September 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: james_taylor: style: Restore margin to bottom of nav-tabs, normalize tab border colors
by commits-noreply＠bitbucket.org 18 Sep '13

18 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eb69169a04ef/ Changeset: eb69169a04ef User: james_taylor Date: 2013-09-18 20:13:36 Summary: style: Restore margin to bottom of nav-tabs, normalize tab border colors Affected #: 3 files diff -r 01f603a2179fce1cb39f5cfde973744585c73918 -r eb69169a04efb1fba610b943fd38a8ceb991d315 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -505,12 +505,12 @@ .nav .open>a,.nav .open>a:hover,.nav .open>a:focus{background-color:#eee;border-color:#303030} .nav .nav-divider{height:1px;margin:7.5px 0;overflow:hidden;background-color:#e5e5e5} .nav>li>a>img{max-width:none} -.nav-tabs{border-bottom:1px solid #ddd}.nav-tabs>li{float:left;margin-bottom:-1px}.nav-tabs>li>a{margin-right:2px;line-height:1.428571429;border:1px solid transparent;border-radius:3px 3px 0 0}.nav-tabs>li>a:hover{border-color:#eee #eee #ddd} -.nav-tabs>li.active>a,.nav-tabs>li.active>a:hover,.nav-tabs>li.active>a:focus{color:#555;background-color:#fff;border:1px solid #ddd;border-bottom-color:transparent;cursor:default} +.nav-tabs{border-bottom:1px solid #bfbfbf}.nav-tabs>li{float:left;margin-bottom:-1px}.nav-tabs>li>a{margin-right:2px;line-height:1.428571429;border:1px solid transparent;border-radius:3px 3px 0 0}.nav-tabs>li>a:hover{border-color:#eee #eee #bfbfbf} +.nav-tabs>li.active>a,.nav-tabs>li.active>a:hover,.nav-tabs>li.active>a:focus{color:#555;background-color:#fff;border:1px solid #bfbfbf;border-bottom-color:transparent;cursor:default} .nav-tabs.nav-justified{width:100%;border-bottom:0}.nav-tabs.nav-justified>li{float:none}.nav-tabs.nav-justified>li>a{text-align:center;margin-bottom:5px} @media (min-width:768px){.nav-tabs.nav-justified>li{display:table-cell;width:1%}.nav-tabs.nav-justified>li>a{margin-bottom:0}}.nav-tabs.nav-justified>li>a{margin-right:0;border-radius:3px} -.nav-tabs.nav-justified>.active>a,.nav-tabs.nav-justified>.active>a:hover,.nav-tabs.nav-justified>.active>a:focus{border:1px solid #ddd} -@media (min-width:768px){.nav-tabs.nav-justified>li>a{border-bottom:1px solid #ddd;border-radius:3px 3px 0 0} .nav-tabs.nav-justified>.active>a,.nav-tabs.nav-justified>.active>a:hover,.nav-tabs.nav-justified>.active>a:focus{border-bottom-color:#fff}} +.nav-tabs.nav-justified>.active>a,.nav-tabs.nav-justified>.active>a:hover,.nav-tabs.nav-justified>.active>a:focus{border:1px solid #bfbfbf} +@media (min-width:768px){.nav-tabs.nav-justified>li>a{border-bottom:1px solid #bfbfbf;border-radius:3px 3px 0 0} .nav-tabs.nav-justified>.active>a,.nav-tabs.nav-justified>.active>a:hover,.nav-tabs.nav-justified>.active>a:focus{border-bottom-color:#fff}} .nav-pills>li{float:left}.nav-pills>li>a{border-radius:5px} .nav-pills>li+li{margin-left:2px} .nav-pills>li.active>a,.nav-pills>li.active>a:hover,.nav-pills>li.active>a:focus{color:#fff;background-color:#303030} @@ -518,8 +518,8 @@ .nav-justified{width:100%}.nav-justified>li{float:none}.nav-justified>li>a{text-align:center;margin-bottom:5px} @media (min-width:768px){.nav-justified>li{display:table-cell;width:1%}.nav-justified>li>a{margin-bottom:0}} .nav-tabs-justified{border-bottom:0}.nav-tabs-justified>li>a{margin-right:0;border-radius:3px} -.nav-tabs-justified>.active>a,.nav-tabs-justified>.active>a:hover,.nav-tabs-justified>.active>a:focus{border:1px solid #ddd} -@media (min-width:768px){.nav-tabs-justified>li>a{border-bottom:1px solid #ddd;border-radius:3px 3px 0 0} .nav-tabs-justified>.active>a,.nav-tabs-justified>.active>a:hover,.nav-tabs-justified>.active>a:focus{border-bottom-color:#fff}} +.nav-tabs-justified>.active>a,.nav-tabs-justified>.active>a:hover,.nav-tabs-justified>.active>a:focus{border:1px solid #bfbfbf} +@media (min-width:768px){.nav-tabs-justified>li>a{border-bottom:1px solid #bfbfbf;border-radius:3px 3px 0 0} .nav-tabs-justified>.active>a,.nav-tabs-justified>.active>a:hover,.nav-tabs-justified>.active>a:focus{border-bottom-color:#fff}} .tabbable:before,.tabbable:after{content:" ";display:table;} .tabbable:after{clear:both} .tabbable:before,.tabbable:after{content:" ";display:table;} @@ -756,9 +756,7 @@ .btn.active,.btn:active{color:inherit} .dropdown-menu{max-width:auto} input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex} -.nav-tabs{border-bottom:1px solid #bfbfbf} -.nav-tabs>li>a:hover{border-color:#eee #eee #bfbfbf} -.nav-tabs>.active>a,.nav-tabs>.active>a:hover{border:1px solid #bfbfbf;border-bottom-color:transparent} +.nav-tabs{margin-bottom:15px} a{text-decoration:underline} label{font-weight:normal} @font-face{font-family:'FontAwesome';src:url('../images/fonts/fontawesome-webfont.eot');src:url('../images/fonts/fontawesome-webfont.eot?#iefix') format('embedded-opentype'),url('../images/fonts/fontawesome-webfont.woff') format('woff'),url('../images/fonts/fontawesome-webfont.ttf') format('truetype');font-weight:normal;font-style:normal}.fa-icon,[class^="fa-icon-"],[class*=" fa-icon-"]{font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat} diff -r 01f603a2179fce1cb39f5cfde973744585c73918 -r eb69169a04efb1fba610b943fd38a8ceb991d315 static/style/src/less/galaxy_bootstrap/overrides.less --- a/static/style/src/less/galaxy_bootstrap/overrides.less +++ b/static/style/src/less/galaxy_bootstrap/overrides.less @@ -57,15 +57,5 @@ // Tabs -- border color is hardcoded in navs.less, change to @btnBorder here .nav-tabs { - border-bottom: 1px solid @btn-default-border; -} -.nav-tabs > li > a { - &:hover { - border-color: @gray-lighter @gray-lighter @btn-default-border; - } -} -.nav-tabs > .active > a, -.nav-tabs > .active > a:hover { - border: 1px solid @btn-default-border; - border-bottom-color: transparent; + margin-bottom: 15px; } \ No newline at end of file diff -r 01f603a2179fce1cb39f5cfde973744585c73918 -r eb69169a04efb1fba610b943fd38a8ceb991d315 static/style/src/less/galaxy_bootstrap/variables.less --- a/static/style/src/less/galaxy_bootstrap/variables.less +++ b/static/style/src/less/galaxy_bootstrap/variables.less @@ -373,15 +373,15 @@ @nav-open-caret-border-color: @white; // Tabs -@nav-tabs-border-color: #ddd; +@nav-tabs-border-color: @border-default-color; @nav-tabs-link-hover-border-color: @gray-lighter; @nav-tabs-active-link-hover-bg: @body-bg; @nav-tabs-active-link-hover-color: @gray; -@nav-tabs-active-link-hover-border-color: #ddd; +@nav-tabs-active-link-hover-border-color: @border-default-color; -@nav-tabs-justified-link-border-color: #ddd; +@nav-tabs-justified-link-border-color: @border-default-color; @nav-tabs-justified-active-link-border-color: @body-bg; // Pills Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: james_taylor: Buttons and submit inputs always get the default .btn style
by commits-noreply＠bitbucket.org 18 Sep '13

18 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/01f603a2179f/ Changeset: 01f603a2179f User: james_taylor Date: 2013-09-18 19:52:07 Summary: Buttons and submit inputs always get the default .btn style Affected #: 5 files diff -r 2d0bcb07596c4c688ed3908391d866831c65c042 -r 01f603a2179fce1cb39f5cfde973744585c73918 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1218,6 +1218,16 @@ select,input,textarea{font:inherit} .form-row select,.form-row textarea,.form-row input[type="text"],.form-row input[type="file"],.form-row input[type="password"]{max-width:90%} textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:1.428571429;border:1px solid #aaa;padding:3px} +input[type="submit"],button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;color:#333;background-color:#fff;border-color:#bfbfbf}input[type="submit"]:focus,button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} +input[type="submit"]:hover,button:hover,input[type="submit"]:focus,button:focus{color:#333;text-decoration:none} +input[type="submit"]:active,button:active,input[type="submit"].active,button.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} +input[type="submit"].disabled,button.disabled,input[type="submit"][disabled],button[disabled],fieldset[disabled] input[type="submit"],fieldset[disabled] button{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} +input[type="submit"] [class^="fa-icon-"],button [class^="fa-icon-"],input[type="submit"] [class*=" fa-icon-"],button [class*=" fa-icon-"]{display:inline;line-height:.6em}input[type="submit"] [class^="fa-icon-"].fa-icon-spin,button [class^="fa-icon-"].fa-icon-spin,input[type="submit"] [class*=" fa-icon-"].fa-icon-spin,button [class*=" fa-icon-"].fa-icon-spin{display:inline-block} +input[type="submit"] [class^="fa-icon-"].pull-left.fa-icon-2x,button [class^="fa-icon-"].pull-left.fa-icon-2x,input[type="submit"] [class*=" fa-icon-"].pull-left.fa-icon-2x,button [class*=" fa-icon-"].pull-left.fa-icon-2x,input[type="submit"] [class^="fa-icon-"].pull-right.fa-icon-2x,button [class^="fa-icon-"].pull-right.fa-icon-2x,input[type="submit"] [class*=" fa-icon-"].pull-right.fa-icon-2x,button [class*=" fa-icon-"].pull-right.fa-icon-2x{margin-top:.35em} +input[type="submit"] [class^="fa-icon-"].fa-icon-spin.icon-large,button [class^="fa-icon-"].fa-icon-spin.icon-large,input[type="submit"] [class*=" fa-icon-"].fa-icon-spin.icon-large,button [class*=" fa-icon-"].fa-icon-spin.icon-large{height:.75em} +input[type="submit"]:hover,button:hover,input[type="submit"]:focus,button:focus,input[type="submit"]:active,button:active,input[type="submit"].active,button.active,.open .dropdown-toggleinput[type="submit"],.open .dropdown-togglebutton{color:#333;background-color:#ebebeb;border-color:#a1a1a1} +input[type="submit"]:active,button:active,input[type="submit"].active,button.active,.open .dropdown-toggleinput[type="submit"],.open .dropdown-togglebutton{background-image:none} +input[type="submit"].disabled,button.disabled,input[type="submit"][disabled],button[disabled],fieldset[disabled] input[type="submit"],fieldset[disabled] button,input[type="submit"].disabled:hover,button.disabled:hover,input[type="submit"][disabled]:hover,button[disabled]:hover,fieldset[disabled] input[type="submit"]:hover,fieldset[disabled] button:hover,input[type="submit"].disabled:focus,button.disabled:focus,input[type="submit"][disabled]:focus,button[disabled]:focus,fieldset[disabled] input[type="submit"]:focus,fieldset[disabled] button:focus,input[type="submit"].disabled:active,button.disabled:active,input[type="submit"][disabled]:active,button[disabled]:active,fieldset[disabled] input[type="submit"]:active,fieldset[disabled] button:active,input[type="submit"].disabled.active,button.disabled.active,input[type="submit"][disabled].active,button[disabled].active,fieldset[disabled] input[type="submit"].active,fieldset[disabled] button.active{background-color:#fff;border-color:#bfbfbf} .search-query{display:inline-block;padding:4px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #aaa;padding-left:14px !important;padding-right:14px !important;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto} .search-query:focus{border-color:rgba(24,132,218,0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075),0 0 8px rgba(82,168,236,0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075),0 0 8px rgba(82,168,236,0.6);outline:0;outline:thin dotted \9;} .search-spinner{position:absolute;display:none;right:6px;top:9px} diff -r 2d0bcb07596c4c688ed3908391d866831c65c042 -r 01f603a2179fce1cb39f5cfde973744585c73918 static/style/blue/sprite-fugue.png Binary file static/style/blue/sprite-fugue.png has changed diff -r 2d0bcb07596c4c688ed3908391d866831c65c042 -r 01f603a2179fce1cb39f5cfde973744585c73918 static/style/blue/sprite-history-buttons.png Binary file static/style/blue/sprite-history-buttons.png has changed diff -r 2d0bcb07596c4c688ed3908391d866831c65c042 -r 01f603a2179fce1cb39f5cfde973744585c73918 static/style/blue/sprite-history-states.png Binary file static/style/blue/sprite-history-states.png has changed diff -r 2d0bcb07596c4c688ed3908391d866831c65c042 -r 01f603a2179fce1cb39f5cfde973744585c73918 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -660,6 +660,11 @@ padding: 3px; } +input[type="submit"], button { + .btn(); + .btn-default(); +} + .search-query { display: inline-block; padding: 4px; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Plugin framework: factor out page serving responsibility, add HookPluginManager subclass and PageServingPluginManager subclass; Visualization registry: inherit from PageServingPluginManager
by commits-noreply＠bitbucket.org 18 Sep '13

18 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2d0bcb07596c/ Changeset: 2d0bcb07596c User: carlfeberhard Date: 2013-09-18 16:53:12 Summary: Plugin framework: factor out page serving responsibility, add HookPluginManager subclass and PageServingPluginManager subclass; Visualization registry: inherit from PageServingPluginManager Affected #: 8 files diff -r b5c08cc6adbb64bb8dfa20070e6df5857483bd00 -r 2d0bcb07596c4c688ed3908391d866831c65c042 config/plugins/visualizations/graphview/config/graphview.xml --- a/config/plugins/visualizations/graphview/config/graphview.xml +++ b/config/plugins/visualizations/graphview/config/graphview.xml @@ -16,5 +16,5 @@ <params><param type="dataset" var_name_in_template="hda" required="true">dataset_id</param></params> - <template>graphview/templates/graphview.mako</template> + <template>graphview.mako</template></visualization> diff -r b5c08cc6adbb64bb8dfa20070e6df5857483bd00 -r 2d0bcb07596c4c688ed3908391d866831c65c042 config/plugins/visualizations/scatterplot/config/scatterplot.xml --- a/config/plugins/visualizations/scatterplot/config/scatterplot.xml +++ b/config/plugins/visualizations/scatterplot/config/scatterplot.xml @@ -11,5 +11,5 @@ <params><param type="dataset" var_name_in_template="hda" required="true">dataset_id</param></params> - <template>scatterplot/templates/scatterplot.mako</template> + <template>scatterplot.mako</template></visualization> diff -r b5c08cc6adbb64bb8dfa20070e6df5857483bd00 -r 2d0bcb07596c4c688ed3908391d866831c65c042 lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -22,6 +22,8 @@ from galaxy.openid.providers import OpenIDProviders from galaxy.tools.data_manager.manager import DataManagers +from galaxy.web.base import pluginframework + import logging log = logging.getLogger( __name__ ) @@ -123,8 +125,11 @@ # Load genome indexer tool. load_genome_index_tools( self.toolbox ) # visualizations registry: associates resources with visualizations, controls how to render - self.visualizations_registry = VisualizationsRegistry.from_config( - self.config.visualizations_plugins_directory, self.config ) + self.visualizations_registry = None + if self.config.visualizations_plugins_directory: + self.visualizations_registry = VisualizationsRegistry( self, + directories_setting=self.config.visualizations_plugins_directory, + template_cache_dir=self.config.template_cache ) # Load security policy. self.security_agent = self.model.security_agent self.host_security_agent = galaxy.security.HostAgent( model=self.security_agent.model, permitted_actions=self.security_agent.permitted_actions ) diff -r b5c08cc6adbb64bb8dfa20070e6df5857483bd00 -r 2d0bcb07596c4c688ed3908391d866831c65c042 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -294,9 +294,7 @@ self.fluent_log = string_as_bool( kwargs.get( 'fluent_log', False ) ) self.fluent_host = kwargs.get( 'fluent_host', 'localhost' ) self.fluent_port = int( kwargs.get( 'fluent_port', 24224 ) ) - # PLUGINS: - self.plugin_frameworks = [] - # visualization framework + # visualization plugin framework self.visualizations_plugins_directory = kwargs.get( 'visualizations_plugins_directory', None ) @property diff -r b5c08cc6adbb64bb8dfa20070e6df5857483bd00 -r 2d0bcb07596c4c688ed3908391d866831c65c042 lib/galaxy/visualization/registry.py --- a/lib/galaxy/visualization/registry.py +++ b/lib/galaxy/visualization/registry.py @@ -39,9 +39,10 @@ """ # ------------------------------------------------------------------- the registry -class VisualizationsRegistry( pluginframework.PluginFramework ): +class VisualizationsRegistry( pluginframework.PageServingPluginManager ): """ 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 @@ -58,31 +59,79 @@ 'sweepster', 'phyloviz' ] - #: directories under plugin_directory that aren't plugins - non_plugin_directories = [] - def __init__( self, registry_filepath, template_cache_dir ): - super( VisualizationsRegistry, self ).__init__( registry_filepath, 'visualizations', template_cache_dir ) + def __str__( self ): + return self.__class__.__name__ + def __init__( self, app, **kwargs ): + self.config_parser = VisualizationsConfigParser() + super( VisualizationsRegistry, self ).__init__( app, 'visualizations', **kwargs ) # what to use to parse query strings into resources/vars for the template self.resource_parser = ResourceParser() log.debug( '%s loaded', str( self ) ) - def load_configuration( self ): + def is_plugin( self, plugin_path ): """ - Builds the registry by parsing the `config/*.xml` files for every plugin - in ``get_plugin_directories`` and stores the results in ``self.listings``. + Determines whether the given filesystem path contains a plugin. - ..note:: - This could be used to re-load a new configuration without restarting - the instance. + 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 """ - try: - self.listings = VisualizationsConfigParser.parse( self.get_plugin_directories() ) + # plugin_path must be a directory, have a config dir + if not os.path.isdir( plugin_path ): + return False + if not 'config' in os.listdir( plugin_path ): + return False + expected_config_filename = '%s.xml' %( os.path.split( plugin_path )[1] ) + if not os.path.isfile( os.path.join( plugin_path, 'config', expected_config_filename ) ): + return False + return True - except Exception, exc: - log.exception( 'Error parsing visualizations plugins %s', self.plugin_directories ) - raise + def load_plugin( self, plugin_path ): + """ + Create the visualization plugin object, parse its configuration file, + and return it. + + Plugin bunches are decorated with: + * config_file : the path to this visualization's config file + * config : the parsed configuration for this visualization + + :type plugin_path: string + :param plugin_path: relative or absolute filesystem path to the plugin + :rtype: ``util.bunch.Bunch`` + :returns: the loaded plugin object + """ + #TODO: possibly move this after the config parsing to allow config to override? + plugin = super( VisualizationsRegistry, self ).load_plugin( plugin_path ) + + # config file is required, otherwise skip this visualization + plugin[ 'config_file' ] = os.path.join( plugin_path, 'config', ( plugin.name + '.xml' ) ) + config = self.config_parser.parse_file( plugin.config_file ) + if not config: + return None + plugin[ 'config' ] = config + + return plugin + + # -- getting resources for visualization templates from link query strings -- + # -- building links to visualizations from objects -- + 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. + """ + #TODO:?? a list of objects? YAGNI? + 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 applicable_visualizations def get_visualization( self, trans, visualization_name, target_object ): """ @@ -90,12 +139,11 @@ `visualization_name` if it's applicable to `target_object` or `None` if it's not. """ - # a little weird to pass trans because this registry is part of the trans.app - listing_data = self.listings.get( visualization_name, None ) - if not listing_data: + visualization = self.plugins.get( visualization_name, None ) + if not visualization: return None - data_sources = listing_data[ 'data_sources' ] + data_sources = visualization.config[ 'data_sources' ] for data_source in data_sources: # currently a model class is required model_class = data_source[ 'model_class' ] @@ -109,11 +157,11 @@ param_data = data_source[ 'to_params' ] url = self.get_visualization_url( trans, target_object, visualization_name, param_data ) - link_text = listing_data.get( 'link_text', None ) + link_text = visualization.config.get( 'link_text', None ) if not link_text: # default to visualization name, titlecase, and replace underscores link_text = visualization_name.title().replace( '_', ' ' ) - render_location = listing_data.get( 'render_location' ) + render_location = visualization.config.get( 'render_location' ) # remap some of these vars for direct use in ui.js, PopupMenu (e.g. text->html) return { 'href' : url, @@ -123,25 +171,12 @@ return None - # -- building links to visualizations from objects -- - 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. - """ - #TODO:?? a list of objects? YAGNI? - applicable_visualizations = [] - for vis_name in self.listings: - url_data = self.get_visualization( trans, vis_name, target_object ) - if url_data: - applicable_visualizations.append( url_data ) - return applicable_visualizations - def is_object_applicable( self, trans, target_object, data_source_tests ): """ Run a visualization's data_source tests to find out if it 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' ] @@ -164,7 +199,6 @@ if test_fn( target_object, test_result ): #log.debug( 'test passed' ) return True - return False def get_visualization_url( self, trans, target_object, visualization_name, param_data ): @@ -219,9 +253,9 @@ Both `params` and `param_modifiers` default to an empty dictionary. """ - visualization = self.listings.get( visualization_name ) - expected_params = visualization.get( 'params', {} ) - param_modifiers = visualization.get( 'param_modifiers', {} ) + visualization = self.plugins.get( visualization_name ) + expected_params = visualization.config.get( 'params', {} ) + param_modifiers = visualization.config.get( 'param_modifiers', {} ) return ( expected_params, param_modifiers ) def query_dict_to_resources( self, trans, controller, visualization_name, query_dict ): @@ -259,13 +293,6 @@ """ VALID_RENDER_LOCATIONS = [ 'galaxy_main', '_top', '_blank' ] - @classmethod - def parse( cls, plugin_directories, debug=False ): - """ - Static class interface. - """ - return cls( debug ).parse_plugins( plugin_directories ) - def __init__( self, debug=False ): self.debug = debug @@ -274,58 +301,19 @@ self.param_parser = ParamParser() self.param_modifier_parser = ParamModifierParser() - def parse_plugins( self, plugin_directories ): - """ - Parses the config files for each plugin sub-dir in `base_path`. - - :param plugin_directories: a list of paths to enabled plugins. - - :returns: registry data in dictionary form - """ - returned = {} - for plugin_path in plugin_directories: - returned.update( self.parse_plugin( plugin_path ) ) - return returned - - def parse_plugin( self, plugin_path ): - """ - Parses any XML files in ``<plugin_path>/config``. - - If an error occurs while parsing a visualizations entry, it is skipped. - :returns: registry data in dictionary form - ..note:: - assumes config files are in a 'config' sub-dir of each plugin - """ - returned = {} - - plugin_config_path = os.path.join( plugin_path, 'config' ) - if not os.path.isdir( plugin_config_path ): - return returned - - for xml_filepath in glob.glob( os.path.join( plugin_config_path, '*.xml' ) ): - try: - visualization_name, visualization = self.parse_file( xml_filepath ) - # skip vis' with parsing errors - don't shutdown the startup - except ParsingException, parse_exc: - log.error( 'Skipped visualization config "%s" due to parsing errors: %s', - xml_filepath, str( parse_exc ), exc_info=self.debug ) - - if visualization: - returned[ visualization_name ] = visualization - log.debug( 'Visualization config loaded for: %s', visualization_name ) - - return returned - def parse_file( self, xml_filepath ): """ Parse the given XML file for visualizations data. :returns: tuple of ( `visualization_name`, `visualization` ) """ - xml_tree = galaxy.util.parse_xml( xml_filepath ) - visualization_conf = xml_tree.getroot() - visualization_name = visualization_conf.get( 'name' ) - visualization = self.parse_visualization( visualization_conf ) - return visualization_name, visualization + try: + xml_tree = galaxy.util.parse_xml( xml_filepath ) + visualization = self.parse_visualization( xml_tree.getroot() ) + return visualization + # skip vis' with parsing errors - don't shutdown the startup + except ParsingException, parse_exc: + log.exception( 'Skipped visualization config "%s" due to parsing errors', xml_filepath ) + return None def parse_visualization( self, xml_tree ): """ diff -r b5c08cc6adbb64bb8dfa20070e6df5857483bd00 -r 2d0bcb07596c4c688ed3908391d866831c65c042 lib/galaxy/web/base/pluginframework.py --- a/lib/galaxy/web/base/pluginframework.py +++ b/lib/galaxy/web/base/pluginframework.py @@ -1,150 +1,106 @@ """ Base class for plugins - frameworks or systems that may: + * add code at startup + * allow hooks to be called +and base class for plugins that: * serve static content * serve templated html * have some configuration at startup """ import os.path -import glob import sys +import imp import pkg_resources pkg_resources.require( 'MarkupSafe' ) pkg_resources.require( 'Mako' ) import mako -from galaxy.util import listify +from galaxy import util +from galaxy.util import odict +from galaxy.util import bunch import logging log = logging.getLogger( __name__ ) # ============================================================================= exceptions -class PluginFrameworkException( Exception ): +class PluginManagerException( Exception ): """Base exception for plugin frameworks. """ pass -class PluginFrameworkConfigException( PluginFrameworkException ): +class PluginManagerConfigException( PluginManagerException ): """Exception for plugin framework configuration errors. """ pass -class PluginFrameworkStaticException( PluginFrameworkException ): - """Exception for plugin framework static directory set up errors. - """ - pass -class PluginFrameworkTemplateException( PluginFrameworkException ): - """Exception for plugin framework template directory - and template rendering errors. - """ - pass # ============================================================================= base -class PluginFramework( object ): +class PluginManager( object ): """ - Plugins are files/directories living outside the Galaxy ``lib`` directory - that serve static files (css, js, images, etc.), use and serve mako templates, - and have some configuration to control the rendering. + Plugins represents an section of code that is not tracked in the + Galaxy repository, allowing the addition of custom code to a Galaxy + installation without changing the code base. - A plugin framework sets up all the above components. + A PluginManager discovers and manages these plugins. + + This is an non-abstract class but it's usefulness is limited and is meant + to be inherited. """ - #: does the class need a config file(s) to be parsed? - has_config = True - #: does the class need static files served? - serves_static = True - #: does the class need template files served? - serves_templates = True - #TODO: allow plugin mako inheritance from existing ``/templates`` files - #uses_galaxy_templates = True - #TODO: possibly better as instance var (or a combo) - #: the directories in ``plugin_directory`` with basenames listed here will - #: be ignored for config, static, and templates - non_plugin_directories = [] - # ------------------------------------------------------------------------- setup - @classmethod - def from_config( cls, config_plugin_directory, config ): + def __init__( self, app, directories_setting=None, skip_bad_plugins=True, **kwargs ): """ - Set up the framework based on data from some config object by: - * constructing it's absolute plugin_directory filepath - * getting a template_cache - * and appending itself to the config object's ``plugin_frameworks`` list + Set up the manager and load all plugins. - .. note:: - precondition: config obj should have attributes: - root, template_cache, and (list) plugin_frameworks + :type app: UniverseApplication + :param app: the application (and it's configuration) using this manager + :type directories_setting: string (default: None) + :param directories_setting: the filesystem path (or paths) + to search for plugins. Can be CSV string of paths. Will be treated as + absolute if a path starts with '/', relative otherwise. + :type skip_bad_plugins: boolean (default: True) + :param skip_bad_plugins: whether to skip plugins that cause + exceptions when loaded or to raise that exception """ - # currently called from (base) app.py - defined here to allow override if needed - if not config_plugin_directory: - return None - try: - # create the plugin path and if plugin dir begins with '/' assume absolute path - full_plugin_filepath = os.path.join( config.root, config_plugin_directory ) - if config_plugin_directory.startswith( os.path.sep ): - full_plugin_filepath = config_plugin_directory - if not os.path.exists( full_plugin_filepath ): - raise PluginFrameworkException( 'Plugin path not found: %s' %( full_plugin_filepath ) ) + log.debug( 'PluginManager.init: %s, %s', directories_setting, kwargs ) + self.directories = [] + self.skip_bad_plugins = skip_bad_plugins + self.plugins = odict.odict() - template_cache = config.template_cache if cls.serves_static else None - plugin = cls( full_plugin_filepath, template_cache ) + self.directories = self.parse_directories_setting( app.config.root, directories_setting ) + #log.debug( '\t directories: %s', self.directories ) - config.plugin_frameworks.append( plugin ) - return plugin + self.load_configuration() + self.load_plugins() - except PluginFrameworkException, plugin_exc: - log.exception( "Error loading framework %s. Skipping...", cls.__class__.__name__ ) - return None + def parse_directories_setting( self, galaxy_root, directories_setting ): + """ + Parse the ``directories_setting`` into a list of relative or absolute + filesystem paths that will be searched to discover plugins. - def __str__( self ): - return '%s(%s)' %( self.__class__.__name__, self.plugin_directories ) + :type galaxy_root: string + :param galaxy_root: the root path of this galaxy installation + :type directories_setting: string (default: None) + :param directories_setting: the filesystem path (or paths) + to search for plugins. Can be CSV string of paths. Will be treated as + absolute if a path starts with '/', relative otherwise. + :rtype: list of strings + :returns: list of filesystem paths + """ + directories = [] + if not directories_setting: + return directories - def __init__( self, plugin_directories, name=None, template_cache_dir=None, debug=False, assert_exists=True ): - """ - :type plugin_directories: string or list - :param plugin_directories: the base directory where plugin code is kept - :type name: (optional) string (default: None) - :param name: the name of this plugin - (that will appear in url pathing, etc.) - :type template_cache_dir: (optional) string (default: None) - :param template_cache_dir: the cache directory to store compiled mako - :type assert_exists: (optional) bool (default: False) - :param assert_exists: If True, each configured plugin directory must exist. - """ - self.plugin_directories = listify( plugin_directories ) - if assert_exists: - for plugin_directory in self.plugin_directories: - if not os.path.isdir( plugin_directory ): - raise PluginFrameworkException( 'Framework plugin directory not found: %s, %s' - % ( self.__class__.__name__, plugin_directory ) ) + for directory in util.listify( directories_setting ): + directory = directory.strip() + if directory.startswith( '/' ): + directory = os.path.join( galaxy_root, directory ) + if not os.path.exists( directory ): + log.warn( '%s, directory not found: %s', self, directory ) + continue + directories.append( directory ) + return directories - #TODO: or pass in from config - self.name = name or os.path.basename( self.plugin_directories[0] ) - - if self.has_config: - self.load_configuration() - # set_up_static_urls will be called during the static middleware creation (if serves_static) - if self.serves_templates: - self.set_up_templates( template_cache_dir ) - - def get_plugin_directories( self ): - """ - Return the plugin directory paths for this plugin. - - Gets any directories within ``plugin_directory`` that are directories - themselves and whose ``basename`` is not in ``plugin_directory``. - """ - # could instead explicitly list on/off in master config file - for plugin_directory in self.plugin_directories: - for plugin_path in glob.glob( os.path.join( plugin_directory, '*' ) ): - if not os.path.isdir( plugin_path ): - continue - - if os.path.basename( plugin_path ) in self.non_plugin_directories: - continue - - yield plugin_path - - # ------------------------------------------------------------------------- config def load_configuration( self ): """ Override to load some framework/plugin specifc configuration. @@ -152,6 +108,348 @@ # Abstract method return True + def load_plugins( self ): + """ + Search ``self.directories`` for potential plugins, load them, and cache + in ``self.plugins``. + :rtype: odict + :returns: ``self.plugins`` + """ + for plugin_path in self.find_plugins(): + try: + plugin = self.load_plugin( plugin_path ) + if not plugin: + log.warn( '%s, plugin load failed: %s. Skipping...', self, plugin_path ) + #NOTE: prevent silent, implicit overwrite here (two plugins in two diff directories) + #TODO: overwriting may be desired + elif plugin.name in self.plugins: + log.warn( '%s, plugin with name already exists: %s. Skipping...', self, plugin.name ) + else: + self.plugins[ plugin.name ] = plugin + log.info( '%s, loaded plugin: %s', self, plugin.name ) + + except Exception, exc: + 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 os.listdir( directory ): + plugin_path = os.path.join( directory, plugin_dir ) + if self.is_plugin( plugin_path ): + yield plugin_path + + 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 + """ + if not os.path.isdir( plugin_path ): + return False + return True + + def load_plugin( self, plugin_path ): + """ + Create, load, and/or initialize the plugin and return it. + + Plugin bunches are decorated with: + * name : the plugin name + * path : the plugin path + + :type plugin_path: string + :param plugin_path: relative or absolute filesystem path to the plugin + :rtype: ``util.bunch.Bunch`` + :returns: the loaded plugin object + """ + plugin = bunch.Bunch( + #TODO: need a better way to define plugin names + # pro: filesystem name ensures uniqueness + # con: rel. inflexible + name = os.path.split( plugin_path )[1], + path = plugin_path + ) + return plugin + + +# ============================================================================= plugin managers using hooks +class HookPluginManager( PluginManager ): + """ + A hook plugin is a directory containing python modules or packages that: + * allow creating, including, and running custom code at specific 'hook' + points/events + * are not tracked in the Galaxy repository and allow adding custom code + to a Galaxy installation + + A HookPluginManager imports the plugin code needed and calls the plugin's + hook functions at the specified time. + """ + #: the python file that will be imported - hook functions should be contained here + loading_point_filename = 'plugin.py' + hook_fn_prefix = 'hook_' + + def is_plugin( self, plugin_path ): + """ + Determines whether the given filesystem path contains a hookable plugin. + + All sub-directories that contain ``loading_point_filename`` 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 + """ + if not super( HookPluginManager, self ).is_plugin( plugin_path ): + return False + #TODO: possibly switch to <plugin.name>.py or __init__.py + if self.loading_point_filename not in os.listdir( plugin_path ): + return False + return True + + def load_plugin( self, plugin_path ): + """ + Import the plugin ``loading_point_filename`` and attach to the plugin bunch. + + Plugin bunches are decorated with: + * name : the plugin name + * path : the plugin path + * module : the plugin code + + :type plugin_path: string + :param plugin_path: relative or absolute filesystem path to the plugin + :rtype: ``util.bunch.Bunch`` + :returns: the loaded plugin object + """ + plugin = super( HookPluginManager, self ).load_plugin( plugin_path ) + + loading_point_name = self.loading_point_filename[:-3] + plugin[ 'module' ] = self.import_plugin_module( loading_point_name, plugin ) + return plugin + + def import_plugin_module( self, loading_point_name, plugin, import_as=None ): + """ + Import the plugin code and cache the module in the plugin object. + + :type loading_point_name: string + :param loading_point_name: name of the python file to import (w/o extension) + :type plugin: ``util.bunch.Bunch`` + :param plugin: the plugin containing the template to render + :type import_as: string + :param import_as: namespace to use for imported module + This will be prepended with the ``__name__`` of this file. + Defaults to ``plugin.name`` + :rtype: ``util.bunch.Bunch`` + :returns: the loaded plugin object + """ + # add this name to import_as (w/ default to plugin.name) to prevent namespace pollution in sys.modules + import_as = '%s.%s' %( __name__, ( import_as or plugin.name ) ) + module_file, pathname, description = imp.find_module( loading_point_name, [ plugin.path ] ) + try: + #TODO: hate this hack but only way to get package imports inside the plugin to work? + sys.path.append( plugin.path ) + # sys.modules will now have import_as in it's list + module = imp.load_module( import_as, module_file, pathname, description ) + finally: + module_file.close() + if plugin.path in sys.path: + sys.path.remove( plugin.path ) + return module + + def run_hook( self, hook_name, *args, **kwargs ): + """ + Search all plugins for a function named ``hook_fn_prefix`` + ``hook_name`` + and run it passing in args and kwargs. + + :type hook_name: string + :param hook_name: name (suffix) of the hook to run + :rtype: 2-tuple containing (list, dict) + :returns: (possibly modified) args, kwargs + """ + #TODO: is hook prefix necessary? + #TODO: could be made more efficient if cached by hook_name in the manager on load_plugin + # (low maint. overhead since no dynamic loading/unloading of plugins) + hook_fn_name = ''.join([ self.hook_fn_prefix, hook_name ]) + for plugin_name, plugin in self.plugins.items(): + hook_fn = getattr( plugin.module, hook_fn_name, None ) + + if hook_fn and hasattr( hook_fn, '__call__' ): + try: + #log.debug( 'calling %s from %s(%s)', hook_fn.func_name, plugin.name, plugin.module ) + hook_fn( *args, **kwargs ) + except Exception, exc: + # fail gracefully and continue with other plugins + log.exception( 'Hook function "%s" failed for plugin "%s"', hook_name, plugin.name ) + + # may have been altered by hook fns, return in order to act like filter + return args, kwargs + + +# ============================================================================= exceptions +class PluginManagerStaticException( PluginManagerException ): + """Exception for plugin framework static directory set up errors. + """ + pass +class PluginManagerTemplateException( PluginManagerException ): + """Exception for plugin framework template directory + and template rendering errors. + """ + pass + + +# ============================================================================= base +class PageServingPluginManager( PluginManager ): + """ + Page serving plugins are files/directories that: + * are not tracked in the Galaxy repository and allow adding custom code + to a Galaxy installation + * serve static files (css, js, images, etc.), + * render templates + + A PageServingPluginManager sets up all the above components. + """ + #TODO: I'm unclear of the utility of this class - it prob. will only have one subclass (vis reg). Fold into? + + #: does the class need static files served? + serves_static = True + #: does the class need template files served? + serves_templates = True + #: default number of templates to search for plugin template lookup + DEFAULT_TEMPLATE_COLLECTION_SIZE = 10 + #: default encoding of plugin templates + DEFAULT_TEMPLATE_ENCODING = 'utf-8' + + def __init__( self, app, base_url, template_cache_dir=None, **kwargs ): + """ + Set up the manager and load all plugins. + + :type app: UniverseApplication + :param app: the application (and it's 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.base_url = base_url + self.template_cache_dir = template_cache_dir + + super( PageServingPluginManager, self ).__init__( app, **kwargs ) + + def is_plugin( self, plugin_path ): + """ + Determines whether the given filesystem path contains a plugin. + + If the manager ``serves_templates`` and a sub-directory contains another + sub-directory named 'templates' it's considered valid. + If the manager ``serves_static`` and a sub-directory contains another + sub-directory named 'static' it's considered valid. + + :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 + """ + if not os.path.isdir( plugin_path ): + return False + #TODO: this is not reliable and forces the inclusion of empty dirs in some situations + if self.serves_templates and not 'templates' in os.listdir( plugin_path ): + return False + if self.serves_static and not 'static' in os.listdir( plugin_path ): + return False + return True + + def load_plugin( self, plugin_path ): + """ + Create the plugin and decorate with static and/or template paths and urls. + + Plugin bunches are decorated with: + * name : the plugin name + * path : the plugin path + * base_url : a url to the plugin + + :type plugin_path: string + :param plugin_path: relative or absolute filesystem path to the plugin + :rtype: ``util.bunch.Bunch`` + :returns: the loaded plugin object + """ + plugin = super( PageServingPluginManager, self ).load_plugin( plugin_path ) + #TODO: urlencode? + plugin[ 'base_url' ] = '/'.join([ self.base_url, plugin.name ]) + plugin = self._set_up_static_plugin( plugin ) + plugin = self._set_up_template_plugin( plugin ) + + return plugin + + def _set_up_static_plugin( self, plugin ): + """ + Decorate the plugin with paths and urls needed to serve static content. + + Plugin bunches are decorated with: + * serves_static : whether this plugin will serve static content + + If the plugin path contains a 'static' sub-dir, the following are added: + * static_path : the filesystem path to the static content + * static_url : the url to use when serving static content + + :type plugin: ``util.bunch.Bunch`` + :param plugin: the plugin to decorate + :rtype: ``util.bunch.Bunch`` + :returns: the loaded plugin object + """ + plugin[ 'serves_static' ] = False + static_path = os.path.join( plugin.path, 'static' ) + if self.serves_static and os.path.isdir( static_path ): + plugin.serves_static = True + plugin[ 'static_path' ] = static_path + plugin[ 'static_url' ] = '/'.join([ plugin.base_url, 'static' ]) + return plugin + + def _set_up_template_plugin( self, plugin ): + """ + Decorate the plugin with paths needed to fill templates. + + Plugin bunches are decorated with: + * serves_templates : whether this plugin will use templates + + If the plugin path contains a 'static' sub-dir, the following are added: + * template_path : the filesystem path to the template sub-dir + * template_lookup : the (currently Mako) TemplateLookup used to search + for templates + + :type plugin: ``util.bunch.Bunch`` + :param plugin: the plugin to decorate + :rtype: ``util.bunch.Bunch`` + :returns: the loaded plugin object + """ + plugin[ 'serves_templates' ] = False + template_path = os.path.join( plugin.path, 'templates' ) + if self.serves_templates and os.path.isdir( template_path ): + plugin.serves_templates = True + plugin[ 'template_path' ] = template_path + plugin[ 'template_lookup' ] = self.build_plugin_template_lookup( plugin ) + return plugin + # ------------------------------------------------------------------------- serving static files def get_static_urls_and_paths( self ): """ @@ -160,81 +458,63 @@ same files. Meant to be passed to a Static url map. + + :rtype: list of 2-tuples + :returns: all urls and paths for each plugin serving static content """ - url_and_paths = [] # called during the static middleware creation (buildapp.py, wrap_in_static) - - # NOTE: this only searches for static dirs two levels deep (i.e. <plugin_directory>/<plugin-name>/static) - for plugin_path in self.get_plugin_directories(): - # that path is a plugin, search for subdirs named static in THAT dir - plugin_static_path = os.path.join( plugin_path, 'static' ) - if not os.path.isdir( plugin_static_path ): - continue - - # build a url for that static subdir and create a Static urlmap entry for it - plugin_name = os.path.splitext( os.path.basename( plugin_path ) )[0] - plugin_url = self.name + '/' + plugin_name + '/static' - url_and_paths.append( ( plugin_url, plugin_static_path ) ) - - return url_and_paths + urls_and_paths = [] + for plugin in self.plugins.values(): + if plugin.serves_static: + urls_and_paths.append( ( plugin.static_url, plugin.static_path ) ) + return urls_and_paths # ------------------------------------------------------------------------- templates - def set_up_templates( self, template_cache_dir ): + def build_plugin_template_lookup( self, plugin ): """ - Add a ``template_lookup`` attribute to the framework that can be passed - to the mako renderer to find templates. + Builds the object that searches for templates (cached or not) when rendering. + + :type plugin: ``util.bunch.Bunch`` + :param plugin: the plugin containing the templates + :rtype: ``Mako.lookup.TemplateLookup`` + :returns: template lookup for this plugin """ - if not template_cache_dir: - raise PluginFrameworkTemplateException( 'Plugins that serve templates require a template_cache_dir' ) - self.template_lookup = self._create_mako_template_lookup( template_cache_dir, self._get_template_paths() ) - return self.template_lookup + if not plugin.serves_templates: + return None + template_lookup = self._create_mako_template_lookup( self.template_cache_dir, plugin.template_path ) + return template_lookup - def _get_template_paths( self ): - """ - Get the paths that will be searched for templates. - """ - return self.plugin_directories - - def _create_mako_template_lookup( self, cache_dir, paths, collection_size=500, output_encoding='utf-8' ): + def _create_mako_template_lookup( self, cache_dir, paths, + collection_size=DEFAULT_TEMPLATE_COLLECTION_SIZE, output_encoding=DEFAULT_TEMPLATE_ENCODING ): """ Create a ``TemplateLookup`` with defaults. + + :rtype: ``Mako.lookup.TemplateLookup`` + :returns: all urls and paths for each plugin serving static content """ + #TODO: possible to add galaxy/templates into the lookup here? return mako.lookup.TemplateLookup( directories = paths, module_directory = cache_dir, collection_size = collection_size, output_encoding = output_encoding ) - #TODO: do we want to remove trans and app from the plugin template context? - def fill_template( self, trans, template_filename, **kwargs ): + def fill_template( self, trans, plugin, template_filename, **kwargs ): """ - Pass control over to trans and render the ``template_filename``. + Pass control over to trans and render ``template_filename``. + + :type trans: ``galaxy.web.framework.GalaxyWebTransaction`` + :param trans: transaction doing the rendering + :type plugin: ``util.bunch.Bunch`` + :param plugin: the plugin containing the template to render + :type template_filename: string + :param template_filename: the path of the template to render relative to + ``plugin.template_path`` + :returns: rendered template """ # defined here to be overridden - return trans.fill_template( template_filename, template_lookup=self.template_lookup, **kwargs ) + return trans.fill_template( template_filename, template_lookup=plugin.template_lookup, **kwargs ) - def fill_template_with_plugin_imports( self, trans, template_filename, **kwargs ): - """ - Returns a rendered plugin template but allows importing modules from inside - the plugin directory within the template. - - ..example:: I.e. given this layout for a plugin: - bler/ - template/ - bler.mako - static/ - conifg/ - my_script.py - this version of `fill_template` allows `bler.mako` to call `import my_script`. - """ - try: - plugin_path = os.path.dirname( os.path.dirname( template_filename ) ) - sys.path.append( plugin_path ) - filled_template = self.fill_template( trans, template_filename, **kwargs ) - - finally: - sys.path.remove( plugin_path ) - - return filled_template - - #TODO: could add plugin template helpers here + #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 diff -r b5c08cc6adbb64bb8dfa20070e6df5857483bd00 -r 2d0bcb07596c4c688ed3908391d866831c65c042 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -193,7 +193,8 @@ if kwargs.get( 'middleware', True ): webapp = wrap_in_middleware( webapp, global_conf, **kwargs ) if asbool( kwargs.get( 'static_enabled', True ) ): - webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=app.config.plugin_frameworks, **kwargs ) + webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=[ app.visualizations_registry ], **kwargs ) + #webapp = wrap_in_static( webapp, global_conf, plugin_frameworks=None, **kwargs ) if asbool(kwargs.get('pack_scripts', False)): pack_scripts() # Close any pooled database connections before forking @@ -362,12 +363,13 @@ # wrap any static dirs for plugins plugin_frameworks = plugin_frameworks or [] - for static_serving_framework in ( framework for framework in plugin_frameworks if framework.serves_static ): - # invert control to each plugin for finding their own static dirs - for plugin_url, plugin_static_path in static_serving_framework.get_static_urls_and_paths(): - plugin_url = '/plugins/' + plugin_url - urlmap[( plugin_url )] = Static( plugin_static_path, cache_time ) - log.debug( 'added url, path to static middleware: %s, %s', plugin_url, plugin_static_path ) + for framework in plugin_frameworks: + if framework and framework.serves_static: + # invert control to each plugin for finding their own static dirs + for plugin_url, plugin_static_path in framework.get_static_urls_and_paths(): + plugin_url = '/plugins/' + plugin_url + urlmap[( plugin_url )] = Static( plugin_static_path, cache_time ) + log.debug( 'added url, path to static middleware: %s, %s', plugin_url, plugin_static_path ) # URL mapper becomes the root webapp return urlmap diff -r b5c08cc6adbb64bb8dfa20070e6df5857483bd00 -r 2d0bcb07596c4c688ed3908391d866831c65c042 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -698,10 +698,10 @@ registry = trans.app.visualizations_registry if not registry: raise HTTPNotFound( 'No visualization registry (possibly disabled in universe_wsgi.ini)' ) - if visualization_name not in registry.listings: + if visualization_name not in registry.plugins: raise HTTPNotFound( 'Unknown or invalid visualization: ' + visualization_name ) # or redirect to list? - registry_listing = registry.listings[ visualization_name ] + plugin = registry.plugins[ visualization_name ] returned = None try: @@ -711,8 +711,8 @@ resources = registry.query_dict_to_resources( trans, self, visualization_name, kwargs ) # look up template and render - template_path = registry_listing[ 'template' ] - returned = registry.fill_template( trans, template_path, + template_path = plugin.config[ 'template' ] + returned = registry.fill_template( trans, plugin, template_path, visualization_name=visualization_name, query_args=kwargs, embedded=embedded, shared_vars={}, **resources ) #NOTE: passing *unparsed* kwargs as query_args Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Typo in toolshed util common.
by commits-noreply＠bitbucket.org 17 Sep '13

17 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b5c08cc6adbb/ Changeset: b5c08cc6adbb User: dannon Date: 2013-09-17 23:31:16 Summary: Typo in toolshed util common. Affected #: 1 file diff -r 1e664910d749be12d6f0ece29028f18b820476a1 -r b5c08cc6adbb64bb8dfa20070e6df5857483bd00 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1186,7 +1186,7 @@ encoded_tool_shed_status_dict = common_util.tool_shed_get( app, tool_shed_url, url ) tool_shed_status_dict = encoding_util.tool_shed_decode( encoded_tool_shed_status_dict ) except Exception, e: - log.exception( "Error attemtping to get tool shed status for installed repository %s: %s" % ( str( repository.name ), str( e ) ) ) + log.exception( "Error attempting to get tool shed status for installed repository %s: %s" % ( str( repository.name ), str( e ) ) ) return {} return tool_shed_status_dict Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 17 Sep '13

17 Sep '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1c9adf19f128/ Changeset: 1c9adf19f128 User: mdshw5 Date: 2013-09-04 16:42:56 Summary: fixed it's > its typos Affected #: 1 file diff -r b9da077a79c3ce0323bd8f8e5aed3e311d1fd8ae -r 1c9adf19f12813b9802e84bbde73ca1e7758a498 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -1,4 +1,3 @@ - <%def name="common_javascripts(repository)"><script type="text/javascript"> $(function(){ @@ -180,7 +179,7 @@ ${repository_type | h} %if render_help: <div class="toolParamHelp" style="clear: both;"> - This repository's type cannot be changed because it's contents are valid only for it's current type or it has been cloned. + This repository's type cannot be changed because its contents are valid only for its current type or it has been cloned. </div> %endif %else: https://bitbucket.org/galaxy/galaxy-central/commits/1e664910d749/ Changeset: 1e664910d749 User: dannon Date: 2013-09-17 22:46:32 Summary: Merged in mdshw5/galaxy-central-toolshed-typos (pull request #210) fixed it's > its typos Affected #: 1 file diff -r 47798b37aed096b344c43c6796b7aae27ef11e90 -r 1e664910d749be12d6f0ece29028f18b820476a1 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -1,4 +1,3 @@ - <%def name="common_javascripts(repository)"><script type="text/javascript"> $(function(){ @@ -180,7 +179,7 @@ ${repository_type | h} %if render_help: <div class="toolParamHelp" style="clear: both;"> - This repository's type cannot be changed because it's contents are valid only for it's current type or it has been cloned. + This repository's type cannot be changed because its contents are valid only for its current type or it has been cloned. </div> %endif %else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 17 Sep '13

17 Sep '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/edc5e6ad3d54/ Changeset: edc5e6ad3d54 User: james_taylor Date: 2013-09-11 22:24:44 Summary: style: use link color for active bg, update tooltip JS Affected #: 5 files diff -r 6cf5d0cbaf96c9910b7e72a83f16d5c6a9f2f34a -r edc5e6ad3d544c47457aaf135c7956d9ac0ab32b static/scripts/libs/bootstrap.js --- a/static/scripts/libs/bootstrap.js +++ b/static/scripts/libs/bootstrap.js @@ -1,8 +1,63 @@ +/* ======================================================================== + * Bootstrap: transition.js v3.0.0 + * http://twbs.github.com/bootstrap/javascript.html#transitions + * ======================================================================== + * Copyright 2013 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ======================================================================== */ -/* =================================================== - * bootstrap-transition.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#transitions - * =================================================== + ++function ($) { "use strict"; + + // CSS TRANSITION SUPPORT (Shoutout: http://www.modernizr.com/) + // ============================================================ + + function transitionEnd() { + var el = document.createElement('bootstrap') + + var transEndEventNames = { + 'WebkitTransition' : 'webkitTransitionEnd' + , 'MozTransition' : 'transitionend' + , 'OTransition' : 'oTransitionEnd otransitionend' + , 'transition' : 'transitionend' + } + + for (var name in transEndEventNames) { + if (el.style[name] !== undefined) { + return { end: transEndEventNames[name] } + } + } + } + + // http://blog.alexmaccaw.com/css-transitions + $.fn.emulateTransitionEnd = function (duration) { + var called = false, $el = this + $(this).one($.support.transition.end, function () { called = true }) + var callback = function () { if (!called) $($el).trigger($.support.transition.end) } + setTimeout(callback, duration) + return this + } + + $(function () { + $.support.transition = transitionEnd() + }) + +}(window.jQuery); +/* ======================================================================== + * Bootstrap: tab.js v3.0.0 + * http://twbs.github.com/bootstrap/javascript.html#tabs + * ======================================================================== * Copyright 2012 Twitter, Inc. * * Licensed under the Apache License, Version 2.0 (the "License"); @@ -16,55 +71,129 @@ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. - * ========================================================== */ + * ======================================================================== */ -!function ($) { ++function ($) { "use strict"; - $(function () { + // TAB CLASS DEFINITION + // ==================== - "use strict"; // jshint ;_; + var Tab = function (element) { + this.element = $(element) + } + Tab.prototype.show = function () { + var $this = this.element + var $ul = $this.closest('ul:not(.dropdown-menu)') + var selector = $this.attr('data-target') - /* CSS TRANSITION SUPPORT (http://www.modernizr.com/) - * ======================================================= */ + if (!selector) { + selector = $this.attr('href') + selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + } - $.support.transition = (function () { + if ($this.parent('li').hasClass('active')) return - var transitionEnd = (function () { + var previous = $ul.find('.active:last a')[0] + var e = $.Event('show.bs.tab', { + relatedTarget: previous + }) - var el = document.createElement('bootstrap') - , transEndEventNames = { - 'WebkitTransition' : 'webkitTransitionEnd' - , 'MozTransition' : 'transitionend' - , 'OTransition' : 'oTransitionEnd' - , 'msTransition' : 'MSTransitionEnd' - , 'transition' : 'transitionend' - } - , name + $this.trigger(e) - for (name in transEndEventNames){ - if (el.style[name] !== undefined) { - return transEndEventNames[name] - } - } + if (e.isDefaultPrevented()) return - }()) + var $target = $(selector) - return transitionEnd && { - end: transitionEnd + this.activate($this.parent('li'), $ul) + this.activate($target, $target.parent(), function () { + $this.trigger({ + type: 'shown.bs.tab' + , relatedTarget: previous + }) + }) + } + + Tab.prototype.activate = function (element, container, callback) { + var $active = container.find('> .active') + var transition = callback + && $.support.transition + && $active.hasClass('fade') + + function next() { + $active + .removeClass('active') + .find('> .dropdown-menu > .active') + .removeClass('active') + + element.addClass('active') + + if (transition) { + element[0].offsetWidth // reflow for transition + element.addClass('in') + } else { + element.removeClass('fade') } - })() + if (element.parent('.dropdown-menu')) { + element.closest('li.dropdown').addClass('active') + } + callback && callback() + } + + transition ? + $active + .one($.support.transition.end, next) + .emulateTransitionEnd(150) : + next() + + $active.removeClass('in') + } + + + // TAB PLUGIN DEFINITION + // ===================== + + var old = $.fn.tab + + $.fn.tab = function ( option ) { + return this.each(function () { + var $this = $(this) + var data = $this.data('bs.tab') + + if (!data) $this.data('bs.tab', (data = new Tab(this))) + if (typeof option == 'string') data[option]() + }) + } + + $.fn.tab.Constructor = Tab + + + // TAB NO CONFLICT + // =============== + + $.fn.tab.noConflict = function () { + $.fn.tab = old + return this + } + + + // TAB DATA-API + // ============ + + $(document).on('click.bs.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) { + e.preventDefault() + $(this).tab('show') }) }(window.jQuery); - -/* ======================================================== - * bootstrap-tab.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#tabs - * ======================================================== +/* ======================================================================== + * Bootstrap: tooltip.js v3.0.0 + * http://twbs.github.com/bootstrap/javascript.html#tooltip + * Inspired by the original jQuery.tipsy by Jason Frame + * ======================================================================== * Copyright 2012 Twitter, Inc. * * Licensed under the Apache License, Version 2.0 (the "License"); @@ -78,452 +207,371 @@ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. - * ======================================================== */ + * ======================================================================== */ -!function ($) { ++function ($) { "use strict"; - "use strict"; // jshint ;_; + // TOOLTIP PUBLIC CLASS DEFINITION + // =============================== + var Tooltip = function (element, options) { + this.type = + this.options = + this.enabled = + this.timeout = + this.hoverState = + this.$element = null - /* TAB CLASS DEFINITION - * ==================== */ - - var Tab = function ( element ) { - this.element = $(element) + this.init('tooltip', element, options) } - Tab.prototype = { + Tooltip.DEFAULTS = { + animation: true + , placement: 'top' + , selector: false + , template: '<div class="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>' + , trigger: 'hover focus' + , title: '' + , delay: 0 + , html: false + , container: 'body' + } - constructor: Tab + Tooltip.prototype.init = function (type, element, options) { + this.enabled = true + this.type = type + this.$element = $(element) + this.options = this.getOptions(options) - , show: function () { - var $this = this.element - , $ul = $this.closest('ul:not(.dropdown-menu)') - , selector = $this.attr('data-target') - , previous - , $target - , e + var triggers = this.options.trigger.split(' ') - if (!selector) { - selector = $this.attr('href') - selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + for (var i = triggers.length; i--;) { + var trigger = triggers[i] + + if (trigger == 'click') { + this.$element.on('click.' + this.type, this.options.selector, $.proxy(this.toggle, this)) + } else if (trigger != 'manual') { + var eventIn = trigger == 'hover' ? 'mouseenter' : 'focus' + var eventOut = trigger == 'hover' ? 'mouseleave' : 'blur' + + this.$element.on(eventIn + '.' + this.type, this.options.selector, $.proxy(this.enter, this)) + this.$element.on(eventOut + '.' + this.type, this.options.selector, $.proxy(this.leave, this)) } + } - if ( $this.parent('li').hasClass('active') ) return + this.options.selector ? + (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) : + this.fixTitle() + } - previous = $ul.find('.active a').last()[0] + Tooltip.prototype.getDefaults = function () { + return Tooltip.DEFAULTS + } - e = $.Event('show', { - relatedTarget: previous - }) + Tooltip.prototype.getOptions = function (options) { + options = $.extend({}, this.getDefaults(), this.$element.data(), options) - $this.trigger(e) + if (options.delay && typeof options.delay == 'number') { + options.delay = { + show: options.delay + , hide: options.delay + } + } + + return options + } + + Tooltip.prototype.getDelegateOptions = function () { + var options = {} + var defaults = this.getDefaults() + + this._options && $.each(this._options, function (key, value) { + if (defaults[key] != value) options[key] = value + }) + + return options + } + + Tooltip.prototype.enter = function (obj) { + var self = obj instanceof this.constructor ? + obj : $(obj.currentTarget)[this.type](this.getDelegateOptions()).data('bs.' + this.type) + + clearTimeout(self.timeout) + + self.hoverState = 'in' + + if (!self.options.delay || !self.options.delay.show) return self.show() + + self.timeout = setTimeout(function () { + if (self.hoverState == 'in') self.show() + }, self.options.delay.show) + } + + Tooltip.prototype.leave = function (obj) { + var self = obj instanceof this.constructor ? + obj : $(obj.currentTarget)[this.type](this.getDelegateOptions()).data('bs.' + this.type) + + clearTimeout(self.timeout) + + self.hoverState = 'out' + + if (!self.options.delay || !self.options.delay.hide) return self.hide() + + self.timeout = setTimeout(function () { + if (self.hoverState == 'out') self.hide() + }, self.options.delay.hide) + } + + Tooltip.prototype.show = function () { + var e = $.Event('show.bs.'+ this.type) + + if (this.hasContent() && this.enabled) { + this.$element.trigger(e) if (e.isDefaultPrevented()) return - $target = $(selector) + var $tip = this.tip() - this.activate($this.parent('li'), $ul) - this.activate($target, $target.parent(), function () { - $this.trigger({ - type: 'shown' - , relatedTarget: previous - }) - }) - } + this.setContent() - , activate: function ( element, container, callback) { - var $active = container.find('> .active') - , transition = callback - && $.support.transition - && $active.hasClass('fade') + if (this.options.animation) $tip.addClass('fade') - function next() { - $active - .removeClass('active') - .find('> .dropdown-menu > .active') - .removeClass('active') + var placement = typeof this.options.placement == 'function' ? + this.options.placement.call(this, $tip[0], this.$element[0]) : + this.options.placement - element.addClass('active') + var autoToken = /\s?auto?\s?/i + var autoPlace = autoToken.test(placement) + if (autoPlace) placement = placement.replace(autoToken, '') || 'top' - if (transition) { - element[0].offsetWidth // reflow for transition - element.addClass('in') - } else { - element.removeClass('fade') - } + $tip + .detach() + .css({ top: 0, left: 0, display: 'block' }) + .addClass(placement) - if ( element.parent('.dropdown-menu') ) { - element.closest('li.dropdown').addClass('active') - } + this.options.container ? $tip.appendTo(this.options.container) : $tip.insertAfter(this.$element) - callback && callback() + var pos = this.getPosition() + var actualWidth = $tip[0].offsetWidth + var actualHeight = $tip[0].offsetHeight + + if (autoPlace) { + var $parent = this.$element.parent() + + var orgPlacement = placement + var docScroll = document.documentElement.scrollTop || document.body.scrollTop + var parentWidth = this.options.container == 'body' ? window.innerWidth : $parent.outerWidth() + var parentHeight = this.options.container == 'body' ? window.innerHeight : $parent.outerHeight() + var parentLeft = this.options.container == 'body' ? 0 : $parent.offset().left + + placement = placement == 'bottom' && pos.top + pos.height + actualHeight - docScroll > parentHeight ? 'top' : + placement == 'top' && pos.top - docScroll - actualHeight < 0 ? 'bottom' : + placement == 'right' && pos.right + actualWidth > parentWidth ? 'left' : + placement == 'left' && pos.left - actualWidth < parentLeft ? 'right' : + placement + + $tip + .removeClass(orgPlacement) + .addClass(placement) } - transition ? - $active.one($.support.transition.end, next) : - next() + var calculatedOffset = this.getCalculatedOffset(placement, pos, actualWidth, actualHeight) - $active.removeClass('in') + this.applyPlacement(calculatedOffset, placement) + this.$element.trigger('shown.bs.' + this.type) } } + Tooltip.prototype.applyPlacement = function(offset, placement) { + var replace + var $tip = this.tip() + var width = $tip[0].offsetWidth + var height = $tip[0].offsetHeight - /* TAB PLUGIN DEFINITION - * ===================== */ + // manually read margins because getBoundingClientRect includes difference + var marginTop = parseInt($tip.css('margin-top'), 10) + var marginLeft = parseInt($tip.css('margin-left'), 10) - $.fn.tab = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('tab') - if (!data) $this.data('tab', (data = new Tab(this))) - if (typeof option == 'string') data[option]() - }) + // we must check for NaN for ie 8/9 + if (isNaN(marginTop)) marginTop = 0 + if (isNaN(marginLeft)) marginLeft = 0 + + offset.top = offset.top + marginTop + offset.left = offset.left + marginLeft + + $tip + .offset(offset) + .addClass('in') + + // check to see if placing tip in new offset caused the tip to resize itself + var actualWidth = $tip[0].offsetWidth + var actualHeight = $tip[0].offsetHeight + + if (placement == 'top' && actualHeight != height) { + replace = true + offset.top = offset.top + height - actualHeight + } + + if (/bottom|top/.test(placement)) { + var delta = 0 + + if (offset.left < 0) { + delta = offset.left * -2 + offset.left = 0 + + $tip.offset(offset) + + actualWidth = $tip[0].offsetWidth + actualHeight = $tip[0].offsetHeight + } + + this.replaceArrow(delta - width + actualWidth, actualWidth, 'left') + } else { + this.replaceArrow(actualHeight - height, actualHeight, 'top') + } + + if (replace) $tip.offset(offset) } - $.fn.tab.Constructor = Tab - - - /* TAB DATA-API - * ============ */ - - $(function () { - $('body').on('click.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) { - e.preventDefault() - $(this).tab('show') - }) - }) - -}(window.jQuery); - -/* =========================================================== - * bootstrap-tooltip.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#tooltips - * Inspired by the original jQuery.tipsy by Jason Frame - * =========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - // Add a special event that is called when an element is destroyed - (function($){ - jQuery.event.special.destroyed = { - remove: function(o) { - if (o.handler) { - o.handler() - } - } - } - })(jQuery) - - /* TOOLTIP PUBLIC CLASS DEFINITION - * =============================== */ - - var Tooltip = function (element, options) { - this.init('tooltip', element, options) + Tooltip.prototype.replaceArrow = function(delta, dimension, position) { + this.arrow().css(position, delta ? (50 * (1 - delta / dimension) + "%") : '') } - Tooltip.prototype = { + Tooltip.prototype.setContent = function () { + var $tip = this.tip() + var title = this.getTitle() - constructor: Tooltip + $tip.find('.tooltip-inner')[this.options.html ? 'html' : 'text'](title) + $tip.removeClass('fade in top bottom left right') + } - , init: function (type, element, options) { - var eventIn - , eventOut + Tooltip.prototype.hide = function () { + var that = this + var $tip = this.tip() + var e = $.Event('hide.bs.' + this.type) - this.type = type - this.$element = $(element) - this.options = this.getOptions(options) - this.enabled = true - - if (this.options.trigger != 'manual') { - eventIn = this.options.trigger == 'hover' ? 'mouseenter' : 'focus' - eventOut = this.options.trigger == 'hover' ? 'mouseleave' : 'blur' - this.$element.on(eventIn, this.options.selector, $.proxy(this.enter, this)) - this.$element.on(eventOut, this.options.selector, $.proxy(this.leave, this)) - } - - // Make sure tooltip is hidden when element is destroyed - this.$element.on( 'destroyed', $.proxy( this.hide, this ) ); - - this.options.selector ? - (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) : - this.fixTitle() + function complete() { + if (that.hoverState != 'in') $tip.detach() } - , getOptions: function (options) { - options = $.extend({}, $.fn[this.type].defaults, options, this.$element.data()) + this.$element.trigger(e) - if (options.delay && typeof options.delay == 'number') { - options.delay = { - show: options.delay - , hide: options.delay - } - } + if (e.isDefaultPrevented()) return - return options - } + $tip.removeClass('in') - , enter: function (e) { - var self = $(e.currentTarget)[this.type](this._options).data(this.type) + $.support.transition && this.$tip.hasClass('fade') ? + $tip + .one($.support.transition.end, complete) + .emulateTransitionEnd(150) : + complete() - if (!self.options.delay || !self.options.delay.show) return self.show() + this.$element.trigger('hidden.bs.' + this.type) - clearTimeout(this.timeout) - self.hoverState = 'in' - this.timeout = setTimeout(function() { - if (self.hoverState == 'in') self.show() - }, self.options.delay.show) - } - - , leave: function (e) { - var self = $(e.currentTarget)[this.type](this._options).data(this.type) - - if (this.timeout) clearTimeout(this.timeout) - if (!self.options.delay || !self.options.delay.hide) return self.hide() - - self.hoverState = 'out' - this.timeout = setTimeout(function() { - if (self.hoverState == 'out') self.hide() - }, self.options.delay.hide) - } - - , show: function () { - var $tip - , inside - , pos - , actualWidth - , actualHeight - , placement - , placementPosition - , $window - , tp - - if (this.hasContent() && this.enabled) { - $tip = this.tip() - this.setContent() - - if (this.options.animation) { - $tip.addClass('fade') - } - - placement = typeof this.options.placement == 'function' ? - this.options.placement.call(this, $tip[0], this.$element[0]) : - this.options.placement - - placementPosition = inside ? placement.split(' ')[1] : placement; - - inside = /in/.test(placement) - - $tip - .remove() - .css({ top: 0, left: 0, display: 'block' }) - .appendTo(inside ? this.$element : document.body) - - pos = this.getPosition(inside) - - actualWidth = $tip[0].offsetWidth - actualHeight = $tip[0].offsetHeight - - switch (placementPosition) { - case 'bottom': - tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2} - break - case 'top': - tp = {top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2} - break - case 'left': - tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth} - break - case 'right': - tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width} - break - } - - // Shift if off screen - $window = $(window) - - // If off the top of the screen, flip - if ( tp.top < $window.scrollTop() && placementPosition == 'top' ) { - tp.top = pos.top + pos.height; - placement = inside ? 'inside bottom' : 'bottom'; - } - - // Shift left or right - var leftShift = 0; - if ( tp.left < $window.scrollLeft() ) { - leftShift = tp.left - $window.scrollLeft(); - } - var t = $window.scrollLeft() + $window.width() - $tip.outerWidth(); - if ( tp.left > t ) { - leftShift = tp.left - t; - } - - tp.left -= leftShift; - - // Shift background to center over element (not implemented for east/west) - switch (inside ? placement.split(' ')[1] : placement) { - case 'bottom': - $tip.find('.tooltip-arrow').css( 'left', ( $tip.outerWidth() / 2 ) + leftShift + "px" ); - break; - case 'top': - $tip.find('.tooltip-arrow').css( 'left', ( $tip.outerWidth() / 2 ) + leftShift + "px" ); - break; - case 'left': - break; - case 'right': - break; - } - - // END GALAXY MODIFICATION - - - $tip - .css(tp) - .addClass(placement) - .addClass('in') - } - } - - , isHTML: function(text) { - // html string detection logic adapted from jQuery - return typeof text != 'string' - || ( text.charAt(0) === "<" - && text.charAt( text.length - 1 ) === ">" - && text.length >= 3 - ) || /^(?:[^<]*<[\w\W]+>[^>]*$)/.exec(text) - } - - , setContent: function () { - var $tip = this.tip() - , title = this.getTitle() - - $tip.find('.tooltip-inner')[this.isHTML(title) ? 'html' : 'text'](title) - $tip.removeClass('fade in top bottom left right') - } - - , hide: function () { - var that = this - , $tip = this.tip() - - $tip.removeClass('in') - - function removeWithAnimation() { - var timeout = setTimeout(function () { - $tip.off($.support.transition.end).remove() - }, 500) - - $tip.one($.support.transition.end, function () { - clearTimeout(timeout) - $tip.remove() - }) - } - - $.support.transition && this.$tip.hasClass('fade') ? - removeWithAnimation() : - $tip.remove() - } - - , fixTitle: function () { - var $e = this.$element - if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') { - $e.attr('data-original-title', $e.attr('title') || '').removeAttr('title') - } - } - - , hasContent: function () { - return this.getTitle() - } - - , getPosition: function (inside) { - return $.extend({}, (inside ? {top: 0, left: 0} : this.$element.offset()), { - width: this.$element[0].offsetWidth - , height: this.$element[0].offsetHeight - }) - } - - , getTitle: function () { - var title - , $e = this.$element - , o = this.options - - title = $e.attr('data-original-title') - || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title) - - return title - } - - , tip: function () { - return this.$tip = this.$tip || $(this.options.template) - } - - , validate: function () { - if (!this.$element[0].parentNode) { - this.hide() - this.$element = null - this.options = null - } - } - - , enable: function () { - this.enabled = true - } - - , disable: function () { - this.enabled = false - } - - , toggleEnabled: function () { - this.enabled = !this.enabled - } - - , toggle: function () { - this[this.tip().hasClass('in') ? 'hide' : 'show']() - } - + return this } + Tooltip.prototype.fixTitle = function () { + var $e = this.$element + if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') { + $e.attr('data-original-title', $e.attr('title') || '').attr('title', '') + } + } - /* TOOLTIP PLUGIN DEFINITION - * ========================= */ + Tooltip.prototype.hasContent = function () { + return this.getTitle() + } - $.fn.tooltip = function ( option ) { + Tooltip.prototype.getPosition = function () { + var el = this.$element[0] + return $.extend({}, (typeof el.getBoundingClientRect == 'function') ? el.getBoundingClientRect() : { + width: el.offsetWidth + , height: el.offsetHeight + }, this.$element.offset()) + } + + Tooltip.prototype.getCalculatedOffset = function (placement, pos, actualWidth, actualHeight) { + return placement == 'bottom' ? { top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2 } : + placement == 'top' ? { top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2 } : + placement == 'left' ? { top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth } : + /* placement == 'right' */ { top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width } + } + + Tooltip.prototype.getTitle = function () { + var title + var $e = this.$element + var o = this.options + + title = $e.attr('data-original-title') + || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title) + + return title + } + + Tooltip.prototype.tip = function () { + return this.$tip = this.$tip || $(this.options.template) + } + + Tooltip.prototype.arrow = function () { + return this.$arrow = this.$arrow || this.tip().find('.tooltip-arrow') + } + + Tooltip.prototype.validate = function () { + if (!this.$element[0].parentNode) { + this.hide() + this.$element = null + this.options = null + } + } + + Tooltip.prototype.enable = function () { + this.enabled = true + } + + Tooltip.prototype.disable = function () { + this.enabled = false + } + + Tooltip.prototype.toggleEnabled = function () { + this.enabled = !this.enabled + } + + Tooltip.prototype.toggle = function (e) { + var self = e ? $(e.currentTarget)[this.type](this.getDelegateOptions()).data('bs.' + this.type) : this + self.tip().hasClass('in') ? self.leave(self) : self.enter(self) + } + + Tooltip.prototype.destroy = function () { + this.hide().$element.off('.' + this.type).removeData('bs.' + this.type) + } + + + // TOOLTIP PLUGIN DEFINITION + // ========================= + + var old = $.fn.tooltip + + $.fn.tooltip = function (option) { return this.each(function () { - var $this = $(this) - , data = $this.data('tooltip') - , options = typeof option == 'object' && option - if (!data) $this.data('tooltip', (data = new Tooltip(this, options))) + var $this = $(this) + var data = $this.data('bs.tooltip') + var options = typeof option == 'object' && option + + if (!data) $this.data('bs.tooltip', (data = new Tooltip(this, options))) if (typeof option == 'string') data[option]() }) } $.fn.tooltip.Constructor = Tooltip - $.fn.tooltip.defaults = { - animation: false - , placement: 'top' - , selector: false - , template: '<div class="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>' - , trigger: 'hover' - , title: '' - , delay: 0 + + // TOOLTIP NO CONFLICT + // =================== + + $.fn.tooltip.noConflict = function () { + $.fn.tooltip = old + return this } }(window.jQuery); diff -r 6cf5d0cbaf96c9910b7e72a83f16d5c6a9f2f34a -r edc5e6ad3d544c47457aaf135c7956d9ac0ab32b static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_main:"#everything",options:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b);$(this.el).hide()}},show:function(b){if(b){this.create(b)}this.$el.fadeIn("fast")},hide:function(){this.$el.fadeOut("fast")},create:function(c){this.$el.remove();if(!c){c=this.options}else{c=_.defaults(c,this.options)}this.setElement(this.template(c.title,c.body));$(this.el_main).append($(this.el));var d=(this.$el).find(".footer");var b=this;if(c.buttons){$.each(c.buttons,function(e,f){d.append($("<button></button>").text(e).click(f)).append(" ")})}else{d.append($("<button></button>").text("Close").click(function(){b.hide()})).append(" ")}},template:function(c,b){return'<div class="modal"><div class="modal-backdrop"></div><div class="modal-dialog galaxy-corner"><div class="modal-content"><div class="header"><span><h3 class="title">'+c+'</h3></span></div><div class="body">'+b+'</div><div class="footer"></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_main:"#everything",options:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b);$(this.el).hide()}},show:function(b){if(b){this.create(b)}this.$el.fadeIn("fast")},hide:function(){this.$el.fadeOut("fast")},create:function(c){this.$el.remove();if(!c){c=this.options}else{c=_.defaults(c,this.options)}this.setElement(this.template(c.title,c.body));$(this.el_main).append($(this.el));var d=(this.$el).find(".buttons");var b=this;if(c.buttons){$.each(c.buttons,function(e,f){d.append($("<button></button>").text(e).click(f)).append(" ")})}else{d.append($("<button></button>").text("Close").click(function(){b.hide()})).append(" ")}},template:function(c,b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+c+'</h3></span></div><div class="modal-body style="min-width: 540px; max-height: 445px;">'+b+'</div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file diff -r 6cf5d0cbaf96c9910b7e72a83f16d5c6a9f2f34a -r edc5e6ad3d544c47457aaf135c7956d9ac0ab32b static/scripts/packed/libs/bootstrap.js --- a/static/scripts/packed/libs/bootstrap.js +++ b/static/scripts/packed/libs/bootstrap.js @@ -1,1 +1,1 @@ -!function(a){a(function(){a.support.transition=(function(){var b=(function(){var e=document.createElement("bootstrap"),d={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd",msTransition:"MSTransitionEnd",transition:"transitionend"},c;for(c in d){if(e.style[c]!==undefined){return d[c]}}}());return b&&{end:b}})()})}(window.jQuery);!function(b){var a=function(c){this.element=b(c)};a.prototype={constructor:a,show:function(){var i=this.element,f=i.closest("ul:not(.dropdown-menu)"),d=i.attr("data-target"),g,c,h;if(!d){d=i.attr("href");d=d&&d.replace(/.*(?=#[^\s]*$)/,"")}if(i.parent("li").hasClass("active")){return}g=f.find(".active a").last()[0];h=b.Event("show",{relatedTarget:g});i.trigger(h);if(h.isDefaultPrevented()){return}c=b(d);this.activate(i.parent("li"),f);this.activate(c,c.parent(),function(){i.trigger({type:"shown",relatedTarget:g})})},activate:function(e,d,h){var c=d.find("> .active"),g=h&&b.support.transition&&c.hasClass("fade");function f(){c.removeClass("active").find("> .dropdown-menu > .active").removeClass("active");e.addClass("active");if(g){e[0].offsetWidth;e.addClass("in")}else{e.removeClass("fade")}if(e.parent(".dropdown-menu")){e.closest("li.dropdown").addClass("active")}h&&h()}g?c.one(b.support.transition.end,f):f();c.removeClass("in")}};b.fn.tab=function(c){return this.each(function(){var e=b(this),d=e.data("tab");if(!d){e.data("tab",(d=new a(this)))}if(typeof c=="string"){d[c]()}})};b.fn.tab.Constructor=a;b(function(){b("body").on("click.tab.data-api",'[data-toggle="tab"], [data-toggle="pill"]',function(c){c.preventDefault();b(this).tab("show")})})}(window.jQuery);!function(b){(function(c){jQuery.event.special.destroyed={remove:function(d){if(d.handler){d.handler()}}}})(jQuery);var a=function(d,c){this.init("tooltip",d,c)};a.prototype={constructor:a,init:function(f,e,d){var 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d=f?c(f.currentTarget)[this.type](this.getDelegateOptions()).data("bs."+this.type):this;d.tip().hasClass("in")?d.leave(d):d.enter(d)};b.prototype.destroy=function(){this.hide().$element.off("."+this.type).removeData("bs."+this.type)};var a=c.fn.tooltip;c.fn.tooltip=function(d){return this.each(function(){var g=c(this);var f=g.data("bs.tooltip");var e=typeof d=="object"&&d;if(!f){g.data("bs.tooltip",(f=new b(this,e)))}if(typeof d=="string"){f[d]()}})};c.fn.tooltip.Constructor=b;c.fn.tooltip.noConflict=function(){c.fn.tooltip=a;return this}}(window.jQuery); \ No newline at end of file diff -r 6cf5d0cbaf96c9910b7e72a83f16d5c6a9f2f34a -r edc5e6ad3d544c47457aaf135c7956d9ac0ab32b static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -422,8 +422,8 @@ .dropdown-menu{position:absolute;top:100%;left:0;z-index:1000;display:none;float:left;min-width:160px;padding:5px 0;margin:2px 0 0;list-style:none;font-size:12px;background-color:#fff;border:1px solid #ccc;border:1px solid rgba(0,0,0,0.15);border-radius:3px;-webkit-box-shadow:0 6px 12px rgba(0,0,0,0.175);box-shadow:0 6px 12px rgba(0,0,0,0.175);background-clip:padding-box}.dropdown-menu.pull-right{right:0;left:auto} .dropdown-menu .divider{height:1px;margin:7.5px 0;overflow:hidden;background-color:#e5e5e5} .dropdown-menu>li>a{display:block;padding:3px 20px;clear:both;font-weight:normal;line-height:1.428571429;color:#333;white-space:nowrap} -.dropdown-menu>li>a:hover,.dropdown-menu>li>a:focus{text-decoration:none;color:#fff;background-color:#00f} -.dropdown-menu>.active>a,.dropdown-menu>.active>a:hover,.dropdown-menu>.active>a:focus{color:#fff;text-decoration:none;outline:0;background-color:#00f} +.dropdown-menu>li>a:hover,.dropdown-menu>li>a:focus{text-decoration:none;color:#fff;background-color:#303030} +.dropdown-menu>.active>a,.dropdown-menu>.active>a:hover,.dropdown-menu>.active>a:focus{color:#fff;text-decoration:none;outline:0;background-color:#303030} .dropdown-menu>.disabled>a,.dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{color:#999} .dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{text-decoration:none;background-color:transparent;background-image:none;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);cursor:not-allowed} .open>.dropdown-menu{display:block} @@ -513,7 +513,7 @@ @media (min-width:768px){.nav-tabs.nav-justified>li>a{border-bottom:1px solid #ddd;border-radius:3px 3px 0 0} .nav-tabs.nav-justified>.active>a,.nav-tabs.nav-justified>.active>a:hover,.nav-tabs.nav-justified>.active>a:focus{border-bottom-color:#fff}} .nav-pills>li{float:left}.nav-pills>li>a{border-radius:5px} .nav-pills>li+li{margin-left:2px} -.nav-pills>li.active>a,.nav-pills>li.active>a:hover,.nav-pills>li.active>a:focus{color:#fff;background-color:#00f} +.nav-pills>li.active>a,.nav-pills>li.active>a:hover,.nav-pills>li.active>a:focus{color:#fff;background-color:#303030} .nav-stacked>li{float:none}.nav-stacked>li+li{margin-top:2px;margin-left:0} .nav-justified{width:100%}.nav-justified>li{float:none}.nav-justified>li>a{text-align:center;margin-bottom:5px} @media (min-width:768px){.nav-justified>li{display:table-cell;width:1%}.nav-justified>li>a{margin-bottom:0}} @@ -659,8 +659,8 @@ .list-group-item>.badge+.badge{margin-right:5px} a.list-group-item{color:#555}a.list-group-item .list-group-item-heading{color:#333} a.list-group-item:hover,a.list-group-item:focus{text-decoration:none;background-color:#f5f5f5} -.list-group-item.active,.list-group-item.active:hover,.list-group-item.active:focus{z-index:2;color:#fff;background-color:#00f;border-color:#00f}.list-group-item.active .list-group-item-heading,.list-group-item.active:hover .list-group-item-heading,.list-group-item.active:focus .list-group-item-heading{color:inherit} -.list-group-item.active .list-group-item-text,.list-group-item.active:hover .list-group-item-text,.list-group-item.active:focus .list-group-item-text{color:#ccf} +.list-group-item.active,.list-group-item.active:hover,.list-group-item.active:focus{z-index:2;color:#fff;background-color:#303030;border-color:#303030}.list-group-item.active .list-group-item-heading,.list-group-item.active:hover .list-group-item-heading,.list-group-item.active:focus .list-group-item-heading{color:inherit} +.list-group-item.active .list-group-item-text,.list-group-item.active:hover .list-group-item-text,.list-group-item.active:focus .list-group-item-text{color:#969696} .list-group-item-heading{margin-top:0;margin-bottom:5px} .list-group-item-text{margin-bottom:0;line-height:1.3} .panel{margin-bottom:17px;background-color:#fff;border:1px solid transparent;border-radius:3px;-webkit-box-shadow:0 1px 1px rgba(0,0,0,0.05);box-shadow:0 1px 1px rgba(0,0,0,0.05)} diff -r 6cf5d0cbaf96c9910b7e72a83f16d5c6a9f2f34a -r edc5e6ad3d544c47457aaf135c7956d9ac0ab32b static/style/src/less/theme/blue.less --- a/static/style/src/less/theme/blue.less +++ b/static/style/src/less/theme/blue.less @@ -11,6 +11,7 @@ @table-border-color: darken(@table-heading-bg,20%); @link-color: #303030; +@component-active-bg: @link-color; @brand-primary: blue; https://bitbucket.org/galaxy/galaxy-central/commits/47798b37aed0/ Changeset: 47798b37aed0 User: james_taylor Date: 2013-09-17 21:18:51 Summary: Fix close/delete icons in workflow editor. Affected #: 3 files diff -r edc5e6ad3d544c47457aaf135c7956d9ac0ab32b -r 47798b37aed096b344c43c6796b7aae27ef11e90 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -199,8 +199,8 @@ .css( { display: 'none' } ) .appendTo( "body" ) .append( - $("<div class='buttons'></div>").append( - $("<img/>").attr("src", galaxy_config.root + 'static/images/delete_icon.png').click( function() { + $("<div class='button'></div>").append( + $("<div/>").addClass("fa-icon-button fa-icon-remove").click( function() { $.each( terminal.connectors, function( _, x ) { if (x) { x.destroy(); @@ -859,12 +859,9 @@ // Fix width to computed width // Now add floats var buttons = $("<div class='buttons' style='float: right;'></div>"); - buttons.append( $("<img/>").attr("src", galaxy_config.root + 'static/images/delete_icon.png').click( function( e ) { + buttons.append( $("<div>").addClass("fa-icon-button fa-icon-remove").click( function( e ) { node.destroy(); - } ).hover( - function() { $(this).attr( "src", galaxy_config.root + "static/images/delete_icon_dark.png" ); }, - function() { $(this).attr( "src", galaxy_config.root + "static/images/delete_icon.png" ); } - ) ); + })); // Place inside container f.appendTo( "#canvas-container" ); // Position in container diff -r edc5e6ad3d544c47457aaf135c7956d9ac0ab32b -r 47798b37aed096b344c43c6796b7aae27ef11e90 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1362,6 +1362,7 @@ .text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc} .text-content th,.text-content td{padding:.8em} .icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;background-repeat:no-repeat;background-position:0px 0px;padding:0} +.fa-icon-button{text-align:center;text-decoration:none;display:inline-block;cursor:pointer;width:16px;height:16px;line-height:8px}.fa-icon-button:hover{color:maroon;-webkit-transition:color .25s linear;transition:color .25s linear} .editable-text{cursor:pointer} .editable-text:hover{cursor:text;border:dotted #999999 1px} .icon-button.multiinput{background:url(../images/documents-stack.png) no-repeat;cursor:pointer;float:none;display:inline-block;margin-left:10px} diff -r edc5e6ad3d544c47457aaf135c7956d9ac0ab32b -r 47798b37aed096b344c43c6796b7aae27ef11e90 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -1339,6 +1339,21 @@ padding: 0; } +.fa-icon-button { + text-align: center; + text-decoration: none; + display: inline-block; + cursor: pointer; + width: 16px; + height: 16px; + line-height: 8px; + // Fade to maroon on hover + &:hover { + color: maroon; + .transition(color .25s linear); + } +} + .editable-text { cursor:pointer; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: MetadataFile shouldn't attempt to create by default without checking exists() first.
by commits-noreply＠bitbucket.org 17 Sep '13

17 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6cf5d0cbaf96/ Changeset: 6cf5d0cbaf96 User: dannon Date: 2013-09-17 20:56:56 Summary: MetadataFile shouldn't attempt to create by default without checking exists() first. Affected #: 1 file diff -r 96a2ab47b882690df5a2a962d3689474e4312e3a -r 6cf5d0cbaf96c9910b7e72a83f16d5c6a9f2f34a lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2416,7 +2416,8 @@ da = self.history_dataset or self.library_dataset if self.object_store_id is None and da is not None: self.object_store_id = da.dataset.object_store_id - da.dataset.object_store.create( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ) + if not da.dataset.object_store.exists( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ): + da.dataset.object_store.create( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ) path = da.dataset.object_store.get_filename( self, extra_dir='_metadata_files', extra_dir_at_root=True, alt_name="metadata_%d.dat" % self.id ) return path except AttributeError: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Richard Burhans: Fix integrated_tool_panel dictionary before writing integrated_tool_panel.xml to keep tools/workflows in multiple sections
by commits-noreply＠bitbucket.org 17 Sep '13

17 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/96a2ab47b882/ Changeset: 96a2ab47b882 User: Richard Burhans Date: 2013-09-17 20:37:36 Summary: Fix integrated_tool_panel dictionary before writing integrated_tool_panel.xml to keep tools/workflows in multiple sections Affected #: 1 file diff -r 48fad71361b3075c85c7d365dd52c106cabad73a -r 96a2ab47b882690df5a2a962d3689474e4312e3a lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -154,8 +154,24 @@ # This will cover cases where the Galaxy administrator manually edited one or more of the tool panel # config files, adding or removing locally developed tools or workflows. The value of integrated_tool_panel # will be False when things like functional tests are the caller. + self.fix_integrated_tool_panel_dict() self.write_integrated_tool_panel_config_file() + def fix_integrated_tool_panel_dict( self ): + # HACK: instead of fixing after the fact, I suggest some combination of: + # 1) adjusting init_tools() and called methods to get this right + # 2) redesigning the code and/or data structure used to read/write integrated_tool_panel.xml + for key, value in self.integrated_tool_panel.iteritems(): + if key.startswith( 'section_' ): + for section_key, section_value in value.elems.iteritems(): + if section_value is None: + if section_key.startswith( 'tool_' ): + tool_id = section_key[5:] + value.elems[section_key] = self.tools_by_id.get( tool_id ) + elif section_key.startswith( 'workflow_' ): + workflow_id = section_key[9:] + value.elems[section_key] = self.workflows_by_id.get( workflow_id ) + def init_tools( self, config_filename ): """ Read the configuration file and load each tool. The following tags are currently supported: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 8 new changesets
by commits-noreply＠bitbucket.org 16 Sep '13

16 Sep '13

8 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5196dc5182f6/ Changeset: 5196dc5182f6 Branch: tool_api_submit User: Kyle Ellrott Date: 2013-06-27 23:23:12 Summary: Adding 'history' parameter to 'get_initial_value' method calls. This allows api based tool requests to build default parameters without having a fixed history attached to the 'trans' class Affected #: 3 files diff -r 63b58d89dedd942ad9842958476dd9d364fe1fe0 -r 5196dc5182f6595b1978cc52359f49547a4a2706 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1814,7 +1814,7 @@ # TODO: Anyway to capture tools that dynamically change their own # outputs? return True - def new_state( self, trans, all_pages=False ): + def new_state( self, trans, all_pages=False, history=None ): """ Create a new `DefaultToolState` for this tool. It will be initialized with default values for inputs. @@ -1828,16 +1828,16 @@ inputs = self.inputs else: inputs = self.inputs_by_page[ 0 ] - self.fill_in_new_state( trans, inputs, state.inputs ) + self.fill_in_new_state( trans, inputs, state.inputs, history=history ) return state - def fill_in_new_state( self, trans, inputs, state, context=None ): + def fill_in_new_state( self, trans, inputs, state, context=None, history=None ): """ Fill in a tool state dictionary with default values for all parameters in the dictionary `inputs`. Grouping elements are filled in recursively. """ context = ExpressionContext( state, context ) for input in inputs.itervalues(): - state[ input.name ] = input.get_initial_value( trans, context ) + state[ input.name ] = input.get_initial_value( trans, context, history=history ) def get_param_html_map( self, trans, page=0, other_values={} ): """ Return a dictionary containing the HTML representation of each @@ -1900,7 +1900,7 @@ state = DefaultToolState() state.decode( encoded_state, self, trans.app ) else: - state = self.new_state( trans ) + state = self.new_state( trans, history=history ) # This feels a bit like a hack. It allows forcing full processing # of inputs even when there is no state in the incoming dictionary # by providing either 'runtool_btn' (the name of the submit button diff -r 63b58d89dedd942ad9842958476dd9d364fe1fe0 -r 5196dc5182f6595b1978cc52359f49547a4a2706 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -69,13 +69,13 @@ """ return value - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): """ Return the starting value of the parameter """ return None - def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ): + def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used, history=None ): """ Get the starting value for the parameter, but if fetching from the history, try to find a value that has not yet been used. already_used is a list of objects that @@ -83,7 +83,7 @@ if a value has already been chosen from the history. This is to support the capability to choose each dataset once """ - return self.get_initial_value(trans, context); + return self.get_initial_value(trans, context, history=history); def get_required_enctype( self ): """ @@ -204,7 +204,7 @@ return form_builder.TextArea( self.name, self.size, value ) else: return form_builder.TextField( self.name, self.size, value ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return self.value class IntegerToolParameter( TextToolParameter ): @@ -271,7 +271,7 @@ if not value and self.optional: return None raise err - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): if self.value: return int( self.value ) else: @@ -340,7 +340,7 @@ if not value and self.optional: return None raise err - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): try: return float( self.value ) except: @@ -383,7 +383,7 @@ return [ 'true' ] def to_python( self, value, app ): return ( value == 'True' ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return self.checked def to_param_dict_string( self, value, other_values={} ): if value: @@ -456,7 +456,7 @@ return value else: raise Exception( "FileToolParameter cannot be persisted" ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return None class FTPFileToolParameter( ToolParameter ): @@ -495,7 +495,7 @@ return None elif isinstance( value, unicode ) or isinstance( value, str ) or isinstance( value, list ): return value - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return None class HiddenToolParameter( ToolParameter ): @@ -516,7 +516,7 @@ self.value = elem.get( 'value' ) def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.HiddenField( self.name, self.value ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return self.value def get_label( self ): return None @@ -539,7 +539,7 @@ return url def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.HiddenField( self.name, self.get_value( trans ) ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return self.value def get_label( self ): # BaseURLToolParameters are ultimately "hidden" parameters @@ -805,7 +805,7 @@ return True # Dynamic, but all dependenceis are known and have values return False - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): # More working around dynamic options for workflow if self.need_late_validation( trans, context ): # Really the best we can do? @@ -1035,7 +1035,7 @@ options.append( ( 'c' + col, col, False ) ) return options - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): if self.default_value is not None: # dataset not ready / in workflow / etc if self.need_late_validation( trans, context ): @@ -1315,7 +1315,7 @@ rval = sanitize_param( rval ) return rval - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): def recurse_options( initial_values, options ): for option in options: if option['selected']: @@ -1503,10 +1503,10 @@ field.add_option( "Selection is Optional", 'None', False ) return field - def get_initial_value( self, trans, context ): - return self.get_initial_value_from_history_prevent_repeats(trans, context, None); + def get_initial_value( self, trans, context, history=None ): + return self.get_initial_value_from_history_prevent_repeats(trans, context, None, history=history); - def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ): + def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used, history=None ): """ NOTE: This is wasteful since dynamic options and dataset collection happens twice (here and when generating HTML). @@ -1515,7 +1515,8 @@ if trans is None or trans.workflow_building_mode: return DummyDataset() assert trans is not None, "DataToolParameter requires a trans" - history = trans.get_history() + if history is None: + history = trans.get_history() assert history is not None, "DataToolParameter requires a history" if self.optional: return None @@ -1687,7 +1688,7 @@ DataToolParameter.__init__( self, tool, elem ) self.value = "None" - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return None def get_html_field( self, trans=None, value=None, other_values={} ): diff -r 63b58d89dedd942ad9842958476dd9d364fe1fe0 -r 5196dc5182f6595b1978cc52359f49547a4a2706 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -34,7 +34,7 @@ into the preferred value form. """ return value - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): """ Return the initial state/value for this group """ @@ -96,7 +96,7 @@ callback( new_prefix, input, d[input.name], parent = d ) else: input.visit_inputs( new_prefix, d[input.name], callback ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): rval = [] for i in range( self.default ): rval_dict = { '__index__': i} @@ -189,14 +189,14 @@ callback( new_prefix, input, d[input.name], parent = d ) else: input.visit_inputs( new_prefix, d[input.name], callback ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): d_type = self.get_datatype( trans, context ) rval = [] for i, ( composite_name, composite_file ) in enumerate( d_type.writable_files.iteritems() ): rval_dict = {} rval_dict['__index__'] = i # create __index__ for input in self.inputs.itervalues(): - rval_dict[ input.name ] = input.get_initial_value( trans, context ) #input.value_to_basic( d[input.name], app ) + rval_dict[ input.name ] = input.get_initial_value( trans, context, history=history ) #input.value_to_basic( d[input.name], app ) rval.append( rval_dict ) return rval def get_uploaded_datasets( self, trans, context, override_name = None, override_info = None ): @@ -476,12 +476,12 @@ callback( prefix, input, value[input.name], parent = value ) else: input.visit_inputs( prefix, value[input.name], callback ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): # State for a conditional is a plain dictionary. rval = {} # Get the default value for the 'test element' and use it # to determine the current case - test_value = self.test_param.get_initial_value( trans, context ) + test_value = self.test_param.get_initial_value( trans, context, history=None ) current_case = self.get_current_case( test_value, trans ) # Store the current case in a special value rval['__current_case__'] = current_case @@ -490,7 +490,7 @@ # Fill in state for selected case child_context = ExpressionContext( rval, context ) for child_input in self.cases[current_case].inputs.itervalues(): - rval[ child_input.name ] = child_input.get_initial_value( trans, child_context ) + rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=None ) return rval class ConditionalWhen( object ): https://bitbucket.org/galaxy/galaxy-central/commits/7ac0ed6f42d6/ Changeset: 7ac0ed6f42d6 Branch: tool_api_submit User: Kyle Ellrott Date: 2013-06-27 23:58:14 Summary: Removing stray print statement Affected #: 1 file diff -r 5196dc5182f6595b1978cc52359f49547a4a2706 -r 7ac0ed6f42d64e24f7bd851193368184a5e28def lib/galaxy/model/migrate/check.py --- a/lib/galaxy/model/migrate/check.py +++ b/lib/galaxy/model/migrate/check.py @@ -44,7 +44,6 @@ # Let this go, it could possibly work with db's we don't support log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect ) # Create engine and metadata - print url, engine_options engine = create_engine( url, **engine_options ) meta = MetaData( bind=engine ) # Try to load dataset table https://bitbucket.org/galaxy/galaxy-central/commits/371e3b451448/ Changeset: 371e3b451448 Branch: tool_api_submit User: Kyle Ellrott Date: 2013-06-28 00:52:08 Summary: The /api/tool submit can define inputs in the payload in the format {'id' : <encoded_id>, 'src' : 'hda'} Affected #: 1 file diff -r 7ac0ed6f42d64e24f7bd851193368184a5e28def -r 371e3b451448bfb7a70139faafc33072a7d2b468 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1575,6 +1575,9 @@ rval = [ trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( v ) for v in value ] elif isinstance( value, trans.app.model.HistoryDatasetAssociation ): rval = value + elif isinstance( value, dict ) and 'src' in value and 'id' in value: + if value['src'] == 'hda': + rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id(value['id']) ) else: rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( value ) if isinstance( rval, list ): https://bitbucket.org/galaxy/galaxy-central/commits/abb889f8c5b7/ Changeset: abb889f8c5b7 Branch: tool_api_submit User: Kyle Ellrott Date: 2013-07-03 22:38:40 Summary: Adding way for API based tools job submissions to copy library dataset into history Affected #: 1 file diff -r 371e3b451448bfb7a70139faafc33072a7d2b468 -r abb889f8c5b75e8b90e8a35617e95ec7c05d28e7 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -30,10 +30,10 @@ # Read params. in_panel = util.string_as_bool( kwds.get( 'in_panel', 'True' ) ) trackster = util.string_as_bool( kwds.get( 'trackster', 'False' ) ) - + # Create return value. try: - return self.app.toolbox.to_dict( trans, in_panel=in_panel, trackster=trackster ) + return self.app.toolbox.to_dict( trans, in_panel=in_panel, trackster=trackster) except Exception, exc: log.error( 'could not convert toolbox to dictionary: %s', str( exc ), exc_info=True ) trans.response.status = 500 @@ -87,6 +87,17 @@ for k, v in payload.iteritems(): if k.startswith("files_"): inputs[k] = v + + #for inputs that are coming from the Library, copy them into the history + input_patch = {} + for k, v in inputs.iteritems(): + if isinstance(v, dict) and v.get('src', '') == 'ldda' and 'id' in v: + ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id(v['id']) ) + if trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ): + input_patch[k] = ldda.to_history_dataset_association(target_history, add_to_history=True) + + for k, v in input_patch.iteritems(): + inputs[k] = v # HACK: add run button so that tool.handle_input will run tool. inputs['runtool_btn'] = 'Execute' https://bitbucket.org/galaxy/galaxy-central/commits/d370b6ba1443/ Changeset: d370b6ba1443 User: Kyle Ellrott Date: 2013-06-27 23:23:12 Summary: Adding 'history' parameter to 'get_initial_value' method calls. This allows api based tool requests to build default parameters without having a fixed history attached to the 'trans' class Affected #: 3 files diff -r 44214ff2a8801dea8714b6cfc7f2d7bd6545e229 -r d370b6ba1443adf67390ae8ca7b8d71a9746b3f6 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1852,7 +1852,7 @@ # TODO: Anyway to capture tools that dynamically change their own # outputs? return True - def new_state( self, trans, all_pages=False ): + def new_state( self, trans, all_pages=False, history=None ): """ Create a new `DefaultToolState` for this tool. It will be initialized with default values for inputs. @@ -1866,16 +1866,16 @@ inputs = self.inputs else: inputs = self.inputs_by_page[ 0 ] - self.fill_in_new_state( trans, inputs, state.inputs ) + self.fill_in_new_state( trans, inputs, state.inputs, history=history ) return state - def fill_in_new_state( self, trans, inputs, state, context=None ): + def fill_in_new_state( self, trans, inputs, state, context=None, history=None ): """ Fill in a tool state dictionary with default values for all parameters in the dictionary `inputs`. Grouping elements are filled in recursively. """ context = ExpressionContext( state, context ) for input in inputs.itervalues(): - state[ input.name ] = input.get_initial_value( trans, context ) + state[ input.name ] = input.get_initial_value( trans, context, history=history ) def get_param_html_map( self, trans, page=0, other_values={} ): """ Return a dictionary containing the HTML representation of each @@ -1938,7 +1938,7 @@ state = DefaultToolState() state.decode( encoded_state, self, trans.app ) else: - state = self.new_state( trans ) + state = self.new_state( trans, history=history ) # This feels a bit like a hack. It allows forcing full processing # of inputs even when there is no state in the incoming dictionary # by providing either 'runtool_btn' (the name of the submit button diff -r 44214ff2a8801dea8714b6cfc7f2d7bd6545e229 -r d370b6ba1443adf67390ae8ca7b8d71a9746b3f6 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -72,13 +72,13 @@ """ return value - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): """ Return the starting value of the parameter """ return None - def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ): + def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used, history=None ): """ Get the starting value for the parameter, but if fetching from the history, try to find a value that has not yet been used. already_used is a list of objects that @@ -86,7 +86,7 @@ if a value has already been chosen from the history. This is to support the capability to choose each dataset once """ - return self.get_initial_value(trans, context); + return self.get_initial_value(trans, context, history=history); def get_required_enctype( self ): """ @@ -216,7 +216,7 @@ return form_builder.TextArea( self.name, self.size, value ) else: return form_builder.TextField( self.name, self.size, value ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return self.value class IntegerToolParameter( TextToolParameter ): @@ -286,7 +286,7 @@ if not value and self.optional: return None raise err - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): if self.value: return int( self.value ) else: @@ -358,7 +358,7 @@ if not value and self.optional: return None raise err - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): try: return float( self.value ) except: @@ -401,7 +401,7 @@ return [ 'true' ] def to_python( self, value, app ): return ( value == 'True' ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return self.checked def to_param_dict_string( self, value, other_values={} ): if value: @@ -474,7 +474,7 @@ return value else: raise Exception( "FileToolParameter cannot be persisted" ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return None class FTPFileToolParameter( ToolParameter ): @@ -513,7 +513,7 @@ return None elif isinstance( value, unicode ) or isinstance( value, str ) or isinstance( value, list ): return value - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return None class HiddenToolParameter( ToolParameter ): @@ -534,7 +534,7 @@ self.value = elem.get( 'value' ) def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.HiddenField( self.name, self.value ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return self.value def get_label( self ): return None @@ -557,7 +557,7 @@ return url def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.HiddenField( self.name, self.get_value( trans ) ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return self.value def get_label( self ): # BaseURLToolParameters are ultimately "hidden" parameters @@ -826,7 +826,7 @@ return True # Dynamic, but all dependenceis are known and have values return False - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): # More working around dynamic options for workflow if self.need_late_validation( trans, context ): # Really the best we can do? @@ -1074,7 +1074,7 @@ options.append( ( 'c' + col, col, False ) ) return options - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): if self.default_value is not None: # dataset not ready / in workflow / etc if self.need_late_validation( trans, context ): @@ -1353,8 +1353,7 @@ else: rval = sanitize_param( rval ) return rval - - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): def recurse_options( initial_values, options ): for option in options: if option['selected']: @@ -1542,10 +1541,10 @@ field.add_option( "Selection is Optional", 'None', False ) return field - def get_initial_value( self, trans, context ): - return self.get_initial_value_from_history_prevent_repeats(trans, context, None); + def get_initial_value( self, trans, context, history=None ): + return self.get_initial_value_from_history_prevent_repeats(trans, context, None, history=history); - def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used ): + def get_initial_value_from_history_prevent_repeats( self, trans, context, already_used, history=None ): """ NOTE: This is wasteful since dynamic options and dataset collection happens twice (here and when generating HTML). @@ -1554,7 +1553,8 @@ if trans is None or trans.workflow_building_mode or trans.webapp.name == 'tool_shed': return DummyDataset() assert trans is not None, "DataToolParameter requires a trans" - history = trans.get_history() + if history is None: + history = trans.get_history() assert history is not None, "DataToolParameter requires a history" if self.optional: return None @@ -1727,7 +1727,7 @@ self.value = "None" self.type = "hidden_data" - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): return None def get_html_field( self, trans=None, value=None, other_values={} ): diff -r 44214ff2a8801dea8714b6cfc7f2d7bd6545e229 -r d370b6ba1443adf67390ae8ca7b8d71a9746b3f6 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -41,8 +41,7 @@ into the preferred value form. """ return value - - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): """ Return the initial state/value for this group """ @@ -109,7 +108,7 @@ callback( new_prefix, input, d[input.name], parent = d ) else: input.visit_inputs( new_prefix, d[input.name], callback ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): rval = [] for i in range( self.default ): rval_dict = { '__index__': i} @@ -202,14 +201,14 @@ callback( new_prefix, input, d[input.name], parent = d ) else: input.visit_inputs( new_prefix, d[input.name], callback ) - def get_initial_value( self, trans, context ): + def get_initial_value( self, trans, context, history=None ): d_type = self.get_datatype( trans, context ) rval = [] for i, ( composite_name, composite_file ) in enumerate( d_type.writable_files.iteritems() ): rval_dict = {} rval_dict['__index__'] = i # create __index__ for input in self.inputs.itervalues(): - rval_dict[ input.name ] = input.get_initial_value( trans, context ) #input.value_to_basic( d[input.name], app ) + rval_dict[ input.name ] = input.get_initial_value( trans, context, history=history ) #input.value_to_basic( d[input.name], app ) rval.append( rval_dict ) return rval def get_uploaded_datasets( self, trans, context, override_name = None, override_info = None ): @@ -489,12 +488,12 @@ callback( prefix, input, value[input.name], parent = value ) else: input.visit_inputs( prefix, value[input.name], callback ) - def get_initial_value( self, trans, context ): - # State for a conditional is a plain dictionary. + def get_initial_value( self, trans, context, history=None ): + # State for a conditional is a plain dictionary. rval = {} # Get the default value for the 'test element' and use it # to determine the current case - test_value = self.test_param.get_initial_value( trans, context ) + test_value = self.test_param.get_initial_value( trans, context, history=None ) current_case = self.get_current_case( test_value, trans ) # Store the current case in a special value rval['__current_case__'] = current_case @@ -503,7 +502,7 @@ # Fill in state for selected case child_context = ExpressionContext( rval, context ) for child_input in self.cases[current_case].inputs.itervalues(): - rval[ child_input.name ] = child_input.get_initial_value( trans, child_context ) + rval[ child_input.name ] = child_input.get_initial_value( trans, child_context, history=None ) return rval class ConditionalWhen( object ): https://bitbucket.org/galaxy/galaxy-central/commits/3e086bca9f63/ Changeset: 3e086bca9f63 User: Kyle Ellrott Date: 2013-06-28 00:52:08 Summary: The /api/tool submit can define inputs in the payload in the format {'id' : <encoded_id>, 'src' : 'hda'} Affected #: 1 file diff -r d370b6ba1443adf67390ae8ca7b8d71a9746b3f6 -r 3e086bca9f63e270da8cbd7e65feb0b22a0ae085 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1613,6 +1613,9 @@ rval = [ trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( v ) for v in value ] elif isinstance( value, trans.app.model.HistoryDatasetAssociation ): rval = value + elif isinstance( value, dict ) and 'src' in value and 'id' in value: + if value['src'] == 'hda': + rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( trans.app.security.decode_id(value['id']) ) else: rval = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( value ) if isinstance( rval, list ): https://bitbucket.org/galaxy/galaxy-central/commits/48fad71361b3/ Changeset: 48fad71361b3 User: Kyle Ellrott Date: 2013-07-03 22:38:40 Summary: Adding way for API based tools job submissions to copy library dataset into history Affected #: 1 file diff -r 3e086bca9f63e270da8cbd7e65feb0b22a0ae085 -r 48fad71361b3075c85c7d365dd52c106cabad73a lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -32,7 +32,7 @@ # Create return value. try: - return self.app.toolbox.to_dict( trans, in_panel=in_panel, trackster=trackster ) + return self.app.toolbox.to_dict( trans, in_panel=in_panel, trackster=trackster) except Exception, exc: log.error( 'could not convert toolbox to dictionary: %s', str( exc ), exc_info=True ) trans.response.status = 500 @@ -86,6 +86,17 @@ for k, v in payload.iteritems(): if k.startswith("files_"): inputs[k] = v + + #for inputs that are coming from the Library, copy them into the history + input_patch = {} + for k, v in inputs.iteritems(): + if isinstance(v, dict) and v.get('src', '') == 'ldda' and 'id' in v: + ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id(v['id']) ) + if trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ): + input_patch[k] = ldda.to_history_dataset_association(target_history, add_to_history=True) + + for k, v in input_patch.iteritems(): + inputs[k] = v # HACK: add run button so that tool.handle_input will run tool. inputs['runtool_btn'] = 'Execute' https://bitbucket.org/galaxy/galaxy-central/commits/e3e7b034cb0b/ Changeset: e3e7b034cb0b Branch: tool_api_submit User: carlfeberhard Date: 2013-09-16 21:45:04 Summary: Close branch tool_api_submit Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Use to_html_string on failed tests tracebacks and stderr
by commits-noreply＠bitbucket.org 16 Sep '13

16 Sep '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/44214ff2a880/ Changeset: 44214ff2a880 User: dan Date: 2013-09-16 17:12:26 Summary: Use to_html_string on failed tests tracebacks and stderr Affected #: 1 file diff -r b65602624e257d96d90fe94de13b483fd70d2f7e -r 44214ff2a8801dea8714b6cfc7f2d7bd6545e229 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -439,7 +439,10 @@ </%def><%def name="render_failed_test( failed_test, pad, parent, row_counter, row_is_header=False )"> - <% encoded_id = trans.security.encode_id( failed_test.id ) %> + <% + from tool_shed.util.shed_util_common import to_html_string + encoded_id = trans.security.encode_id( failed_test.id ) + %><tr class="datasetRow" %if parent is not None: parent="${parent}" @@ -450,8 +453,8 @@ <tr><td bgcolor="#FFFFCC"><b>Tool id:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Tool version:</b> ${failed_test.tool_id | h}</td></tr><tr><td><b>Test:</b> ${failed_test.test_id | h}</td></tr> - <tr><td><b>Stderr:</b><br/>${failed_test.stderr | h}</td></tr> - <tr><td><b>Traceback:</b><br/>${failed_test.traceback | h}</td></tr> + <tr><td><b>Stderr:</b><br/>${ to_html_string( failed_test.stderr ) }</td></tr> + <tr><td><b>Traceback:</b><br/>${ to_html_string( failed_test.traceback ) }</td></tr></table></td></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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