:' % args.basepath + for element in os.listdir( args.basepath ): + print element + return 0 + +if __name__ == '__main__': + description = 'Clean out or list the contents of the provided tool dependency path. Remove if ' + description += 'the --delete command line argument is provided.' + parser = argparse.ArgumentParser( description=description ) + parser.add_argument( '--delete', + dest='delete', + required=False, + action='store_true', + default=False, + help='Whether to delete all folders and files or list them on exit.' ) + parser.add_argument( '--basepath', + dest='basepath', + required=True, + action='store', + metavar='name', + help='The base path where tool dependencies are installed.' ) + args = parser.parse_args() + sys.exit( main( args ) ) 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.

1 0

commit/galaxy-central: greg: Fix imports in various functional test scripts.
by commits-noreply＠bitbucket.org 17 Dec '13

17 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/786c58661b64/ Changeset: 786c58661b64 User: greg Date: 2013-12-17 17:20:23 Summary: Fix imports in various functional test scripts. Affected #: 5 files diff -r a2bad69f03f4786309ba80ff305ebdd7b68f93fa -r 786c58661b6429a7bcdb0978df1da74dddbd656d test/base/tool_shed_util.py --- a/test/base/tool_shed_util.py +++ b/test/base/tool_shed_util.py @@ -15,6 +15,9 @@ log = logging.getLogger(__name__) +# Set a 10 minute timeout for repository installation. +repository_installation_timeout = 600 + def get_installed_repository_info( elem, last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision, tool_path ): """ Return the GALAXY_TEST_FILE_DIR, the containing repository name and the change set revision for the tool elem. diff -r a2bad69f03f4786309ba80ff305ebdd7b68f93fa -r 786c58661b6429a7bcdb0978df1da74dddbd656d test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1,39 +1,38 @@ -import pkg_resources -pkg_resources.require( "twill==0.9" ) - +import difflib +import filecmp +import logging +import os +import re +import pprint +import shutil import StringIO -import os -import filecmp +import subprocess +import tarfile +import tempfile import time import unittest import urllib -import logging -import difflib -import tarfile import zipfile -import tempfile -import re -import shutil -import subprocess -import pprint -import twill -import twill.commands as tc -from twill.other_packages._mechanize_dist import ClientForm -pkg_resources.require( "elementtree" ) -pkg_resources.require( "MarkupSafe" ) -from markupsafe import escape -from elementtree import ElementTree from galaxy.web import security from galaxy.web.framework.helpers import iff from galaxy.util.json import from_json_string from base.asserts import verify_assertions -buffer = StringIO.StringIO() +from galaxy import eggs +eggs.require( "elementtree" ) +eggs.require( 'twill' ) + +from elementtree import ElementTree + +import twill +import twill.commands as tc +from twill.other_packages._mechanize_dist import ClientForm #Force twill to log to a buffer -- FIXME: Should this go to stdout and be captured by nose? -twill.set_output(buffer) -tc.config('use_tidy', 0) +buffer = StringIO.StringIO() +twill.set_output( buffer ) +tc.config( 'use_tidy', 0 ) # Dial ClientCookie logging down (very noisy) logging.getLogger( "ClientCookie.cookies" ).setLevel( logging.WARNING ) diff -r a2bad69f03f4786309ba80ff305ebdd7b68f93fa -r 786c58661b6429a7bcdb0978df1da74dddbd656d test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -1,9 +1,22 @@ +import logging +import os +import re +import test_db_util +import time +import urllib + import galaxy.model as model import galaxy.model.tool_shed_install as install_model -import common, string, os, re, test_db_util, simplejson, logging, time, sys -import galaxy.util as util -from base.twilltestcase import tc, from_json_string, TwillTestCase, security, urllib -from tool_shed.util.encoding_util import tool_shed_encode, tool_shed_decode +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 log = logging.getLogger( __name__ ) @@ -52,7 +65,7 @@ if install_parameters: iri_ids = install_parameters.group(1) # In some cases, the returned iri_ids are of the form: "[u'<encoded id>', u'<encoded id>']" - # This regex ensures that non-hex characters are stripped out of the list, so that util.listify/decode_id + # This regex ensures that non-hex characters are stripped out of the list, so that galaxy.util.listify/decode_id # will handle them correctly. It's safe to pass the cleaned list to manage_repositories, because it can parse # comma-separated values. repository_ids = str( iri_ids ) @@ -60,9 +73,9 @@ encoded_kwd = install_parameters.group(2) reinstalling = install_parameters.group(3) url = '/admin_toolshed/manage_repositories?operation=install&tool_shed_repository_ids=%s&encoded_kwd=%s&reinstalling=%s' % \ - ( ','.join( util.listify( repository_ids ) ), encoded_kwd, reinstalling ) + ( ','.join( galaxy.util.listify( repository_ids ) ), encoded_kwd, reinstalling ) self.visit_url( url ) - return util.listify( repository_ids ) + return galaxy.util.listify( repository_ids ) def install_repository( self, repository_info_dict, install_tool_dependencies=True, install_repository_dependencies=True, strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[], @@ -161,9 +174,9 @@ 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 180 seconds, or 3 minutes. - if timeout_counter > common.repository_installation_timeout: - raise AssertionError( 'Repository installation timed out, %d seconds elapsed, repository state is %s.' % \ - ( timeout_counter, repository.status ) ) + # 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 ) ) break time.sleep( 1 ) diff -r a2bad69f03f4786309ba80ff305ebdd7b68f93fa -r 786c58661b6429a7bcdb0978df1da74dddbd656d test/tool_shed/base/common.py --- a/test/tool_shed/base/common.py +++ b/test/tool_shed/base/common.py @@ -33,6 +33,3 @@ ''' new_repository_dependencies_line = ''' <repository toolshed="${toolshed_url}" name="${repository_name}" owner="${owner}" changeset_revision="${changeset_revision}"${prior_installation_required} />''' - -# Set a 3 minute timeout for repository installation. This should be sufficient, since we're not installing tool dependencies. -repository_installation_timeout = 180 \ No newline at end of file diff -r a2bad69f03f4786309ba80ff305ebdd7b68f93fa -r 786c58661b6429a7bcdb0978df1da74dddbd656d test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -12,16 +12,27 @@ import urllib import galaxy.webapps.tool_shed.util.hgweb_config import galaxy.model.tool_shed_install as galaxy_model -import galaxy.util as util +import galaxy.util + +from base.tool_shed_util import repository_installation_timeout +from base.twilltestcase import TwillTestCase +from galaxy.util.json import from_json_string +from galaxy.web import security +from tool_shed.util.encoding_util import tool_shed_encode from tool_shed.util import shed_util_common as suc from tool_shed.util import xml_util -from base.twilltestcase import tc, from_json_string, TwillTestCase, security, urllib -from tool_shed.util.encoding_util import tool_shed_encode, tool_shed_decode from galaxy import eggs -eggs.require('mercurial') -from mercurial import hg, ui, commands +eggs.require( 'mercurial' ) +eggs.require( 'twill' ) + from mercurial.util import Abort +from mercurial import commands +from mercurial import hg +from mercurial import ui + +import twill.commands as tc + log = logging.getLogger( __name__ ) @@ -848,7 +859,7 @@ if install_parameters: iri_ids = install_parameters.group(1) # In some cases, the returned iri_ids are of the form: "[u'<encoded id>', u'<encoded id>']" - # This regex ensures that non-hex characters are stripped out of the list, so that util.listify/decode_id + # This regex ensures that non-hex characters are stripped out of the list, so that galaxy.util.listify/decode_id # will handle them correctly. It's safe to pass the cleaned list to manage_repositories, because it can parse # comma-separated values. repository_ids = str( iri_ids ) @@ -856,9 +867,9 @@ encoded_kwd = install_parameters.group(2) reinstalling = install_parameters.group(3) url = '/admin_toolshed/manage_repositories?operation=install&tool_shed_repository_ids=%s&encoded_kwd=%s&reinstalling=%s' % \ - ( ','.join( util.listify( repository_ids ) ), encoded_kwd, reinstalling ) + ( ','.join( galaxy.util.listify( repository_ids ) ), encoded_kwd, reinstalling ) self.visit_galaxy_url( url ) - return util.listify( repository_ids ) + return galaxy.util.listify( repository_ids ) def install_repositories_from_search_results( self, repositories, install_tool_dependencies=False, strings_displayed=[], strings_not_displayed=[], **kwd ): @@ -1327,7 +1338,7 @@ def verify_installed_repository_data_table_entries( self, required_data_table_entries ): # The value of the received required_data_table_entries will be something like: [ 'sam_fa_indexes' ] - data_tables = util.parse_xml( self.shed_tool_data_table_conf ) + data_tables = xml_util.parse_xml( self.shed_tool_data_table_conf ) found = False # With the tool shed, the "path" attribute that is hard-coded into the tool_data_tble_conf.xml # file is ignored. This is because the tool shed requires the directory location to which this @@ -1445,8 +1456,8 @@ while galaxy_repository.status not in final_states: test_db_util.ga_refresh( galaxy_repository ) timeout_counter = timeout_counter + 1 - # This timeout currently defaults to 180 seconds, or 3 minutes. - if timeout_counter > common.repository_installation_timeout: + # This timeout currently defaults to 10 minutes. + if timeout_counter > repository_installation_timeout: raise AssertionError( 'Repository installation timed out, %d seconds elapsed, repository state is %s.' % \ ( timeout_counter, galaxy_repository.status ) ) break 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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galaxy-commits December 2013