mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Visualizations registry: refactor the relationship between plugins, the visualization controller, rendering, and rendering saved visualizations, minor fixes; Extend testing; Scatterplot: fix baseUrl resolution when used in own window
This commit is contained in:
Carl Eberhard
@@ -20,7 +20,8 @@ var ScatterplotDisplay = Backbone.View.extend({
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var view = this,
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config = this.model.get( 'config' ),
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//TODO: very tied to datasets - should be generalized eventually
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xhr = jQuery.getJSON(((typeof parent.galaxy_config.root == 'undefined') ? '/' : parent.galaxy_config.root) + 'api/datasets/' + this.dataset.id, {
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baseUrl = ( window.parent && parent.galaxy_config )? parent.galaxy_config.root : '/',
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xhr = jQuery.getJSON( baseUrl + 'api/datasets/' + this.dataset.id, {
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data_type : 'raw_data',
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provider : 'dataset-column',
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limit : config.pagination.perPage,
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File diff suppressed because one or more lines are too long
@@ -129,7 +129,7 @@ class VisualizationPlugin( pluginframework.Plugin, ServesStaticPluginMixin, Serv
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self.config = config
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base_url = context.get( 'base_url', '' )
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self.base_url = '/'.join([ base_url, self.name ])
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self.base_url = '/'.join([ base_url, self.name ]) if base_url else self.name
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self._set_up_static_plugin()
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@@ -139,87 +139,79 @@ class VisualizationPlugin( pluginframework.Plugin, ServesStaticPluginMixin, Serv
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self.resource_parser = resource_parser.ResourceParser( app )
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def render( self, trans=None, visualization=None, config=None, embedded=None, **kwargs ):
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def render( self, trans=None, embedded=None, **kwargs ):
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"""
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Return the text of the rendered plugin webpage/fragment.
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Render and return the text of the non-saved plugin webpage/fragment.
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"""
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if visualization:
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return self._render_saved( visualization, config, trans=trans, embedded=embedded, **kwargs )
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config = {}
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context = self._default_context_vars( embedded=embedded, **kwargs )
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return self._render( config, trans=trans, embedded=embedded, context=context, **kwargs )
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# get the config for passing to the template from the kwargs dict, parsed using the plugin's params setting
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config_from_kwargs = self._query_dict_to_config( trans, kwargs )
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config = utils.OpenObject( **config_from_kwargs )
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# further parse config to resources (models, etc.) used in template based on registry config
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resources = self._query_dict_to_resources( trans, config )
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# if a saved visualization, pass in the encoded visualization id or None if a new render
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encoded_visualization_id = None
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visualization_display_name = self.config[ 'name' ]
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title = kwargs.get( 'title', None )
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return self._fill_template( trans,
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visualization_name=self.name,
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visualization_display_name=visualization_display_name,
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title=title,
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def render_saved( self, visualization, config, trans=None, embedded=None, **kwargs ):
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"""
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Render and return the text of the plugin webpage/fragment using the
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config/data of a saved visualization.
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"""
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context = self._default_context_vars( embedded=embedded, **kwargs )
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# update any values that were loaded from the Visualization
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context.update( dict(
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title=visualization.latest_revision.title,
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saved_visualization=visualization,
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visualization_id=encoded_visualization_id,
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visualization_id=trans.security.encode_id( visualization.id ),
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))
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return self._render( config, trans=trans, embedded=embedded, context=context, **kwargs )
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embedded=embedded,
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# ---- non-public
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def _default_context_vars( self, **kwargs ):
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"""
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Meta variables passed to the template/renderer to describe the visualization
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being rendered.
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These are the defaults used when a saved visualization isn't present to
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provide them.
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"""
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return dict(
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visualization_name=self.name,
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visualization_display_name=self.config[ 'name' ],
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title=kwargs.get( 'title', None ),
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saved_visualization=None,
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visualization_id=None,
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# NOTE: passing *unparsed* kwargs as query
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query=kwargs,
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# NOTE: vars is a dictionary for shared data in the template
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# this feels hacky to me but it's what mako recommends:
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# http://docs.makotemplates.org/en/latest/runtime.html
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vars={},
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config=config,
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**resources
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)
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def _render_saved( self, visualization, config, trans=None, embedded=None, **kwargs ):
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def _render( self, config, context, trans=None, embedded=None, **kwargs ):
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"""
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Return the text of the saved visualization.
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Build/fetch the variables needed to render the visualization and call the renderer.
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"""
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config = config or {}
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template_args = {}
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# get the config for passing to the template from the kwargs dict, parsed using the plugin's params setting
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config = config or {}
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config_from_kwargs = self._query_dict_to_config( trans, kwargs )
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config.update( config_from_kwargs )
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config = utils.OpenObject( **config )
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template_args[ 'config' ] = config
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# further parse config to resources (models, etc.) used in template based on registry config
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resources = self._query_dict_to_resources( trans, config )
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template_args.update( resources )
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# if a saved visualization, pass in the encoded visualization id or None if a new render
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encoded_visualization_id = trans.security.encode_id( visualization.id )
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# add any extra variables dealing with the visualization itself, saved visualizations, etc.
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template_args.update( context )
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visualization_display_name = self.config[ 'name' ]
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title = visualization.latest_revision.title
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template_args.update( embedded=embedded )
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return self._fill_template( trans, **template_args )
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return self._fill_template( trans,
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visualization_name=self.name,
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visualization_display_name=visualization_display_name,
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title=title,
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saved_visualization=visualization,
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visualization_id=encoded_visualization_id,
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embedded=embedded,
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# NOTE: passing *unparsed* kwargs as query
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query=kwargs,
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# NOTE: vars is a dictionary for shared data in the template
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# this feels hacky to me but it's what mako recommends:
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# http://docs.makotemplates.org/en/latest/runtime.html
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vars={},
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config=config,
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**resources
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)
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# ---------------- getting resources for visualization templates from link query strings
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def _fill_template( self, trans, **kwargs ):
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# NOTE: (mako specific) vars is a dictionary for shared data in the template
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# this feels hacky to me but it's what mako recommends:
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# http://docs.makotemplates.org/en/latest/runtime.html
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kwargs.update( vars={} )
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template_filename = self.config[ 'entry_point' ][ 'file' ]
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return trans.fill_template( template_filename, template_lookup=self.template_lookup, **kwargs )
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# ---------------- getting resources for visualization templates from link query strings
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def _get_resource_params_and_modifiers( self ):
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"""
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Get params and modifiers for the given visualization as a 2-tuple.
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@@ -8,6 +8,7 @@ import os
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import weakref
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from galaxy.web import url_for
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import galaxy.exceptions
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from galaxy.web.base import pluginframework
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from galaxy.visualization.plugins import config_parser
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@@ -114,6 +115,14 @@ class VisualizationsRegistry( pluginframework.PageServingPluginManager ):
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))
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return plugin
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def get_plugin( self, key ):
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"""
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Wrap to throw error if plugin not in registry.
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"""
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if key not in self.plugins:
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raise galaxy.exceptions.ObjectNotFound( 'Unknown or invalid visualization: ' + key )
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return self.plugins[ key ]
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# -- building links to visualizations from objects --
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def get_visualizations( self, trans, target_object ):
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"""
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@@ -716,38 +716,14 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio
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help="A description of the visualization; annotation is shown alongside published visualizations."),
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template="visualization/create.mako" )
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#
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# Visualizations.
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#
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# ------------------------- registry.
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@web.expose
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@web.require_login( "use Galaxy visualizations", use_panels=True )
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def saved( self, trans, id=None, revision=None, type=None, config=None, title=None, **kwargs ):
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"""
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"""
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DEFAULT_VISUALIZATION_NAME = 'Unnamed Visualization'
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# post to saved in order to save a visualization
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# TODO: re-route this one to clear up signature
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if trans.request.method == 'POST':
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if type is None or config is None:
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return HTTPBadRequest( 'A visualization type and config are required to save a visualization' )
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if isinstance( config, basestring ):
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config = loads( config )
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title = title or DEFAULT_VISUALIZATION_NAME
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# TODO: allow saving to (updating) a specific revision - should be part of UsesVisualization
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# TODO: would be easier if this returned the visualization directly
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# check security if posting to existing visualization
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if id is not None:
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visualization = self.get_visualization( trans, id, check_ownership=True, check_accessible=False )
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# ??: on not owner: error raised, but not returned (status = 200)
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# TODO: there's no security check in save visualization (if passed an id)
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returned = self.save_visualization( trans, config, type, id, title )
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# redirect to GET to prevent annoying 'Do you want to post again?' dialog on page reload
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render_url = web.url_for( controller='visualization', action='saved', id=returned.get( 'vis_id' ) )
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return trans.response.send_redirect( render_url )
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self._POST_to_saved( trans, id=id, revision=revision, type=type, config=config, title=title, **kwargs )
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if id is None:
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return HTTPBadRequest( 'A valid visualization id is required to load a visualization' )
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@@ -760,11 +736,15 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio
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# re-add title to kwargs for passing to render
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if title:
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kwargs[ 'title' ] = title
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return self.render( trans, visualization.type, visualization, config=config, **kwargs )
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plugin = self._get_plugin_from_registry( trans, visualization.type )
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try:
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return plugin.render_saved( visualization, config, trans=trans, **kwargs )
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except Exception, exception:
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self._handle_plugin_error( trans, visualization.type, exception )
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@web.expose
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@web.require_login( "use Galaxy visualizations", use_panels=True )
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def render( self, trans, visualization_name, visualization=None, config=None, embedded=None, **kwargs ):
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def render( self, trans, visualization_name, embedded=None, **kwargs ):
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"""
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Render the appropriate visualization template, parsing the `kwargs`
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into appropriate variables and resources (such as ORM models)
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@@ -772,32 +752,66 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio
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URL: /visualization/show/{visualization_name}
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"""
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config = config or {}
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# validate name vs. registry
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registry = trans.app.visualizations_registry
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if not registry:
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raise HTTPNotFound( 'No visualization registry (possibly disabled in galaxy.ini)' )
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if visualization_name not in registry.plugins:
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raise HTTPNotFound( 'Unknown or invalid visualization: ' + visualization_name )
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plugin = registry.plugins[ visualization_name ]
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returned = None
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plugin = self._get_plugin_from_registry( trans, visualization_name )
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try:
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returned = plugin.render( controller=self, trans=trans,
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visualization=visualization, config=config, embedded=embedded, **kwargs )
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return plugin.render( trans=trans, embedded=embedded, **kwargs )
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except Exception, exception:
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log.exception( 'error rendering visualization (%s): %s', visualization_name, str( exception ) )
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if trans.debug:
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raise
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returned = trans.show_error_message(
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"There was an error rendering the visualization. " +
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"Contact your Galaxy administrator if the problem persists." +
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"<br/>Details: " + str( exception ), use_panels=False )
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self._handle_plugin_error( trans, visualization_name, exception )
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return returned
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def _POST_to_saved( self, trans, id=None, revision=None, type=None, config=None, title=None, **kwargs ):
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"""
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Save the visualiztion info (revision, type, config, title, etc.) to
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the Visualization at `id` or to a new Visualization if `id` is None.
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Uses POST/redirect/GET after a successful save, redirecting to GET.
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"""
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DEFAULT_VISUALIZATION_NAME = 'Unnamed Visualization'
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# post to saved in order to save a visualization
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if type is None or config is None:
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return HTTPBadRequest( 'A visualization type and config are required to save a visualization' )
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if isinstance( config, basestring ):
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config = loads( config )
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title = title or DEFAULT_VISUALIZATION_NAME
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# TODO: allow saving to (updating) a specific revision - should be part of UsesVisualization
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# TODO: would be easier if this returned the visualization directly
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# check security if posting to existing visualization
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if id is not None:
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self.get_visualization( trans, id, check_ownership=True, check_accessible=False )
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# ??: on not owner: error raised, but not returned (status = 200)
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# TODO: there's no security check in save visualization (if passed an id)
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returned = self.save_visualization( trans, config, type, id, title )
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# redirect to GET to prevent annoying 'Do you want to post again?' dialog on page reload
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render_url = web.url_for( controller='visualization', action='saved', id=returned.get( 'vis_id' ) )
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return trans.response.send_redirect( render_url )
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def _get_plugin_from_registry( self, trans, visualization_name ):
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"""
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Get the named plugin from the registry.
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:raises HTTPNotFound: if registry has been turned off in config.
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:raises HTTPNotFound: if visualization_name isn't a registered plugin.
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"""
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if not trans.app.visualizations_registry:
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raise HTTPNotFound( 'No visualization registry (possibly disabled in galaxy.ini)' )
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return trans.app.visualizations_registry.get_plugin( visualization_name )
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def _handle_plugin_error( self, trans, visualization_name, exception ):
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"""
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Log, raise if debugging; log and show html message if not.
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"""
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log.exception( 'error rendering visualization (%s): %s', visualization_name, str( exception ) )
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if trans.debug:
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raise
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return trans.show_error_message(
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"There was an error rendering the visualization. " +
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"Contact your Galaxy administrator if the problem persists." +
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"<br/>Details: " + str( exception ), use_panels=False )
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#
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# Visualizations.
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#
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@web.expose
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@web.require_login()
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def trackster(self, trans, **kwargs):
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@@ -833,7 +847,7 @@ class VisualizationController( BaseUIController, SharableMixin, UsesVisualizatio
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app['viz_config'] = self.get_visualization_config( trans, vis )
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# backup id
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app['id'] = id;
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app['id'] = id
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# add dataset id
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app['add_dataset'] = new_dataset_id
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@@ -0,0 +1,112 @@
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"""
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"""
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import os
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import imp
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import unittest
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test_utils = imp.load_source( 'test_utils',
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os.path.join( os.path.dirname( __file__), '..', 'unittest_utils', 'utility.py' ) )
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import galaxy_mock
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from galaxy.visualization.plugins import plugin as vis_plugin
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from galaxy.visualization.plugins import resource_parser
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# -----------------------------------------------------------------------------
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glx_dir = test_utils.get_galaxy_root()
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template_cache_dir = os.path.join( glx_dir, 'database', 'compiled_templates' )
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addtional_templates_dir = os.path.join( glx_dir, 'config', 'plugins', 'visualizations', 'common', 'templates' )
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vis_reg_path = 'config/plugins/visualizations'
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config1 = """\
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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE visualization SYSTEM "../../visualization.dtd">
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<visualization name="scatterplot">
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<data_sources>
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<data_source>
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<model_class>HistoryDatasetAssociation</model_class>
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<test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test>
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<to_param param_attr="id">dataset_id</to_param>
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</data_source>
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</data_sources>
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<params>
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<param type="dataset" var_name_in_template="hda" required="true">dataset_id</param>
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</params>
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<template>scatterplot.mako</template>
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</visualization>
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"""
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# -----------------------------------------------------------------------------
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class VisualizationsPlugin_TestCase( unittest.TestCase ):
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def test_default_init( self ):
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"""
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"""
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vis_dir = galaxy_mock.MockDir({
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'config' : {
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'vis1.xml' : ''
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},
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'static' : {},
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'templates' : {},
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})
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config = dict()
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plugin = vis_plugin.VisualizationPlugin( galaxy_mock.MockApp(), vis_dir.root_path,
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'myvis', config )
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self.assertEqual( plugin.name, 'myvis' )
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self.assertEqual( plugin.path, vis_dir.root_path )
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self.assertEqual( plugin.config, {} )
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self.assertEqual( plugin.base_url, 'myvis' )
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# static
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self.assertTrue( plugin.serves_static )
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self.assertEqual( plugin.static_path, vis_dir.root_path + '/static' )
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self.assertEqual( plugin.static_url, 'myvis/static' )
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# template
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self.assertTrue( plugin.serves_templates )
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self.assertEqual( plugin.template_path, vis_dir.root_path + '/templates' )
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self.assertEqual( plugin.template_lookup.__class__.__name__, 'TemplateLookup' )
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# resource parser
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self.assertIsInstance( plugin.resource_parser, resource_parser.ResourceParser )
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def test_init_with_context( self ):
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"""
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"""
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vis_dir = galaxy_mock.MockDir({
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'config' : {
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'vis1.xml' : ''
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},
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'static' : {},
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'templates' : {},
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})
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config = dict()
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context = dict(
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base_url='u/wot/m8',
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template_cache_dir='template_cache',
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additional_template_paths=[ 'one' ]
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)
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plugin = vis_plugin.VisualizationPlugin( galaxy_mock.MockApp(), vis_dir.root_path,
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'myvis', config, context=context )
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self.assertEqual( plugin.base_url, 'u/wot/m8/myvis' )
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# static
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self.assertEqual( plugin.static_url, 'u/wot/m8/myvis/static' )
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# template
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self.assertEqual( plugin.template_lookup.__class__.__name__, 'TemplateLookup' )
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def test_init_without_static_or_templates( self ):
|
||||
"""
|
||||
"""
|
||||
vis_dir = galaxy_mock.MockDir({
|
||||
'config' : {
|
||||
'vis1.xml' : ''
|
||||
}
|
||||
})
|
||||
plugin = vis_plugin.VisualizationPlugin( galaxy_mock.MockApp(), vis_dir.root_path,
|
||||
'myvis', dict() )
|
||||
self.assertFalse( plugin.serves_static )
|
||||
self.assertFalse( plugin.serves_templates )
|
||||
# not sure what this would do, but...
|
||||
|
||||
# -----------------------------------------------------------------------------
|
||||
# TODO: config parser tests (in separate file)
|
||||
|
||||
if __name__ == '__main__':
|
||||
unittest.main()
|
||||
Reference in New Issue
Block a user