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 (
    interactive_environments,
    resource_parser,
    utils
)
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 {}
        self.app = app
        self.path = path
        self.name = name
        self.config = config
        base_url = context.get('base_url', '')
        self.base_url = '/'.join((base_url, self.name)) if base_url else self.name
        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'] = f"{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,
            visualization_id=trans.security.encode_id(visualization.id),
        ))
        return self._render(render_vars, trans=trans, embedded=embedded)

[docs]    def to_dict(self):
        return {
            'name': self.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 self.name in self.app.visualizations_registry.BUILT_IN_VISUALIZATIONS:
            return url_for(controller='visualization', action=self.name)
        return url_for('visualization_plugin', visualization_name=self.name)

    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(f'Visualization has no static path: {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_name=self.name,
            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:
        #   http://docs.makotemplates.org/en/latest/runtime.html
        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(
                    admin_mail=trans.app.config.error_email_to)
                if trans.app.config.error_email_to 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:
        #   http://docs.makotemplates.org/en/latest/runtime.html
        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(trans.app).get_or_create_api_key(trans.user)
            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', visualization_name=self.name)


[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(f'/{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 outfile.read()