Source code for galaxy.visualization.plugins.plugin

Visualization plugins: instantiate/deserialize data and models
from a query string and render a webpage based on those data.
import copy
import logging
import os

import mako.lookup

from galaxy.managers import api_keys
from galaxy.visualization.plugins import (
from galaxy.web import url_for

log = logging.getLogger(__name__)

[docs]class ServesTemplatesPluginMixin: """ An object that renders (mako) template files from the server. """ #: default number of templates to search for plugin template lookup DEFAULT_TEMPLATE_COLLECTION_SIZE = 10 def _set_up_template_plugin(self, template_cache_dir, additional_template_paths=None, **kwargs): """ Detect and set up template paths if the plugin serves templates. """ self.serves_templates = False if self._is_template_plugin(): self.template_path = self._build_template_path() self.template_lookup = self._build_template_lookup(template_cache_dir, additional_template_paths=additional_template_paths) self.serves_templates = True return self.serves_templates def _is_template_plugin(self): return os.path.isdir(self._build_template_path()) def _build_template_path(self): return os.path.join(self.path, 'templates') def _build_template_lookup(self, template_cache_dir, additional_template_paths=None, collection_size=DEFAULT_TEMPLATE_COLLECTION_SIZE): """ Build a mako template filename lookup for the plugin. """ template_lookup_paths = self.template_path if additional_template_paths: template_lookup_paths = [template_lookup_paths] + additional_template_paths return mako.lookup.TemplateLookup( directories=template_lookup_paths, module_directory=template_cache_dir, collection_size=collection_size)
[docs]class VisualizationPlugin(ServesTemplatesPluginMixin): """ A plugin that instantiates resources, serves static files, and uses mako templates to render web pages. """
[docs] def __init__(self, app, path, name, config, context=None, **kwargs): context = context or {} = app self.path = path = name self.config = config base_url = context.get('base_url', '') self.base_url = '/'.join((base_url, if base_url else self.static_path = self._get_static_path(self.path) if self.static_path and os.path.exists(os.path.join(self.static_path, 'logo.png')): self.config['logo'] = self.static_path + '/logo.png' template_cache_dir = context.get('template_cache_dir', None) additional_template_paths = context.get('additional_template_paths', []) self._set_up_template_plugin(template_cache_dir, additional_template_paths=additional_template_paths) self.resource_parser = resource_parser.ResourceParser(app)
[docs] def render(self, trans=None, embedded=None, **kwargs): """ Render and return the text of the non-saved plugin webpage/fragment. """ # not saved - no existing config config = {} # set up render vars based on plugin.config and kwargs render_vars = self._build_render_vars(config, trans=trans, **kwargs) return self._render(render_vars, trans=trans, embedded=embedded)
[docs] def render_saved(self, visualization, trans=None, embedded=None, **kwargs): """ Render and return the text of the plugin webpage/fragment using the config/data of a saved visualization. """ config = self._get_saved_visualization_config(visualization, **kwargs) # pass the saved visualization config for parsing into render vars render_vars = self._build_render_vars(config, trans=trans, **kwargs) # update any values that were loaded from the saved Visualization render_vars.update(dict( title=visualization.latest_revision.title, saved_visualization=visualization,, )) return self._render(render_vars, trans=trans, embedded=embedded)
[docs] def to_dict(self): return { 'name':, 'html': self.config.get('name'), 'description': self.config.get('description'), 'logo': self.config.get('logo'), 'title': self.config.get('title'), 'target': self.config.get('render_target', 'galaxy_main'), 'embeddable': self.config.get('embeddable'), 'entry_point': self.config.get('entry_point'), 'settings': self.config.get('settings'), 'groups': self.config.get('groups'), 'specs': self.config.get('specs'), 'href': self._get_url() }
def _get_url(self): if in return url_for(controller='visualization', return url_for('visualization_plugin', def _get_static_path(self, path): if '/config/' in path: match = path.split('/config/')[-1] return os.path.join('./static', match, 'static') else: log.debug('Visualization has no static path: %s.' % path) def _get_saved_visualization_config(self, visualization, revision=None, **kwargs): """ Return the config of a saved visualization and revision. If no revision given, default to latest revision. """ # TODO: allow loading a specific revision - should be part of UsesVisualization return copy.copy(visualization.latest_revision.config) # ---- non-public def _build_render_vars(self, config, trans=None, **kwargs): """ Build all the variables that will be passed into the renderer. """ render_vars = {} # Meta variables passed to the template/renderer to describe the visualization being rendered. render_vars.update(, visualization_display_name=self.config['name'], title=kwargs.get('title', None), saved_visualization=None, visualization_id=None, visualization_plugin=self.to_dict(), # NOTE: passing *unparsed* kwargs as query query=kwargs, ) # config based on existing or kwargs config = self._build_config(config, trans=trans, **kwargs) render_vars['config'] = config # further parse config to resources (models, etc.) used in template based on registry config resources = self._config_to_resources(trans, config) render_vars.update(resources) return render_vars def _build_config(self, config, trans=None, **kwargs): """ Build the configuration for this new/saved visualization by combining any existing config and the kwargs (gen. from the url query). """ # first, pull from any existing config if config: config = copy.copy(config) else: config = {} # then, overwrite with keys/values from kwargs (gen. a query string) config_from_kwargs = self._kwargs_to_config(trans, kwargs) config.update(config_from_kwargs) # to object format for easier querying config = utils.OpenObject(**config) return config # TODO: the difference between config & resources is unclear in this section - is it needed? def _kwargs_to_config(self, trans, kwargs): """ Given a kwargs dict (gen. a query string dict from a controller action), parse and return any key/value pairs found in the plugin's `params` section. """ expected_params = self.config.get('params', {}) config = self.resource_parser.parse_config(trans, expected_params, kwargs) return config def _config_to_resources(self, trans, config): """ Instantiate/deserialize the resources (HDAs, LDDAs, etc.) given in a visualization config into models/variables a visualization renderer can use. """ expected_params = self.config.get('params', {}) param_modifiers = self.config.get('param_modifiers', {}) resources = self.resource_parser.parse_parameter_dictionary(trans, expected_params, config, param_modifiers) return resources def _render(self, render_vars, trans=None, embedded=None, **kwargs): """ Render the visualization via Mako and the plugin's template file. """ render_vars['embedded'] = self._parse_embedded(embedded) # NOTE: (mako specific) vars is a dictionary for shared data in the template # this feels hacky to me but it's what mako recommends: # render_vars.update(vars={}) template_filename = self.config['entry_point']['file'] return trans.fill_template(template_filename, template_lookup=self.template_lookup, **render_vars) def _parse_embedded(self, embedded): """ Parse information on dimensions, readonly, etc. from the embedded query val. """ # as is for now return embedded
[docs]class InteractiveEnvironmentPlugin(VisualizationPlugin): """ Serves web-based REPLs such as Jupyter and RStudio. """ INTENV_REQUEST_FACTORY = interactive_environments.InteractiveEnvironmentRequest
[docs] def __init__(self, app, path, name, config, context=None, **kwargs): # TODO: this is a hack until we can get int envs seperated from the vis reg and into their own framework context['base_url'] = 'interactive_environments' super().__init__(app, path, name, config, context=context, **kwargs)
def _error_template(self, trans): return trans.fill_template('message.mako', message='Loading the interactive environment failed, please contact the {admin_tag} for assistance'.format( admin_tag='<a href="mailto:{admin_mail}">Galaxy administrator</a>'.format( if else 'Galaxy administrator'), status='error') def _render(self, render_vars, trans=None, embedded=None, **kwargs): """ Override to add interactive environment specific template vars. """ render_vars['embedded'] = self._parse_embedded(embedded) # NOTE: (mako specific) vars is a dictionary for shared data in the template # this feels hacky to me but it's what mako recommends: # render_vars.update(vars={}) # No longer needed but being left around for a few releases as jupyter-galaxy # as an external visualization plugin is deprecated in favor of core interactive # environment plugin. if 'get_api_key' not in render_vars: def get_api_key(): return api_keys.ApiKeyManager( render_vars['get_api_key'] = get_api_key if 'plugin_path' not in render_vars: render_vars['plugin_path'] = os.path.abspath(self.path) if self.config.get('plugin_type', 'visualization') == "interactive_environment": try: request = self.INTENV_REQUEST_FACTORY(trans, self) except Exception: log.exception("IE plugin request handling failed") return self._error_template(trans) render_vars["ie_request"] = request template_filename = self.config['entry_point']['file'] try: return trans.fill_template(template_filename, template_lookup=self.template_lookup, **render_vars) except Exception: log.exception("IE plugin template fill failed") return self._error_template(trans) def _get_url(self): return url_for('interactive_environment_plugin',
[docs]class ScriptVisualizationPlugin(VisualizationPlugin): """ A visualization plugin that starts by loading a single (js) script. The script is loaded into a pre-defined mako template: `config/plugins/visualizations/common/templates/script_entry_point.mako` """ MAKO_TEMPLATE = 'script_entry_point.mako' def _is_template_plugin(self): """ Override to always yield true since this plugin type always uses the pre-determined mako template. """ return True def _render(self, render_vars, trans=None, embedded=None, **kwargs): """ Override to add script attributes and point mako at the script entry point template. """ render_vars['embedded'] = self._parse_embedded(embedded) render_vars['static_url'] = url_for('/%s/' % self.static_path) render_vars.update(vars={}) render_vars.update({ "script_attributes": self.config['entry_point']['attr'] }) template_filename = os.path.join(self.MAKO_TEMPLATE) return trans.fill_template(template_filename, template_lookup=self.template_lookup, **render_vars)
[docs]class ChartVisualizationPlugin(ScriptVisualizationPlugin): MAKO_TEMPLATE = 'chart_entry_point.mako'
[docs]class StaticFileVisualizationPlugin(VisualizationPlugin): """ A visualization plugin that starts by loading a static html file defined in the visualization's config file. """ # TODO: these are not embeddable by their nature - update config # TODO: should do render/render_saved here since most of the calc done there is unneeded in this case def _render(self, render_vars, trans=None, embedded=None, **kwargs): """ Render the static file simply by reading and returning it. """ render_vars['embedded'] = self._parse_embedded(embedded) render_vars.update(vars={}) static_file_path = self.config['entry_point']['file'] static_file_path = os.path.join(self.path, static_file_path) with open(static_file_path) as outfile: return