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

commit/galaxy-central: dannon: Toolshed workflow import: add storedworkflowannotation in addition to just the step annotations (oops)
by commits-noreply＠bitbucket.org 18 Jun '13

18 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f720e8e003f7/ Changeset: f720e8e003f7 User: dannon Date: 2013-06-18 20:24:33 Summary: Toolshed workflow import: add storedworkflowannotation in addition to just the step annotations (oops) Affected #: 1 file diff -r ff17100de392abf7fba9327949308ab2594d2d07 -r f720e8e003f750a8c1f9c4f72ac4acadae9e761d lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -420,7 +420,8 @@ repository_id=repository_id, changeset_revision=changeset_revision ) # Save the workflow in the Galaxy database. - stored_workflow = workflow_util.save_workflow( trans, workflow ) + # Pass workflow_dict along to create annotation at this point + stored_workflow = workflow_util.save_workflow( trans, workflow, workflow_dict ) # Use the latest version of the saved workflow. workflow = stored_workflow.latest_workflow if workflow_name: 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: Enable workflow step annotations for toolshed imported workflows.
by commits-noreply＠bitbucket.org 18 Jun '13

18 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff17100de392/ Changeset: ff17100de392 User: dannon Date: 2013-06-18 20:04:21 Summary: Enable workflow step annotations for toolshed imported workflows. Affected #: 1 file diff -r 81a2bb351c1a0f545a1f69b5514a29d96eb4575a -r ff17100de392abf7fba9327949308ab2594d2d07 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -12,9 +12,7 @@ from tool_shed.util import metadata_util from tool_shed.util import tool_util -import pkg_resources - -pkg_resources.require( "SVGFig" ) +eggs.require( "SVGFig" ) import svgfig log = logging.getLogger( __name__ ) @@ -386,6 +384,28 @@ workflow.has_errors = True # Stick this in the step temporarily. step.temp_input_connections = step_dict[ 'input_connections' ] + + # This should be considered a *temporary* hack. + # Usually we'd use the UsesAnnotation mixin, but + # that's not possible here. This entire module + # needs to die and get replaced with the regular + # galaxy/workflow methods. + from galaxy.util.sanitize_html import sanitize_html + annotation = step_dict.get( 'annotation', '') + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + new_step_annotation = trans.model.WorkflowStepAnnotationAssociation() + new_step_annotation.annotation = annotation + new_step_annotation.user = trans.user + step.annotations.append(new_step_annotation) + # Unpack and add post-job actions. + post_job_actions = step_dict.get( 'post_job_actions', {} ) + for name, pja_dict in post_job_actions.items(): + trans.model.PostJobAction( pja_dict[ 'action_type' ], + step, pja_dict[ 'output_name' ], + pja_dict[ 'action_arguments' ] ) + # End temporary hack + steps.append( step ) steps_by_external_id[ step_dict[ 'id' ] ] = step # Second pass to deal with connections between steps. 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: Remove import_from_myexp method since myexperiment.org uses the standard workflow import now (http://myexperiment.rubyforge.org/svn/trunk/app/views/workflows/galaxy/_run_options.rhtml)
by commits-noreply＠bitbucket.org 18 Jun '13

18 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/81a2bb351c1a/ Changeset: 81a2bb351c1a User: dannon Date: 2013-06-18 19:16:05 Summary: Remove import_from_myexp method since myexperiment.org uses the standard workflow import now (http://myexperiment.rubyforge.org/svn/trunk/app/views/workflows/galaxy/_run…) Affected #: 1 file diff -r fcffbe5a0a4c4e53d4f091df004118613abda807 -r 81a2bb351c1a0f545a1f69b5514a29d96eb4575a lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -891,56 +891,6 @@ @web.expose @web.require_login( "use workflows" ) - def import_from_myexp( self, trans, myexp_id, **kwd ): - """ - Imports a workflow from the myExperiment website. - Authenticates either by using HTTP basic, or with a cookie. - !!! This isn't currently used. MyExperiment uses the generic import_workflow method !!! - """ - # Parse parameters - myexp_username = kwd.get( 'myexp_username', None ) - myexp_password = kwd.get( 'myexp_password', None ) - myexp_cookie = kwd.get( 'myexp_cookie', None ) - # Get workflow content. - conn = httplib.HTTPConnection( trans.app.config.get( "myexperiment_url", self.__myexp_url ) ) - # NOTE: blocks web thread. - headers = {} - if myexp_username and myexp_password: - auth_header = base64.b64encode( '%s:%s' % ( myexp_username, myexp_password )) - headers = { "Authorization" : "Basic %s" % auth_header } - elif myexp_cookie: - headers = { "Cookie" : "myexperiment_session=%s" % myexp_cookie } - conn.request( "GET", "/workflow.xml?id=%s&elements=content" % myexp_id, headers=headers ) - response = conn.getresponse() - response_data = response.read() - conn.close() - if response.status == 200: - parser = SingleTagContentsParser( "content" ) - parser.feed( response_data ) - workflow_content = base64.b64decode( parser.tag_content ) - # Process workflow JSON and create workflow. - workflow_dict = from_json_string( workflow_content ) - # Create workflow. - workflow, missing_tool_tups = self._workflow_from_dict( trans, workflow_dict, source="myExperiment" ) - workflow = workflow.latest_workflow - if missing_tool_tups: - # TODO: handle the case where the imported workflow requires tools that are not available in - # the local Galaxy instance. - pass - - # Provide user feedback. - workflow_list_str = " <br>Return to <a href='%s'>workflow list." % url_for( controller='workflow', action='list' ) - if response.status != 200: - return trans.show_error_message( "There was a problem importing the workflow. Error: %s %s" % (response_data, workflow_list_str) ) - if workflow.has_errors: - return trans.show_warn_message( "Imported, but some steps in this workflow have validation errors. %s" % workflow_list_str ) - if workflow.has_cycles: - return trans.show_warn_message( "Imported, but this workflow contains cycles. %s" % workflow_list_str ) - else: - return trans.show_message( "Workflow '%s' imported. %s" % (workflow.name, workflow_list_str) ) - - @web.expose - @web.require_login( "use workflows" ) def export_to_myexp( self, trans, id, myexp_username, myexp_password ): """ Exports a workflow to myExperiment website. 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: jgoecks: Return empty string rather than None because Mako functions write by default; add comments as well.
by commits-noreply＠bitbucket.org 18 Jun '13

18 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/fcffbe5a0a4c/ Changeset: fcffbe5a0a4c User: jgoecks Date: 2013-06-18 18:43:38 Summary: Return empty string rather than None because Mako functions write by default; add comments as well. Affected #: 1 file diff -r d6d2f0287e6ff6d3dc2e4cf3ed4778b77e2abda9 -r fcffbe5a0a4c4e53d4f091df004118613abda807 templates/refresh_frames.mako --- a/templates/refresh_frames.mako +++ b/templates/refresh_frames.mako @@ -1,9 +1,11 @@ ## Include JavaScript code to refresh Galaxy application frames as needed. <%def name="handle_refresh_frames()"> + ## If no refresh frames, print nothing. <% - if not refresh_frames: return + if not refresh_frames: return '' %> + ## Write JavaScript to refresh specified frames. <script type="text/javascript"> %if 'everything' in refresh_frames: parent.location.href="${h.url_for( controller='root' )}"; 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: Tools/Workflows: Handle loading saved tool states that may not have rerun_remap_job_id in state.
by commits-noreply＠bitbucket.org 18 Jun '13

18 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d6d2f0287e6f/ Changeset: d6d2f0287e6f User: dannon Date: 2013-06-18 18:20:18 Summary: Tools/Workflows: Handle loading saved tool states that may not have rerun_remap_job_id in state. Affected #: 1 file diff -r f3fed61f4575620827fbf992781ef230bb9042ba -r d6d2f0287e6ff6d3dc2e4cf3ed4778b77e2abda9 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -848,7 +848,10 @@ # Restore from string values = json_fix( simplejson.loads( value ) ) self.page = values.pop( "__page__" ) - self.rerun_remap_job_id = values.pop( "__rerun_remap_job_id__" ) + if '__rerun_remap_job_id__' in values: + self.rerun_remap_job_id = values.pop( "__rerun_remap_job_id__" ) + else: + self.rerun_remap_job_id = None self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True ) class ToolOutput( object ): 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 18 Jun '13

18 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/76f9ddde5f5e/ Changeset: 76f9ddde5f5e User: jgoecks Date: 2013-06-18 17:41:46 Summary: Turns out min-height is needed to propagate tool background correctly. Affected #: 2 files diff -r e55155b6010e398102a738fb575fa40115c2d864 -r 76f9ddde5f5ee7c0069b487b101734fe883f165e static/style/base.less --- a/static/style/base.less +++ b/static/style/base.less @@ -1718,6 +1718,7 @@ { color: @base_text; background: @menu_bg_over; + min-height: 100%; padding: 0px 5px; } diff -r e55155b6010e398102a738fb575fa40115c2d864 -r 76f9ddde5f5ee7c0069b487b101734fe883f165e static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1142,7 +1142,7 @@ div.historyItemBody div{padding-top:2px;} pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} -.toolMenuContainer{color:#303030;background:#dfe5f9;padding:0px 5px;} +.toolMenuContainer{color:#303030;background:#dfe5f9;min-height:100%;padding:0px 5px;} div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} div.toolSectionWrapper{margin-bottom:5px;} div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} https://bitbucket.org/galaxy/galaxy-central/commits/f3fed61f4575/ Changeset: f3fed61f4575 User: jgoecks Date: 2013-06-18 17:46:16 Summary: Fix import for edit_attributes page. Affected #: 1 file diff -r 76f9ddde5f5ee7c0069b487b101734fe883f165e -r f3fed61f4575620827fbf992781ef230bb9042ba templates/webapps/galaxy/dataset/edit_attributes.mako --- a/templates/webapps/galaxy/dataset/edit_attributes.mako +++ b/templates/webapps/galaxy/dataset/edit_attributes.mako @@ -1,6 +1,6 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/message.mako" name="message_ns" import="handle_refresh_frames" /> +<%namespace file="/refresh_frames.mako" import="handle_refresh_frames" /><%def name="title()">${_('Edit Dataset Attributes')}</%def> @@ -10,7 +10,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${message_ns.handle_refresh_frames()} + ${handle_refresh_frames()} ${h.js( "libs/jquery/jquery.autocomplete", "galaxy.autocom_tagging" )} </%def> 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: jgoecks: Remove tool menu container height because it is not needed.
by commits-noreply＠bitbucket.org 18 Jun '13

18 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e55155b6010e/ Changeset: e55155b6010e User: jgoecks Date: 2013-06-18 17:26:52 Summary: Remove tool menu container height because it is not needed. Affected #: 2 files diff -r 736a8371a9a15ff0e0b53c65c218a445103c0b08 -r e55155b6010e398102a738fb575fa40115c2d864 static/style/base.less --- a/static/style/base.less +++ b/static/style/base.less @@ -1718,7 +1718,6 @@ { color: @base_text; background: @menu_bg_over; - height: 100%; padding: 0px 5px; } diff -r 736a8371a9a15ff0e0b53c65c218a445103c0b08 -r e55155b6010e398102a738fb575fa40115c2d864 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1142,7 +1142,7 @@ div.historyItemBody div{padding-top:2px;} pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto;}pre.peek th{color:white;background:#023858;} pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Menlo,Monaco,"Courier New",monospace;font-size:10px;} -.toolMenuContainer{color:#303030;background:#dfe5f9;height:100%;padding:0px 5px;} +.toolMenuContainer{color:#303030;background:#dfe5f9;padding:0px 5px;} div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px;} div.toolSectionWrapper{margin-bottom:5px;} div.toolSectionDetailsInner{margin-left:5px;margin-right:5px;} 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: jgoecks: Update jQuery library to 1.9.2 and jquery.event.drag/drop to 2.2; add jquery.migrate library because many jQuery plugins rely on deprecated features. Remove live() in favor of click(). Pack scripts and templates.
by commits-noreply＠bitbucket.org 18 Jun '13

18 Jun '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/736a8371a9a1/ Changeset: 736a8371a9a1 User: jgoecks Date: 2013-06-18 16:51:12 Summary: Update jQuery library to 1.9.2 and jquery.event.drag/drop to 2.2; add jquery.migrate library because many jQuery plugins rely on deprecated features. Remove live() in favor of click(). Pack scripts and templates. Affected #: 67 files diff -r d20c3481acb6581b239b20a34078f927dcc2a3c2 -r 736a8371a9a15ff0e0b53c65c218a445103c0b08 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -412,7 +412,7 @@ } // Set up input element. - $("#" + click_to_edit_elt).live("click", function() { + $("#" + click_to_edit_elt).click(function() { // Check if this is already active if ( $("#renaming-active").length > 0) { return; diff -r d20c3481acb6581b239b20a34078f927dcc2a3c2 -r 736a8371a9a15ff0e0b53c65c218a445103c0b08 static/scripts/libs/jquery/jquery.event.drag.js --- a/static/scripts/libs/jquery/jquery.event.drag.js +++ b/static/scripts/libs/jquery/jquery.event.drag.js @@ -1,11 +1,11 @@ /*! - * jquery.event.drag - v 2.1.0 + * jquery.event.drag - v 2.2 * Copyright (c) 2010 Three Dub Media - http://threedubmedia.com * Open Source MIT License - http://threedubmedia.com/code/license */ // Created: 2008-06-04 -// Updated: 2010-09-15 -// REQUIRES: jquery 1.4.2+ +// Updated: 2012-05-21 +// REQUIRES: jquery 1.7.x ;(function( $ ){ @@ -43,7 +43,10 @@ // the key name for stored drag data datakey: "dragdata", - + + // prevent bubbling for better performance + noBubble: true, + // count bound related events add: function( obj ){ // read the interaction data @@ -115,11 +118,7 @@ if ( dd.handle && !$( event.target ).closest( dd.handle, event.currentTarget ).length ) return; - // store/reset some initial attributes - if ( event.type == "touchstart" ){ - drag.touched = this; - drag.touchFix( event, dd ); - } + drag.touched = event.type == 'touchstart' ? this : null; dd.propagates = 1; dd.mousedown = this; dd.interactions = [ drag.interaction( this, dd ) ]; @@ -158,17 +157,6 @@ return false; }, - // fix event properties for touch events - touchFix: function( event, dd ){ - var orig = event.originalEvent, i = 0; - // iOS webkit: touchstart, touchmove, touchend - if ( orig && orig.changedTouches ){ - event.pageX = orig.changedTouches[0].pageX; - event.pageY = orig.changedTouches[0].pageY; - } - //console.log( event.type, event ); - }, - // returns an interaction object interaction: function( elem, dd ){ var offset = $( elem )[ dd.relative ? "position" : "offset" ]() || { top:0, left:0 }; @@ -183,9 +171,7 @@ // handle drag-releatd DOM events handler: function( event ){ // read the data before hijacking anything - var dd = event.data; - if ( drag.touched ) - drag.touchFix( event, dd ); + var dd = event.data; // handle various events switch ( event.type ){ // mousemove, check distance, start dragging @@ -217,22 +203,20 @@ // mouseup, stop dragging case 'touchend': case 'mouseup': + default: if ( drag.touched ) $event.remove( drag.touched, "touchmove touchend", drag.handler ); // remove touch events else $event.remove( document, "mousemove mouseup", drag.handler ); // remove page events if ( dd.dragging ){ - if ( dd.drop !== false && $special.drop ) + if ( dd.drop !== false && $special.drop ) $special.drop.handler( event, dd ); // "drop" drag.hijack( event, "dragend", dd ); // trigger "dragend" - } else { - drag.hijack( event, "dragclickonly", dd ); // trigger "dragclickonly" - } + } drag.textselect( true ); // enable text selection // if suppressing click events... - if ( dd.click === false && dd.dragging ){ + if ( dd.click === false && dd.dragging ) $.data( dd.mousedown, "suppress.click", new Date().getTime() + 5 ); - } dd.dragging = drag.touched = false; // deactivate element break; } @@ -244,7 +228,7 @@ if ( !dd ) return; // remember the original event and type - var orig = { event:event.originalEvent, type: event.type }, + var orig = { event:event.originalEvent, type:event.type }, // is the event drag related or drog related? mode = type.indexOf("drop") ? "drag" : "drop", // iteration vars @@ -269,8 +253,10 @@ $( elem || ia[ mode ] || dd.droppable ).each(function( p, subject ){ // identify drag or drop targets individually callback.target = subject; + // force propagtion of the custom event + event.isPropagationStopped = function(){ return false; }; // handle the event - result = subject ? $event.handle.call( subject, event, callback ) : null; + result = subject ? $event.dispatch.call( subject, event, callback ) : null; // stop the drag interaction for this element if ( result === false ){ if ( mode == "drag" ){ @@ -378,17 +364,39 @@ } }; -// patch $.event.handle to allow suppressing clicks -var orighandle = $event.handle; -$event.handle = function( event ){ +// patch $.event.$dispatch to allow suppressing clicks +var $dispatch = $event.dispatch; +$event.dispatch = function( event ){ if ( $.data( this, "suppress."+ event.type ) - new Date().getTime() > 0 ){ $.removeData( this, "suppress."+ event.type ); return; } - return orighandle.apply( this, arguments ); + return $dispatch.apply( this, arguments ); +}; + +// event fix hooks for touch events... +var touchHooks = +$event.fixHooks.touchstart = +$event.fixHooks.touchmove = +$event.fixHooks.touchend = +$event.fixHooks.touchcancel = { + props: "clientX clientY pageX pageY screenX screenY".split( " " ), + filter: function( event, orig ) { + if ( orig ){ + var touched = ( orig.touches && orig.touches[0] ) + || ( orig.changedTouches && orig.changedTouches[0] ) + || null; + // iOS webkit: touchstart, touchmove, touchend + if ( touched ) + $.each( touchHooks.props, function( i, prop ){ + event[ prop ] = touched[ prop ]; + }); + } + return event; + } }; // share the same special event configuration with related events... $special.draginit = $special.dragstart = $special.dragend = drag; -})( jQuery ); +})( jQuery ); \ No newline at end of file diff -r d20c3481acb6581b239b20a34078f927dcc2a3c2 -r 736a8371a9a15ff0e0b53c65c218a445103c0b08 static/scripts/libs/jquery/jquery.event.drop.js --- a/static/scripts/libs/jquery/jquery.event.drop.js +++ b/static/scripts/libs/jquery/jquery.event.drop.js @@ -1,341 +1,302 @@ -/*! - * jquery.event.drop - v 2.0.0 - * Copyright (c) 2010 Three Dub Media - http://threedubmedia.com - * Open Source MIT License - http://threedubmedia.com/code/license - */ -// Created: 2008-06-04 -// Updated: 2010-06-08 -// REQUIRES: jquery 1.4.2+, jquery.event.drag 2+ - -;(function($){ // secure $ jQuery alias - -// Events: drop, dropinit, dropstart, dropend - -// add the jquery instance method -$.fn.drop = function( str, arg, opts ){ - // figure out the event type - var type = typeof str == "string" ? str : "", - // figure out the event handler... - fn = $.isFunction( str ) ? str : $.isFunction( arg ) ? arg : null; - // fix the event type - if ( type.indexOf("drop") !== 0 ) - type = "drop"+ type; - // were options passed - opts = ( str == fn ? arg : opts ) || {}; - // trigger or bind event handler - return fn ? this.bind( type, opts, fn ) : this.trigger( type ); -}; - -// DROP MANAGEMENT UTILITY -// returns filtered drop target elements, caches their positions -$.drop = function( opts ){ - opts = opts || {}; - // safely set new options... - drop.multi = opts.multi === true ? Infinity : - opts.multi === false ? 1 : !isNaN( opts.multi ) ? opts.multi : drop.multi; - drop.delay = opts.delay || drop.delay; - drop.tolerance = $.isFunction( opts.tolerance ) ? opts.tolerance : - opts.tolerance === null ? null : drop.tolerance; - drop.mode = opts.mode || drop.mode || 'intersect'; -}; - -// local refs (increase compression) -var $event = $.event, -$special = $event.special, -// configure the drop special event -drop = $.event.special.drop = { - - // these are the default settings - multi: 1, // allow multiple drop winners per dragged element - delay: 20, // async timeout delay - mode: 'overlap', // drop tolerance mode - - // internal cache - targets: [], - - // the key name for stored drop data - datakey: "dropdata", - - // the namespace for internal live events - livekey: "livedrop", - - // count bound related events - add: function( obj ){ - // read the interaction data - var data = $.data( this, drop.datakey ); - // count another realted event - data.related += 1; - // bind the live "dropinit" delegator - if ( !data.live && obj.selector ){ - data.live = true; - $event.add( this, "dropinit."+ drop.livekey, drop.delegate ); - } - }, - - // forget unbound related events - remove: function(){ - $.data( this, drop.datakey ).related -= 1; - }, - - // configure the interactions - setup: function(){ - // check for related events - if ( $.data( this, drop.datakey ) ) - return; - // initialize the drop element data - var data = { - related: 0, - active: [], - anyactive: 0, - winner: 0, - location: {} - }; - // store the drop data on the element - $.data( this, drop.datakey, data ); - // store the drop target in internal cache - drop.targets.push( this ); - }, - - // destroy the configure interaction - teardown: function(){ - // check for related events - if ( $.data( this, drop.datakey ).related ) - return; - // remove the stored data - $.removeData( this, drop.datakey ); - // remove the "live" delegation - $event.remove( this, "dropinit", drop.delegate ); - // reference the targeted element - var element = this; - // remove from the internal cache - drop.targets = $.grep( drop.targets, function( target ){ - return ( target !== element ); - }); - }, - - // shared event handler - handler: function( event, dd ){ - // local vars - var results, $targets; - // make sure the right data is available - if ( !dd ) - return; - // handle various events - switch ( event.type ){ - // draginit, from $.event.special.drag - case 'mousedown': // DROPINIT >> - // collect and assign the drop targets - $targets = $( drop.targets ); - if ( typeof dd.drop == "string" ) - $targets = $targets.filter( dd.drop ); - // reset drop data winner properties - $targets.each(function(){ - var data = $.data( this, drop.datakey ); - data.active = []; - data.anyactive = 0; - data.winner = 0; - }); - // set available target elements - dd.droppable = $targets; - // hold any live elements - drop.delegates = []; - // activate drop targets for the initial element being dragged - $special.drag.hijack( event, "dropinit", dd ); - // flatten all the live elements - drop.delegates = $.unique( $special.drag.flatten( drop.delegates ) ); - break; - // drag, from $.event.special.drag - case 'mousemove': // TOLERATE >> - drop.event = event; // store the mousemove event - if ( !drop.timer ) - // monitor drop targets - drop.tolerate( dd ); - break; - // dragend, from $.event.special.drag - case 'mouseup': // DROP >> DROPEND >> - drop.timer = clearTimeout( drop.timer ); // delete timer - if ( dd.propagates ){ - $special.drag.hijack( event, "drop", dd ); - $special.drag.hijack( event, "dropend", dd ); - // cleanout live events... - $.each( drop.delegates || [], function(){ - $event.remove( this, '.'+ drop.livekey ); - }); - } - break; - } - }, - - // identify potential delegate elements - delegate: function( event ){ - // local refs - var elems = [], $targets, - // element event structure - events = $.data( this, "events" ) || {}; - // query live events - $.each( events.live || [], function( i, obj ){ - // no event type matches - if ( obj.preType.indexOf("drop") !== 0 ) - return; - // locate the elements to delegate - $targets = $( event.currentTarget ).find( obj.selector ); - // no element found - if ( !$targets.length ) - return; - // take each target... - $targets.each(function(){ - // add an event handler - $event.add( this, obj.origType +'.'+ drop.livekey, obj.origHandler, obj.data ); - // remember new elements - if ( $.inArray( this, elems ) < 0 ) - elems.push( this ); - }); - }); - drop.delegates.push( elems ); - return elems.length ? $( elems ) : false; - }, - - // returns the location positions of an element - locate: function( elem, index ){ - var data = $.data( elem, drop.datakey ), - $elem = $( elem ), - posi = $elem.offset() || {}, - height = $elem.outerHeight(), - width = $elem.outerWidth(), - location = { - elem: elem, - width: width, - height: height, - top: posi.top, - left: posi.left, - right: posi.left + width, - bottom: posi.top + height - }; - // drag elements might not have dropdata - if ( data ){ - data.location = location; - data.index = index; - data.elem = elem; - } - return location; - }, - - // test the location positions of an element against another OR an X,Y coord - contains: function( target, test ){ // target { location } contains test [x,y] or { location } - return ( ( test[0] || test.left ) >= target.left && ( test[0] || test.right ) <= target.right - && ( test[1] || test.top ) >= target.top && ( test[1] || test.bottom ) <= target.bottom ); - }, - - // stored tolerance modes - modes: { // fn scope: "$.event.special.drop" object - // target with mouse wins, else target with most overlap wins - 'intersect': function( event, proxy, target ){ - return this.contains( target, [ event.pageX, event.pageY ] ) ? // check cursor - 1e9 : this.modes.overlap.apply( this, arguments ); // check overlap - }, - // target with most overlap wins - 'overlap': function( event, proxy, target ){ - // calculate the area of overlap... - return Math.max( 0, Math.min( target.bottom, proxy.bottom ) - Math.max( target.top, proxy.top ) ) - * Math.max( 0, Math.min( target.right, proxy.right ) - Math.max( target.left, proxy.left ) ); - }, - // proxy is completely contained within target bounds - 'fit': function( event, proxy, target ){ - return this.contains( target, proxy ) ? 1 : 0; - }, - // center of the proxy is contained within target bounds - 'middle': function( event, proxy, target ){ - return this.contains( target, [ proxy.left + proxy.width * .5, proxy.top + proxy.height * .5 ] ) ? 1 : 0; - } - }, - - // sort drop target cache by by winner (dsc), then index (asc) - sort: function( a, b ){ - return ( b.winner - a.winner ) || ( a.index - b.index ); - }, - - // async, recursive tolerance execution - tolerate: function( dd ){ - // declare local refs - var i, drp, drg, data, arr, len, elem, - // interaction iteration variables - x = 0, ia, end = dd.interactions.length, - // determine the mouse coords - xy = [ drop.event.pageX, drop.event.pageY ], - // custom or stored tolerance fn - tolerance = drop.tolerance || drop.modes[ drop.mode ]; - // go through each passed interaction... - do if ( ia = dd.interactions[x] ){ - // check valid interaction - if ( !ia ) - return; - // initialize or clear the drop data - ia.drop = []; - // holds the drop elements - arr = []; - len = ia.droppable.length; - // determine the proxy location, if needed - if ( tolerance ) - drg = drop.locate( ia.proxy ); - // reset the loop - i = 0; - // loop each stored drop target - do if ( elem = ia.droppable[i] ){ - data = $.data( elem, drop.datakey ); - drp = data.location; - if ( !drp ) continue; - // find a winner: tolerance function is defined, call it - data.winner = tolerance ? tolerance.call( drop, drop.event, drg, drp ) - // mouse position is always the fallback - : drop.contains( drp, xy ) ? 1 : 0; - arr.push( data ); - } while ( ++i < len ); // loop - // sort the drop targets - arr.sort( drop.sort ); - // reset the loop - i = 0; - // loop through all of the targets again - do if ( data = arr[ i ] ){ - // winners... - if ( data.winner && ia.drop.length < drop.multi ){ - // new winner... dropstart - if ( !data.active[x] && !data.anyactive ){ - // check to make sure that this is not prevented - if ( $special.drag.hijack( drop.event, "dropstart", dd, x, data.elem )[0] !== false ){ - data.active[x] = 1; - data.anyactive += 1; - } - // if false, it is not a winner - else - data.winner = 0; - } - // if it is still a winner - if ( data.winner ) - ia.drop.push( data.elem ); - } - // losers... - else if ( data.active[x] && data.anyactive == 1 ){ - // former winner... dropend - $special.drag.hijack( drop.event, "dropend", dd, x, data.elem ); - data.active[x] = 0; - data.anyactive -= 1; - } - } while ( ++i < len ); // loop - } while ( ++x < end ) // loop - // check if the mouse is still moving or is idle - if ( drop.last && xy[0] == drop.last.pageX && xy[1] == drop.last.pageY ) - delete drop.timer; // idle, don't recurse - else // recurse - drop.timer = setTimeout(function(){ - drop.tolerate( dd ); - }, drop.delay ); - // remember event, to compare idleness - drop.last = drop.event; - } - -}; - -// share the same special event configuration with related events... -$special.dropinit = $special.dropstart = $special.dropend = drop; - +/*! + * jquery.event.drop - v 2.2 + * Copyright (c) 2010 Three Dub Media - http://threedubmedia.com + * Open Source MIT License - http://threedubmedia.com/code/license + */ +// Created: 2008-06-04 +// Updated: 2012-05-21 +// REQUIRES: jquery 1.7.x, event.drag 2.2 + +;(function($){ // secure $ jQuery alias + +// Events: drop, dropstart, dropend + +// add the jquery instance method +$.fn.drop = function( str, arg, opts ){ + // figure out the event type + var type = typeof str == "string" ? str : "", + // figure out the event handler... + fn = $.isFunction( str ) ? str : $.isFunction( arg ) ? arg : null; + // fix the event type + if ( type.indexOf("drop") !== 0 ) + type = "drop"+ type; + // were options passed + opts = ( str == fn ? arg : opts ) || {}; + // trigger or bind event handler + return fn ? this.bind( type, opts, fn ) : this.trigger( type ); +}; + +// DROP MANAGEMENT UTILITY +// returns filtered drop target elements, caches their positions +$.drop = function( opts ){ + opts = opts || {}; + // safely set new options... + drop.multi = opts.multi === true ? Infinity : + opts.multi === false ? 1 : !isNaN( opts.multi ) ? opts.multi : drop.multi; + drop.delay = opts.delay || drop.delay; + drop.tolerance = $.isFunction( opts.tolerance ) ? opts.tolerance : + opts.tolerance === null ? null : drop.tolerance; + drop.mode = opts.mode || drop.mode || 'intersect'; +}; + +// local refs (increase compression) +var $event = $.event, +$special = $event.special, +// configure the drop special event +drop = $.event.special.drop = { + + // these are the default settings + multi: 1, // allow multiple drop winners per dragged element + delay: 20, // async timeout delay + mode: 'overlap', // drop tolerance mode + + // internal cache + targets: [], + + // the key name for stored drop data + datakey: "dropdata", + + // prevent bubbling for better performance + noBubble: true, + + // count bound related events + add: function( obj ){ + // read the interaction data + var data = $.data( this, drop.datakey ); + // count another realted event + data.related += 1; + }, + + // forget unbound related events + remove: function(){ + $.data( this, drop.datakey ).related -= 1; + }, + + // configure the interactions + setup: function(){ + // check for related events + if ( $.data( this, drop.datakey ) ) + return; + // initialize the drop element data + var data = { + related: 0, + active: [], + anyactive: 0, + winner: 0, + location: {} + }; + // store the drop data on the element + $.data( this, drop.datakey, data ); + // store the drop target in internal cache + drop.targets.push( this ); + }, + + // destroy the configure interaction + teardown: function(){ + var data = $.data( this, drop.datakey ) || {}; + // check for related events + if ( data.related ) + return; + // remove the stored data + $.removeData( this, drop.datakey ); + // reference the targeted element + var element = this; + // remove from the internal cache + drop.targets = $.grep( drop.targets, function( target ){ + return ( target !== element ); + }); + }, + + // shared event handler + handler: function( event, dd ){ + // local vars + var results, $targets; + // make sure the right data is available + if ( !dd ) + return; + // handle various events + switch ( event.type ){ + // draginit, from $.event.special.drag + case 'mousedown': // DROPINIT >> + case 'touchstart': // DROPINIT >> + // collect and assign the drop targets + $targets = $( drop.targets ); + if ( typeof dd.drop == "string" ) + $targets = $targets.filter( dd.drop ); + // reset drop data winner properties + $targets.each(function(){ + var data = $.data( this, drop.datakey ); + data.active = []; + data.anyactive = 0; + data.winner = 0; + }); + // set available target elements + dd.droppable = $targets; + // activate drop targets for the initial element being dragged + $special.drag.hijack( event, "dropinit", dd ); + break; + // drag, from $.event.special.drag + case 'mousemove': // TOLERATE >> + case 'touchmove': // TOLERATE >> + drop.event = event; // store the mousemove event + if ( !drop.timer ) + // monitor drop targets + drop.tolerate( dd ); + break; + // dragend, from $.event.special.drag + case 'mouseup': // DROP >> DROPEND >> + case 'touchend': // DROP >> DROPEND >> + drop.timer = clearTimeout( drop.timer ); // delete timer + if ( dd.propagates ){ + $special.drag.hijack( event, "drop", dd ); + $special.drag.hijack( event, "dropend", dd ); + } + break; + + } + }, + + // returns the location positions of an element + locate: function( elem, index ){ + var data = $.data( elem, drop.datakey ), + $elem = $( elem ), + posi = $elem.offset() || {}, + height = $elem.outerHeight(), + width = $elem.outerWidth(), + location = { + elem: elem, + width: width, + height: height, + top: posi.top, + left: posi.left, + right: posi.left + width, + bottom: posi.top + height + }; + // drag elements might not have dropdata + if ( data ){ + data.location = location; + data.index = index; + data.elem = elem; + } + return location; + }, + + // test the location positions of an element against another OR an X,Y coord + contains: function( target, test ){ // target { location } contains test [x,y] or { location } + return ( ( test[0] || test.left ) >= target.left && ( test[0] || test.right ) <= target.right + && ( test[1] || test.top ) >= target.top && ( test[1] || test.bottom ) <= target.bottom ); + }, + + // stored tolerance modes + modes: { // fn scope: "$.event.special.drop" object + // target with mouse wins, else target with most overlap wins + 'intersect': function( event, proxy, target ){ + return this.contains( target, [ event.pageX, event.pageY ] ) ? // check cursor + 1e9 : this.modes.overlap.apply( this, arguments ); // check overlap + }, + // target with most overlap wins + 'overlap': function( event, proxy, target ){ + // calculate the area of overlap... + return Math.max( 0, Math.min( target.bottom, proxy.bottom ) - Math.max( target.top, proxy.top ) ) + * Math.max( 0, Math.min( target.right, proxy.right ) - Math.max( target.left, proxy.left ) ); + }, + // proxy is completely contained within target bounds + 'fit': function( event, proxy, target ){ + return this.contains( target, proxy ) ? 1 : 0; + }, + // center of the proxy is contained within target bounds + 'middle': function( event, proxy, target ){ + return this.contains( target, [ proxy.left + proxy.width * .5, proxy.top + proxy.height * .5 ] ) ? 1 : 0; + } + }, + + // sort drop target cache by by winner (dsc), then index (asc) + sort: function( a, b ){ + return ( b.winner - a.winner ) || ( a.index - b.index ); + }, + + // async, recursive tolerance execution + tolerate: function( dd ){ + // declare local refs + var i, drp, drg, data, arr, len, elem, + // interaction iteration variables + x = 0, ia, end = dd.interactions.length, + // determine the mouse coords + xy = [ drop.event.pageX, drop.event.pageY ], + // custom or stored tolerance fn + tolerance = drop.tolerance || drop.modes[ drop.mode ]; + // go through each passed interaction... + do if ( ia = dd.interactions[x] ){ + // check valid interaction + if ( !ia ) + return; + // initialize or clear the drop data + ia.drop = []; + // holds the drop elements + arr = []; + len = ia.droppable.length; + // determine the proxy location, if needed + if ( tolerance ) + drg = drop.locate( ia.proxy ); + // reset the loop + i = 0; + // loop each stored drop target + do if ( elem = ia.droppable[i] ){ + data = $.data( elem, drop.datakey ); + drp = data.location; + if ( !drp ) continue; + // find a winner: tolerance function is defined, call it + data.winner = tolerance ? tolerance.call( drop, drop.event, drg, drp ) + // mouse position is always the fallback + : drop.contains( drp, xy ) ? 1 : 0; + arr.push( data ); + } while ( ++i < len ); // loop + // sort the drop targets + arr.sort( drop.sort ); + // reset the loop + i = 0; + // loop through all of the targets again + do if ( data = arr[ i ] ){ + // winners... + if ( data.winner && ia.drop.length < drop.multi ){ + // new winner... dropstart + if ( !data.active[x] && !data.anyactive ){ + // check to make sure that this is not prevented + if ( $special.drag.hijack( drop.event, "dropstart", dd, x, data.elem )[0] !== false ){ + data.active[x] = 1; + data.anyactive += 1; + } + // if false, it is not a winner + else + data.winner = 0; + } + // if it is still a winner + if ( data.winner ) + ia.drop.push( data.elem ); + } + // losers... + else if ( data.active[x] && data.anyactive == 1 ){ + // former winner... dropend + $special.drag.hijack( drop.event, "dropend", dd, x, data.elem ); + data.active[x] = 0; + data.anyactive -= 1; + } + } while ( ++i < len ); // loop + } while ( ++x < end ) // loop + // check if the mouse is still moving or is idle + if ( drop.last && xy[0] == drop.last.pageX && xy[1] == drop.last.pageY ) + delete drop.timer; // idle, don't recurse + else // recurse + drop.timer = setTimeout(function(){ + drop.tolerate( dd ); + }, drop.delay ); + // remember event, to compare idleness + drop.last = drop.event; + } + +}; + +// share the same special event configuration with related events... +$special.dropinit = $special.dropstart = $special.dropend = drop; + })(jQuery); // confine scope \ No newline at end of file This diff is so big that we needed to truncate the remainder. 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 18 Jun '13

18 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d20c3481acb6/ Changeset: d20c3481acb6 User: greg Date: 2013-06-18 15:44:13 Summary: Fix for handing comments as the last element in a set_environment tag set in tool dependency definitions. Contributed by Adam Novak. Affected #: 1 file diff -r 7a6bc7485be9da1b07ac5bf8d9d62dcff327b5ba -r d20c3481acb6581b239b20a34078f927dcc2a3c2 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -431,7 +431,8 @@ if env_var_dict: env_var_dicts.append( env_var_dict ) if env_var_dicts: - action_dict[ env_elem.tag ] = env_var_dicts + # The last child of an <action type="set_environment"> might be a comment, so manually set it to be 'environment_variable'. + action_dict[ 'environment_variable' ] = env_var_dicts else: continue elif action_type == 'set_environment_for_install': https://bitbucket.org/galaxy/galaxy-central/commits/ddeb00845879/ Changeset: ddeb00845879 Branch: stable User: greg Date: 2013-06-18 15:44:13 Summary: Fix for handing comments as the last element in a set_environment tag set in tool dependency definitions. Contributed by Adam Novak. Affected #: 1 file diff -r f295092476c781987d5a31e44e7a19a372a461aa -r ddeb0084587994c3a0b9d1504950b4639ab7e7e8 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -431,7 +431,8 @@ if env_var_dict: env_var_dicts.append( env_var_dict ) if env_var_dicts: - action_dict[ env_elem.tag ] = env_var_dicts + # The last child of an <action type="set_environment"> might be a comment, so manually set it to be 'environment_variable'. + action_dict[ 'environment_variable' ] = env_var_dicts else: continue elif action_type == 'set_environment_for_install': 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.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 18 Jun '13

18 Jun '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/564f28960281/ Changeset: 564f28960281 User: dannon Date: 2013-06-18 14:59:17 Summary: Fix tool panel rendering user requirement logic. Affected #: 1 file diff -r d2d4b6ac2139f1623301990462a5e63b2952dcc1 -r 564f289602814adae34ec716c18a2d9ea0ebf1ff templates/webapps/galaxy/root/tool_menu.mako --- a/templates/webapps/galaxy/root/tool_menu.mako +++ b/templates/webapps/galaxy/root/tool_menu.mako @@ -29,7 +29,7 @@ Galaxy.toolPanel = tool_panel; ## Populate tool panel if (a) anonymous use possible or (b) user is logged in. - %if trans.app.config.require_login and trans.user: + %if trans.user or not trans.app.config.require_login: tool_panel.reset( tool_panel.parse( ${h.to_json_string( trans.app.toolbox.to_dict( trans ) )} ) ); %endif @@ -90,4 +90,4 @@ </div></div> -</%def> \ No newline at end of file +</%def> https://bitbucket.org/galaxy/galaxy-central/commits/7a6bc7485be9/ Changeset: 7a6bc7485be9 User: dannon Date: 2013-06-18 15:01:15 Summary: Merge Affected #: 1 file diff -r 564f289602814adae34ec716c18a2d9ea0ebf1ff -r 7a6bc7485be9da1b07ac5bf8d9d62dcff327b5ba templates/refresh_frames.mako --- a/templates/refresh_frames.mako +++ b/templates/refresh_frames.mako @@ -1,9 +1,10 @@ ## Include JavaScript code to refresh Galaxy application frames as needed. <%def name="handle_refresh_frames()"> - <script type="text/javascript"><% if not refresh_frames: return %> + + <script type="text/javascript"> %if 'everything' in refresh_frames: parent.location.href="${h.url_for( controller='root' )}"; %endif 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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