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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 (
from galaxy.visualization.plugins import (
    plugin as vis_plugins,

log = logging.getLogger(__name__)

[docs]class VisualizationsRegistry: """ 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" #: built-in visualizations 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: galaxy.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 = {} 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``. """ 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) 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 if os.path.isdir(plugin_path): for plugin_subdir in sorted(os.listdir(plugin_path)): plugin_subpath = os.path.join(plugin_path, plugin_subdir) if self._is_plugin(plugin_subpath): yield plugin_subpath # 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 = f"{os.path.split(plugin_path)[1]}.xml" 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", (f"{plugin_name}.xml")) if os.path.exists(config_file): config = self.config_parser.parse_file(config_file) if config is not None: # config may be none if the visualization is disabled plugin = self._build_plugin(plugin_name, plugin_path, config) return plugin else: raise ObjectNotFound(f"Visualization XML not found: {config_file}.") def _build_plugin(self, plugin_name, plugin_path, config): # TODO: as builder not factory # default class plugin_class = vis_plugins.VisualizationPlugin # js only if config["entry_point"]["type"] == "script": plugin_class = vis_plugins.ScriptVisualizationPlugin # js only using charts environment elif config["entry_point"]["type"] == "chart": plugin_class = vis_plugins.ChartVisualizationPlugin # from a static file (html, etc) elif config["entry_point"]["type"] == "html": plugin_class = vis_plugins.StaticFileVisualizationPlugin return 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, ), )
[docs] def get_plugin(self, key): """ Wrap to throw error if plugin not in registry. """ if key not in self.plugins: raise ObjectNotFound(f"Unknown or invalid visualization: {key}") return self.plugins[key]
[docs] def get_plugins(self, embeddable=None): result = [] for plugin in self.plugins.values(): if embeddable and not plugin.config.get("embeddable"): continue result.append(plugin.to_dict()) return sorted(result, key=lambda k: k.get("html"))
# -- 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. """ 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 sorted(applicable_visualizations, key=lambda k: k.get("html"))
[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. """ if (visualization := self.plugins.get(visualization_name, None)) is not None: data_sources = visualization.config["data_sources"] for data_source in data_sources: model_class = data_source["model_class"] if isinstance(target_object, model_class): tests = data_source["tests"] if tests is None or self.is_object_applicable(trans, target_object, tests): return visualization.to_dict()
[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