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Source code for galaxy.visualization.plugins.registry
"""
Lower level of visualization framework which does three main things:
- associate visualizations with objects
- create urls to visualizations based on some target object(s)
- unpack a query string into the desired objects needed for rendering
"""
import logging
import os
import weakref
from galaxy.exceptions import ObjectNotFound
from galaxy.util import (
config_directories_from_setting,
odict,
parse_xml
)
from galaxy.visualization.plugins import (
config_parser,
plugin as vis_plugins,
utils as vis_utils
)
from galaxy.web import url_for
log = logging.getLogger(__name__)
[docs]class VisualizationsRegistry(object):
"""
Main responsibilities are:
- discovering visualization plugins in the filesystem
- testing if an object has a visualization that can be applied to it
- generating a link to controllers.visualization.render with
the appropriate params
- validating and parsing params into resources (based on a context)
used in the visualization template
"""
#: base url to controller endpoint
BASE_URL = 'visualizations'
#: name of files to search for additional template lookup directories
TEMPLATE_PATHS_CONFIG = 'additional_template_paths.xml'
# these should be handled somewhat differently - and be passed onto their resp. methods in ctrl.visualization
# TODO: change/remove if/when they can be updated to use this system
#: any built in visualizations that have their own render method in ctrls/visualization
BUILT_IN_VISUALIZATIONS = [
'trackster',
'circster',
'sweepster',
'phyloviz'
]
def __str__(self):
return self.__class__.__name__
[docs] def __init__(self, app, template_cache_dir=None, directories_setting=None, skip_bad_plugins=True, **kwargs):
"""
Set up the manager and load all visualization plugins.
:type app: UniverseApplication
:param app: the application (and its configuration) using this manager
:type base_url: string
:param base_url: url to prefix all plugin urls with
:type template_cache_dir: string
:param template_cache_dir: filesytem path to the directory where cached
templates are kept
"""
self.app = weakref.ref(app)
self.config_parser = config_parser.VisualizationsConfigParser()
self.base_url = self.BASE_URL
self.template_cache_dir = template_cache_dir
self.additional_template_paths = []
self.directories = []
self.skip_bad_plugins = skip_bad_plugins
self.plugins = odict.odict()
self.directories = config_directories_from_setting(directories_setting, app.config.root)
self._load_configuration()
self._load_plugins()
def _load_configuration(self):
"""
Load framework wide configuration, including:
additional template lookup directories
"""
for directory in self.directories:
possible_path = os.path.join(directory, self.TEMPLATE_PATHS_CONFIG)
if os.path.exists(possible_path):
added_paths = self._parse_additional_template_paths(possible_path, directory)
self.additional_template_paths.extend(added_paths)
def _parse_additional_template_paths(self, config_filepath, base_directory):
"""
Parse an XML config file at `config_filepath` for template paths
(relative to `base_directory`) to add to each plugin's template lookup.
Allows having a set of common templates for import/inheritance in
plugin templates.
:type config_filepath: string
:param config_filepath: filesystem path to the config file
:type base_directory: string
:param base_directory: path prefixed to new, relative template paths
"""
additional_paths = []
xml_tree = parse_xml(config_filepath)
paths_list = xml_tree.getroot()
for rel_path_elem in paths_list.findall('path'):
if rel_path_elem.text is not None:
additional_paths.append(os.path.join(base_directory, rel_path_elem.text))
return additional_paths
def _load_plugins(self):
"""
Search ``self.directories`` for potential plugins, load them, and cache
in ``self.plugins``.
:rtype: odict
:returns: ``self.plugins``
"""
for plugin_path in self._find_plugins():
try:
plugin = self._load_plugin(plugin_path)
if plugin and plugin.name not in self.plugins:
self.plugins[plugin.name] = plugin
log.info('%s, loaded plugin: %s', self, plugin.name)
# NOTE: prevent silent, implicit overwrite here (two plugins in two diff directories)
# TODO: overwriting may be desired
elif plugin and plugin.name in self.plugins:
log.warning('%s, plugin with name already exists: %s. Skipping...', self, plugin.name)
except Exception:
if not self.skip_bad_plugins:
raise
log.exception('Plugin loading raised exception: %s. Skipping...', plugin_path)
return self.plugins
def _find_plugins(self):
"""
Return the directory paths of plugins within ``self.directories``.
Paths are considered a plugin path if they pass ``self.is_plugin``.
:rtype: string generator
:returns: paths of valid plugins
"""
# due to the ordering of listdir, there is an implicit plugin loading order here
# could instead explicitly list on/off in master config file
for directory in self.directories:
for plugin_dir in sorted(os.listdir(directory)):
plugin_path = os.path.join(directory, plugin_dir)
if self._is_plugin(plugin_path):
yield plugin_path
# TODO: add fill_template fn that is able to load extra libraries beforehand (and remove after)
# TODO: add template helpers specific to the plugins
# TODO: some sort of url_for for these plugins
def _is_plugin(self, plugin_path):
"""
Determines whether the given filesystem path contains a plugin.
In this base class, all sub-directories are considered plugins.
:type plugin_path: string
:param plugin_path: relative or absolute filesystem path to the
potential plugin
:rtype: bool
:returns: True if the path contains a plugin
"""
# plugin_path must be a directory, have a config dir, and a config file matching the plugin dir name
if not os.path.isdir(plugin_path):
# super won't work here - different criteria
return False
if 'config' not in os.listdir(plugin_path):
return False
expected_config_filename = '%s.xml' % (os.path.split(plugin_path)[1])
if not os.path.isfile(os.path.join(plugin_path, 'config', expected_config_filename)):
return False
return True
def _load_plugin(self, plugin_path):
"""
Create the visualization plugin object, parse its configuration file,
and return it.
:type plugin_path: string
:param plugin_path: relative or absolute filesystem path to the plugin
:rtype: ``VisualizationPlugin``
:returns: the loaded plugin
"""
plugin_name = os.path.split(plugin_path)[1]
# TODO: this is the standard/older way to config
config_file = os.path.join(plugin_path, 'config', (plugin_name + '.xml'))
config = self.config_parser.parse_file(config_file)
# config file is required, otherwise skip this visualization
if not config:
return None
plugin = self._build_plugin(plugin_name, plugin_path, config)
return plugin
def _build_plugin(self, plugin_name, plugin_path, config):
# TODO: as builder not factory
# default class
plugin_class = vis_plugins.VisualizationPlugin
# jupyter, etc
if config['plugin_type'] == 'interactive_environment':
plugin_class = vis_plugins.InteractiveEnvironmentPlugin
# js only
elif config['entry_point']['type'] == 'script':
plugin_class = vis_plugins.ScriptVisualizationPlugin
# from a static file (html, etc)
elif config['entry_point']['type'] == 'html':
plugin_class = vis_plugins.StaticFileVisualizationPlugin
plugin = plugin_class(self.app(), plugin_path, plugin_name, config, context=dict(
base_url=self.base_url,
template_cache_dir=self.template_cache_dir,
additional_template_paths=self.additional_template_paths
))
return plugin
[docs] def get_plugin(self, key):
"""
Wrap to throw error if plugin not in registry.
"""
if key not in self.plugins:
raise ObjectNotFound('Unknown or invalid visualization: ' + key)
return self.plugins[key]
# -- building links to visualizations from objects --
[docs] def get_visualizations(self, trans, target_object):
"""
Get the names of visualizations usable on the `target_object` and
the urls to call in order to render the visualizations.
"""
# TODO:?? a list of objects? YAGNI?
applicable_visualizations = []
for vis_name in self.plugins:
url_data = self.get_visualization(trans, vis_name, target_object)
if url_data:
applicable_visualizations.append(url_data)
return applicable_visualizations
[docs] def get_visualization(self, trans, visualization_name, target_object):
"""
Return data to build a url to the visualization with the given
`visualization_name` if it's applicable to `target_object` or
`None` if it's not.
"""
# log.debug( 'VisReg.get_visualization: %s, %s', visualization_name, target_object )
visualization = self.plugins.get(visualization_name, None)
if not visualization:
return None
data_sources = visualization.config['data_sources']
for data_source in data_sources:
# log.debug( 'data_source: %s', data_source )
# currently a model class is required
model_class = data_source['model_class']
# log.debug( '\t model_class: %s', model_class )
if not isinstance(target_object, model_class):
continue
# log.debug( '\t passed model_class' )
# TODO: not true: must have test currently
tests = data_source['tests']
if tests and not self.is_object_applicable(trans, target_object, tests):
continue
# log.debug( '\t passed tests' )
param_data = data_source['to_params']
url = self.get_visualization_url(trans, target_object, visualization, param_data)
display_name = visualization.config.get('name', None)
render_target = visualization.config.get('render_target', 'galaxy_main')
embeddable = visualization.config.get('embeddable', False)
# remap some of these vars for direct use in ui.js, PopupMenu (e.g. text->html)
return {
'href' : url,
'html' : display_name,
'target' : render_target,
'embeddable': embeddable
}
return None
[docs] def is_object_applicable(self, trans, target_object, data_source_tests):
"""
Run a visualization's data_source tests to find out if
it can be applied to the target_object.
"""
# log.debug( 'is_object_applicable( self, trans, %s, %s )', target_object, data_source_tests )
for test in data_source_tests:
test_type = test['type']
result_type = test['result_type']
test_result = test['result']
test_fn = test['fn']
# log.debug( '%s %s: %s, %s, %s, %s', str( target_object ), 'is_object_applicable',
# test_type, result_type, test_result, test_fn )
if test_type == 'isinstance':
# parse test_result based on result_type (curr: only datatype has to do this)
if result_type == 'datatype':
# convert datatypes to their actual classes (for use with isinstance)
datatype_class_name = test_result
test_result = trans.app.datatypes_registry.get_datatype_class_by_name(datatype_class_name)
if not test_result:
# but continue (with other tests) if can't find class by that name
# if self.debug:
# log.warning( 'visualizations_registry cannot find class (%s)' +
# ' for applicability test on: %s, id: %s', datatype_class_name,
# target_object, getattr( target_object, 'id', '' ) )
continue
# NOTE: tests are OR'd, if any test passes - the visualization can be applied
if test_fn(target_object, test_result):
# log.debug( '\t test passed' )
return True
return False
[docs] def get_visualization_url(self, trans, target_object, visualization, param_data):
"""
Generates a url for the visualization with `visualization`
for use with the given `target_object` with a query string built
from the configuration data in `param_data`.
"""
# precondition: the target_object should be usable by the visualization (accrd. to data_sources)
# convert params using vis.data_source.to_params
params = self.get_url_params(trans, target_object, param_data)
# we want existing visualizations to work as normal but still be part of the registry (without mod'ing)
# so generate their urls differently
url = None
if visualization.name in self.BUILT_IN_VISUALIZATIONS:
url = url_for(controller='visualization', action=visualization.name, **params)
# TODO: needs to be split off as it's own registry
elif isinstance(visualization, vis_plugins.InteractiveEnvironmentPlugin):
url = url_for('interactive_environment_plugin', visualization_name=visualization.name, **params)
else:
url = url_for('visualization_plugin', visualization_name=visualization.name, **params)
# TODO:?? not sure if embedded would fit/used here? or added in client...
return url
[docs] def get_url_params(self, trans, target_object, param_data):
"""
Convert the applicable objects and assoc. data into a param dict
for a url query string to add to the url that loads the visualization.
"""
params = {}
for to_param_name, to_param_data in param_data.items():
# TODO??: look into params as well? what is required, etc.
target_attr = to_param_data.get('param_attr', None)
assign = to_param_data.get('assign', None)
# one or the other is needed
# assign takes precedence (goes last, overwrites)?
# NOTE this is only one level
if target_attr and vis_utils.hasattr_recursive(target_object, target_attr):
params[to_param_name] = vis_utils.getattr_recursive(target_object, target_attr)
if assign:
params[to_param_name] = assign
# NOTE!: don't expose raw ids: encode id, _id
# TODO: double encodes if from config
if params:
params = trans.security.encode_dict_ids(params)
return params