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Use class instead of substrings to identify integrated tool panel tools, sections, workflows, and section labels when saving and updating the panel.

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This commit is contained in:
Dave Bouvier
2014-01-10 15:02:20 -05:00
parent d6ce2f475f
commit 60094ca499
2 changed files with 26 additions and 32 deletions
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lib/galaxy/tools/__init__.py
+22 -21
View File
@@ -62,6 +62,7 @@ from galaxy.util.template import fill_template
from galaxy.web import url_for
from galaxy.web.form_builder import SelectField
from galaxy.model.item_attrs import Dictifiable
from galaxy.model import Workflow
from tool_shed.util import shed_util_common
from .loader import load_tool, template_macro_params
@@ -142,13 +143,13 @@ class ToolBox( object, Dictifiable ):
# 1) adjusting init_tools() and called methods to get this right
# 2) redesigning the code and/or data structure used to read/write integrated_tool_panel.xml
for key, value in self.integrated_tool_panel.iteritems():
if key.startswith( 'section_' ):
if isinstance( value, ToolSection ):
for section_key, section_value in value.elems.iteritems():
if section_value is None:
if section_key.startswith( 'tool_' ):
if isinstance( section_value, Tool ):
tool_id = section_key[5:]
value.elems[section_key] = self.tools_by_id.get( tool_id )
elif section_key.startswith( 'workflow_' ):
elif isinstance( section_value, Workflow ):
workflow_id = section_key[9:]
value.elems[section_key] = self.workflows_by_id.get( workflow_id )
@@ -252,19 +253,19 @@ class ToolBox( object, Dictifiable ):
def load_tool_panel( self ):
for key, val in self.integrated_tool_panel.items():
if key.startswith( 'tool_' ):
if isinstance( val, Tool ):
tool_id = key.replace( 'tool_', '', 1 )
if tool_id in self.tools_by_id:
self.__add_tool_to_tool_panel( tool_id, self.tool_panel, section=False )
elif key.startswith( 'workflow_' ):
elif isinstance( val, Workflow ):
workflow_id = key.replace( 'workflow_', '', 1 )
if workflow_id in self.workflows_by_id:
workflow = self.workflows_by_id[ workflow_id ]
self.tool_panel[ key ] = workflow
log.debug( "Loaded workflow: %s %s" % ( workflow_id, workflow.name ) )
elif key.startswith( 'label_' ):
elif isinstance( val, ToolSectionLabel ):
self.tool_panel[ key ] = val
elif key.startswith( 'section_' ):
elif isinstance( val, ToolSection ):
elem = ElementTree.Element( 'section' )
elem.attrib[ 'id' ] = val.id or ''
elem.attrib[ 'name' ] = val.name or ''
@@ -276,13 +277,13 @@ class ToolBox( object, Dictifiable ):
tool_id = section_key.replace( 'tool_', '', 1 )
if tool_id in self.tools_by_id:
self.__add_tool_to_tool_panel( tool_id, section, section=True )
elif section_key.startswith( 'workflow_' ):
elif isinstance( section_val, Workflow ):
workflow_id = section_key.replace( 'workflow_', '', 1 )
if workflow_id in self.workflows_by_id:
workflow = self.workflows_by_id[ workflow_id ]
section.elems[ section_key ] = workflow
log.debug( "Loaded workflow: %s %s" % ( workflow_id, workflow.name ) )
elif section_key.startswith( 'label_' ):
elif isinstance( val, ToolSectionLabel ):
if section_val:
section.elems[ section_key ] = section_val
log.debug( "Loaded label: %s" % ( section_val.text ) )
@@ -315,7 +316,7 @@ class ToolBox( object, Dictifiable ):
elif section_elem.tag == 'label':
key = 'label_%s' % section_elem.get( 'id' )
section.elems[ key ] = None
key = 'section_%s' % elem.get( 'id' )
key = elem.get( 'id' )
self.integrated_tool_panel[ key ] = section
elif elem.tag == 'label':
key = 'label_%s' % elem.get( 'id' )
@@ -331,28 +332,28 @@ class ToolBox( object, Dictifiable ):
os.write( fd, '<toolbox>\n' )
for key, item in self.integrated_tool_panel.items():
if item:
if key.startswith( 'tool_' ):
if isinstance( item, Tool ):
os.write( fd, ' <tool id="%s" />\n' % item.id )
elif key.startswith( 'workflow_' ):
elif isinstance( item, Workflow ):
os.write( fd, ' <workflow id="%s" />\n' % item.id )
elif key.startswith( 'label_' ):
elif isinstance( item, ToolSectionLabel ):
label_id = item.id or ''
label_text = item.text or ''
label_version = item.version or ''
os.write( fd, ' <label id="%s" text="%s" version="%s" />\n' % ( label_id, label_text, label_version ) )
elif key.startswith( 'section_' ):
elif isinstance( item, ToolSection ):
section_id = item.id or ''
section_name = item.name or ''
section_version = item.version or ''
os.write( fd, ' <section id="%s" name="%s" version="%s">\n' % ( section_id, section_name, section_version ) )
for section_key, section_item in item.elems.items():
if section_key.startswith( 'tool_' ):
if isinstance( section_item, Tool ):
if section_item:
os.write( fd, ' <tool id="%s" />\n' % section_item.id )
elif section_key.startswith( 'workflow_' ):
elif isinstance( section_item, Workflow ):
if section_item:
os.write( fd, ' <workflow id="%s" />\n' % section_item.id )
elif section_key.startswith( 'label_' ):
elif isinstance( section_item, ToolSectionLabel ):
if section_item:
label_id = section_item.id or ''
label_text = section_item.text or ''
@@ -576,7 +577,7 @@ class ToolBox( object, Dictifiable ):
integrated_panel_dict.insert( index, key, label )
def load_section_tag_set( self, elem, tool_path, load_panel_dict, index=None ):
key = 'section_' + elem.get( "id" )
key = elem.get( "id" )
if key in self.tool_panel:
section = self.tool_panel[ key ]
elems = section.elems
@@ -1078,14 +1079,14 @@ class Tool( object, Dictifiable ):
def get_panel_section( self ):
for key, item in self.app.toolbox.integrated_tool_panel.items():
if item:
if key.startswith( 'tool_' ):
if isinstance( item, Tool ):
if item.id == self.id:
return '', ''
if key.startswith( 'section_' ):
if isinstance( item, ToolSection ):
section_id = item.id or ''
section_name = item.name or ''
for section_key, section_item in item.elems.items():
if section_key.startswith( 'tool_' ):
if isinstance( section_item, Tool ):
if section_item:
if section_item.id == self.id:
return section_id, section_name
lib/tool_shed/util/tool_util.py
+4 -11
View File
@@ -466,11 +466,7 @@ def get_list_of_copied_sample_files( repo, ctx, dir ):
return sample_files, deleted_sample_files
def get_or_create_tool_section( trans, tool_panel_section_id, new_tool_panel_section_label=None ):
if tool_panel_section_id.startswith( 'section_' ):
tool_panel_section_key = tool_panel_section_id
tool_panel_section_id.lstrip( 'section_' )
else:
tool_panel_section_key = 'section_%s' % str( tool_panel_section_id )
tool_panel_section_key = str( tool_panel_section_id )
if tool_panel_section_key in trans.app.toolbox.tool_panel:
# Appending a tool to an existing section in trans.app.toolbox.tool_panel
tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ]
@@ -680,16 +676,13 @@ def handle_tool_panel_section( trans, tool_panel_section_id=None, new_tool_panel
# received tool_panel_section_id must be the id retrieved from a tool panel config (e.g., tool_conf.xml, which
# may have getext). If new_tool_panel_section_label is received, a new section will be added to the tool panel.
if new_tool_panel_section_label:
section_id = 'section_%s' % str( new_tool_panel_section_label.lower().replace( ' ', '_' ) )
section_id = str( new_tool_panel_section_label.lower().replace( ' ', '_' ) )
tool_panel_section_key, tool_section = \
get_or_create_tool_section( trans,
tool_panel_section_id=section_id,
new_tool_panel_section_label=new_tool_panel_section_label )
elif tool_panel_section_id:
if tool_panel_section_id.startswith( 'section_' ):
tool_panel_section_key = str( tool_panel_section_id )
else:
tool_panel_section_key = 'section_%s' % str( tool_panel_section_id )
tool_panel_section_key = str( tool_panel_section_id )
tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ]
else:
return None, None
@@ -1000,7 +993,7 @@ def remove_from_tool_panel( trans, repository, shed_tool_conf, uninstall ):
for config_elem in config_elems:
if config_elem.tag == 'section':
# Get the section key for the in-memory tool panel.
section_key = 'section_%s' % str( config_elem.get( "id" ) )
section_key = str( config_elem.get( "id" ) )
# Generate the list of tool elements to remove.
tool_elems_to_remove = []
for tool_elem in config_elem: