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Merge ToolConfWatchers and separate from Toolbox #3821

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merged 7 commits into from
Apr 7, 2017
Merged

Merge ToolConfWatchers and separate from Toolbox #3821

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c857388
Merge ToolConfWatchers and separate from Toolbox
mvdbeek Mar 27, 2017
1a5e337
Move ConfigWatchers into galaxy.webapps.galaxy.config_watchers
mvdbeek Apr 3, 2017
f79fb90
Move ToolWatcher from Toolbox to ConfigWatchers class
mvdbeek Apr 3, 2017
63f1efd
Fix toolshed startup
mvdbeek Apr 3, 2017
c4e6671
Fix import order in config_watchers.py
mvdbeek Apr 3, 2017
b037332
Avoid race-condition between multiple instances of ToolConfWatchers
mvdbeek Apr 3, 2017
2c7089d
Fix TS tests
mvdbeek Apr 3, 2017
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3 changes: 3 additions & 0 deletions lib/galaxy/app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
from galaxy.visualization.data_providers.registry import DataProviderRegistry
from galaxy.visualization.plugins.registry import VisualizationsRegistry
from galaxy.tools.special_tools import load_lib_tools
from galaxy.tools.toolbox.watcher import ConfigWatchers
from galaxy.tours import ToursRegistry
from galaxy.webhooks import WebhooksRegistry
from galaxy.sample_tracking import external_service_types
Expand Down Expand Up @@ -112,6 +113,8 @@ def __init__( self, **kwargs ):
self.datatypes_registry.load_external_metadata_tool( self.toolbox )
# Load history import/export tools.
load_lib_tools( self.toolbox )
# Watch various config files for immediate reload
self.watchers = ConfigWatchers(self)
# visualizations registry: associates resources with visualizations, controls how to render
self.visualizations_registry = VisualizationsRegistry(
self,
Expand Down
4 changes: 2 additions & 2 deletions lib/galaxy/queue_worker.py
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Expand Up @@ -106,7 +106,7 @@ def _get_new_toolbox(app):
if app.config.migrated_tools_config not in tool_configs:
tool_configs.append(app.config.migrated_tools_config)
start = time.time()
new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app, app.toolbox._tool_conf_watcher)
new_toolbox = tools.ToolBox(tool_configs, app.config.tool_path, app)
new_toolbox.data_manager_tools = app.toolbox.data_manager_tools
app.datatypes_registry.load_datatype_converters(new_toolbox, use_cached=True)
load_lib_tools(new_toolbox)
Expand All @@ -124,7 +124,7 @@ def reload_data_managers(app, **kwargs):
app._configure_tool_data_tables(from_shed_config=False)
reload_tool_data_tables(app)
reload_count = app.data_managers._reload_count
app.data_managers = DataManagers(app, conf_watchers=app.data_managers.conf_watchers)
app.data_managers = DataManagers(app)
app.data_managers._reload_count = reload_count + 1


Expand Down
9 changes: 1 addition & 8 deletions lib/galaxy/tools/__init__.py
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Expand Up @@ -29,10 +29,7 @@
)
from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper
from galaxy.managers import histories
from galaxy.queue_worker import (
reload_toolbox,
send_control_task
)
from galaxy.queue_worker import send_control_task
from galaxy.tools.actions import DefaultToolAction
from galaxy.tools.actions.data_manager import DataManagerToolAction
from galaxy.tools.actions.data_source import DataSourceToolAction
Expand Down Expand Up @@ -193,12 +190,8 @@ def __init__( self, config_filenames, tool_root_dir, app, tool_conf_watcher=None
config_filenames=config_filenames,
tool_root_dir=tool_root_dir,
app=app,
tool_conf_watcher=tool_conf_watcher
)

def handle_reload_toolbox(self):
reload_toolbox(self.app)

def handle_panel_update(self, section_dict):
"""
Sends a panel update to all threads/processes.
Expand Down
113 changes: 48 additions & 65 deletions lib/galaxy/tools/data_manager/manager.py
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Expand Up @@ -7,14 +7,9 @@

from galaxy import util
from galaxy.queue_worker import (
reload_data_managers,
send_control_task
)
from galaxy.tools.data import TabularToolDataTable
from galaxy.tools.toolbox.watcher import (
get_tool_conf_watcher,
get_tool_data_dir_watcher
)
from galaxy.util.odict import odict
from galaxy.util.template import fill_template
from tool_shed.util import (
Expand All @@ -30,7 +25,7 @@


class DataManagers( object ):
def __init__( self, app, xml_filename=None, conf_watchers=None ):
def __init__( self, app, xml_filename=None):
self.app = app
self.data_managers = odict()
self.managed_data_tables = odict()
Expand All @@ -43,31 +38,6 @@ def __init__( self, app, xml_filename=None, conf_watchers=None ):
self.load_from_xml( filename )
if self.app.config.shed_data_manager_config_file:
self.load_from_xml( self.app.config.shed_data_manager_config_file, store_tool_path=False, replace_existing=True )
if conf_watchers:
self.conf_watchers = conf_watchers
else:
self.conf_watchers = self.get_conf_watchers()

def get_conf_watchers(self):
"""
Sets up monitoring of data manager related config files.
These are the data_manager_conf.xml and shed_data_manager_conf.xml files
as well as any loc file in the tool-data directory.
"""
conf_watchers = []
conf_watchers.extend([(get_tool_conf_watcher(lambda: reload_data_managers(self.app)), filename) for filename in util.listify(self.filename) if filename])
if self.app.config.shed_data_manager_config_file:
conf_watchers.append((get_tool_conf_watcher(lambda: reload_data_managers(self.app)), self.app.config.shed_data_manager_config_file))
[watcher.watch_file(filename) for watcher, filename in conf_watchers]
tool_data_watcher = get_tool_data_dir_watcher(self.app.tool_data_tables, self.app.config)
tool_data_watcher.watch_directory(self.app.config.tool_data_path)
if self.app.config.shed_tool_data_path:
tool_data_watcher.watch_directory(self.app.config.shed_tool_data_path)
conf_watchers.append((tool_data_watcher, self.app.tool_data_tables.tool_data_path))
return [watcher for watcher, filename in conf_watchers]

def shutdown(self):
[watcher.shutdown() for watcher in self.conf_watchers]

def load_from_xml( self, xml_filename, store_tool_path=True, replace_existing=False ):
try:
Expand Down Expand Up @@ -166,46 +136,58 @@ def load_from_element( self, elem, tool_path ):
self.version = elem.get( 'version', self.version )
tool_shed_repository_id = None
tool_guid = None

if path is None:
tool_elem = elem.find( 'tool' )
assert tool_elem is not None, "Error loading tool for data manager. Make sure that a tool_file attribute or a tool tag set has been defined:\n%s" % ( util.xml_to_string( elem ) )
path = tool_elem.get( "file", None )
tool_guid = tool_elem.get( "guid", None )
# need to determine repository info so that dependencies will work correctly
tool_shed_url = tool_elem.find( 'tool_shed' ).text
# Handle protocol changes.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.data_managers.app, tool_shed_url )
# The protocol is not stored in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
repository_name = tool_elem.find( 'repository_name' ).text
repository_owner = tool_elem.find( 'repository_owner' ).text
installed_changeset_revision = tool_elem.find( 'installed_changeset_revision' ).text
self.tool_shed_repository_info_dict = dict( tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision )
tool_shed_repository = \
repository_util.get_installed_repository( self.data_managers.app,
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision )
if tool_shed_repository is None:
log.warning( 'Could not determine tool shed repository from database. This should only ever happen when running tests.' )
# we'll set tool_path manually here from shed_conf_file
tool_shed_repository_id = None
try:
tool_path = util.parse_xml( elem.get( 'shed_conf_file' ) ).getroot().get( 'tool_path', tool_path )
except Exception as e:
log.error( 'Error determining tool_path for Data Manager during testing: %s', e )
if tool_guid in self.data_managers.app.tool_cache._tool_paths_by_id:
path = self.data_managers.app.tool_cache._tool_paths_by_id[tool_guid]
tool = self.data_managers.app.tool_cache.get_tool(path)
tool_shed_repository = tool.tool_shed_repository
self.tool_shed_repository_info_dict = dict(tool_shed=tool_shed_repository.tool_shed,
name=tool_shed_repository.name,
owner=tool_shed_repository.owner,
installed_changeset_revision=tool_shed_repository.installed_changeset_revision)
tool_shed_repository_id = self.data_managers.app.security.encode_id(tool_shed_repository.id)
tool_path = ""
else:
tool_shed_repository_id = self.data_managers.app.security.encode_id( tool_shed_repository.id )
# use shed_conf_file to determine tool_path
shed_conf_file = elem.get( "shed_conf_file", None )
if shed_conf_file:
shed_conf = self.data_managers.app.toolbox.get_shed_config_dict_by_filename( shed_conf_file, None )
if shed_conf:
tool_path = shed_conf.get( "tool_path", tool_path )
tool_shed_url = tool_elem.find( 'tool_shed' ).text
# Handle protocol changes.
tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.data_managers.app, tool_shed_url )
# The protocol is not stored in the database.
tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed_url )
repository_name = tool_elem.find( 'repository_name' ).text
repository_owner = tool_elem.find( 'repository_owner' ).text
installed_changeset_revision = tool_elem.find( 'installed_changeset_revision' ).text
self.tool_shed_repository_info_dict = dict( tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision )
tool_shed_repository = \
repository_util.get_installed_repository( self.data_managers.app,
tool_shed=tool_shed,
name=repository_name,
owner=repository_owner,
installed_changeset_revision=installed_changeset_revision )
if tool_shed_repository is None:
log.warning( 'Could not determine tool shed repository from database. This should only ever happen when running tests.' )
# we'll set tool_path manually here from shed_conf_file
tool_shed_repository_id = None
try:
tool_path = util.parse_xml( elem.get( 'shed_conf_file' ) ).getroot().get( 'tool_path', tool_path )
except Exception as e:
log.error( 'Error determining tool_path for Data Manager during testing: %s', e )
else:
tool_shed_repository_id = self.data_managers.app.security.encode_id( tool_shed_repository.id )
# use shed_conf_file to determine tool_path
shed_conf_file = elem.get( "shed_conf_file", None )
if shed_conf_file:
shed_conf = self.data_managers.app.toolbox.get_shed_config_dict_by_filename( shed_conf_file, None )
if shed_conf:
tool_path = shed_conf.get( "tool_path", tool_path )
assert path is not None, "A tool file path could not be determined:\n%s" % ( util.xml_to_string( elem ) )
self.load_tool( os.path.join( tool_path, path ),
guid=tool_guid,
Expand Down Expand Up @@ -287,7 +269,8 @@ def load_tool( self, tool_filename, guid=None, data_manager_id=None, tool_shed_r
tool = toolbox.load_hidden_tool( tool_filename,
guid=guid,
data_manager_id=data_manager_id,
repository_id=tool_shed_repository_id )
repository_id=tool_shed_repository_id,
use_cached=True )
self.data_managers.app.toolbox.data_manager_tools[ tool.id ] = tool
self.tool = tool
return tool
Expand Down
34 changes: 3 additions & 31 deletions lib/galaxy/tools/toolbox/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@
from .parser import ensure_tool_conf_item, get_toolbox_parser
from .tags import tool_tag_manager
from .watcher import (
get_tool_conf_watcher,
get_tool_watcher
)

Expand All @@ -47,11 +46,10 @@ class AbstractToolBox( Dictifiable, ManagesIntegratedToolPanelMixin, object ):
workflows optionally in labelled sections.
"""

def __init__( self, config_filenames, tool_root_dir, app, tool_conf_watcher=None ):
def __init__( self, config_filenames, tool_root_dir, app ):
"""
Create a toolbox from the config files named by `config_filenames`, using
`tool_root_dir` as the base directory for finding individual tool config files.
When reloading the toolbox, tool_conf_watcher will be provided.
"""
# The _dynamic_tool_confs list contains dictionaries storing
# information about the tools defined in each shed-related
Expand All @@ -76,16 +74,6 @@ def __init__( self, config_filenames, tool_root_dir, app, tool_conf_watcher=None
self._tool_root_dir = tool_root_dir
self.app = app
self._tool_watcher = get_tool_watcher( self, app.config )
if tool_conf_watcher:
self._tool_conf_watcher = tool_conf_watcher # Avoids (re-)starting threads in uwsgi
else:
if hasattr(self.app, 'tool_cache'):
# Normal galaxy instances should have a tool_cache,
# but the toolshed does not.
tool_cache = self.app.tool_cache
else:
tool_cache = None
self._tool_conf_watcher = get_tool_conf_watcher(reload_callback=lambda: self.handle_reload_toolbox(), tool_cache=tool_cache)
self._filter_factory = FilterFactory( self )
self._tool_tag_manager = tool_tag_manager( app )
self._init_tools_from_configs( config_filenames )
Expand All @@ -94,13 +82,6 @@ def __init__( self, config_filenames, tool_root_dir, app, tool_conf_watcher=None
self._load_tool_panel()
self._save_integrated_tool_panel()

def handle_reload_toolbox(self):
"""Extension-point for Galaxy-app specific reload logic.

This abstract representation of the toolbox shouldn't have details about
interacting with the rest of the Galaxy app or message queues, etc....
"""

def handle_panel_update(self, section_dict):
"""Extension-point for Galaxy-app specific reload logic.

Expand Down Expand Up @@ -188,10 +169,6 @@ def _init_tools_from_config( self, config_filename ):
tool_path=tool_path,
config_elems=config_elems )
self._dynamic_tool_confs.append( shed_tool_conf_dict )
# This explicitly monitors shed_tool_confs, otherwise need to add <toolbox monitor="true">>
self._tool_conf_watcher.watch_file(config_filename)
if tool_conf_source.parse_monitor():
self._tool_conf_watcher.watch_file(config_filename)

def load_item( self, item, tool_path, panel_dict=None, integrated_panel_dict=None, load_panel_dict=True, guid=None, index=None, internal=False ):
with self.app._toolbox_lock:
Expand Down Expand Up @@ -948,11 +925,6 @@ def shutdown(self):
except Exception as e:
exception = e

try:
self._tool_conf_watcher.shutdown()
except Exception as e:
exception = exception or e

if exception:
raise exception

Expand Down Expand Up @@ -1066,8 +1038,8 @@ class BaseGalaxyToolBox(AbstractToolBox):
shouldn't really depend on.
"""

def __init__(self, config_filenames, tool_root_dir, app, tool_conf_watcher=None):
super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app, tool_conf_watcher=tool_conf_watcher)
def __init__(self, config_filenames, tool_root_dir, app):
super(BaseGalaxyToolBox, self).__init__(config_filenames, tool_root_dir, app)
self._init_dependency_manager()

@property
Expand Down
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