mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well.
Refactor tool_form.mako to use base_panels.mako instead of its own custom HTML.
This commit is contained in:
Kanwei Li
@@ -1463,6 +1463,11 @@ class Tool:
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elif isinstance( input, SelectToolParameter ):
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input_values[ input.name ] = SelectToolParameterWrapper(
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input, input_values[ input.name ], self.app, other_values = param_dict )
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elif isinstance( input, LibraryDatasetToolParameter ):
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input_values[ input.name ] = LibraryDatasetValueWrapper(
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input, input_values[ input.name ], param_dict )
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else:
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input_values[ input.name ] = InputValueWrapper(
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input, input_values[ input.name ], param_dict )
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@@ -2013,6 +2018,31 @@ class RawObjectWrapper( object ):
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def __getattr__( self, key ):
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return getattr( self.obj, key )
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class LibraryDatasetValueWrapper( object ):
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"""
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Wraps an input so that __str__ gives the "param_dict" representation.
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"""
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def __init__( self, input, value, other_values={} ):
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self.input = input
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self.value = value
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self._other_values = other_values
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def __str__( self ):
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return self.value.name
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def templates( self ):
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if not self.value:
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return None
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template_data = {}
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for temp_info in self.value.info_association:
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template = temp_info.template
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content = temp_info.info.content
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tmp_dict = {}
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for field in template.fields:
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tmp_dict[field['label']] = content[field['name']]
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template_data[template.name] = tmp_dict
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return template_data
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def __getattr__( self, key ):
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return getattr( self.value, key )
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class InputValueWrapper( object ):
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"""
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Wraps an input so that __str__ gives the "param_dict" representation.
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@@ -1272,7 +1272,7 @@ class DataToolParameter( ToolParameter ):
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displayed as radio buttons and multiple selects as a set of checkboxes
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TODO: The following must be fixed to test correctly for the new security_check tag in the DataToolParameter ( the last test below is broken )
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Nate's next passs at the dataset security stuff will dramatically alter this anyway.
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Nate's next pass at the dataset security stuff will dramatically alter this anyway.
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"""
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def __init__( self, tool, elem ):
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@@ -1522,6 +1522,38 @@ class DataToolParameter( ToolParameter ):
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ref = ref()
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return ref
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class LibraryDatasetToolParameter( ToolParameter ):
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"""
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Parameter that lets users select a LDDA from a modal window, then use it within the wrapper.
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"""
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def __init__( self, tool, elem ):
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ToolParameter.__init__( self, tool, elem )
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def get_html_field( self, trans=None, value=None, other_values={} ):
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return form_builder.LibraryField( self.name, value=value, trans=trans )
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def get_initial_value( self, trans, context ):
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return None
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def from_html( self, value, trans, other_values={} ):
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if not value:
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return None
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elif isinstance( value, trans.app.model.LibraryDatasetDatasetAssociation ):
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return value
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else:
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return trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( value ) )
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def to_string( self, value, app ):
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if not value:
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return None
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return value.id
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def to_python( self, value, app ):
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if not value:
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return value
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return app.model.context.query( app.model.LibraryDatasetDatasetAssociation ).get( value )
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# class RawToolParameter( ToolParameter ):
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# """
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# Completely nondescript parameter, HTML representation is provided as text
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@@ -1570,19 +1602,20 @@ class DataToolParameter( ToolParameter ):
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# self.html = form_builder.HiddenField( self.name, trans.history.id ).get_html()
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# return self.html
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parameter_types = dict( text = TextToolParameter,
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integer = IntegerToolParameter,
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float = FloatToolParameter,
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boolean = BooleanToolParameter,
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genomebuild = GenomeBuildParameter,
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select = SelectToolParameter,
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data_column = ColumnListParameter,
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hidden = HiddenToolParameter,
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baseurl = BaseURLToolParameter,
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file = FileToolParameter,
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ftpfile = FTPFileToolParameter,
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data = DataToolParameter,
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drill_down = DrillDownSelectToolParameter )
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parameter_types = dict( text = TextToolParameter,
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integer = IntegerToolParameter,
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float = FloatToolParameter,
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boolean = BooleanToolParameter,
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genomebuild = GenomeBuildParameter,
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select = SelectToolParameter,
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data_column = ColumnListParameter,
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hidden = HiddenToolParameter,
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baseurl = BaseURLToolParameter,
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file = FileToolParameter,
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ftpfile = FTPFileToolParameter,
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data = DataToolParameter,
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library_data = LibraryDatasetToolParameter,
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drill_down = DrillDownSelectToolParameter )
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class UnvalidatedValue( object ):
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"""
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@@ -652,6 +652,27 @@ class HistoryField( BaseField ):
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return self.value
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else:
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return '-'
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class LibraryField( BaseField ):
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def __init__( self, name, value=None, trans=None ):
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self.name = name
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self.ldda = value
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self.trans = trans
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def get_html( self, disabled=False ):
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if not self.ldda:
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ldda = ""
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text = "Choose a library dataset"
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else:
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ldda = self.trans.security.encode_id(self.ldda.id)
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text = self.ldda.name
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return '<a href="javascript:void(0);" class="add-librarydataset">%s</a> \
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<input type="hidden" name="%s" value="%s">' % ( text, self.name, escape( str(ldda), quote=True ) )
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def get_display_text(self):
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if self.ldda:
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return self.ldda.name
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else:
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return 'None'
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def get_suite():
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"""Get unittest suite for this module"""
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@@ -725,4 +725,5 @@ $(document).ready( function() {
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}
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return anchor;
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});
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});
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@@ -214,7 +214,7 @@ function show_modal( title, body, buttons, extra_buttons, init_fn ) {
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init_fn();
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}
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};
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function show_in_overlay( options ) {
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var width = options.width || '600';
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var height = options.height || '400';
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@@ -226,9 +226,9 @@ function show_in_overlay( options ) {
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show_modal( null, $( "<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='" + image_path + "/closebox.png'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) );
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$("#close_button").bind( "click", function() { hide_modal(); } );
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}
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// Tab management
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$(function() {
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$(".tab").each( function() {
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var submenu = $(this).children( ".submenu" );
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+7
-9
@@ -1,15 +1,13 @@
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<% _=n_ %>
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<html>
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<head>
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<title>${self.title()}</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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${self.metas()}
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${self.stylesheets()}
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${self.javascripts()}
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</head>
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<head>
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<title>${self.title()}</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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${self.metas()}
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${self.stylesheets()}
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${self.javascripts()}
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</head>
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<body>
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${next.body()}
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</body>
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+47
-47
@@ -155,13 +155,13 @@
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## Override
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</%def>
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<%def name="overlay( title='', content='' )">
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<%def name="overlay( title='', content='', visible=False )">
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<%def name="title()"></%def>
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<%def name="content()"></%def>
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<div id="overlay"
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%if not self.overlay_visible:
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style="display: none;"
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%if not visible:
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style="display: none;"
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%endif
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>
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##
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@@ -169,21 +169,21 @@
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## Need a table here for centering in IE6
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<table class="dialog-box-container" border="0" cellpadding="0" cellspacing="0"
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%if not self.overlay_visible:
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%if not visible:
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style="display: none;"
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%endif
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><tr><td>
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<div class="dialog-box-wrapper">
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<div class="dialog-box">
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<div class="unified-panel-header">
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<div class="unified-panel-header-inner"><span class='title'>${title}</span></div>
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</div>
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<div class="body">${content}</div>
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<div>
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<div class="buttons" style="display: none; float: right;"></div>
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<div class="extra_buttons" style="display: none; padding: 5px;"></div>
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<div style="clear: both;"></div>
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</div>
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<div class="unified-panel-header">
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<div class="unified-panel-header-inner"><span class='title'>${title}</span></div>
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</div>
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<div class="body">${content}</div>
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<div>
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<div class="buttons" style="display: none; float: right;"></div>
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<div class="extra_buttons" style="display: none; padding: 5px;"></div>
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<div style="clear: both;"></div>
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</div>
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</div>
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</div>
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</td></tr></table>
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@@ -198,45 +198,45 @@
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<html>
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${self.init()}
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<head>
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<title>${self.title()}</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<meta name = "viewport" content = "maximum-scale=1.0">
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${self.stylesheets()}
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${self.javascripts()}
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<title>${self.title()}</title>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<meta name = "viewport" content = "maximum-scale=1.0">
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${self.stylesheets()}
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${self.javascripts()}
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</head>
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<body scroll="no" class="${self.body_class}">
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<div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 600px;">
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## Background displays first
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<div id="background"></div>
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## Layer iframes over backgrounds
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<div id="masthead">
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${self.masthead()}
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</div>
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<div id="messagebox" class="panel-${self.message_box_class}-message">
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%if self.message_box_visible:
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${self.message_box_content()}
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<div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%; min-width: 600px;">
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## Background displays first
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<div id="background"></div>
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## Layer iframes over backgrounds
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<div id="masthead">
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${self.masthead()}
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</div>
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<div id="messagebox" class="panel-${self.message_box_class}-message">
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%if self.message_box_visible:
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${self.message_box_content()}
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%endif
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</div>
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${self.overlay(visible=self.overlay_visible)}
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%if self.has_left_panel:
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<div id="left">
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${self.left_panel()}
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</div>
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<div id="left-border">
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<div id="left-border-inner" style="display: none;"></div>
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</div>
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%endif
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<div id="center">
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${self.center_panel()}
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</div>
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%if self.has_right_panel:
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<div id="right-border"><div id="right-border-inner" style="display: none;"></div></div>
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<div id="right">
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${self.right_panel()}
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</div>
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%endif
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</div>
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${self.overlay()}
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%if self.has_left_panel:
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<div id="left">
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${self.left_panel()}
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</div>
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<div id="left-border">
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<div id="left-border-inner" style="display: none;"></div>
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</div>
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%endif
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<div id="center">
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${self.center_panel()}
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</div>
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%if self.has_right_panel:
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<div id="right-border"><div id="right-border-inner" style="display: none;"></div></div>
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<div id="right">
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${self.right_panel()}
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</div>
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%endif
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</div>
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## Allow other body level elements
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</body>
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## Scripts can be loaded later since they progressively add features to
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@@ -174,14 +174,14 @@
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<%def name="init()">
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<%
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if trans.app.config.cloud_controller_instance:
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self.has_left_panel=False
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self.has_right_panel=False
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self.active_view="cloud"
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else:
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self.has_left_panel=True
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self.has_right_panel=True
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self.active_view="analysis"
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if trans.app.config.cloud_controller_instance:
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self.has_left_panel=False
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self.has_right_panel=False
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self.active_view="cloud"
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else:
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self.has_left_panel=True
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self.has_right_panel=True
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self.active_view="analysis"
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%>
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%if trans.app.config.require_login and not trans.user:
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<script type="text/javascript">
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@@ -219,7 +219,7 @@
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elif m_c is not None:
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center_url = h.url_for( controller=m_c, action=m_a )
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elif trans.app.config.cloud_controller_instance:
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center_url = h.url_for( controller='cloud', action='list' )
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center_url = h.url_for( controller='cloud', action='list' )
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else:
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center_url = h.url_for( '/static/welcome.html' )
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%>
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+259
-233
@@ -1,203 +1,230 @@
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<!-- -->
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<%inherit file="/base.mako"/>
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<%namespace file="/base_panels.mako" import="overlay" />
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<%
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from galaxy.util.expressions import ExpressionContext
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%>
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<%def name="stylesheets()">
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${h.css( "autocomplete_tagging", "panel_layout", "base", "library" )}
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</%def>
|
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|
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<html>
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<%def name="javascripts()">
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${h.js( "jquery", "galaxy.panels", "galaxy.base", "jquery.autocomplete", "jstorage" )}
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<script type="text/javascript">
|
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$(function() {
|
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$(window).bind("refresh_on_change", function() {
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$(':file').each( function() {
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var file = $(this);
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var file_value = file.val();
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if (file_value) {
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// disable file input, since we don't want to upload the file on refresh
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var file_name = $(this).attr("name");
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file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } );
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// create a new hidden field which stores the filename and has the original name of the file input
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var new_file_input = $(document.createElement('input'));
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new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } );
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file.after(new_file_input);
|
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}
|
||||
});
|
||||
});
|
||||
|
||||
<head>
|
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<title>Galaxy</title>
|
||||
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
|
||||
${h.css( "base", "autocomplete_tagging" )}
|
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${h.js( "jquery", "galaxy.base", "jquery.autocomplete" )}
|
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<script type="text/javascript">
|
||||
$(function() {
|
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$(window).bind("refresh_on_change", function() {
|
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$(':file').each( function() {
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var file = $(this);
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var file_value = file.val();
|
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if (file_value) {
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// disable file input, since we don't want to upload the file on refresh
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var file_name = $(this).attr("name");
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file.attr( { name: 'replaced_file_input_' + file_name, disabled: true } );
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// create a new hidden field which stores the filename and has the original name of the file input
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var new_file_input = $(document.createElement('input'));
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new_file_input.attr( { "type": "hidden", "value": file_value, "name": file_name } );
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file.after(new_file_input);
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// For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements
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$( 'li ul.toolParameterExpandableCollapsable' ).each( function() {
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var el = $(this),
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parent_li = el.parent('li'),
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sub_ul = el.remove();
|
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parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() {
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sub_ul.toggle();
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(this).html( sub_ul.is(":hidden") ? '[+]' : '[-]' );
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});
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parent_li.append( sub_ul );
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});
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|
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$( 'ul ul.toolParameterExpandableCollapsable' ).each( function(i) {
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||||
var el = $(this);
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||||
if (el.attr("default_state") === "collapsed") {
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el.hide();
|
||||
}
|
||||
});
|
||||
});
|
||||
|
||||
// For drilldown parameters: add expand/collapse buttons and collapse initially-collapsed elements
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||||
$( 'li ul.toolParameterExpandableCollapsable' ).each( function() {
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||||
var el = $(this),
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||||
parent_li = el.parent('li'),
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||||
sub_ul = el.remove();
|
||||
|
||||
parent_li.find( 'span' ).wrapInner( '<a/>' ).find( 'a' ).click( function() {
|
||||
sub_ul.toggle();
|
||||
(this).html( sub_ul.is(":hidden") ? '[+]' : '[-]' );
|
||||
});
|
||||
parent_li.append( sub_ul );
|
||||
});
|
||||
|
||||
$( 'ul ul.toolParameterExpandableCollapsable' ).each( function(i) {
|
||||
var el = $(this);
|
||||
if (el.attr("default_state") === "collapsed") {
|
||||
el.hide();
|
||||
|
||||
function checkUncheckAll( name, check ) {
|
||||
$("input[name='" + name + "'][type='checkbox']").attr('checked', !!check);
|
||||
}
|
||||
});
|
||||
|
||||
function checkUncheckAll( name, check ) {
|
||||
$("input[name='" + name + "'][type='checkbox']").attr('checked', !!check);
|
||||
}
|
||||
|
||||
// Inserts the Select All / Unselect All buttons for checkboxes
|
||||
$("div.checkUncheckAllPlaceholder").each( function() {
|
||||
var check_name = $(this).attr("checkbox_name");
|
||||
select_link = $("<a class='action-button'></a>").text("Select All").click(function() {
|
||||
checkUncheckAll(check_name, true);
|
||||
|
||||
// Inserts the Select All / Unselect All buttons for checkboxes
|
||||
$("div.checkUncheckAllPlaceholder").each( function() {
|
||||
var check_name = $(this).attr("checkbox_name");
|
||||
select_link = $("<a class='action-button'></a>").text("Select All").click(function() {
|
||||
checkUncheckAll(check_name, true);
|
||||
});
|
||||
unselect_link = $("<a class='action-button'></a>").text("Unselect All").click(function() {
|
||||
checkUncheckAll(check_name, false);
|
||||
});
|
||||
$(this).append(select_link).append(" ").append(unselect_link);
|
||||
});
|
||||
unselect_link = $("<a class='action-button'></a>").text("Unselect All").click(function() {
|
||||
checkUncheckAll(check_name, false);
|
||||
|
||||
$(".add-librarydataset").live("click", function() {
|
||||
var link = $(this);
|
||||
$.ajax({
|
||||
url: "/tracks/list_libraries",
|
||||
error: function(xhr, ajaxOptions, thrownError) { alert( "Grid failed" ); console.log(xhr, ajaxOptions, thrownError); },
|
||||
success: function(table_html) {
|
||||
show_modal(
|
||||
"Select Library Dataset",
|
||||
table_html, {
|
||||
"Cancel": function() {
|
||||
hide_modal();
|
||||
},
|
||||
"Select": function() {
|
||||
$('input[name=ldda_ids]:checked').each(function() {
|
||||
var name = $.trim( $(this).siblings("div").find("a").text() );
|
||||
var id = $(this).val();
|
||||
link.text(name);
|
||||
link.siblings("input[type=hidden]").val(id);
|
||||
});
|
||||
hide_modal();
|
||||
}
|
||||
}
|
||||
);
|
||||
}
|
||||
});
|
||||
});
|
||||
$(this).append(select_link).append(" ").append(unselect_link);
|
||||
});
|
||||
});
|
||||
|
||||
%if not add_frame.debug:
|
||||
if( window.name != "galaxy_main" ) {
|
||||
location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' );
|
||||
}
|
||||
%endif
|
||||
%if not add_frame.debug:
|
||||
if( window.name != "galaxy_main" ) {
|
||||
location.replace( '${h.url_for( controller='root', action='index', tool_id=tool.id )}' );
|
||||
}
|
||||
%endif
|
||||
|
||||
</script>
|
||||
</head>
|
||||
</script>
|
||||
|
||||
<body>
|
||||
<%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )">
|
||||
<% other_values = ExpressionContext( tool_state, other_values ) %>
|
||||
%for input_index, input in enumerate( inputs.itervalues() ):
|
||||
%if not input.visible:
|
||||
<% pass %>
|
||||
%elif input.type == "repeat":
|
||||
<div class="repeat-group">
|
||||
<div class="form-title-row"><b>${input.title_plural}</b></div>
|
||||
<% repeat_state = tool_state[input.name] %>
|
||||
%for i in range( len( repeat_state ) ):
|
||||
<div class="repeat-group-item">
|
||||
<%
|
||||
if input.name in errors:
|
||||
rep_errors = errors[input.name][i]
|
||||
else:
|
||||
rep_errors = dict()
|
||||
index = repeat_state[i]['__index__']
|
||||
%>
|
||||
<div class="form-title-row"><b>${input.title} ${i + 1}</b></div>
|
||||
${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )}
|
||||
<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div>
|
||||
</div>
|
||||
%if rep_errors.has_key( '__index__' ):
|
||||
<div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div>
|
||||
%endif
|
||||
%endfor
|
||||
<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div>
|
||||
</div>
|
||||
%elif input.type == "conditional":
|
||||
<%
|
||||
group_state = tool_state[input.name]
|
||||
group_errors = errors.get( input.name, {} )
|
||||
current_case = group_state['__current_case__']
|
||||
group_prefix = prefix + input.name + "|"
|
||||
%>
|
||||
%if input.value_ref_in_group:
|
||||
${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )}
|
||||
%endif
|
||||
${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )}
|
||||
%elif input.type == "upload_dataset":
|
||||
%if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before
|
||||
</%def>
|
||||
|
||||
<%def name="do_inputs( inputs, tool_state, errors, prefix, other_values=None )">
|
||||
<%
|
||||
from galaxy.util.expressions import ExpressionContext
|
||||
other_values = ExpressionContext( tool_state, other_values )
|
||||
%>
|
||||
%for input_index, input in enumerate( inputs.itervalues() ):
|
||||
%if not input.visible:
|
||||
<% pass %>
|
||||
%elif input.type == "repeat":
|
||||
<div class="repeat-group">
|
||||
<div class="form-title-row"><strong>${input.title_plural}</strong></div>
|
||||
<% repeat_state = tool_state[input.name] %>
|
||||
%for i in range( len( repeat_state ) ):
|
||||
<div class="repeat-group-item">
|
||||
<%
|
||||
if input.name in errors:
|
||||
rep_errors = errors[input.name][0]
|
||||
rep_errors = errors[input.name][i]
|
||||
else:
|
||||
rep_errors = dict()
|
||||
index = repeat_state[i]['__index__']
|
||||
%>
|
||||
${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )}
|
||||
%else:
|
||||
<div class="repeat-group">
|
||||
<div class="form-title-row"><b>${input.group_title( other_values )}</b></div>
|
||||
<%
|
||||
repeat_state = tool_state[input.name]
|
||||
%>
|
||||
%for i in range( len( repeat_state ) ):
|
||||
<div class="repeat-group-item">
|
||||
<%
|
||||
if input.name in errors:
|
||||
rep_errors = errors[input.name][i]
|
||||
else:
|
||||
rep_errors = dict()
|
||||
index = repeat_state[i]['__index__']
|
||||
%>
|
||||
<div class="form-title-row"><b>File Contents for ${input.title_by_index( trans, i, other_values )}</b></div>
|
||||
${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )}
|
||||
##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div>
|
||||
</div>
|
||||
%endfor
|
||||
##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div>
|
||||
</div>
|
||||
<div class="form-title-row"><strong>${input.title} ${i + 1}</strong></div>
|
||||
${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )}
|
||||
<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div>
|
||||
</div>
|
||||
%if rep_errors.has_key( '__index__' ):
|
||||
<div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${rep_errors['__index__']}</span></div>
|
||||
%endif
|
||||
%endfor
|
||||
<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div>
|
||||
</div>
|
||||
%elif input.type == "conditional":
|
||||
<%
|
||||
group_state = tool_state[input.name]
|
||||
group_errors = errors.get( input.name, {} )
|
||||
current_case = group_state['__current_case__']
|
||||
group_prefix = prefix + input.name + "|"
|
||||
%>
|
||||
%if input.value_ref_in_group:
|
||||
${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )}
|
||||
%endif
|
||||
${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )}
|
||||
%elif input.type == "upload_dataset":
|
||||
%if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before
|
||||
<%
|
||||
if input.name in errors:
|
||||
rep_errors = errors[input.name][0]
|
||||
else:
|
||||
rep_errors = dict()
|
||||
%>
|
||||
${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )}
|
||||
%else:
|
||||
${row_for_param( prefix, input, tool_state, errors, other_values )}
|
||||
%endif
|
||||
%endfor
|
||||
</%def>
|
||||
|
||||
<%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )">
|
||||
<%
|
||||
if parent_errors.has_key( param.name ):
|
||||
cls = "form-row form-row-error"
|
||||
else:
|
||||
cls = "form-row"
|
||||
|
||||
label = param.get_label()
|
||||
|
||||
field = param.get_html_field( trans, parent_state[ param.name ], other_values )
|
||||
field.refresh_on_change = param.refresh_on_change
|
||||
|
||||
# Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully.
|
||||
field_html = field.get_html( prefix )
|
||||
if type( field_html ) is not unicode:
|
||||
field_html = unicode( field_html, 'utf-8' )
|
||||
|
||||
if param.type == "hidden":
|
||||
return field_html
|
||||
%>
|
||||
<div class="${cls}">
|
||||
%if label:
|
||||
<label for="${param.name}">${label}:</label>
|
||||
%endif
|
||||
<div class="form-row-input">${field_html}</div>
|
||||
%if parent_errors.has_key( param.name ):
|
||||
<div class="form-row-error-message">
|
||||
<div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div>
|
||||
<div class="repeat-group">
|
||||
<div class="form-title-row"><strong>${input.group_title( other_values )}</strong></div>
|
||||
<%
|
||||
repeat_state = tool_state[input.name]
|
||||
%>
|
||||
%for i in range( len( repeat_state ) ):
|
||||
<div class="repeat-group-item">
|
||||
<%
|
||||
if input.name in errors:
|
||||
rep_errors = errors[input.name][i]
|
||||
else:
|
||||
rep_errors = dict()
|
||||
index = repeat_state[i]['__index__']
|
||||
%>
|
||||
<div class="form-title-row"><strong>File Contents for ${input.title_by_index( trans, i, other_values )}</strong></div>
|
||||
${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )}
|
||||
##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div>
|
||||
</div>
|
||||
%endfor
|
||||
##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div>
|
||||
</div>
|
||||
%endif
|
||||
|
||||
%if param.help:
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
${param.help}
|
||||
</div>
|
||||
%endif
|
||||
|
||||
<div style="clear: both"></div>
|
||||
|
||||
</div>
|
||||
</%def>
|
||||
|
||||
%if add_frame.from_noframe:
|
||||
<div class="warningmessage">
|
||||
%else:
|
||||
${row_for_param( prefix, input, tool_state, errors, other_values )}
|
||||
%endif
|
||||
%endfor
|
||||
</%def>
|
||||
|
||||
<%def name="row_for_param( prefix, param, parent_state, parent_errors, other_values )">
|
||||
<%
|
||||
if parent_errors.has_key( param.name ):
|
||||
cls = "form-row form-row-error"
|
||||
else:
|
||||
cls = "form-row"
|
||||
|
||||
label = param.get_label()
|
||||
|
||||
field = param.get_html_field( trans, parent_state[ param.name ], other_values )
|
||||
field.refresh_on_change = param.refresh_on_change
|
||||
|
||||
# Field may contain characters submitted by user and these characters may be unicode; handle non-ascii characters gracefully.
|
||||
field_html = field.get_html( prefix )
|
||||
if type( field_html ) is not unicode:
|
||||
field_html = unicode( field_html, 'utf-8' )
|
||||
|
||||
if param.type == "hidden":
|
||||
return field_html
|
||||
%>
|
||||
<div class="${cls}">
|
||||
%if label:
|
||||
<label for="${param.name}">${label}:</label>
|
||||
%endif
|
||||
<div class="form-row-input">${field_html}</div>
|
||||
%if parent_errors.has_key( param.name ):
|
||||
<div class="form-row-error-message">
|
||||
<div><img style="vertical-align: middle;" src="${h.url_for('/static/style/error_small.png')}"> <span style="vertical-align: middle;">${parent_errors[param.name]}</span></div>
|
||||
</div>
|
||||
%endif
|
||||
|
||||
%if param.help:
|
||||
<div class="toolParamHelp" style="clear: both;">
|
||||
${param.help}
|
||||
</div>
|
||||
%endif
|
||||
|
||||
<div style="clear: both;"></div>
|
||||
|
||||
</div>
|
||||
</%def>
|
||||
|
||||
<% overlay(visible=False) %>
|
||||
|
||||
%if add_frame.from_noframe:
|
||||
<div class="warningmessage">
|
||||
<strong>Welcome to Galaxy</strong>
|
||||
<hr/>
|
||||
It appears that you found this tool from a link outside of Galaxy.
|
||||
@@ -205,60 +232,59 @@ $(function() {
|
||||
<a href="${h.url_for( controller='root' )}" target="_top">welcome page</a>.
|
||||
To learn more about what Galaxy is and what it can do for you, please visit
|
||||
the <a href="$add_frame.wiki_url" target="_top">Galaxy wiki</a>.
|
||||
</div>
|
||||
<br/>
|
||||
</div>
|
||||
<br/>
|
||||
%endif
|
||||
|
||||
## handle calculating the redict url for the special case where we have nginx proxy
|
||||
## upload and need to do url_for on the redirect portion of the tool action
|
||||
<%
|
||||
try:
|
||||
tool_url = h.url_for(tool.action)
|
||||
except AttributeError:
|
||||
assert len(tool.action) == 2
|
||||
tool_url = tool.action[0] + h.url_for(tool.action[1])
|
||||
%>
|
||||
<div class="toolForm" id="${tool.id}">
|
||||
%if tool.has_multiple_pages:
|
||||
<div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div>
|
||||
%else:
|
||||
<div class="toolFormTitle">${tool.name}</div>
|
||||
%endif
|
||||
|
||||
## handle calculating the redict url for the special case where we have nginx proxy
|
||||
## upload and need to do url_for on the redirect portion of the tool action
|
||||
<%
|
||||
try:
|
||||
tool_url = h.url_for(tool.action)
|
||||
except AttributeError:
|
||||
assert len(tool.action) == 2
|
||||
tool_url = tool.action[0] + h.url_for(tool.action[1])
|
||||
%><div class="toolForm" id="${tool.id}">
|
||||
%if tool.has_multiple_pages:
|
||||
<div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div>
|
||||
%else:
|
||||
<div class="toolFormTitle">${tool.name}</div>
|
||||
%endif
|
||||
<div class="toolFormBody">
|
||||
<form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}">
|
||||
<input type="hidden" name="tool_id" value="${tool.id}">
|
||||
<input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}">
|
||||
%if tool.display_by_page[tool_state.page]:
|
||||
${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )}
|
||||
<input type="submit" class="primary-button" name="runtool_btn" value="Execute">
|
||||
%else:
|
||||
${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )}
|
||||
<div class="form-row">
|
||||
%if tool_state.page == tool.last_page:
|
||||
<input type="submit" class="primary-button" name="runtool_btn" value="Execute">
|
||||
%else:
|
||||
<input type="submit" class="primary-button" name="runtool_btn" value="Next step">
|
||||
%endif
|
||||
</div>
|
||||
%endif
|
||||
</form>
|
||||
<div class="toolFormBody">
|
||||
<form id="tool_form" name="tool_form" action="${tool_url}" enctype="${tool.enctype}" target="${tool.target}" method="${tool.method}">
|
||||
<input type="hidden" name="tool_id" value="${tool.id}">
|
||||
<input type="hidden" name="tool_state" value="${util.object_to_string( tool_state.encode( tool, app ) )}">
|
||||
%if tool.display_by_page[tool_state.page]:
|
||||
${trans.fill_template_string( tool.display_by_page[tool_state.page], context=tool.get_param_html_map( trans, tool_state.page, tool_state.inputs ) )}
|
||||
<input type="submit" class="primary-button" name="runtool_btn" value="Execute">
|
||||
%else:
|
||||
${do_inputs( tool.inputs_by_page[ tool_state.page ], tool_state.inputs, errors, "" )}
|
||||
<div class="form-row">
|
||||
%if tool_state.page == tool.last_page:
|
||||
<input type="submit" class="primary-button" name="runtool_btn" value="Execute">
|
||||
%else:
|
||||
<input type="submit" class="primary-button" name="runtool_btn" value="Next step">
|
||||
%endif
|
||||
</div>
|
||||
%endif
|
||||
</form>
|
||||
</div>
|
||||
</div>
|
||||
%if tool.help:
|
||||
<div class="toolHelp">
|
||||
<div class="toolHelpBody">
|
||||
<%
|
||||
if tool.has_multiple_pages:
|
||||
tool_help = tool.help_by_page[tool_state.page]
|
||||
else:
|
||||
tool_help = tool.help
|
||||
|
||||
# Convert to unicode to display non-ascii characters.
|
||||
if type( tool_help ) is not unicode:
|
||||
tool_help = unicode( tool_help, 'utf-8')
|
||||
%>
|
||||
${tool_help}
|
||||
</div>
|
||||
</div>
|
||||
%if tool.help:
|
||||
<div class="toolHelp">
|
||||
<div class="toolHelpBody">
|
||||
<%
|
||||
if tool.has_multiple_pages:
|
||||
tool_help = tool.help_by_page[tool_state.page]
|
||||
else:
|
||||
tool_help = tool.help
|
||||
|
||||
# Convert to unicode to display non-ascii characters.
|
||||
if type( tool_help ) is not unicode:
|
||||
tool_help = unicode( tool_help, 'utf-8')
|
||||
%>
|
||||
${tool_help}
|
||||
</div>
|
||||
</div>
|
||||
%endif
|
||||
</body>
|
||||
</html>
|
||||
%endif
|
||||
|
||||
Reference in New Issue
Block a user