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Merge latest central.

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This commit is contained in:
John Chilton
2013-12-05 11:02:57 -06:00
parent 19b6904b98 8aa3adf55f
commit c8b32ba00d
1 changed files with 236 additions and 96 deletions
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lib/tool_shed/util/container_util.py
+236 -96
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@@ -327,19 +327,30 @@ def add_orphan_settings_to_tool_dependencies( tool_dependencies, tools ):
# "set_environment": [{"name": "R_SCRIPT_PATH", "type": "set_environment"}]
new_set_environment_dict_list = []
for env_requirements_dict in requirements_dict:
name = env_requirements_dict[ 'name' ]
type = env_requirements_dict[ 'type' ]
if tool_dependency_is_orphan( type, name, None, tools ):
env_requirements_dict[ 'is_orphan' ] = True
try:
name = env_requirements_dict[ 'name' ]
type = env_requirements_dict[ 'type' ]
if tool_dependency_is_orphan( type, name, None, tools ):
env_requirements_dict[ 'is_orphan' ] = True
except Exception, e:
name = str( e )
type = 'unknown'
is_orphan = 'unknown'
new_set_environment_dict_list.append( env_requirements_dict )
new_tool_dependencies[ td_key ] = new_set_environment_dict_list
else:
# {"R/2.15.1": {"name": "R", "readme": "some string", "type": "package", "version": "2.15.1"}
name = requirements_dict[ 'name' ]
type = requirements_dict[ 'type' ]
version = requirements_dict[ 'version']
if tool_dependency_is_orphan( type, name, version, tools ):
requirements_dict[ 'is_orphan' ] = True
try:
name = requirements_dict[ 'name' ]
type = requirements_dict[ 'type' ]
version = requirements_dict[ 'version']
if tool_dependency_is_orphan( type, name, version, tools ):
requirements_dict[ 'is_orphan' ] = True
except Exception, e:
name = str( e )
type = 'unknown'
version = 'unknown'
is_orphan = 'unknown'
new_tool_dependencies[ td_key ] = requirements_dict
return new_tool_dependencies
@@ -358,16 +369,24 @@ def build_data_managers_folder( trans, folder_id, data_managers, label=None ):
# Insert a header row.
data_manager_id += 1
data_manager = DataManager( id=data_manager_id,
name='Name',
version='Version',
data_tables='Data Tables' )
name='Name',
version='Version',
data_tables='Data Tables' )
folder.valid_data_managers.append( data_manager )
for data_manager_dict in data_managers.itervalues():
data_manager_id += 1
try:
name = data_manager_dict.get( 'name', '' )
version = data_manager_dict.get( 'version', '' )
data_tables = ", ".join( data_manager_dict.get( 'data_tables', '' ) )
except Exception, e:
name = str( e )
version = 'unknown'
data_tables = 'unknown'
data_manager = DataManager( id=data_manager_id,
name=data_manager_dict.get( 'name', '' ),
version=data_manager_dict.get( 'version', '' ),
data_tables=", ".join( data_manager_dict.get( 'data_tables', '' ) ) )
name=name,
version=version,
data_tables=data_tables )
folder.valid_data_managers.append( data_manager )
else:
data_managers_root_folder = None
@@ -412,13 +431,27 @@ def build_datatypes_folder( trans, folder_id, datatypes, label='Datatypes' ):
else:
num_display_app_containers = 0
datatype_id += 1
try:
extension = datatypes_dict.get( 'extension', '' )
type = datatypes_dict.get( 'dtype', '' )
mimetype = datatypes_dict.get( 'mimetype', '' )
subclass = datatypes_dict.get( 'subclass', '' )
converters = num_converters
display_app_containers = num_display_app_containers
except Exception, e:
extension = str( e )
type = 'unknown'
mimetype = 'unknown'
subclass = 'unknown'
converters = 'unknown'
display_app_containers = 'unknown'
datatype = Datatype( id=datatype_id,
extension=datatypes_dict.get( 'extension', '' ),
type=datatypes_dict.get( 'dtype', '' ),
mimetype=datatypes_dict.get( 'mimetype', '' ),
subclass=datatypes_dict.get( 'subclass', '' ),
converters=num_converters,
display_app_containers=num_display_app_containers )
extension=extension,
type=type,
mimetype=mimetype,
subclass=subclass,
converters=converters,
display_app_containers=display_app_containers )
folder.datatypes.append( datatype )
else:
datatypes_root_folder = None
@@ -439,22 +472,22 @@ def build_invalid_data_managers_folder( trans, folder_id, data_managers, error_m
# Insert a header row.
data_manager_id += 1
data_manager = InvalidDataManager( id=data_manager_id,
index='Element Index',
error='Error' )
index='Element Index',
error='Error' )
folder.invalid_data_managers.append( data_manager )
if error_messages:
for error_message in error_messages:
data_manager_id += 1
data_manager = InvalidDataManager( id=data_manager_id,
index=0,
error=error_message )
index=0,
error=error_message )
folder.invalid_data_managers.append( data_manager )
has_errors = True
for data_manager_dict in data_managers:
data_manager_id += 1
data_manager = InvalidDataManager( id=data_manager_id,
index=data_manager_dict.get( 'index', 0 ) + 1,
error=data_manager_dict.get( 'error_message', '' ) )
index=data_manager_dict.get( 'index', 0 ) + 1,
error=data_manager_dict.get( 'error_message', '' ) )
folder.invalid_data_managers.append( data_manager )
has_errors = True
else:
@@ -523,10 +556,16 @@ def build_invalid_tool_dependencies_root_folder( trans, folder_id, invalid_tool_
for td_key, requirements_dict in invalid_tool_dependencies_dict.items():
folder_id += 1
invalid_tool_dependency_id += 1
name = requirements_dict[ 'name' ]
type = requirements_dict[ 'type' ]
version = requirements_dict[ 'version' ]
error = requirements_dict[ 'error' ]
try:
name = requirements_dict[ 'name' ]
type = requirements_dict[ 'type' ]
version = requirements_dict[ 'version' ]
error = requirements_dict[ 'error' ]
except Exception, e:
name = 'unknown'
type = 'unknown'
version = 'unknown'
error = str( e )
key = generate_tool_dependencies_key( name, version, type )
label = "Version <b>%s</b> of the <b>%s</b> <b>%s</b>" % ( version, name, type )
folder = Folder( id=folder_id,
@@ -923,8 +962,8 @@ def build_tools_folder( trans, folder_id, tool_dicts, repository, changeset_revi
repository_installation_status = None
for tool_dict in tool_dicts:
if not isinstance( tool_dict, dict ):
# Due to some previous bug (hopefully not current) invalid tool strings may be included in the recived
# list of tool_dicts. For example, the picard repository metadata has 2 invalid tools in the recieved
# Due to some previous bug (hopefully not current) invalid tool strings may be included in the received
# list of tool_dicts. For example, the picard repository metadata has 2 invalid tools in the received
# list of supposedly valid tools: 'rgPicardASMetrics.xml', 'rgPicardGCBiasMetrics.xml'.
continue
container_object_tool_id += 1
@@ -933,17 +972,28 @@ def build_tools_folder( trans, folder_id, tool_dicts, repository, changeset_revi
# 'requirements': [{'version': '1.56.0', 'type': 'package', 'name': 'picard'}],
requirements_str = ''
for requirement_dict in requirements:
requirement_name = str( requirement_dict.get( 'name', 'unknown' ) )
requirement_type = str( requirement_dict.get( 'type', 'unknown' ) )
try:
requirement_name = str( requirement_dict.get( 'name', 'unknown' ) )
requirement_type = str( requirement_dict.get( 'type', 'unknown' ) )
except Exception, e:
requirement_name = str( e )
requirement_type = 'unknown'
requirements_str += '%s (%s), ' % ( requirement_name, requirement_type )
requirements_str = requirements_str.rstrip( ', ' )
else:
requirements_str = 'none'
tool_config = str( tool_dict.get( 'tool_config', 'missing' ) )
tool_id = str( tool_dict.get( 'id', 'missing' ) )
name = str( tool_dict.get( 'name', 'missing' ) )
description = str( tool_dict.get( 'description', '' ) )
version = str( tool_dict.get( 'description', 'missing' ) )
try:
tool_config = str( tool_dict.get( 'tool_config', 'missing' ) )
tool_id = str( tool_dict.get( 'id', 'unknown' ) )
name = str( tool_dict.get( 'name', 'unknown' ) )
description = str( tool_dict.get( 'description', '' ) )
version = str( tool_dict.get( 'description', 'unknown' ) )
except Exception, e:
tool_config = str( e )
tool_id = 'unknown'
name = 'unknown'
description = ''
version = 'unknown'
tool = Tool( id=container_object_tool_id,
tool_config=tool_config,
tool_id=tool_id,
@@ -1012,12 +1062,21 @@ def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='
is_orphan = False
if is_orphan:
folder.description = not_used_by_local_tools_description
name = set_environment_dict.get( 'name', None )
type = set_environment_dict[ 'type' ]
repository_id = set_environment_dict.get( 'repository_id', None )
td_id = set_environment_dict.get( 'tool_dependency_id', None )
try:
name = set_environment_dict.get( 'name', None )
type = set_environment_dict[ 'type' ]
repository_id = set_environment_dict.get( 'repository_id', None )
td_id = set_environment_dict.get( 'tool_dependency_id', None )
except Exception, e:
name = str( e )
type = 'unknown'
repository_id = 'unknown'
td_id = 'unknown'
if trans.webapp.name == 'galaxy':
installation_status = set_environment_dict.get( 'status', 'Never installed' )
try:
installation_status = set_environment_dict.get( 'status', 'Never installed' )
except Exception, e:
installation_status = str( e )
else:
installation_status = None
tool_dependency = ToolDependency( id=tool_dependency_id,
@@ -1037,13 +1096,23 @@ def build_tool_dependencies_folder( trans, folder_id, tool_dependencies, label='
is_orphan = False
if is_orphan:
folder.description = not_used_by_local_tools_description
name = requirements_dict[ 'name' ]
version = requirements_dict[ 'version' ]
type = requirements_dict[ 'type' ]
repository_id = requirements_dict.get( 'repository_id', None )
td_id = requirements_dict.get( 'tool_dependency_id', None )
try:
name = requirements_dict[ 'name' ]
version = requirements_dict[ 'version' ]
type = requirements_dict[ 'type' ]
repository_id = requirements_dict.get( 'repository_id', None )
td_id = requirements_dict.get( 'tool_dependency_id', None )
except Exception, e:
name = str( e )
version = 'unknown'
type = 'unknown'
repository_id = 'unknown'
td_id = 'unknown'
if trans.webapp.name == 'galaxy':
installation_status = requirements_dict.get( 'status', 'Never installed' )
try:
installation_status = requirements_dict.get( 'status', 'Never installed' )
except Exception, e:
installation_status = str( e )
else:
installation_status = None
tool_dependency = ToolDependency( id=tool_dependency_id,
@@ -1109,14 +1178,24 @@ def build_tool_test_results_folder( trans, folder_id, tool_test_results_dicts, l
folder_id += 1
test_environment_folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder )
containing_folder.folders.append( test_environment_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', '' )
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', '' )
try:
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', '' )
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', '' )
except Exception, e:
architecture = str( e )
galaxy_database_version = ''
galaxy_revision = ''
python_version = ''
system = ''
tool_shed_database_version = ''
tool_shed_mercurial_version = ''
tool_shed_revision = ''
test_environment = TestEnvironment( id=1,
architecture=architecture,
galaxy_database_version=galaxy_database_version,
@@ -1134,8 +1213,11 @@ def build_tool_test_results_folder( trans, folder_id, tool_test_results_dicts, l
not_tested_folder = Folder( id=folder_id, key='not_tested', label='Not tested', parent=containing_folder )
containing_folder.folders.append( not_tested_folder )
not_tested_id = 0
not_tested = NotTested( id=not_tested_id,
reason=not_tested_dict.get( 'reason', '' ) )
try:
reason = not_tested_dict.get( 'reason', '' )
except Exception, e:
reason = str( e )
not_tested = NotTested( id=not_tested_id, reason=reason )
not_tested_folder.not_tested.append( not_tested )
passed_tests_dicts = tool_test_results_dict.get( 'passed_tests', [] )
if len( passed_tests_dicts ) > 0:
@@ -1145,10 +1227,18 @@ def build_tool_test_results_folder( trans, folder_id, tool_test_results_dicts, l
passed_test_id = 0
for passed_tests_dict in passed_tests_dicts:
passed_test_id += 1
try:
test_id = passed_tests_dict.get( 'test_id' '' )
tool_id = passed_tests_dict.get( 'tool_id', '' )
tool_version = passed_tests_dict.get( 'tool_version', '' )
except Exception, e:
test_id = str( e )
tool_id = 'unknown'
tool_version = 'unknown'
passed_test = PassedTest( id=passed_test_id,
test_id=passed_tests_dict.get( 'test_id' '' ),
tool_id=passed_tests_dict.get( 'tool_id', '' ),
tool_version=passed_tests_dict.get( 'tool_version', '' ) )
test_id=test_id,
tool_id=tool_id,
tool_version=tool_version )
passed_tests_folder.passed_tests.append( passed_test )
failed_tests_dicts = tool_test_results_dict.get( 'failed_tests', [] )
if len( failed_tests_dicts ) > 0:
@@ -1157,16 +1247,25 @@ def build_tool_test_results_folder( trans, folder_id, tool_test_results_dicts, l
containing_folder.folders.append( failed_tests_folder )
failed_test_id = 0
for failed_tests_dict in failed_tests_dicts:
# TODO: Remove this when invalid test data is eliminated.
if isinstance( failed_tests_dict, list ):
failed_tests_dict = failed_tests_dict[ 0 ]
failed_test_id += 1
try:
stderr = failed_tests_dict.get( 'stderr', '' )
test_id = failed_tests_dict.get( 'test_id', '' )
tool_id = failed_tests_dict.get( 'tool_id', '' )
tool_version = failed_tests_dict.get( 'tool_version', '' )
traceback = failed_tests_dict.get( 'traceback', '' )
except Exception, e:
stderr = 'unknown'
test_id = 'unknown'
tool_id = 'unknown'
tool_version = 'unknown'
traceback = str( e )
failed_test = FailedTest( id=failed_test_id,
stderr=failed_tests_dict.get( 'stderr', '' ),
test_id=failed_tests_dict.get( 'test_id', '' ),
tool_id=failed_tests_dict.get( 'tool_id', '' ),
tool_version=failed_tests_dict.get( 'tool_version', '' ),
traceback=failed_tests_dict.get( 'traceback', '' ) )
stderr=stderr,
test_id=test_id,
tool_id=tool_id,
tool_version=tool_version,
traceback=traceback )
failed_tests_folder.failed_tests.append( failed_test )
missing_test_components_dicts = tool_test_results_dict.get( 'missing_test_components', [] )
if len( missing_test_components_dicts ) > 0:
@@ -1179,11 +1278,21 @@ def build_tool_test_results_folder( trans, folder_id, tool_test_results_dicts, l
missing_test_component_id = 0
for missing_test_components_dict in missing_test_components_dicts:
missing_test_component_id += 1
try:
missing_components = missing_test_components_dict.get( 'missing_components', '' )
tool_guid = missing_test_components_dict.get( 'tool_guid', '' )
tool_id = missing_test_components_dict.get( 'tool_id', '' )
tool_version = missing_test_components_dict.get( 'tool_version', '' )
except Exception, e:
missing_components = str( e )
tool_guid = 'unknown'
tool_id = 'unknown'
tool_version = 'unknown'
missing_test_component = MissingTestComponent( id=missing_test_component_id,
missing_components=missing_test_components_dict.get( 'missing_components', '' ),
tool_guid=missing_test_components_dict.get( 'tool_guid', '' ),
tool_id=missing_test_components_dict.get( 'tool_id', '' ),
tool_version=missing_test_components_dict.get( 'tool_version', '' ) )
missing_components=missing_components,
tool_guid=tool_guid,
tool_id=tool_id,
tool_version=tool_version )
missing_test_components_folder.missing_test_components.append( missing_test_component )
installation_error_dict = tool_test_results_dict.get( 'installation_errors', {} )
if len( installation_error_dict ) > 0:
@@ -1215,13 +1324,24 @@ def build_tool_test_results_folder( trans, folder_id, tool_test_results_dicts, l
installation_error_base_folder.folders.append( current_repository_folder )
for current_repository_error_dict in current_repository_installation_error_dicts:
repository_installation_error_id += 1
repository_installation_error = \
RepositoryInstallationError( id=repository_installation_error_id,
tool_shed=str( current_repository_error_dict.get( 'tool_shed', '' ) ),
name=str( current_repository_error_dict.get( 'name', '' ) ),
owner=str( current_repository_error_dict.get( 'owner', '' ) ),
changeset_revision=str( current_repository_error_dict.get( 'changeset_revision', '' ) ),
error_message=current_repository_error_dict.get( 'error_message', '' ) )
try:
r_tool_shed = str( current_repository_error_dict.get( 'tool_shed', '' ) )
r_name = str( current_repository_error_dict.get( 'name', '' ) )
r_owner = str( current_repository_error_dict.get( 'owner', '' ) )
r_changeset_revision = str( current_repository_error_dict.get( 'changeset_revision', '' ) )
r_error_message = current_repository_error_dict.get( 'error_message', '' )
except Exception, e:
r_tool_shed = 'unknown'
r_name = 'unknown'
r_owner = 'unknown'
r_changeset_revision = 'unknown'
r_error_message = str( e )
repository_installation_error = RepositoryInstallationError( id=repository_installation_error_id,
tool_shed=r_tool_shed,
name=r_name,
owner=r_owner,
changeset_revision=r_changeset_revision,
error_message=r_error_message )
current_repository_folder.current_repository_installation_errors.append( repository_installation_error )
if len( repository_dependency_installation_error_dicts ) > 0:
folder_id += 1
@@ -1232,13 +1352,24 @@ def build_tool_test_results_folder( trans, folder_id, tool_test_results_dicts, l
installation_error_base_folder.folders.append( repository_dependencies_folder )
for repository_dependency_error_dict in repository_dependency_installation_error_dicts:
repository_installation_error_id += 1
repository_installation_error = \
RepositoryInstallationError( id=repository_installation_error_id,
tool_shed=str( repository_dependency_error_dict.get( 'tool_shed', '' ) ),
name=str( repository_dependency_error_dict.get( 'name', '' ) ),
owner=str( repository_dependency_error_dict.get( 'owner', '' ) ),
changeset_revision=str( repository_dependency_error_dict.get( 'changeset_revision', '' ) ),
error_message=repository_dependency_error_dict.get( 'error_message', '' ) )
try:
rd_tool_shed = str( repository_dependency_error_dict.get( 'tool_shed', '' ) )
rd_name = str( repository_dependency_error_dict.get( 'name', '' ) )
rd_owner = str( repository_dependency_error_dict.get( 'owner', '' ) )
rd_changeset_revision = str( repository_dependency_error_dict.get( 'changeset_revision', '' ) )
rd_error_message = repository_dependency_error_dict.get( 'error_message', '' )
except Exception, e:
rd_tool_shed = 'unknown'
rd_name = 'unknown'
rd_owner = 'unknown'
rd_changeset_revision = 'unknown'
rd_error_message = str( e )
repository_installation_error = RepositoryInstallationError( id=repository_installation_error_id,
tool_shed=rd_tool_shed,
name=rd_name,
owner=rd_owner,
changeset_revision=rd_changeset_revision,
error_message=rd_error_message )
repository_dependencies_folder.repository_installation_errors.append( repository_installation_error )
if len( tool_dependency_installation_error_dicts ) > 0:
# [{'error_message': 'some traceback string' 'type': 'package', 'name': 'MIRA', 'version': '4.0'}]
@@ -1251,12 +1382,21 @@ def build_tool_test_results_folder( trans, folder_id, tool_test_results_dicts, l
tool_dependency_error_id = 0
for tool_dependency_error_dict in tool_dependency_installation_error_dicts:
tool_dependency_error_id += 1
tool_dependency_installation_error = \
ToolDependencyInstallationError( id=tool_dependency_error_id,
type=str( tool_dependency_error_dict.get( 'type', '' ) ),
name=str( tool_dependency_error_dict.get( 'name', '' ) ),
version=str( tool_dependency_error_dict.get( 'version', '' ) ),
error_message=tool_dependency_error_dict.get( 'error_message', '' ) )
try:
td_type = str( tool_dependency_error_dict.get( 'type', '' ) )
td_name = str( tool_dependency_error_dict.get( 'name', '' ) )
td_version = str( tool_dependency_error_dict.get( 'version', '' ) )
td_error_message = tool_dependency_error_dict.get( 'error_message', '' )
except Exception, e:
td_type = 'unknown'
td_name = 'unknown'
td_version = 'unknown'
td_error_message = str( e )
tool_dependency_installation_error = ToolDependencyInstallationError( id=tool_dependency_error_id,
type=td_type,
name=td_name,
version=td_version,
error_message=td_error_message )
tool_dependencies_folder.tool_dependency_installation_errors.append( tool_dependency_installation_error )
else:
tool_test_results_root_folder = None