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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 1486: Between page reloads, Drill Down parameter typ...
by greg＠scofield.bx.psu.edu 02 Sep '08

02 Sep '08

details: http://www.bx.psu.edu/hg/galaxy/rev/9e956e7b738f changeset: 1486:9e956e7b738f user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Aug 27 16:36:41 2008 -0400 description: Between page reloads, Drill Down parameter type will now keep parent nodes expanded when a descendant is selected. 3 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py lib/galaxy/web/form_builder.py templates/tool_form.tmpl diffs (142 lines): diff -r 19c03a96b338 -r 9e956e7b738f lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Wed Aug 27 15:51:59 2008 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Wed Aug 27 16:36:41 2008 -0400 @@ -729,13 +729,13 @@ >>> print p.get_html() <div><ul class="toolParameterExpandableCollapsable"> <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="checkbox" name="some_name" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable"> + <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> <li><input type="checkbox" name="some_name" value="option1"">Option 1 </li> <li><input type="checkbox" name="some_name" value="option2"">Option 2 </li> <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="checkbox" name="some_name" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable"> + <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> <li><input type="checkbox" name="some_name" value="option3"">Option 3 </li> <li><input type="checkbox" name="some_name" value="option4"">Option 4 @@ -766,13 +766,13 @@ >>> print p.get_html() <div><ul class="toolParameterExpandableCollapsable"> <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="radio" name="some_name" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable"> + <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> <li><input type="radio" name="some_name" value="option1"">Option 1 </li> <li><input type="radio" name="some_name" value="option2"">Option 2 </li> <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="radio" name="some_name" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable"> + <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> <li><input type="radio" name="some_name" value="option3"">Option 3 </li> <li><input type="radio" name="some_name" value="option4"">Option 4 diff -r 19c03a96b338 -r 9e956e7b738f lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py Wed Aug 27 15:51:59 2008 -0400 +++ b/lib/galaxy/web/form_builder.py Wed Aug 27 16:36:41 2008 -0400 @@ -203,13 +203,13 @@ >>> print t.get_html() <div><ul class="toolParameterExpandableCollapsable"> <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="checkbox" name="foo" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable"> + <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> <li><input type="checkbox" name="foo" value="option1"">Option 1 </li> <li><input type="checkbox" name="foo" value="option2"">Option 2 </li> <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="checkbox" name="foo" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable"> + <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> <li><input type="checkbox" name="foo" value="option3"">Option 3 </li> <li><input type="checkbox" name="foo" value="option4"">Option 4 @@ -225,13 +225,13 @@ >>> print t.get_html() <div><ul class="toolParameterExpandableCollapsable"> <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="radio" name="foo" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable"> + <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> <li><input type="radio" name="foo" value="option1"">Option 1 </li> <li><input type="radio" name="foo" value="option2"">Option 2 </li> <li><span class="toolParameterExpandableCollapsable">[+]</span><input type="radio" name="foo" value="heading1"">Heading 1 - <ul class="toolParameterExpandableCollapsable"> + <ul class="toolParameterExpandableCollapsable" default_state="collapsed"> <li><input type="radio" name="foo" value="option3"">Option 3 </li> <li><input type="radio" name="foo" value="option4"">Option 4 @@ -266,22 +266,36 @@ else: self.refresh_on_change_text = '' def get_html( self, prefix="" ): - def recurse_options( html, options ): + def find_expanded_options( expanded_options, options, parent_options = [] ): + for option in options: + if option['value'] in self.value: + expanded_options.extend( parent_options ) + if option['options']: + new_parents = list( parent_options ) + [ option['value'] ] + find_expanded_options( expanded_options, option['options'], new_parents ) + def recurse_options( html, options, expanded_options = [] ): for option in options: selected = ( option['value'] in self.value ) if selected: selected = ' checked' else: selected = '' if option['options']: - html.append( '<li><span class="toolParameterExpandableCollapsable">[+]</span><input type="%s" name="%s%s" value="%s"%s">%s' % ( self.display, prefix, self.name, option['value'], selected, option['name']) ) - html.append( '<ul class="toolParameterExpandableCollapsable">') - recurse_options( html, option['options'] ) + default_state = 'collapsed' + default_icon = '[+]' + if option['value'] in expanded_options: + default_state = 'expanded' + default_icon = '[-]' + html.append( '<li><span class="toolParameterExpandableCollapsable">%s</span><input type="%s" name="%s%s" value="%s"%s">%s' % ( default_icon, self.display, prefix, self.name, option['value'], selected, option['name']) ) + html.append( '<ul class="toolParameterExpandableCollapsable" default_state="%s">' % default_state ) + recurse_options( html, option['options'], expanded_options ) html.append( '</ul>') else: html.append( '<li><input type="%s" name="%s%s" value="%s"%s">%s' % ( self.display, prefix, self.name, option['value'], selected, option['name']) ) html.append( '</li>' ) rval = [] rval.append( '<div><ul class="toolParameterExpandableCollapsable">' ) - recurse_options( rval, self.options ) + expanded_options = [] + find_expanded_options( expanded_options, self.options ) + recurse_options( rval, self.options, expanded_options ) rval.append( '</ul></div>' ) return '\n'.join( rval ) diff -r 19c03a96b338 -r 9e956e7b738f templates/tool_form.tmpl --- a/templates/tool_form.tmpl Wed Aug 27 15:51:59 2008 -0400 +++ b/templates/tool_form.tmpl Wed Aug 27 16:36:41 2008 -0400 @@ -126,7 +126,7 @@ <input type="submit" class="primary-button" name="runtool_btn" value="Execute"> #else - + <div style="display: none;"> #if $tool_state.page == $tool.last_page <input type="submit" class="primary-button" name="runtool_btn" value="Execute"> @@ -142,7 +142,7 @@ <input type="submit" class="primary-button" name="runtool_btn" value="Next step"> #end if </div> - + #end if </form> @@ -178,7 +178,7 @@ } }); \$( 'ul ul' ).each( function(i) { - if ( \$( this )[0].className == 'toolParameterExpandableCollapsable' ) + if ( \$( this )[0].className == 'toolParameterExpandableCollapsable' && this.attributes.getNamedItem( 'default_state' ).value == 'collapsed' ) { \$( this ).hide(); }

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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 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 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 28 Aug '08

28 Aug '08

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

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

27 Aug '08

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[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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