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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

import galaxy.model
from galaxy.exceptions import ObjectNotFound
from galaxy.util import config_directories_from_setting
from galaxy.visualization.plugins import (
    config_parser,
    plugin as vis_plugins,
)
from galaxy.visualization.plugins.datasource_testing import is_object_applicable

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 directory of visualizations BASE_DIR = "static/plugins/visualizations" #: base url to controller endpoint BASE_URL = "visualizations" #: built-in visualizations BUILT_IN_VISUALIZATIONS = ["trackster"] 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.skip_bad_plugins = skip_bad_plugins self.plugins = {} self.directories = config_directories_from_setting(directories_setting, app.config.root) self.directories.append(os.path.join(app.config.root, self.BASE_DIR)) self._load_plugins()
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: if not os.path.isdir(directory): continue 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 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 expected_config_filename = f"{os.path.basename(plugin_path)}.xml" return os.path.isfile(os.path.join(plugin_path, "static", expected_config_filename)) 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] config_file = os.path.join(plugin_path, "static", f"{plugin_name}.xml") if os.path.exists(config_file): config = self.config_parser.parse_file(config_file) if config is not None: plugin = self._build_plugin(plugin_name, plugin_path, config) return plugin raise ObjectNotFound(f"Visualization XML not found in config or static paths for: {plugin_name}.") def _build_plugin(self, plugin_name, plugin_path, config): # from mako if config["entry_point"]["type"] == "mako": plugin_class = vis_plugins.VisualizationPlugin else: # default from js plugin_class = vis_plugins.ScriptVisualizationPlugin return plugin_class( self.app(), plugin_path, plugin_name, config, context=dict( base_url=self.base_url, template_cache_dir=self.template_cache_dir, ), )
[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]
# -- building links to visualizations from objects --
[docs] def get_visualizations(self, trans, target_object=None, embeddable=None): """ Get the names of visualizations usable on the `target_object` and the urls to call in order to render the visualizations. """ result = [] for vis_name, vis_plugin in self.plugins.items(): if vis_plugin.config.get("hidden"): continue if embeddable and not vis_plugin.config.get("embeddable"): continue if target_object is not None and self.get_visualization(trans, vis_name, target_object) is None: continue result.append(vis_plugin.to_dict()) return sorted(result, 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"] model_class = getattr(galaxy.model, model_class, None) if model_class and isinstance(target_object, model_class): tests = data_source["tests"] if tests is None or is_object_applicable(trans, target_object, tests): return visualization.to_dict()