1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/7756b29bea29/
Changeset: 7756b29bea29
User: greg
Date: 2013-11-28 03:25:03
Summary: Fix a debug statement.
Affected #: 1 file
diff -r 849898bb73009a5be2387a03e44ff8afdeed12cc -r 7756b29bea292228d3472a7f613f5be5adee38a2 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
@@ -380,7 +380,7 @@
# 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 about repository %s from the API: %s' % ( str( name ), error_message ) )
+ log.debug( 'Error getting additional details from the API: %s' % str( error_message ) )
else:
# Don't test empty repositories.
changeset_revision = baseline_repository_dict[ 'changeset_revision' ]
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 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/849898bb7300/
Changeset: 849898bb7300
User: greg
Date: 2013-11-28 03:20:38
Summary: Handle errors attempting to get the list of repositories to test for the Tool Shed's install and test framework.
Affected #: 1 file
diff -r 3c7edca24e5aa0563e7078b56469730fd2bc27a1 -r 849898bb73009a5be2387a03e44ff8afdeed12cc 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
@@ -620,130 +620,137 @@
changeset_revision = str( repository_dict[ 'changeset_revision' ] )
# Populate the tool_test_results_dict.
tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, encoded_repository_metadata_id )
- # The preparation script ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered
- # information in the 'test_environment' and possibly the 'missing_test_components' entries of the first
- # tool_test_results_dict in the list of tool_test_results_dicts. We need to be careful to not lose this
- # information.
- tool_test_results_dict = tool_test_results_dicts.pop( 0 )
- # See if this repository should be skipped for any reason.
- skip_this_repository = 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:
- skip_this_repository = True
- skip_reason = reason
- break
- if skip_this_repository:
- tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason )
- params = dict( tools_functionally_correct=False,
- do_not_test=False )
- # TODO: do something usefule 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." % ( changeset_revision, name, owner ) )
+ if error_message:
+ log.debug( error_message )
else:
- if error_message:
- log.debug( error_message )
+ # The preparation script ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered
+ # information in the 'test_environment' and possibly the 'missing_test_components' entries of the first
+ # tool_test_results_dict in the list of tool_test_results_dicts. We need to be careful to not lose this
+ # information.
+ try:
+ tool_test_results_dict = tool_test_results_dicts.pop( 0 )
+ except Exception, e:
+ log.exception( "Invalid list of tool_test_results_dicts %s: %s" % ( str( tool_test_results_dicts ), str( e ) ) )
+ continue
+ # See if this repository should be skipped for any reason.
+ skip_this_repository = 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:
+ skip_this_repository = True
+ skip_reason = reason
+ break
+ if skip_this_repository:
+ tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason )
+ params = dict( tools_functionally_correct=False,
+ do_not_test=False )
+ # TODO: do something usefule 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." % ( changeset_revision, name, owner ) )
else:
- test_environment_dict = tool_test_results_dict.get( 'test_environment', None )
- test_environment_dict = get_test_environment( test_environment_dict )
- # 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" )
- test_environment_dict[ 'time_tested' ] = now
- 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 )
- # TODO: do something usefule 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 )
+ log.debug( error_message )
+ else:
+ test_environment_dict = tool_test_results_dict.get( 'test_environment', None )
+ test_environment_dict = get_test_environment( test_environment_dict )
+ # 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" )
+ test_environment_dict[ 'time_tested' ] = now
+ 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 )
+ # TODO: do something usefule 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( 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_dicts,
+ 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() ) )
- # 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 usefule 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[ '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_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 usefule 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[ '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
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 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/8b613225f1de/
Changeset: 8b613225f1de
User: Dave Bouvier
Date: 2013-11-27 21:37:02
Summary: Fix imports.
Affected #: 1 file
diff -r 11028b31d3f024ef920c3168d3f752bc13ba3ad8 -r 8b613225f1def637af4774b860578a77a7fb0fe4 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
@@ -15,6 +15,7 @@
import ConfigParser
import galaxy.webapps.tool_shed.config as tool_shed_config
import galaxy.webapps.tool_shed.model.mapping
+import tool_shed.util.shed_util_common as suc
import logging
import shutil
import tempfile
@@ -31,8 +32,6 @@
from mercurial import __version__
from optparse import OptionParser
from time import strftime
-from tool_shed.util.shed_util_common import clone_repository
-from tool_shed.util.shed_util_common import get_configured_ui
log = logging.getLogger( 'check_repositories_for_functional_tests' )
assert sys.version_info[ :2 ] >= ( 2, 6 )
@@ -129,9 +128,9 @@
testable_revision = False
# Clone the repository up to the changeset revision we're checking.
repo_dir = repository.repo_path( app )
- repo = hg.repository( get_configured_ui(), repo_dir )
+ repo = hg.repository( suc.get_configured_ui(), repo_dir )
work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-cafr" )
- cloned_ok, error_message = clone_repository( repo_dir, work_dir, changeset_revision )
+ cloned_ok, error_message = suc.clone_repository( repo_dir, work_dir, changeset_revision )
if cloned_ok:
# Iterate through all the directories in the cloned changeset revision and determine whether there's a
# directory named test-data. If this directory is not present update the metadata record for the changeset
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.