mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Add the ability to enter a new tool panel section label when installing repositories with tools from a tool shed in addition to being able to choose an existing tool panel section for containing the tools. Also clean up code related to message displayed when a local Galaxy instance is missing tools required by an imported workflow.
This commit is contained in:
Greg Von Kuster
@@ -22,6 +22,7 @@ from Cheetah.Template import Template
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pkg_resources.require( 'elementtree' )
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from elementtree import ElementTree, ElementInclude
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from elementtree.ElementTree import Element
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log = logging.getLogger( __name__ )
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@@ -3,7 +3,7 @@ from galaxy import model
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from galaxy.model.orm import *
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from galaxy.web.framework.helpers import time_ago, iff, grids
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from galaxy.tools.search import ToolBoxSearch
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from galaxy.tools import json_fix
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from galaxy.tools import ToolSection, json_fix
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import logging
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log = logging.getLogger( __name__ )
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@@ -403,7 +403,7 @@ class RepositoryListGrid( grids.Grid ):
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def get_value( self, trans, grid, tool_shed_repository ):
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return tool_shed_repository.tool_shed
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# Grid definition
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title = "Tool shed repositories"
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title = "Installed tool shed repositories"
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model_class = model.ToolShedRepository
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template='/admin/tool_shed_repository/grid.mako'
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default_sort_key = "name"
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@@ -807,28 +807,45 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
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status = kwd.get( 'status', 'done' )
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tool_shed_url = kwd[ 'tool_shed_url' ]
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repo_info_dict = kwd[ 'repo_info_dict' ]
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new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' )
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tool_panel_section = kwd.get( 'tool_panel_section', '' )
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if kwd.get( 'select_tool_panel_section_button', False ):
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shed_tool_conf = kwd[ 'shed_tool_conf' ]
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# Get the tool path.
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for k, tool_path in trans.app.toolbox.shed_tool_confs.items():
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if k == shed_tool_conf:
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break
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if 'tool_panel_section' in kwd:
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section_key = 'section_%s' % kwd[ 'tool_panel_section' ]
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tool_section = trans.app.toolbox.tool_panel[ section_key ]
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if new_tool_panel_section or tool_panel_section:
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if new_tool_panel_section:
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section_id = new_tool_panel_section.lower().replace( ' ', '_' )
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new_section_key = 'section_%s' % str( section_id )
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if new_section_key in trans.app.toolbox.tool_panel:
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# Appending a tool to an existing section in trans.app.toolbox.tool_panel
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log.debug( "Appending to tool panel section: %s" % new_tool_panel_section )
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tool_section = trans.app.toolbox.tool_panel[ new_section_key ]
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else:
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# Appending a new section to trans.app.toolbox.tool_panel
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log.debug( "Loading new tool panel section: %s" % new_tool_panel_section )
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elem = Element( 'section' )
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elem.attrib[ 'name' ] = new_tool_panel_section
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elem.attrib[ 'id' ] = section_id
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tool_section = ToolSection( elem )
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trans.app.toolbox.tool_panel[ new_section_key ] = tool_section
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else:
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section_key = 'section_%s' % tool_panel_section
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tool_section = trans.app.toolbox.tool_panel[ section_key ]
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# Decode the encoded repo_info_dict param value.
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repo_info_dict = tool_shed_decode( repo_info_dict )
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# Clone the repository to the configured location.
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current_working_dir = os.getcwd()
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installed_repository_names = []
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for name, repo_info_tuple in repo_info_dict.items():
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description, repository_clone_url, changeset_revision = repo_info_tuple
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clone_dir = os.path.join( tool_path, self.__generate_tool_path( repository_clone_url, changeset_revision ) )
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if os.path.exists( clone_dir ):
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# Repository and revision has already been cloned.
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# TODO: implement the ability to re-install or revert an existing repository.
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message += 'Revision <b>%s</b> of repository <b>%s</b> has already been installed. Updating an existing repository is not yet supported.<br/>' % \
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( changeset_revision, name )
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status = 'error'
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message += 'Revision <b>%s</b> of repository <b>%s</b> was previously installed.<br/>' % ( changeset_revision, name )
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else:
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os.makedirs( clone_dir )
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log.debug( 'Cloning %s...' % repository_clone_url )
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@@ -892,9 +909,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
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if trans.app.toolbox_search.enabled:
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# If search support for tools is enabled, index the new installed tools.
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trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox )
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message += 'Revision <b>%s</b> of repository <b>%s</b> has been loaded into tool panel section <b>%s</b>.<br/>' % \
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( changeset_revision, name, tool_section.name )
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#return trans.show_ok_message( message )
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installed_repository_names.append( name )
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else:
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tmp_stderr = open( tmp_name, 'rb' )
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message += '%s<br/>' % tmp_stderr.read()
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@@ -905,6 +920,19 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
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message += '%s<br/>' % tmp_stderr.read()
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tmp_stderr.close()
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status = 'error'
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if installed_repository_names:
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installed_repository_names.sort()
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message += 'These %d repositories were installed and all tools were loaded into tool panel section <b>%s</b>:<br/>' % \
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( len( installed_repository_names ), tool_section.name )
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for i, repo_name in enumerate( installed_repository_names ):
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if i == len( installed_repository_names ) -1:
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message += '%s.<br/>' % repo_name
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else:
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message += '%s, ' % repo_name
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return trans.response.send_redirect( web.url_for( controller='admin',
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action='browse_tool_shed_repositories',
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message=message,
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status=status ) )
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else:
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message = 'Choose the section in your tool panel to contain the installed tools.'
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status = 'error'
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@@ -921,6 +949,7 @@ class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuota, QuotaParamP
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shed_tool_conf=shed_tool_conf,
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shed_tool_conf_select_field=shed_tool_conf_select_field,
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tool_panel_section_select_field=tool_panel_section_select_field,
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new_tool_panel_section=new_tool_panel_section,
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message=message,
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status=status )
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@web.expose
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@@ -1115,10 +1115,10 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
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workflow_name = tool_shed_decode( workflow_name )
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# The following parameters will have a value only if the import originated
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# from a tool shed repository installed locally.
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local_file = kwd.get( 'local_file', '' )
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installed_repository_file = kwd.get( 'installed_repository_file', '' )
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repository_id = kwd.get( 'repository_id', '' )
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if local_file and not import_button:
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workflow_file = open( local_file, 'rb' )
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if installed_repository_file and not import_button:
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workflow_file = open( installed_repository_file, 'rb' )
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workflow_text = workflow_file.read()
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workflow_file.close()
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import_button = True
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@@ -1197,27 +1197,26 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
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if shed_url.endswith( '/' ):
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shed_url = shed_url.rstrip( '/' )
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url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, trans.request.host, webapp )
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if missing_tool_tups:
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url += '&tool_id='
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for missing_tool_tup in missing_tool_tups:
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missing_tool_id = missing_tool_tup[0]
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url += '&tool_id=%s' % missing_tool_id
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url += '%s,' % missing_tool_id
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message += '<a href="%s">%s</a><br/>' % ( url, shed_name )
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status = 'error'
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if local_file or tool_shed_url:
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if installed_repository_file or tool_shed_url:
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# Another Galaxy panels Hack: The request did not originate from the Galaxy
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# workflow view, so we don't need to render the Galaxy panels.
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return trans.response.send_redirect( web.url_for( controller='admin',
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action='center',
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webapp='galaxy',
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message=message,
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status=status ) )
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action = 'center'
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else:
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# Another Galaxy panels hack: The request originated from the Galaxy
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# workflow view, so we need to render the Galaxy panels.
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return trans.response.send_redirect( web.url_for( controller='admin',
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action='index',
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webapp='galaxy',
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message=message,
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status=status ) )
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action = 'index'
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return trans.response.send_redirect( web.url_for( controller='admin',
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action=action,
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webapp='galaxy',
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message=message,
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status=status ) )
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else:
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# TODO: Figure out what to do here...
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pass
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@@ -1228,7 +1227,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn
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url = 'http://%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \
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( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message )
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return trans.response.send_redirect( url )
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elif local_file:
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elif installed_repository_file:
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# The workflow was read from a file included with an installed tool shed repository.
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message = "Workflow <b>%s</b> imported successfully." % workflow.name
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return trans.response.send_redirect( web.url_for( controller='admin',
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@@ -23,7 +23,7 @@
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<br/>
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<div class="toolForm">
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<div class="toolFormTitle">Load tools into tool panel</div>
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<div class="toolFormTitle">Choose section to load tools into tool panel</div>
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<div class="toolFormBody">
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<form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin', action='install_tool_shed_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict )}" method="post" >
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%if shed_tool_conf_select_field:
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@@ -40,10 +40,17 @@
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<input type="hidden" name="shed_tool_conf" value="${shed_tool_conf}"/>
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%endif
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<div class="form-row">
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<label>Tool panel section:</label>
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<label>Add new tool panel section:</label>
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<input name="new_tool_panel_section" type="textfield" value="${new_tool_panel_section}" size="40"/>
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<div class="toolParamHelp" style="clear: both;">
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Add a new tool panel section or choose an existing section in your tool panel below to contain the installed tools.
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</div>
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</div>
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<div class="form-row">
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<label>Select existing tool panel section:</label>
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${tool_panel_section_select_field.get_html()}
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<div class="toolParamHelp" style="clear: both;">
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Choose the section in your tool panel to contain the installed tools.
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Choose an existing section in your tool panel to contain the installed tools.
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</div>
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</div>
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<div class="form-row">
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@@ -103,7 +103,7 @@
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<div class="menubutton" style="float: left;" id="workflow-${index}-popup">
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${workflow_name}
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<div popupmenu="workflow-${index}-popup">
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<a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', local_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a>
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<a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a>
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</div>
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</div>
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</td>
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