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[hg] galaxy 1485: Bugfix for workflow editor.
by greg＠scofield.bx.psu.edu 02 Sep '08

02 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/19c03a96b338 changeset: 1485:19c03a96b338 user: James Taylor <james(a)jamestaylor.org> date: Wed Aug 27 15:51:59 2008 -0400 description: Bugfix for workflow editor. 1 file(s) affected in this change: static/scripts/galaxy.workflow_editor.canvas.js diffs (13 lines): diff -r 30fefdf743c2 -r 19c03a96b338 static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Wed Aug 27 15:35:14 2008 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Wed Aug 27 15:51:59 2008 -0400 @@ -483,7 +483,8 @@ // zIndex tracking for bring to front zmax = $("#canvas-container").data( "zmax" ) if ( ! zmax ) { - zmax = 0; + // Start above level where connectors are drawn + zmax = 20; } f.css( "zIndex", zmax + 1 ); $("#canvas-container").data( "zmax", zmax + 1 );

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[hg] galaxy 1488: Another IE fix for stacking / deleting workflo...
by greg＠scofield.bx.psu.edu 02 Sep '08

02 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/dcaed9f80caf changeset: 1488:dcaed9f80caf user: James Taylor <james(a)jamestaylor.org> date: Thu Aug 28 13:57:23 2008 -0400 description: Another IE fix for stacking / deleting workflow editor nodes. 1 file(s) affected in this change: static/scripts/galaxy.workflow_editor.canvas.js diffs (27 lines): diff -r a7248362c37b -r dcaed9f80caf static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Thu Aug 28 13:38:54 2008 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Thu Aug 28 13:57:23 2008 -0400 @@ -446,16 +446,18 @@ parent.show_form_for_tool( "<div>No node selected</div>" ); }, activate_node : function( node ) { - this.clear_active_node(); - parent.show_form_for_tool( node.form_html, node ); - node.make_active(); - this.active_node = node; + if ( this.active_node != node ) { + this.clear_active_node(); + parent.show_form_for_tool( node.form_html, node ); + node.make_active(); + this.active_node = node; + } }, node_changed : function ( node ) { this.has_changes = true; if ( this.active_node == node ) { // Reactive with new form_html - this.activate_node( node ); + parent.show_form_for_tool( node.form_html, node ); } } });

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[hg] galaxy 1487: A better fix for bring-to-front stacking in wo...
by greg＠scofield.bx.psu.edu 02 Sep '08

02 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/a7248362c37b changeset: 1487:a7248362c37b user: James Taylor <james(a)jamestaylor.org> date: Thu Aug 28 13:38:54 2008 -0400 description: A better fix for bring-to-front stacking in workflow editor 2 file(s) affected in this change: static/scripts/galaxy.workflow_editor.canvas.js templates/workflow/editor.mako diffs (71 lines): diff -r 9e956e7b738f -r a7248362c37b static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Wed Aug 27 16:36:41 2008 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Thu Aug 28 13:38:54 2008 -0400 @@ -259,7 +259,12 @@ $(this.element).addClass( "toolForm-active" ); }, make_inactive : function () { - $(this.element).removeClass( "toolForm-active" ); + // Keep inactive nodes stacked from most to least recently active + // by moving element to the end of parent's node list + var element = this.element.get(0); + (function(p) { p.removeChild( element ); p.appendChild( element ) })(element.parentNode); + // Remove active class + $(element).removeClass( "toolForm-active" ); }, init_field_data : function ( data ) { var f = this.element; @@ -480,14 +485,6 @@ function() { $(this).attr( 'src', "../images/delete_icon_dark.png" ) }, function() { $(this).attr( 'src', "../images/delete_icon.png" ) } ) ); - // zIndex tracking for bring to front - zmax = $("#canvas-container").data( "zmax" ) - if ( ! zmax ) { - // Start above level where connectors are drawn - zmax = 20; - } - f.css( "zIndex", zmax + 1 ); - $("#canvas-container").data( "zmax", zmax + 1 ); // Place inside container f.appendTo( "#canvas-container" ); // Position in container @@ -508,16 +505,11 @@ // containment: $("#shim"), // grow: true, click: function( e, ui ) { - // Bring to front - zmax = $("#canvas-container").data( "zmax" ) - $(this).css( "zIndex", zmax + 1 ); - $("#canvas-container").data( "zmax", zmax + 1 ); // Make active workflow.activate_node( node ); }, start: function( e, ui ) { workflow.activate_node( node ); - $(this).css( 'z-index', $("#canvas-container").data( "zmax" ) + 1000 ); }, drag: function( e, ui ) { $(this).find( ".terminal" ).each( function() { @@ -525,10 +517,6 @@ }) }, stop: function( e, ui ) { - // Bring to front - zmax = $("#canvas-container").data( "zmax" ) - $(this).css( "zIndex", zmax + 1 ); - $("#canvas-container").data( "zmax", zmax + 1 ); // Redraw $(this).find( ".terminal" ).each( function() { this.terminal.redraw(); diff -r 9e956e7b738f -r a7248362c37b templates/workflow/editor.mako --- a/templates/workflow/editor.mako Wed Aug 27 16:36:41 2008 -0400 +++ b/templates/workflow/editor.mako Thu Aug 28 13:38:54 2008 -0400 @@ -394,6 +394,7 @@ } div.toolForm-active { + z-index: 1001; border: solid #8080FF 4px; margin: 3px; }

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[hg] galaxy 1484: More fixes for twill 0.9.
by greg＠scofield.bx.psu.edu 02 Sep '08

02 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/30fefdf743c2 changeset: 1484:30fefdf743c2 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Aug 27 15:35:14 2008 -0400 description: More fixes for twill 0.9. 1 file(s) affected in this change: test/base/twilltestcase.py diffs (47 lines): diff -r 8e81eced2601 -r 30fefdf743c2 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Aug 27 12:06:47 2008 -0400 +++ b/test/base/twilltestcase.py Wed Aug 27 15:35:14 2008 -0400 @@ -18,6 +18,7 @@ # Dial ClientCookie logging down (very noisy) logging.getLogger( "ClientCookie.cookies" ).setLevel( logging.WARNING ) +#log = logging.getLogger( __name__ ) class TwillTestCase( unittest.TestCase ): @@ -412,7 +413,7 @@ #Check for onchange attribute, submit a change if required for i, f in enumerate( tc.showforms() ): if i == form - 1: - break + break for i, control in enumerate( f.controls ): try: if 'refresh_on_change' in control.attrs.keys(): @@ -447,21 +448,19 @@ tc.formvalue(str(form), str(i+1), str(elem) ) #Create a new submit control, allows form to refresh, instead of going to next page control = ClientForm.SubmitControl('SubmitControl','___refresh_grouping___',{'name':'refresh_grouping'}) - control.add_to_form(tc.showforms()[form-1]) + control.add_to_form( f ) + control.fixup() #submit for refresh tc.submit('___refresh_grouping___') #start over submit_form() return self.submit_form(form, button, **kwd) - except: continue - + except Exception, e: + # Log.debug("In submit_form, caught exception: %s" %str( e )) + continue for key, value in kwd.items(): # needs to be able to handle multiple values per key if not isinstance(value, list): value = [ value ] - - for i, f in enumerate( tc.showforms() ): - if i == form - 1: - break for i, control in enumerate( f.controls ): if control.name == key: control.clear()

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[hg] galaxy 1483: Allow the user to optionally set a reference s...
by greg＠scofield.bx.psu.edu 02 Sep '08

02 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/8e81eced2601 changeset: 1483:8e81eced2601 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Aug 27 12:06:47 2008 -0400 description: Allow the user to optionally set a reference sequence in GMAJ. 1 file(s) affected in this change: tools/visualization/GMAJ.xml diffs (23 lines): diff -r c77dea3e745a -r 8e81eced2601 tools/visualization/GMAJ.xml --- a/tools/visualization/GMAJ.xml Tue Aug 26 17:07:44 2008 -0400 +++ b/tools/visualization/GMAJ.xml Wed Aug 27 12:06:47 2008 -0400 @@ -3,6 +3,7 @@ <command interpreter="python">GMAJ.py $out_file1 $maf_input $gmaj_file $filenames_file</command> <inputs> <param name="maf_input" type="data" format="maf" label="Alignment File" optional="False"/> + <param name="refseq" label="Reference Sequence" value="" type="text" help="Leave empty to allow interactive selection."/> <repeat name="annotations" title="Annotations"> <param name="species" type="select" label="Species of Annotation" multiple="False"> <options> @@ -70,7 +71,11 @@ title = "Galaxy: $maf_input.name" alignfile = input.maf +#if $refseq.value: +refseq = $refseq +#else: refseq = any +#end if tabext = .bed .gff .gtf #if $nowarn.value: nowarn = $nowarn

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welcome page
by Cathy Riemer 29 Aug '08

29 Aug '08

I had to smile when I saw the "Noodly Appendages". :-) -Cathy

2 1

Main is at rev 1482:c77dea3e745a
by Greg Von Kuster 27 Aug '08

27 Aug '08

1 0

[hg] galaxy 1482: Fix for new twill version 0.9.
by greg＠scofield.bx.psu.edu 27 Aug '08

27 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/c77dea3e745a changeset: 1482:c77dea3e745a user: Greg Von Kuster <greg(a)bx.psu.edu> date: Tue Aug 26 17:07:44 2008 -0400 description: Fix for new twill version 0.9. 1 file(s) affected in this change: test/base/twilltestcase.py diffs (36 lines): diff -r ed448639d90e -r c77dea3e745a test/base/twilltestcase.py --- a/test/base/twilltestcase.py Tue Aug 26 10:39:47 2008 -0400 +++ b/test/base/twilltestcase.py Tue Aug 26 17:07:44 2008 -0400 @@ -7,7 +7,7 @@ import twill import twill.commands as tc -from twill.other_packages import ClientForm +from twill.other_packages._mechanize_dist import ClientForm from elementtree import ElementTree buffer = StringIO.StringIO() @@ -410,7 +410,10 @@ def submit_form( self, form=1, button="runtool_btn", **kwd ): """Populates and submits a form from the keyword arguments""" #Check for onchange attribute, submit a change if required - for i, control in enumerate(tc.showforms()[form-1].controls): + for i, f in enumerate( tc.showforms() ): + if i == form - 1: + break + for i, control in enumerate( f.controls ): try: if 'refresh_on_change' in control.attrs.keys(): changed = False @@ -456,7 +459,10 @@ if not isinstance(value, list): value = [ value ] - for i, control in enumerate(tc.showforms()[form-1].controls): + for i, f in enumerate( tc.showforms() ): + if i == form - 1: + break + for i, control in enumerate( f.controls ): if control.name == key: control.clear() if control.is_of_kind("text"):

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[hg] galaxy 1481: Upgraded twill to 0.9.
by greg＠scofield.bx.psu.edu 27 Aug '08

27 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/ed448639d90e changeset: 1481:ed448639d90e user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Aug 26 10:39:47 2008 -0400 description: Upgraded twill to 0.9. 1 file(s) affected in this change: eggs.ini diffs (21 lines): diff -r 6de3006c62b3 -r ed448639d90e eggs.ini --- a/eggs.ini Mon Aug 25 15:28:57 2008 -0400 +++ b/eggs.ini Tue Aug 26 10:39:47 2008 -0400 @@ -41,7 +41,7 @@ simplejson = 1.5 SQLAlchemy = 0.3.11 Tempita = 0.1 -twill = 0.8.3 +twill = 0.9 WebError = 0.8a WebHelpers = 0.2 WebOb = 0.8.5 @@ -86,7 +86,7 @@ simplejson = http://cheeseshop.python.org/packages/source/s/simplejson/simplejson-1.5.ta… SQLAlchemy = http://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-0.3.11.tar.gz Tempita = http://pypi.python.org/packages/source/T/Tempita/Tempita-0.1.tar.gz -twill = http://darcs.idyll.org/~t/projects/twill-0.8.3.tar.gz +twill = http://darcs.idyll.org/~t/projects/twill-0.9.tar.gz WebError = http://pypi.python.org/packages/source/W/WebError/WebError-0.8a.tar.gz WebHelpers = http://pypi.python.org/packages/source/W/WebHelpers/WebHelpers-0.2.tar.gz WebOb = http://pypi.python.org/packages/source/W/WebOb/WebOb-0.8.5.tar.gz

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[hg] galaxy 1479: Internet explorer fixes and support -- popup m...
by greg＠scofield.bx.psu.edu 27 Aug '08

27 Aug '08

details: http://www.bx.psu.edu/hg/galaxy/rev/b671c301674a changeset: 1479:b671c301674a user: James Taylor <james(a)jamestaylor.org> date: Fri Aug 22 17:47:43 2008 -0400 description: Internet explorer fixes and support -- popup menus and dialogs work better on IE6+, workflow editor works on IE7 (using excanvas). It actually *nearly* works on IE6 but there are some layout problems that are probably not worth wasting time on. If any IE users can test this that would be great! 13 file(s) affected in this change: static/june_2007_style/base.css.tmpl static/june_2007_style/blue/base.css static/june_2007_style/blue/panel_layout.css static/june_2007_style/panel_layout.css.tmpl static/scripts/galaxy.base.js static/scripts/galaxy.panels.js static/scripts/galaxy.ui.scrollPanel.js static/scripts/galaxy.workflow_editor.canvas.js static/scripts/packed/galaxy.base.js static/scripts/packed/galaxy.panels.js static/scripts/packed/galaxy.workflow_editor.canvas.js templates/workflow/editor.mako templates/workflow/index.mako diffs (648 lines): diff -r 6eac08f7edcf -r b671c301674a static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Fri Aug 22 17:44:32 2008 -0400 +++ b/static/june_2007_style/base.css.tmpl Fri Aug 22 17:47:43 2008 -0400 @@ -358,7 +358,7 @@ font-weight: bold; display: inline-block; cursor: pointer; - margin: -1px; padding: 2px; + padding: 2px; border: solid #aaaaaa 1px; padding-right: 0.5em; padding-left: 0.5em; diff -r 6eac08f7edcf -r b671c301674a static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Fri Aug 22 17:44:32 2008 -0400 +++ b/static/june_2007_style/blue/base.css Fri Aug 22 17:47:43 2008 -0400 @@ -356,7 +356,7 @@ font-weight: bold; display: inline-block; cursor: pointer; - margin: -1px; padding: 2px; + padding: 2px; border: solid #aaaaaa 1px; padding-right: 0.5em; padding-left: 0.5em; diff -r 6eac08f7edcf -r b671c301674a static/june_2007_style/blue/panel_layout.css --- a/static/june_2007_style/blue/panel_layout.css Fri Aug 22 17:44:32 2008 -0400 +++ b/static/june_2007_style/blue/panel_layout.css Fri Aug 22 17:47:43 2008 -0400 @@ -244,14 +244,6 @@ top: 0; left: 0; width: 100%; height: 100%; z-index: 20000; } -#overlay-inner { - width: 100%; height: 100%; - background-color:#FFF; - filter:alpha(opacity=75); - -moz-opacity: 0.75; - opacity: 0.75; - z-index: 20000; -} .dialog-box-container { position: relative; @@ -259,15 +251,11 @@ margin-right: auto; margin-left: auto; } -.dialog-box-underlay { - position: absolute; - left: -1em; - right: -1em; - top: -1em; - bottom: -1em; - opacity: 0.5; - background: black; - z-index: -1; + +.dialog-box-wrapper { + position: relative; + padding: 1em; + background-color: rgba(0,0,0,0.5); -moz-border-radius: 1em; -webkit-border-radius: 1em; } diff -r 6eac08f7edcf -r b671c301674a static/june_2007_style/panel_layout.css.tmpl --- a/static/june_2007_style/panel_layout.css.tmpl Fri Aug 22 17:44:32 2008 -0400 +++ b/static/june_2007_style/panel_layout.css.tmpl Fri Aug 22 17:47:43 2008 -0400 @@ -244,30 +244,17 @@ z-index: 20000; } -#overlay-inner { - width: 100%; height: 100%; - background-color:#FFF; - filter:alpha(opacity=75); - -moz-opacity: 0.75; - opacity: 0.75; - z-index: 20000; -} - .dialog-box-container { position: relative; margin-top: 80px; margin-right: auto; margin-left: auto; } -.dialog-box-underlay { - position: absolute; - left: -1em; - right: -1em; - top: -1em; - bottom: -1em; - opacity: 0.5; - background: black; - z-index: -1; + +.dialog-box-wrapper { + position: relative; + padding: 1em; + background-color: rgba(0,0,0,0.5); -moz-border-radius: 1em; -webkit-border-radius: 1em; } diff -r 6eac08f7edcf -r b671c301674a static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/galaxy.base.js Fri Aug 22 17:47:43 2008 -0400 @@ -29,13 +29,10 @@ function ensure_popup_helper() { // And the helper below the popup menus if ( $( "#popup-helper" ).length == 0 ) { - var e = $("<div id='popup-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; z-index: 15000;'></div>"); - if ( $.browser.ie ) { - // Element will not capture drags in ie without nonzero opacity, - // but causes flashing in firefox with nonzero opacity - e.css( "opacity", "0.01" ); - } - e.appendTo("body").hide(); + $( "<div id='popup-helper'/>" ).css( { + background: 'white', opacity: 0, zIndex: 15000, + position: 'absolute', top: 0, left: 0, width: '100%', height: '100%' + } ).appendTo( "body" ).hide(); } } diff -r 6eac08f7edcf -r b671c301674a static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/galaxy.panels.js Fri Aug 22 17:47:43 2008 -0400 @@ -6,13 +6,10 @@ function ensure_dd_helper() { // Insert div that covers everything when dragging the borders if ( jq( "#DD-helper" ).length == 0 ) { - var e = jq("<div id='DD-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; z-index: 9000;'></div>"); - if ( jq.browser.ie ) { - // Element will not capture drags in ie without nonzero opacity, - // but causes flashing in firefox with nonzero opacity - e.css( "opacity", "0.01" ); - } - e.appendTo("body").hide(); + $( "<div id='DD-helper'/>" ).css( { + background: 'white', opacity: 0, zIndex: 9000, + position: 'absolute', top: 0, left: 0, width: '100%', height: '100%' + } ).appendTo( "body" ).hide(); } } @@ -179,6 +176,46 @@ return { handle_minwidth_hint: handle_minwidth_hint }; }; +// Modal dialog boxes + +function hide_modal() { + $(".dialog-box-container" ).fadeOut( function() { $("#overlay").hide(); } ); +}; + +function show_modal( title, body, buttons, extra_buttons ) { + $( ".dialog-box" ).find( ".title" ).html( title ); + var b = $( ".dialog-box" ).find( ".buttons" ).html( "" ); + if ( buttons ) { + $.each( buttons, function( name, value ) { + b.append( $( '<button/>' ).text( name ).click( value ) ); + b.append( " " ); + }); + b.show(); + } else { + b.hide(); + } + var b = $( ".dialog-box" ).find( ".extra_buttons" ).html( "" ); + if ( extra_buttons ) { + $.each( extra_buttons, function( name, value ) { + b.append( $( '<button/>' ).text( name ).click( value ) ); + b.append( " " ); + }); + b.show(); + } else { + b.hide(); + } + if ( body == "progress" ) { + body = $( "<img src='../images/yui/rel_interstitial_loading.gif')' />" ); + } + $( ".dialog-box" ).find( ".body" ).html( body ); + if ( ! $(".dialog-box-container").is( ":visible" ) ) { + $("#overlay").show(); + $(".dialog-box-container").fadeIn() + } +}; + +// Popup -- is this up to date? + function make_popupmenu( button_element, options ) { var menu_element = $( "<div class='popupmenu'><div class='popupmenu-top'><div class='popupmenu-top-inner'/></div></div>" ).appendTo( "body" ); $.each( options, function( k, v ) { diff -r 6eac08f7edcf -r b671c301674a static/scripts/galaxy.ui.scrollPanel.js --- a/static/scripts/galaxy.ui.scrollPanel.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/galaxy.ui.scrollPanel.js Fri Aug 22 17:47:43 2008 -0400 @@ -18,7 +18,7 @@ element_w = element.width(), element_h = element.height(), moved = false, - close = 5, + close_dist = 5, nudge = 23, // Legal panel range p_min_x = - ( panel_w - viewport_w ), @@ -34,21 +34,21 @@ mouse_x = ui.position.left + instance.offset.click.left; mouse_y = ui.position.top + instance.offset.click.top; // Move it - if ( ( panel_pos.left < p_max_x ) && ( mouse_x - close < min_vis_x ) ) { + if ( ( panel_pos.left < p_max_x ) && ( mouse_x - close_dist < min_vis_x ) ) { var t = Math.min( nudge, p_max_x - panel_pos.left ); panel.css( "left", panel_pos.left + t ); moved = true; instance.offset.parent.left += t; ui.position.left -= t } - if ( ( ! moved ) && ( panel_pos.left > p_min_x ) && ( mouse_x + close > max_vis_x ) ) { + if ( ( ! moved ) && ( panel_pos.left > p_min_x ) && ( mouse_x + close_dist > max_vis_x ) ) { var t = Math.min( nudge, panel_pos.left - p_min_x ); panel.css( "left", panel_pos.left - t ); moved = true; instance.offset.parent.left -= t; ui.position.left += t; } - if ( ( ! moved ) && ( panel_pos.top < p_max_y ) && ( mouse_y - close < min_vis_y ) ) { + if ( ( ! moved ) && ( panel_pos.top < p_max_y ) && ( mouse_y - close_dist < min_vis_y ) ) { var t = Math.min( nudge, p_max_y - panel_pos.top ); panel.css( "top", panel_pos.top + t ); // Firefox sometimes moves by less, so we need to check. Yuck. @@ -57,7 +57,7 @@ ui.position.top -= amount_moved; moved = true; } - if ( ( ! moved ) && ( panel_pos.top > p_min_y ) && ( mouse_y + close > max_vis_y ) ) { + if ( ( ! moved ) && ( panel_pos.top > p_min_y ) && ( mouse_y + close_dist > max_vis_y ) ) { var t = Math.min( nudge, panel_pos.top - p_min_x ); panel.css( "top", ( panel_pos.top - t ) + "px" ); // Firefox sometimes moves by less, so we need to check. Yuck. diff -r 6eac08f7edcf -r b671c301674a static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/galaxy.workflow_editor.canvas.js Fri Aug 22 17:47:43 2008 -0400 @@ -32,15 +32,16 @@ this.datatype = datatype; } -OutputTerminal.prototype.__proto__ = Terminal.prototype; +OutputTerminal.prototype = new Terminal; function InputTerminal( element, datatypes ) { Terminal.call( this, element ); this.datatypes = datatypes; } -InputTerminal.prototype = { - __proto__: Terminal.prototype, +InputTerminal.prototype = new Terminal; + +$.extend( InputTerminal.prototype, { can_accept: function ( other ) { if ( this.connectors.length < 1 ) { for ( t in this.datatypes ) { @@ -53,7 +54,7 @@ } return false; } -} +}); function Connector( handle1, handle2 ) { this.canvas = null; @@ -81,6 +82,10 @@ var canvas_container = $("#canvas-container"); if ( ! this.canvas ) { this.canvas = document.createElement( "canvas" ); + // excanvas specific hack + if ( window.G_vmlCanvasManager ) { + G_vmlCanvasManager.initElement( this.canvas ); + } canvas_container.append( $(this.canvas) ); if ( this.dragging ) { this.canvas.style.zIndex = "300" } } @@ -182,14 +187,14 @@ t.remove(); }))) .bind( "mouseleave", function() { - $(this).fadeOut( "fast", function() { $(this).remove() } ) + $(this).remove(); }); // Position it and show t.css( { top: $(this).offset().top - 2, left: $(this).offset().left - t.width(), 'padding-right': $(this).width() } - ).fadeIn( "fast" ); + ).show(); } }, function() {} @@ -272,12 +277,12 @@ var node = this; var b = f.find( ".toolFormBody" ); b.find( "div" ).remove(); - var ibox = $("<div class='inputs'/>").appendTo( b ); + var ibox = $("<div class='inputs'></div>").appendTo( b ); $.each( data.data_inputs, function( i, input ) { - t = $("<div class='terminal input-terminal'></div>") + var t = $("<div class='terminal input-terminal'></div>"); node.enable_input_terminal( t, input.name, input.extensions ); - ibox.append( $("<div class='form-row dataRow input-data-row' name='" + input.name + "'>" + input.label + "</div></div>" ).prepend( t ) ); - }); + ibox.append( $("<div class='form-row dataRow input-data-row' name='" + input.name + "'>" + input.label + "</div>" ).prepend( t ) ); + }); if ( ( data.data_inputs.length > 0 ) && ( data.data_outputs.length > 0 ) ) { b.append( $( "<div class='rule'></div>" ) ); } @@ -305,8 +310,8 @@ } // Update input rows var old_body = el.find( "div.inputs" ); - var new_body = $("<div class='inputs'/>"); - old = old_body.find( "div.input-data-row") + var new_body = $("<div class='inputs'></div>"); + var old = old_body.find( "div.input-data-row") $.each( data.data_inputs, function( i, input ) { var t = $("<div class='terminal input-terminal'></div>"); node.enable_input_terminal( t, input.name, input.extensions ); @@ -322,7 +327,7 @@ $(this).remove(); }); // Append to new body - new_body.append( $("<div class='form-row dataRow input-data-row' name='" + input.name + "'>" + input.label + "</div></div>" ).prepend( t ) ); + new_body.append( $("<div class='form-row dataRow input-data-row' name='" + input.name + "'>" + input.label + "</div>" ).prepend( t ) ); }); old_body.replaceWith( new_body ); // Cleanup any leftover terminals @@ -468,13 +473,21 @@ f.append( b ) // Fix width to computed width // Now add floats - var buttons = $("<div class='buttons' style='float: right'></div>"); - buttons.append( $("<img src='../images/delete_icon.png' />").click( function() { + var buttons = $("<div class='buttons' style='float: right;'></div>"); + buttons.append( $("<img src='../images/delete_icon.png' />").click( function( e ) { node.destroy(); } ).hover( function() { $(this).attr( 'src', "../images/delete_icon_dark.png" ) }, function() { $(this).attr( 'src', "../images/delete_icon.png" ) } ) ); + // zIndex tracking for bring to front + zmax = $("#canvas-container").data( "zmax" ) + if ( ! zmax ) { + zmax = 0; + } + f.css( "zIndex", zmax + 1 ); + $("#canvas-container").data( "zmax", zmax + 1 ); + // Place inside container f.appendTo( "#canvas-container" ); // Position in container var o = $("#canvas-container").position(); @@ -494,13 +507,16 @@ // containment: $("#shim"), // grow: true, click: function( e, ui ) { - var element = $(this).data("draggable").element.get(0); - (function(p) { p.removeChild( element ); p.appendChild( element ) })(element.parentNode) + // Bring to front + zmax = $("#canvas-container").data( "zmax" ) + $(this).css( "zIndex", zmax + 1 ); + $("#canvas-container").data( "zmax", zmax + 1 ); + // Make active workflow.activate_node( node ); }, start: function( e, ui ) { workflow.activate_node( node ); - $(this).css( 'z-index', '1000' ); + $(this).css( 'z-index', $("#canvas-container").data( "zmax" ) + 1000 ); }, drag: function( e, ui ) { $(this).find( ".terminal" ).each( function() { @@ -508,9 +524,11 @@ }) }, stop: function( e, ui ) { - var element = $(this).data("draggable").element.get(0); - (function(p) { p.removeChild( element ); p.appendChild( element ) })(element.parentNode) - $(this).css( 'z-index', '100' ); + // Bring to front + zmax = $("#canvas-container").data( "zmax" ) + $(this).css( "zIndex", zmax + 1 ); + $("#canvas-container").data( "zmax", zmax + 1 ); + // Redraw $(this).find( ".terminal" ).each( function() { this.terminal.redraw(); }); diff -r 6eac08f7edcf -r b671c301674a static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/packed/galaxy.base.js Fri Aug 22 17:47:43 2008 -0400 @@ -1,1 +1,1 @@ -jQuery(document).ready(function(){jQuery("a[@confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[@popupmenu]").each(function(){var B={};$(this).find("a").each(function(){var C=$(this).attr("confirm"),D=$(this).attr("href"),E=$(this).attr("target");B[$(this).text()]=function(){if(!C||confirm(C)){var F=window;if(E=="_parent"){F=window.parent}F.location=D}}});var A=$("#"+$(this).attr("popupmenu"));make_popupmenu(A,B);$(this).remove();A.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){var A=$("<div id='popup-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; z-index: 15000;'></div>");if($.browser.ie){A.css("opacity","0.01")}A.appendTo("body").hide()}}function make_popupmenu(D,B){ensure_popup_helper();var A=$("<div class='popupmenu'></div>").appendTo("body");$.each(B,function(G,F){$("<div class='popupmenu-item' />").html(G).click(F).appendTo(A)});var C=functi on(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E=function(F){var G=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.pageY-2,left:F.pageX-2});return false};$(D).click(E)}; \ No newline at end of file +jQuery(document).ready(function(){jQuery("a[@confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});jQuery("div[@popupmenu]").each(function(){var B={};$(this).find("a").each(function(){var C=$(this).attr("confirm"),D=$(this).attr("href"),E=$(this).attr("target");B[$(this).text()]=function(){if(!C||confirm(C)){var F=window;if(E=="_parent"){F=window.parent}F.location=D}}});var A=$("#"+$(this).attr("popupmenu"));make_popupmenu(A,B);$(this).remove();A.show()})});function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",top:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(D,B){ensure_popup_helper();var A=$("<div class='popupmenu'></div>").appendTo("body");$.each(B,function(G,F){$("<div class='popupmenu-item' />").html(G).click(F).appendTo(A)});var C=function(){$(A).unbind().hide();$("#popup-helper").unbind().hide()};var E =function(F){var G=$(D).offset();$("#popup-helper").mousedown(C).show();$(A).click(C).css({top:-1000}).show().css({top:F.pageY-2,left:F.pageX-2});return false};$(D).click(E)}; \ No newline at end of file diff -r 6eac08f7edcf -r b671c301674a static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/packed/galaxy.panels.js Fri Aug 22 17:47:43 2008 -0400 @@ -1,1 +1,1 @@ -var hidden_width=7;var border_tweak=9;var jq=jQuery;function ensure_dd_helper(){if(jq("#DD-helper").length==0){var A=jq("<div id='DD-helper' style='background: white; opacity: 0.00; top: 0; left: 0; width: 100%; height: 100%; position: absolute; z-index: 9000;'></div>");if(jq.browser.ie){A.css("opacity","0.01")}A.appendTo("body").hide()}}function make_left_panel(E,A,B){var D=false;var C=null;resize=function(F){var 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false},drag:function(F,G){x=G.position.left;x=Math.min(400,Math.max(100,x));if(D){jq(E).css("left",0);jq(B).removeClass("hidden");D=false}resize(x);G.position.left=x;G.position.top=$(this).data("draggable").originalPosition.top},click:function(){toggle()}}).find("div").show()}function make_right_panel(A,E,G){var I=false;var F=false;var C=null;var D=function(J){jq(A).css("width",J);jq(E).css("right",J+9);jq(G).css("right",J).css("left","");if(document.recalc){document.recalc()}};var H=function(){if(I){jq(G).removeClass("hover");jq(G).animate({right:C},"fast");jq(A).css("right",-C).show().animate({right:0},"fast",function(){D(C);jq(G).removeClass("hidden")});I=false}else{C=jq(document).width()-jq(G).position().left-border_tweak;jq(E).css("right",hidden_width+1);if(document.recalc){document.recalc()}jq(G).removeClass("hover");jq(A).animate({right:-C},"fast");jq(G).anima te({right:-1},"fast",function(){jq(this).addClass("hidden")});I=true}F=false};var B=function(J){var 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$(D).height()+9,left:F.left+$(D).width()-$(A).width()})};$(D).click(E)}; \ No newline at end of file diff -r 6eac08f7edcf -r b671c301674a static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js Fri Aug 22 17:44:32 2008 -0400 +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js Fri Aug 22 17:47:43 2008 -0400 @@ -1,1 +1,1 @@ -function Terminal(A){this.element=A;this.connectors=[]}Terminal.prototype={connect:function(A){this.connectors.push(A);if(this.node){this.node.changed()}},disconnect:function(A){this.connectors.splice($.inArray(A,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(A,B){B.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(A,B){B.destroy()})}};function OutputTerminal(A,B){Terminal.call(this,A);this.datatype=B}OutputTerminal.prototype.__proto__=Terminal.prototype;function InputTerminal(A,B){Terminal.call(this,A);this.datatypes=B}InputTerminal.prototype={__proto__:Terminal.prototype,can_accept:function(A){if(this.connectors.length<1){for(t in this.datatypes){if(A.datatype=="input"){return true}if(issubtype(A.datatype,this.datatypes[t])){return true}}}return false}};function Connector(B,A){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototype ,{connect:function(B,A){this.handle1=B;this.handle1.connect(this);this.handle2=A;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var C=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");C.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var L=function(S){return $(S).offset().left-C.offset().left};var G=function(S){return $(S).offset().top-C.offset().top};var F=L(this.handle1.element)+5;var E=G(this.handle1.element)+5;var N=L(this.handle2.element)+5;var K=G(this.handle2.element)+5;var D=100;var I=Math.min(F,N);var A=Math.max(F,N);var H=Math.min(E,K);var R=Math.max(E,K);var B=Math.min(Math.max(Math.abs(R-H)/2,100),300);var M=I-D;var Q=H-D;var O=A-I+2*D;var J=R-H+2*D;this.canvas.style.left=M+"px";this.canvas.style.top=Q+"px";this.canvas.setAttribute("width",O);this.canvas.setAttribute("h eight",J);F-=M;E-=Q;N-=M;K-=Q;var P=this.canvas.getContext("2d");P.lineCap="round";P.strokeStyle=this.outer_color;P.lineWidth=7;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke();P.strokeStyle=this.inner_color;P.lineWidth=5;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke()}});function Node(A){this.element=A;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new InputTerminal(this,B);D.node=node;D.name=A;$(this).droppable({tolerance:"intersect",accept:function(E){E=E.get(0);return(E.terminal)&&(D.can_accept(E.terminal))},activeClass:"input-terminal-active",over:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(I,G){var E=$(this).data("droppable");var F=G.draggable.get(0).terminal;var H= E.element.get(0).terminal;var J=new Connector();J.connect(F,H);J.redraw()}});$(this).hoverIntent(function(){if(D.connectors.length>0){var E=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).fadeOut("fast",function(){$(this).remove()})});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).fadeIn("fast")}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);E.terminal=new OutputTerm inal(E);var F=new Connector();this.drag_temp_connector=F;F.dragging=true;F.connect(this.terminal,E.terminal);return E},drag:function(F,E){h=E.helper.get(0);h.terminal.redraw()},stop:function(F,E){this.drag_temp_connector.destroy()}});node.output_terminals[A]=D})},redraw:function(){$.each(this.input_terminals,function(A,B){B.redraw()});$.each(this.output_terminals,function(A,B){B.redraw()})},destroy:function(){$.each(this.input_terminals,function(A,B){B.destroy();$(B.element).droppable("destroy")});$.each(this.output_terminals,function(A,B){B.destroy();$(B.element).draggable("destroy")});$(this.element).draggable("destroy").remove();workflow.remove_node(this)},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){$(this.element).removeClass("toolForm-active")},init_field_data:function(D){var C=this.element;if(D.type){this.type=D.type}this.form_html=D.form_html;this.tool_state=D.tool_state;this.tool_errors=D.tool_errors;if(this.tool_error s){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var B=this;var A=C.find(".toolFormBody");A.find("div").remove();var E=$("<div class='inputs'/>").appendTo(A);$.each(D.data_inputs,function(G,F){t=$("<div class='terminal input-terminal'></div>");B.enable_input_terminal(t,F.name,F.extensions);E.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div></div>").prepend(t))});if((D.data_inputs.length>0)&&(D.data_outputs.length>0)){A.append($("<div class='rule'></div>"))}$.each(D.data_outputs,function(I,F){var H=$("<div class='terminal output-terminal'></div>");B.enable_output_terminal(H,F.name,F.extension);var G=F.name;if(F.extension!="input"){G=G+" ("+F.extension+")"}A.append($("<div class='form-row dataRow'>"+G+"</div>").append(H))});workflow.node_changed(this)},update_field_data:function(D){var B=$(this.element),C=this;this.tool_state=D.tool_state;this.form_html=D.form_html;this.tool_errors=D.tool_errors;if(this.tool_errors ){B.addClass("tool-node-error")}else{B.removeClass("tool-node-error")}var E=B.find("div.inputs");var A=$("<div class='inputs'/>");old=E.find("div.input-data-row");$.each(D.data_inputs,function(H,F){var G=$("<div class='terminal input-terminal'></div>");C.enable_input_terminal(G,F.name,F.extensions);E.find("div[name="+F.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var I=this.terminal.connectors[0];if(I){G[0].terminal.connectors[0]=I;I.handle2=G[0].terminal}});$(this).remove()});A.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div></div>").prepend(G))});E.replaceWith(A);E.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(C){var A=$(this.element).find(".toolFormBody");A.find("div").remove();var B="<div style='color: red; text-style: italic;'>"+C+"</div>";this.form_html=B;A.html(B);workflow.node_changed(this)},changed:function(){workflow .node_changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(A){A.id=this.id_counter;this.id_counter++;this.nodes[A.id]=A;this.has_changes=true;A.workflow=this},remove_node:function(A){if(this.active_node==A){this.clear_active_node()}delete this.nodes[A.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(B,A){A.destroy();wf.remove_node(A)})},to_simple:function(){var A={};$.each(this.nodes,function(B,D){var E={};$.each(D.input_terminals,function(F,G){E[G.name]=null;$.each(G.connectors,function(H,I){E[G.name]={id:I.handle1.node.id,output_name:I.handle1.name}})});var C={id:D.id,type:D.type,tool_id:D.tool_id,tool_state:D.tool_state,tool_errors:D.tool_errors,input_connections:E,position:$(D.element).position()};A[D.id]=C});return{steps:A}},from_simple:function(A){wf=this;var B=0;wf.name=A.name;$.each(A.steps,function(E,D){var C=prebuild_node("tool",D. name,D.tool_id);C.init_field_data(D);if(D.position){C.element.css({top:D.position.top,left:D.position.left})}C.id=D.id;wf.nodes[C.id]=C;B=Math.max(B,parseInt(E))});wf.id_counter=B+1;$.each(A.steps,function(E,D){var C=wf.nodes[E];$.each(D.input_connections,function(G,F){if(F){var H=wf.nodes[F.id];var I=new Connector();I.connect(H.output_terminals[F.output_name],C.input_terminals[G]);I.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive()}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(A){this.clear_active_node();parent.show_form_for_tool(A.form_html,A);A.make_active();this.active_node=A},node_changed:function(A){this.has_changes=true;if(this.active_node==A){this.activate_node(A)}}});function prebuild_node(H,F,K){var E=$("<div class='toolForm toolFormInCanvas'></div>");var C=new Node(E);C.type=H;if(H=="tool"){C.tool_id=K}var J=$("<div class='toolFormTitle unselectable'>"+F+"</div>");E.append(J);E.css( "left",$(window).scrollLeft()+20);E.css("top",$(window).scrollTop()+20);var I=$("<div class='toolFormBody'></div>");var D="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";I.append(D);C.form_html=D;E.append(I);var G=$("<div class='buttons' style='float: right'></div>");G.append($("<img src='../images/delete_icon.png' />").click(function(){C.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));E.appendTo("#canvas-container");var B=$("#canvas-container").position();E.css({left:(-B.left)+10,top:(-B.top)+10});var A=E.width();G.prependTo(J);A+=(G.width()+10);E.css("width",A);$(E).draggable({cursor:"move",scrollPanel:true,panel:$("#canvas-container"),scrollSensitivity:10,scrollSpeed:20,click:function(N,M){var L=$(this).data("draggable").element.get(0);(function(O){O.removeChild(L);O.appendChild(L)})(L.parentNode);workflow.activate _node(C)},start:function(M,L){workflow.activate_node(C);$(this).css("z-index","1000")},drag:function(M,L){$(this).find(".terminal").each(function(){this.terminal.redraw()})},stop:function(N,M){var L=$(this).data("draggable").element.get(0);(function(O){O.removeChild(L);O.appendChild(L)})(L.parentNode);$(this).css("z-index","100");$(this).find(".terminal").each(function(){this.terminal.redraw()});workflow.node_changed(this)}});return C}var ext_to_type=null;var type_to_type=null;function issubtype(B,A){B=ext_to_type[B];A=ext_to_type[A];return(A in type_to_type[B])}function populate_datatype_info(A){ext_to_type=A.ext_to_class_name;type_to_type=A.class_to_classes}; \ No newline at end of file +function Terminal(A){this.element=A;this.connectors=[]}Terminal.prototype={connect:function(A){this.connectors.push(A);if(this.node){this.node.changed()}},disconnect:function(A){this.connectors.splice($.inArray(A,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(A,B){B.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(A,B){B.destroy()})}};function OutputTerminal(A,B){Terminal.call(this,A);this.datatype=B}OutputTerminal.prototype=new Terminal;function InputTerminal(A,B){Terminal.call(this,A);this.datatypes=B}InputTerminal.prototype=new Terminal;$.extend(InputTerminal.prototype,{can_accept:function(A){if(this.connectors.length<1){for(t in this.datatypes){if(A.datatype=="input"){return true}if(issubtype(A.datatype,this.datatypes[t])){return true}}}return false}});function Connector(B,A){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365"}$.extend(Connector.prototy pe,{connect:function(B,A){this.handle1=B;this.handle1.connect(this);this.handle2=A;this.handle2.connect(this)},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var C=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}C.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var L=function(S){return $(S).offset().left-C.offset().left};var G=function(S){return $(S).offset().top-C.offset().top};var F=L(this.handle1.element)+5;var E=G(this.handle1.element)+5;var N=L(this.handle2.element)+5;var K=G(this.handle2.element)+5;var D=100;var I=Math.min(F,N);var A=Math.max(F,N);var H=Math.min(E,K);var R=Math.max(E,K);var B=Math.min(Math.max(Math.abs(R-H)/2,100),300);var M=I-D;var Q=H-D;var O=A-I+2*D;var J=R-H+2*D;this.canvas.style.left=M+"px";this.canvas.styl e.top=Q+"px";this.canvas.setAttribute("width",O);this.canvas.setAttribute("height",J);F-=M;E-=Q;N-=M;K-=Q;var P=this.canvas.getContext("2d");P.lineCap="round";P.strokeStyle=this.outer_color;P.lineWidth=7;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke();P.strokeStyle=this.inner_color;P.lineWidth=5;P.beginPath();P.moveTo(F,E);P.bezierCurveTo(F+B,E,N-B,K,N,K);P.stroke()}});function Node(A){this.element=A;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new InputTerminal(this,B);D.node=node;D.name=A;$(this).droppable({tolerance:"intersect",accept:function(E){E=E.get(0);return(E.terminal)&&(D.can_accept(E.terminal))},activeClass:"input-terminal-active",over:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#BBFFBB"},out:function(F,E){E.helper.get(0).terminal.connectors[0].inner_color="#FFFFFF"},drop:function(I ,G){var E=$(this).data("droppable");var F=G.draggable.get(0).terminal;var H=E.element.get(0).terminal;var J=new Connector();J.connect(F,H);J.redraw()}});$(this).hoverIntent(function(){if(D.connectors.length>0){var E=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='buttons'></div>").append($("<img src='../images/delete_icon.png' />").click(function(){$.each(D.connectors,function(G,F){F.destroy()});E.remove()}))).bind("mouseleave",function(){$(this).remove()});E.css({top:$(this).offset().top-2,left:$(this).offset().left-E.width(),"padding-right":$(this).width()}).show()}},function(){});node.input_terminals[A]=D})},enable_output_terminal:function(C,A,B){node=this;$(C).each(function(){var D=this.terminal=new OutputTerminal(this,B);D.node=node;D.name=A;$(this).draggable({scrollPanel:true,panel:$("#canvas-container"),helper:function(){var E=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container"). get(0);E.terminal=new OutputTerminal(E);var F=new Connector();this.drag_temp_connector=F;F.dragging=true;F.connect(this.terminal,E.terminal);return E},drag:function(F,E){h=E.helper.get(0);h.terminal.redraw()},stop:function(F,E){this.drag_temp_connector.destroy()}});node.output_terminals[A]=D})},redraw:function(){$.each(this.input_terminals,function(A,B){B.redraw()});$.each(this.output_terminals,function(A,B){B.redraw()})},destroy:function(){$.each(this.input_terminals,function(A,B){B.destroy();$(B.element).droppable("destroy")});$.each(this.output_terminals,function(A,B){B.destroy();$(B.element).draggable("destroy")});$(this.element).draggable("destroy").remove();workflow.remove_node(this)},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){$(this.element).removeClass("toolForm-active")},init_field_data:function(D){var C=this.element;if(D.type){this.type=D.type}this.form_html=D.form_html;this.tool_state=D.tool_state;this.tool_errors= D.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var B=this;var A=C.find(".toolFormBody");A.find("div").remove();var E=$("<div class='inputs'></div>").appendTo(A);$.each(D.data_inputs,function(H,F){var G=$("<div class='terminal input-terminal'></div>");B.enable_input_terminal(G,F.name,F.extensions);E.append($("<div class='form-row dataRow input-data-row' name='"+F.name+"'>"+F.label+"</div>").prepend(G))});if((D.data_inputs.length>0)&&(D.data_outputs.length>0)){A.append($("<div class='rule'></div>"))}$.each(D.data_outputs,function(I,F){var H=$("<div class='terminal output-terminal'></div>");B.enable_output_terminal(H,F.name,F.extension);var G=F.name;if(F.extension!="input"){G=G+" ("+F.extension+")"}A.append($("<div class='form-row dataRow'>"+G+"</div>").append(H))});workflow.node_changed(this)},update_field_data:function(E){var C=$(this.element),D=this;this.tool_state=E.tool_state;this.form_html=E.form_html;this.tool_error s=E.tool_errors;if(this.tool_errors){C.addClass("tool-node-error")}else{C.removeClass("tool-node-error")}var F=C.find("div.inputs");var B=$("<div class='inputs'></div>");var A=F.find("div.input-data-row");$.each(E.data_inputs,function(I,G){var H=$("<div class='terminal input-terminal'></div>");D.enable_input_terminal(H,G.name,G.extensions);F.find("div[name="+G.name+"]").each(function(){$(this).find(".input-terminal").each(function(){var J=this.terminal.connectors[0];if(J){H[0].terminal.connectors[0]=J;J.handle2=H[0].terminal}});$(this).remove()});B.append($("<div class='form-row dataRow input-data-row' name='"+G.name+"'>"+G.label+"</div>").prepend(H))});F.replaceWith(B);F.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(C){var A=$(this.element).find(".toolFormBody");A.find("div").remove();var B="<div style='color: red; text-style: italic;'>"+C+"</div>";this.form_html=B;A.html(B);workflow.node_change d(this)},changed:function(){workflow.node_changed(this)}});function Workflow(){this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false}$.extend(Workflow.prototype,{add_node:function(A){A.id=this.id_counter;this.id_counter++;this.nodes[A.id]=A;this.has_changes=true;A.workflow=this},remove_node:function(A){if(this.active_node==A){this.clear_active_node()}delete this.nodes[A.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(B,A){A.destroy();wf.remove_node(A)})},to_simple:function(){var A={};$.each(this.nodes,function(B,D){var E={};$.each(D.input_terminals,function(F,G){E[G.name]=null;$.each(G.connectors,function(H,I){E[G.name]={id:I.handle1.node.id,output_name:I.handle1.name}})});var C={id:D.id,type:D.type,tool_id:D.tool_id,tool_state:D.tool_state,tool_errors:D.tool_errors,input_connections:E,position:$(D.element).position()};A[D.id]=C});return{steps:A}},from_simple:function(A){wf=this;var B=0;wf.name=A.name;$.each(A.steps,functio n(E,D){var C=prebuild_node("tool",D.name,D.tool_id);C.init_field_data(D);if(D.position){C.element.css({top:D.position.top,left:D.position.left})}C.id=D.id;wf.nodes[C.id]=C;B=Math.max(B,parseInt(E))});wf.id_counter=B+1;$.each(A.steps,function(E,D){var C=wf.nodes[E];$.each(D.input_connections,function(G,F){if(F){var H=wf.nodes[F.id];var I=new Connector();I.connect(H.output_terminals[F.output_name],C.input_terminals[G]);I.redraw()}})})},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive()}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(A){this.clear_active_node();parent.show_form_for_tool(A.form_html,A);A.make_active();this.active_node=A},node_changed:function(A){this.has_changes=true;if(this.active_node==A){this.activate_node(A)}}});function prebuild_node(H,F,K){var E=$("<div class='toolForm toolFormInCanvas'></div>");var C=new Node(E);C.type=H;if(H=="tool"){C.tool_id=K}var J=$("<div class='toolFormTitle unselectab le'>"+F+"</div>");E.append(J);E.css("left",$(window).scrollLeft()+20);E.css("top",$(window).scrollTop()+20);var I=$("<div class='toolFormBody'></div>");var D="<div><img height='16' align='middle' src='../images/loading_small_white_bg.gif'/> loading tool info...</div>";I.append(D);C.form_html=D;E.append(I);var G=$("<div class='buttons' style='float: right;'></div>");G.append($("<img src='../images/delete_icon.png' />").click(function(L){C.destroy()}).hover(function(){$(this).attr("src","../images/delete_icon_dark.png")},function(){$(this).attr("src","../images/delete_icon.png")}));zmax=$("#canvas-container").data("zmax");if(!zmax){zmax=0}E.css("zIndex",zmax+1);$("#canvas-container").data("zmax",zmax+1);E.appendTo("#canvas-container");var B=$("#canvas-container").position();E.css({left:(-B.left)+10,top:(-B.top)+10});var A=E.width();G.prependTo(J);A+=(G.width()+10);E.css("width",A);$(E).draggable({cursor:"move",scrollPanel:true,panel:$("#canvas-container"),scrollSensitivity:10, scrollSpeed:20,click:function(M,L){zmax=$("#canvas-container").data("zmax");$(this).css("zIndex",zmax+1);$("#canvas-container").data("zmax",zmax+1);workflow.activate_node(C)},start:function(M,L){workflow.activate_node(C);$(this).css("z-index",$("#canvas-container").data("zmax")+1000)},drag:function(M,L){$(this).find(".terminal").each(function(){this.terminal.redraw()})},stop:function(M,L){zmax=$("#canvas-container").data("zmax");$(this).css("zIndex",zmax+1);$("#canvas-container").data("zmax",zmax+1);$(this).find(".terminal").each(function(){this.terminal.redraw()});workflow.node_changed(this)}});return C}var ext_to_type=null;var type_to_type=null;function issubtype(B,A){B=ext_to_type[B];A=ext_to_type[A];return(A in type_to_type[B])}function populate_datatype_info(A){ext_to_type=A.ext_to_class_name;type_to_type=A.class_to_classes}; \ No newline at end of file diff -r 6eac08f7edcf -r b671c301674a templates/workflow/editor.mako --- a/templates/workflow/editor.mako Fri Aug 22 17:44:32 2008 -0400 +++ b/templates/workflow/editor.mako Fri Aug 22 17:47:43 2008 -0400 @@ -14,8 +14,11 @@ <%def name="javascripts()"> - ## ${parent.javascripts()} - + ${parent.javascripts()} + +  <script type='text/javascript' src="/static/scripts/jquery.js"> </script> <script type='text/javascript' src="/static/scripts/jquery.ui.js"> </script> <script type='text/javascript' src="/static/scripts/galaxy.ui.scrollPanel.js"> </script> @@ -23,46 +26,6 @@ <script type='text/javascript' src="/static/scripts/jquery.form.js"> </script> <script type='text/javascript' src="/static/scripts/jquery.json.js"> </script> - <script type='text/javascript'> - /* Dialog and menu handling tools to be moved to galaxy.layout.js */ - - function hide_modal() { - $(".dialog-box-container" ).fadeOut( function() { $("#overlay").hide(); } ); - }; - - function show_modal( title, body, buttons, extra_buttons ) { - $( ".dialog-box" ).find( ".title" ).html( title ); - var b = $( ".dialog-box" ).find( ".buttons" ).html( "" ); - if ( buttons ) { - $.each( buttons, function( name, value ) { - b.append( $( '<button/>' ).text( name ).click( value ) ); - b.append( " " ); - }); - b.show(); - } else { - b.hide(); - } - var b = $( ".dialog-box" ).find( ".extra_buttons" ).html( "" ); - if ( extra_buttons ) { - $.each( extra_buttons, function( name, value ) { - b.append( $( '<button/>' ).text( name ).click( value ) ); - b.append( " " ); - }); - b.show(); - } else { - b.hide(); - } - if ( body == "progress" ) { - body = $( "<img src='${h.url_for('/static/images/yui/rel_interstitial_loading.gif')}'/>" ); - } - $( ".dialog-box" ).find( ".body" ).html( body ); - if ( ! $(".dialog-box-container").is( ":visible" ) ) { - $("#overlay").show(); - $(".dialog-box-container").fadeIn() - } - }; - </script> - <script type='text/javascript' src="/static/scripts/galaxy.workflow_editor.canvas.js"> </script> <script type='text/javascript'> @@ -70,38 +33,34 @@ $( function() { // Initialize workflow state reset(); - // Shim (the background of the editor area) causes loss of focus - // $("#shim").click( workflow.clear_active_node ).hoverIntent( { - // over: function () { $("div.toolForm").fadeTo( "fast", 0.7 ) }, - // out: function () { $("div.toolForm").fadeTo( "fast", 1.0 ) }, - // interval: 300 - // }); // Load the datatype info - $.getJSON( "${h.url_for( action='get_datatypes' )}", function( data ) { - populate_datatype_info( data ); - // Load workflow definition - $.ajax( { - url: "${h.url_for( action='load_workflow' )}", - data: { id: "${trans.security.encode_id( workflow_id )}", "_": "true" }, - dataType: 'json', - success: function( data ) { - reset(); - workflow.from_simple( data ); - workflow.has_changes = false; - scroll_to_nodes(); - hide_modal(); - }, - beforeSubmit: function( data ) { - show_modal( "Loading workflow", "progress" ); - } - }); + $.ajax( { + url: "${h.url_for( action='get_datatypes' )}", + dataType: "json", + cache: false, + success: function( data ) { + populate_datatype_info( data ); + // Load workflow definition + $.ajax( { + url: "${h.url_for( action='load_workflow' )}", + data: { id: "${trans.security.encode_id( workflow_id )}", "_": "true" }, + dataType: 'json', + cache: false, + success: function( data ) { + reset(); + workflow.from_simple( data ); + workflow.has_changes = false; + scroll_to_nodes(); + hide_modal(); + }, + beforeSubmit: function( data ) { + show_modal( "Loading workflow", "progress" ); + } + }); + } }); $(document).ajaxError( function ( e, x ) { - // $("#error-display").empty() - // .append( $("<div/>").html( x.responseText ) ) - // .append( $("<div><a>close</a></div>" ).click( function() { $("#error-display").hide(); } ) ) - // .show(); show_modal( "Server error", x.responseText, { "Ignore error" : hide_modal } ); return false; }); @@ -272,7 +231,7 @@ save_current_workflow( do_close ); } }, { - "Don't Save": do_close, + "Don't Save": do_close } ); } else { window.document.location = "${next_url}" @@ -410,20 +369,10 @@ margin: 5px; } - #error-display { - display: none; - position: fixed; - top: 5%; left: 5%; width: 90%; height: 90%; - border: solid red 10px; - background: #FFDDDD; - z-index: 50000; - overflow: auto; - } - canvas { position: absolute; z-index: 10; } canvas.dragging { position: absolute; z-index: 1000; } - .input-terminal { width: 12px; height: 12px; background: url(${h.url_for('/static/style/workflow_circle_open.png')}); position: absolute; bottom: 0; left: -16px; z-index: 1500; } - .output-terminal { width: 12px; height: 12px; background: url(${h.url_for('/static/style/workflow_circle_open.png')}); position: absolute; bottom: 0; right: -16px; z-index: 1500; } + .input-terminal { width: 12px; height: 12px; background: url(${h.url_for('/static/style/workflow_circle_open.png')}); position: absolute; top: 0; left: -16px; z-index: 1500; } + .output-terminal { width: 12px; height: 12px; background: url(${h.url_for('/static/style/workflow_circle_open.png')}); position: absolute; top: 0; right: -16px; z-index: 1500; } .drag-terminal { width: 12px; height: 12px; background: url(${h.url_for('/static/style/workflow_circle_drag.png')}); position: absolute; z-index: 1500; } .input-terminal-active { background: url(${h.url_for('/static/style/workflow_circle_green.png')}); } ## .input-terminal-hover { background: yellow; border: solid black 1px; } @@ -504,13 +453,11 @@ </style> </%def> - -<div id="error-display"></div> <div id="overlay"> ## Need a table here for centering in IE6 <table class="dialog-box-container" border="0" cellpadding="0" cellspacing="0"><tr><td> - <div style="position: relative;"> + <div class="dialog-box-wrapper"> <div class="dialog-box"> <div class="unified-panel-header"> <div class="unified-panel-header-inner"><span class='title'>Loading workflow editor...</span></div> @@ -522,7 +469,6 @@ <div style="clear: both;"></div> </div> </div> - <div class="dialog-box-underlay"></div> </div> </td></tr></table> </div> @@ -558,9 +504,9 @@ %if "[[" in tool.description and "]]" in tool.description: ${tool.description.replace( '[[', '<a id="link-${tool.id}" href="javascript:add_node_for_tool( ${tool.id} )">' % tool.id ).replace( "]]", "</a>" )} %elif tool.name: - <a id="link-${tool.id}" href="javascript:add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.name}</a> ${tool.description} + <a id="link-${tool.id}" href="#" onclick="add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.name}</a> ${tool.description} %else: - <a id="link-${tool.id}" href="javascript:add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.description}</a> + <a id="link-${tool.id}" href="#" onclick="add_node_for_tool( '${tool.id}', '${tool.name}' )">${tool.description}</a> %endif </div> %else: @@ -588,7 +534,7 @@ <div id="__workflow__input__" class="toolSectionBody"> <div class="toolSectionBg"> <div class="toolTitle"> - <a href="javascript:add_node_for_module( 'data_input', 'Input Dataset' )">Input dataset</a> + <a href="#" onclick="add_node_for_module( 'data_input', 'Input Dataset' )">Input dataset</a> </div> </div> </div> diff -r 6eac08f7edcf -r b671c301674a templates/workflow/index.mako --- a/templates/workflow/index.mako Fri Aug 22 17:44:32 2008 -0400 +++ b/templates/workflow/index.mako Fri Aug 22 17:47:43 2008 -0400 @@ -21,16 +21,15 @@ </div> %endif -<div> - <div style="float: right;"> - <a class="action-button" href="${h.url_for( action='create' )}"> - <img src="${h.url_for('/static/images/silk/add.png')}" /> - <span>Add a new workflow</span> - </a> - </div> - <h2>Your workflows</h2> +<h2>Your workflows</h2> + +<div style="float: right; margin-top: -2.5em;"> + <a class="action-button" href="${h.url_for( action='create' )}"> + <img src="${h.url_for('/static/images/silk/add.png')}" /> + <span>Add a new workflow</span> + </a> </div> - + %if workflows: <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%"> <tr class="header">

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