1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/61eacb9ce6d5/ Changeset: 61eacb9ce6d5 User: greg Date: 2013-11-25 21:09:50 Summary: More fixes for the tool shed's install and test framework - the test environment including time last tested should now display correctly again (among other fixes). Affected #: 5 files

diff -r 1fbb0cb8dd5865185b186e609d747668510a25a8 -r 61eacb9ce6d54a3cc217e7d826963a9a7370adf7 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -170,6 +170,7 @@ if key in [ 'tools_functionally_correct', 'time_last_tested' ]: # Automatically update repository_metadata.time_last_tested. repository_metadata.time_last_tested = datetime.datetime.utcnow() + flush_needed = True flush_needed = True if flush_needed: trans.sa_session.add( repository_metadata )

diff -r 1fbb0cb8dd5865185b186e609d747668510a25a8 -r 61eacb9ce6d54a3cc217e7d826963a9a7370adf7 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -7,7 +7,6 @@ import tempfile import time

-from datetime import datetime from optparse import OptionParser from time import strftime

@@ -119,21 +118,11 @@ missing_test_components = [] repository = repository_metadata.repository records_checked += 1 - # Create the repository_status dictionary, using the dictionary from the previous test run if available. + # Create the tool_test_results_dict dictionary, using the dictionary from the previous test run if available. if repository_metadata.tool_test_results: - repository_status = repository_metadata.tool_test_results + tool_test_results_dict = repository_metadata.tool_test_results else: - repository_status = {} - # Initialize the repository_status dictionary with the information about the current test environment. - last_test_environment = repository_status.get( 'test_environment', None ) - if last_test_environment is None: - test_environment = get_test_environment() - else: - test_environment = get_test_environment( last_test_environment ) - test_environment[ 'tool_shed_database_version' ] = get_database_version( app ) - test_environment[ 'tool_shed_mercurial_version' ] = __version__.version - test_environment[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) - repository_status[ 'test_environment' ] = test_environment + tool_test_results_dict = {} # Check the next repository revision. changeset_revision = str( repository_metadata.changeset_revision ) name = repository.name @@ -262,6 +251,11 @@ if 'missing_components' in invalid_test: print '# %s' % invalid_test[ 'missing_components' ] if not info_only: + test_environment_dict = tool_test_results_dict.get( 'test_environment', {} ) + test_environment_dict[ 'tool_shed_database_version' ] = get_database_version( app ) + test_environment_dict[ 'tool_shed_mercurial_version' ] = __version__.version + test_environment_dict[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) + tool_test_results_dict[ 'test_environment' ] = test_environment_dict # The repository_metadata.time_last_tested column is not changed by this script since no testing is performed here. if missing_test_components: # If functional test definitions or test data are missing, set do_not_test = True if no tool with valid tests has been @@ -278,8 +272,8 @@ repository_metadata.do_not_test = True repository_metadata.tools_functionally_correct = False repository_metadata.missing_test_components = True - repository_status[ 'missing_test_components' ] = missing_test_components - repository_metadata.tool_test_results = repository_status + tool_test_results_dict[ 'missing_test_components' ] = missing_test_components + repository_metadata.tool_test_results = tool_test_results_dict app.sa_session.add( repository_metadata ) app.sa_session.flush() stop = time.time()

diff -r 1fbb0cb8dd5865185b186e609d747668510a25a8 -r 61eacb9ce6d54a3cc217e7d826963a9a7370adf7 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -235,7 +235,7 @@ class TestEnvironment( object ): """Tool test environment object"""

- def __init__( self, id=None, architecture=None, galaxy_database_version=None, galaxy_revision=None, python_version=None, system=None, time_last_tested=None, + def __init__( self, id=None, architecture=None, galaxy_database_version=None, galaxy_revision=None, python_version=None, system=None, time_tested=None, tool_shed_database_version=None, tool_shed_mercurial_version=None, tool_shed_revision=None ): self.id = id self.architecture = architecture @@ -243,7 +243,7 @@ self.galaxy_revision = galaxy_revision self.python_version = python_version self.system = system - self.time_last_tested = time_last_tested + self.time_tested = time_tested self.tool_shed_database_version = tool_shed_database_version self.tool_shed_mercurial_version = tool_shed_mercurial_version self.tool_shed_revision = tool_shed_revision @@ -743,11 +743,6 @@ ) if repository_metadata: metadata = repository_metadata.metadata - tool_test_results = repository_metadata.tool_test_results - try: - time_last_tested = time_ago( repository_metadata.time_last_tested ) - except: - time_last_tested = None lock = threading.Lock() lock.acquire( True ) try: @@ -836,12 +831,17 @@ label='Valid tools' ) containers_dict[ 'valid_tools' ] = valid_tools_root_folder # Tool test results container. - if 'tool_test_results' not in exclude and tool_test_results and len( tool_test_results ) > 1: - # Only create and populate this folder if there are actual tool test results to display, since the display of the 'Test environment' - # folder by itself can be misleading. We check for more than a single entry in the tool_test_results dictionary because it may have - # only the "test_environment" entry, but we want at least 1 of "passed_tests", "failed_tests", "installation_errors", "missing_test_components" - # "skipped_tests", "not_tested" or any other entry that may be added in the future. - folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, folder_id, tool_test_results, time_last_tested=time_last_tested ) + tool_test_results = repository_metadata.tool_test_results + # Only create and populate this folder if there are actual tool test results to display. + if can_display_tool_test_results( tool_test_results, exclude=exclude ): + time_tested = repository_metadata.time_last_tested + if time_tested is not None: + time_tested = time_ago( time_tested ) + folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, + folder_id, + tool_test_results, + time_tested, + label='Tool test results' ) containers_dict[ 'tool_test_results' ] = tool_test_results_root_folder # Workflows container. if metadata: @@ -1052,30 +1052,39 @@ tool_dependencies_root_folder = None return folder_id, tool_dependencies_root_folder

-def build_tool_test_results_folder( trans, folder_id, tool_test_results_dict, label='Tool test results', time_last_tested=None ): +def build_tool_test_results_folder( trans, folder_id, tool_test_results_dict, time_tested, label='Tool test results' ): """Return a folder hierarchy containing tool dependencies.""" # This container is displayed only in the tool shed. if tool_test_results_dict: folder_id += 1 tool_test_results_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) - if test_environment_dict: + if test_environment_dict is not None: folder_id += 1 test_results_folder = Folder( id=folder_id, key='test_results', label=label, parent=tool_test_results_root_folder ) tool_test_results_root_folder.folders.append( test_results_folder ) folder_id += 1 folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=test_results_folder ) test_results_folder.folders.append( folder ) + architecture = test_environment_dict.get( 'architecture', '' ) + galaxy_database_version = test_environment_dict.get( 'galaxy_database_version', '' ) + galaxy_revision = test_environment_dict.get( 'galaxy_revision', '' ) + python_version = test_environment_dict.get( 'python_version', '' ) + system = test_environment_dict.get( 'system', '' ) + time_tested = time_tested + tool_shed_database_version = test_environment_dict.get( 'tool_shed_database_version', '' ) + tool_shed_mercurial_version = test_environment_dict.get( 'tool_shed_mercurial_version', '' ) + tool_shed_revision = test_environment_dict.get( 'tool_shed_revision', '' ) test_environment = TestEnvironment( id=1, - architecture=test_environment_dict.get( 'architecture', '' ), - galaxy_database_version=test_environment_dict.get( 'galaxy_database_version', '' ), - galaxy_revision=test_environment_dict.get( 'galaxy_revision', '' ), - python_version=test_environment_dict.get( 'python_version', '' ), - system=test_environment_dict.get( 'system', '' ), - time_last_tested=time_last_tested, - tool_shed_database_version=test_environment_dict.get( 'tool_shed_database_version', '' ), - tool_shed_mercurial_version=test_environment_dict.get( 'tool_shed_mercurial_version', '' ), - tool_shed_revision=test_environment_dict.get( 'tool_shed_revision', '' ) ) + architecture=architecture, + galaxy_database_version=galaxy_database_version, + galaxy_revision=galaxy_revision, + python_version=python_version, + system=system, + time_tested=time_tested, + tool_shed_database_version=tool_shed_database_version, + tool_shed_mercurial_version=tool_shed_mercurial_version, + tool_shed_revision=tool_shed_revision ) folder.test_environments.append( test_environment ) not_tested_dict = tool_test_results_dict.get( 'not_tested', {} ) if not_tested_dict: @@ -1238,6 +1247,26 @@ workflows_root_folder = None return folder_id, workflows_root_folder

+def can_display_tool_test_results( tool_test_results_dict, exclude=None ): + # Only create and populate the tool_test_results container if there are actual tool test results to display. + if exclude is None: + exclude = [] + if 'tool_test_results' in exclude: + return False + if tool_test_results_dict: + # We check for more than a single entry in the tool_test_results dictionary because it may have + # only the "test_environment" entry, but we want at least 1 of "passed_tests", "failed_tests", + # "installation_errors", "missing_test_components" "skipped_tests", "not_tested" or any other + # entry that may be added in the future. + display_entries = [ 'failed_tests', 'installation_errors', 'missing_test_components', 'not_tested', 'passed_tests', 'skipped_tests' ] + for k, v in tool_test_results_dict.items(): + if k in display_entries: + # We've discovered an entry that can be displayed, so see if it has a value since displaying + # empty lists is not desired. + if v: + return True + return False + def cast_empty_repository_dependency_folders( folder, repository_dependency_id ): """ Change any empty folders contained within the repository dependencies container into a repository dependency since it has no repository dependencies

diff -r 1fbb0cb8dd5865185b186e609d747668510a25a8 -r 61eacb9ce6d54a3cc217e7d826963a9a7370adf7 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -909,7 +909,7 @@ id="libraryItem-rte-${encoded_id}"><td style="padding-left: ${pad+20}px;"><table class="grid" id="test_environment"> - <tr><td><b>Time tested:</b> ${test_environment.time_last_tested | h}</td></tr> + <tr><td><b>Time tested:</b> ${test_environment.time_tested | h}</td></tr><tr><td><b>System:</b> ${test_environment.system | h}</td></tr><tr><td><b>Architecture:</b> ${test_environment.architecture | h}</td></tr><tr><td><b>Python version:</b> ${test_environment.python_version | h}</td></tr>

diff -r 1fbb0cb8dd5865185b186e609d747668510a25a8 -r 61eacb9ce6d54a3cc217e7d826963a9a7370adf7 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -21,7 +21,6 @@ import threading import unittest import urllib -import urllib2 from time import strftime

# Assume we are run from the galaxy root directory, add lib to the python path @@ -42,8 +41,8 @@ sys.path = new_path

from functional_tests import generate_config_file + from galaxy import eggs -from galaxy.util import unicodify

eggs.require( "nose" ) eggs.require( "NoseHTML" ) @@ -53,10 +52,14 @@ eggs.require( "PasteDeploy" ) eggs.require( "Cheetah" ) eggs.require( "simplejson" ) +eggs.require( 'mercurial' )

import simplejson import twill

+from datetime import datetime +from mercurial import __version__ + # This should not be required, but it is under certain conditions, thanks to this bug: http://code.google.com/p/python-nose/issues/detail?id=284 eggs.require( "pysqlite" )

@@ -76,13 +79,20 @@ import tool_shed.util.shed_util_common as suc from tool_shed.util import tool_dependency_util

+from galaxy.web.framework.helpers import time_ago + import nose.core import nose.config import nose.loader import nose.plugins.manager from nose.plugins import Plugin

-from base.util import parse_tool_panel_config, get_database_version, get_test_environment, get_repository_current_revision +from base.util import get_database_version +from base.util import get_repository_current_revision +from base.util import get_test_environment +from base.util import parse_tool_panel_config + +from galaxy.util import unicodify

from common import update

@@ -472,29 +482,27 @@ return repository_dicts, error_message

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) + """ + 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_from_api( tool_shed_url, metadata_revision_id ): +def get_tool_test_results_dict( tool_shed_url, encoded_repository_metadata_id ): error_message = '' - api_path = [ 'api', 'repository_revisions', metadata_revision_id ] + api_path = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] api_url = get_api_url( base=tool_shed_url, parts=api_path ) repository_metadata, error_message = json_from_url( api_url ) if error_message: return None, error_message tool_test_results = repository_metadata.get( 'tool_test_results', {} ) - # If, for some reason, the script that checks for functional tests has not run, tool_test_results will be None. - if tool_test_results is None: - return {}, error_message return tool_test_results, error_message

-def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, repository_status_dict, results_dict ): +def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, tool_test_results_dict, results_dict ): """Handle missing repository or tool dependencies for an installed repository.""" # If a tool dependency fails to install correctly, this should be considered an installation error, # and functional tests should be skipped, since the tool dependency needs to be correctly installed @@ -508,7 +516,7 @@ name=dependency.name, version=dependency.version, error_message=dependency.error_message ) - repository_status_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) + tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) for dependency in repository.missing_repository_dependencies: log.debug( 'Missing repository dependency %s changeset revision %s owned by %s: %s' % \ ( str( dependency.name ), str( dependency.changeset_revision ), str( dependency.owner ), unicodify( dependency.error_message ) ) ) @@ -517,12 +525,12 @@ owner=dependency.owner, changeset_revision=dependency.changeset_revision, error_message=dependency.error_message ) - repository_status_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) + 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 ) - register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) + register_test_result( galaxy_tool_shed_url, 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'. @@ -629,27 +637,13 @@ # "tool_shed_url": "http://toolshed.local:10001", # "url": "/api/repository_revisions/529fd61ab1c6cc36", # "user_id": "529fd61ab1c6cc36" } - metadata_revision_id = repository_dict.get( 'id', None ) + 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' ] ) - # Populate the repository_status_dict. - repository_status_dict, error_message = get_tool_test_results_from_api( galaxy_tool_shed_url, metadata_revision_id ) - if error_message: - return None, error_message - if 'test_environment' not in repository_status_dict: - repository_status_dict[ 'test_environment' ] = {} - test_environment = get_test_environment( repository_status_dict[ 'test_environment' ] ) - test_environment[ 'galaxy_database_version' ] = get_database_version( app ) - test_environment[ 'galaxy_revision'] = get_repository_current_revision( os.getcwd() ) - repository_status_dict[ 'test_environment' ] = test_environment - repository_status_dict[ 'passed_tests' ] = [] - repository_status_dict[ 'failed_tests' ] = [] - repository_status_dict[ 'skip_reason' ] = None - repository_status_dict[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) # See if this repository should be skipped for any reason. skip_this_repository = False skip_reason = None @@ -661,82 +655,104 @@ skip_reason = reason break if skip_this_repository: - repository_status_dict[ 'not_tested' ] = dict( reason=skip_reason ) + tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) params = dict( tools_functionally_correct=False, do_not_test=False ) - register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) + register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) log.debug( "Not testing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) ) else: - repository, error_message = install_repository( app, repository_dict ) + # Populate the tool_test_results_dict. + tool_test_results_dict, error_message = get_tool_test_results_dict( galaxy_tool_shed_url, encoded_repository_metadata_id ) if error_message: - repository_status_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 ) - repository_status_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) - params = dict( tools_functionally_correct=False, - test_install_error=True, - do_not_test=False ) - register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) - try: - if deactivate: - # We are deactivating this repository and all of its repository dependencies. - deactivate_repository( app, repository_dict ) + log.debug( error_message ) + else: + # The preparation script ~/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. We need to be careful to not lose this information. For all other repositories, + # no changes will have been made to this dictionary by the preparation script, and tool_test_results_dict will be None. + # Initialize the tool_test_results_dict dictionary with the information about the current test environment. + test_environment_dict = tool_test_results_dict.get( 'test_environent', None ) + test_environment_dict = get_test_environment( test_environment_dict ) + test_environment_dict[ 'galaxy_database_version' ] = get_database_version( app ) + test_environment_dict[ 'galaxy_revision' ] = get_repository_current_revision( os.getcwd() ) + 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=[] ) + 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 ) + + register_test_result( galaxy_tool_shed_url, 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( app, repository_dict ) + except: + log.exception( 'Encountered error attempting to deactivate or uninstall %s.', str( repository_dict[ 'name' ] ) ) + results_dict[ 'repositories_failed_install' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) + 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_dict, + results_dict ) else: - # We are uninstalling this repository and all of its repository dependencies. - uninstall_repository( app, repository_dict ) - except: - log.exception( 'Encountered error attempting to deactivate or uninstall %s.', str( repository_dict[ 'name' ] ) ) - results_dict[ 'repositories_failed_install' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - 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() ) ) - if 'missing_test_components' not in repository_status_dict: - repository_status_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, - repository_status_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, repository_status_dict, results_dict ) - except Exception, e: - exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) - log.exception( exception_message ) - repository_status_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 ) - register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) - results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) - total_repositories_tested += 1 + # 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_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 ) + register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) + results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) + total_repositories_tested += 1 results_dict[ 'total_repositories_tested' ] = total_repositories_tested return results_dict, error_message

@@ -794,12 +810,20 @@ return exclude_list

def register_test_result( url, test_results_dict, repository_dict, params ): - """Update the repository metadata tool_test_results and appropriate flags using the API.""" + """ + Update the repository metadata tool_test_results and appropriate flags using the Tool SHed API. This method + updates tool_test_results with the relevant data, sets the do_not_test and tools_functionally correct flags + to the appropriate values and updates the time_last_tested field to the value of the received time_tested. + """ if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: return {} else: metadata_revision_id = repository_dict.get( 'id', None ) + log.debug("RRR In register_test_result, metadata_revision_id: %s" % str( metadata_revision_id )) if metadata_revision_id is not None: + # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. + time_tested = datetime.utcnow() + test_results_dict[ 'time_last_tested' ] = time_ago( time_tested ) params[ 'tool_test_results' ] = test_results_dict url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) try: @@ -876,7 +900,7 @@ for repository in repositories_by_owner[ owner ]: print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] )

-def test_repository_tools( app, repository, repository_dict, repository_status_dict, results_dict ): +def test_repository_tools( app, repository, repository_dict, tool_test_results_dict, results_dict ): """Test tools contained in the received repository.""" name = str( repository.name ) owner = str( repository.owner ) @@ -898,12 +922,12 @@ test_identifier = '%s/%s' % ( owner, name ) passed_tests = plugin.getTestStatus( test_identifier ) break - repository_status_dict[ 'passed_tests' ] = [] + 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 ) - repository_status_dict[ 'passed_tests' ].append( test_result ) + tool_test_results_dict[ 'passed_tests' ].append( test_result ) if success: # This repository's tools passed all functional tests. Update the repository_metadata table in the tool shed's database # to reflect that. Call the register_test_result method, which executes a PUT request to the repository_revisions API @@ -913,20 +937,16 @@ params = dict( tools_functionally_correct=True, do_not_test=False, test_install_error=False ) - register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) + register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( str( changeset_revision ), str( name ) ) ) else: - repository_status_dict[ 'failed_tests' ].append( extract_log_data( result, from_tool_test=True ) ) - # Call the register_test_result method, which executes a PUT request to the repository_revisions API controller with the outcome - # of the tests, and updates tool_test_results with the relevant log data. - # This also sets the do_not_test and tools_functionally correct flags to the appropriate values, and updates the time_last_tested - # field to today's date. + tool_test_results_dict[ 'failed_tests' ].append( extract_log_data( result, from_tool_test=True ) ) results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_dict ) params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=str( set_do_not_test ) ) - register_test_result( galaxy_tool_shed_url, repository_status_dict, repository_dict, params ) + register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed successfully but did not pass functional tests.' % \ ( str( changeset_revision ), str( name ) ) ) # Run the uninstall method. This removes tool functional test methods from the test_toolbox module and uninstalls the @@ -1256,7 +1276,7 @@ return 1

if __name__ == "__main__": - # The repository_status_dict should always have the following structure: + # The tool_test_results_dict should always have the following structure: # { # "test_environment": # {

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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