commit/galaxy-central: greg: Get all necessary information for installing a tool shed repository via a request from Galaxy rather than sending it from the tool shed.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/ee9cd81ccce2/
changeset: ee9cd81ccce2
user: greg
date: 2012-07-06 20:12:38
summary: Get all necessary information for installing a tool shed repository via a request from Galaxy rather than sending it from the tool shed.
affected #: 3 files
diff -r c04a803228753159987fbed332398aff5df17c15 -r ee9cd81ccce258a973c53f62489e54630d5d3fad lib/galaxy/web/controllers/admin_toolshed.py
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -545,194 +545,6 @@
status=status ) )
@web.expose
@web.require_admin
- def install_repository( self, trans, **kwd ):
- if not trans.app.toolbox.shed_tool_confs:
- message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one shed tool configuration file name with a '
- message += '<b><toolbox></b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation '
- message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose '
- message += '<b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the '
- message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_to..." '
- message += 'target="_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the '
- message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed" target="_blank">Galaxy tool shed wiki</a> for all of the details.'
- return trans.show_error_message( message )
- message = kwd.get( 'message', '' )
- status = kwd.get( 'status', 'done' )
- tool_shed_url = kwd[ 'tool_shed_url' ]
- # The value of repo_info_dicts is a list of one or more dictionaries, each associated with a tool shed repository that will be installed.
- encoded_repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] )
- repo_info_dicts = [ tool_shed_decode( repo_info_dict ) for repo_info_dict in encoded_repo_info_dicts ]
- # Every repository will be installed into the same tool panel section or all will be installed outside of any sections.
- new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' )
- tool_panel_section = kwd.get( 'tool_panel_section', '' )
- # One or more repositories may include tools, but not necessarily all of them.
- includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) )
- includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) )
- install_tool_dependencies = kwd.get( 'install_tool_dependencies', '' )
- tool_section = None
- if not includes_tools or ( includes_tools and kwd.get( 'select_tool_panel_section_button', False ) ):
- if includes_tools:
- install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies )
- shed_tool_conf = kwd[ 'shed_tool_conf' ]
- else:
- install_tool_dependencies = False
- # If installing a repository that includes no tools, get the relative tool_path from the file to which the
- # migrated_tools_config setting points.
- shed_tool_conf = trans.app.config.migrated_tools_config
- # Get the tool path by searching the list of shed_tool_confs for the dictionary that contains the information about shed_tool_conf.
- for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs:
- config_filename = shed_tool_conf_dict[ 'config_filename' ]
- if config_filename == shed_tool_conf:
- tool_path = shed_tool_conf_dict[ 'tool_path' ]
- break
- else:
- file_name = strip_path( config_filename )
- if file_name == shed_tool_conf:
- tool_path = shed_tool_conf_dict[ 'tool_path' ]
- break
- # Make sure all tool_shed_repository records exist.
- created_or_updated_tool_shed_repositories = []
- for repo_info_dict in repo_info_dicts:
- for name, repo_info_tuple in repo_info_dict.items():
- description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
- clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, changeset_revision ) )
- relative_install_dir = os.path.join( clone_dir, name )
- owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) )
- # Make sure the repository was not already installed.
- installed_tool_shed_repository, installed_changeset_revision = self.repository_was_previously_installed( trans,
- tool_shed_url,
- name,
- repo_info_tuple,
- clone_dir )
- if installed_tool_shed_repository:
- message += "The tool shed repository <b>%s</b> with owner <b>%s</b> and changeset revision <b>%s</b> " % ( name, owner, changeset_revision )
- if installed_changeset_revision != changeset_revision:
- message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision
- else:
- message += "was previously installed. "
- if installed_tool_shed_repository.uninstalled:
- message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. "
- elif installed_tool_shed_repository.deleted:
- message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. "
- if installed_changeset_revision != changeset_revision:
- message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's "
- message += "<b>Repository Actions</b> pop-up menu. "
- status = 'error'
- if len( repo_info_dicts ) == 1:
- new_kwd = dict( message=message, status=status )
- return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
- action='browse_repositories',
- **new_kwd ) )
- else:
- print "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name
- tool_shed_repository = create_or_update_tool_shed_repository( app=trans.app,
- name=name,
- description=description,
- installed_changeset_revision=changeset_revision,
- ctx_rev=ctx_rev,
- repository_clone_url=repository_clone_url,
- metadata_dict={},
- status=trans.model.ToolShedRepository.installation_status.NEW,
- current_changeset_revision=changeset_revision,
- owner=owner,
- dist_to_shed=False )
- created_or_updated_tool_shed_repositories.append( tool_shed_repository )
- if created_or_updated_tool_shed_repositories:
- if includes_tools and ( new_tool_panel_section or tool_panel_section ):
- if new_tool_panel_section:
- section_id = new_tool_panel_section.lower().replace( ' ', '_' )
- tool_panel_section_key = 'section_%s' % str( 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
- log.debug( "Appending to tool panel section: %s" % new_tool_panel_section )
- tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ]
- else:
- # Appending a new section to trans.app.toolbox.tool_panel
- log.debug( "Loading new tool panel section: %s" % new_tool_panel_section )
- elem = Element( 'section' )
- elem.attrib[ 'name' ] = new_tool_panel_section
- elem.attrib[ 'id' ] = section_id
- elem.attrib[ 'version' ] = ''
- tool_section = tools.ToolSection( elem )
- trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section
- else:
- tool_panel_section_key = 'section_%s' % tool_panel_section
- tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ]
- else:
- tool_panel_section_key = None
- tool_section = None
- tsrids_list = [ trans.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ]
- new_kwd = dict( includes_tool_dependencies=kwd.get( 'includes_tool_dependencies', False ),
- includes_tools=kwd.get( 'includes_tools', False ),
- install_tool_dependencies=install_tool_dependencies,
- repo_info_dicts=kwd[ 'repo_info_dicts' ],
- message=message,
- new_tool_panel_section=kwd.get( 'new_tool_panel_section', '' ),
- shed_tool_conf=kwd[ 'shed_tool_conf' ],
- status=status,
- tool_panel_section=kwd.get( 'tool_panel_section', '' ),
- tool_path=tool_path,
- tool_panel_section_key=tool_panel_section_key,
- tool_shed_repository_ids=tsrids_list,
- tool_shed_url=kwd[ 'tool_shed_url' ] )
- encoded_kwd = tool_shed_encode( new_kwd )
- tsrids_str = ','.join( tsrids_list )
- return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
- action='initiate_repository_installation',
- shed_repository_ids=tsrids_str,
- encoded_kwd=encoded_kwd,
- reinstalling=False ) )
- else:
- kwd[ 'message' ] = message
- kwd[ 'status' ] = status
- return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
- action='manage_repositories',
- **kwd ) )
- if len( trans.app.toolbox.shed_tool_confs ) > 1:
- shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans )
- shed_tool_conf = None
- else:
- shed_tool_conf_dict = trans.app.toolbox.shed_tool_confs[0]
- shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ]
- shed_tool_conf = shed_tool_conf.replace( './', '', 1 )
- shed_tool_conf_select_field = None
- tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
- if includes_tools and len( repo_info_dicts ) == 1:
- # If we're installing a single repository that contains a readme file, get it's contents to display.
- repo_info_dict = repo_info_dicts[ 0 ]
- name = repo_info_dict.keys()[ 0 ]
- repo_info_tuple = repo_info_dict[ name ]
- description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
- url = '%srepository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy&no_reset=true' % \
- ( tool_shed_url, name, repository_owner, changeset_revision )
- response = urllib2.urlopen( url )
- raw_text = response.read()
- response.close()
- readme_text = ''
- for i, line in enumerate( raw_text ):
- readme_text = '%s%s' % ( readme_text, to_html_str( line ) )
- if len( readme_text ) > MAX_CONTENT_SIZE:
- large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE )
- readme_text = '%s%s' % ( readme_text, to_html_str( large_str ) )
- break
- else:
- readme_text = ''
- install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=True )
- return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako',
- tool_shed_url=tool_shed_url,
- encoded_repo_info_dicts=kwd[ 'repo_info_dicts' ],
- repo_info_dicts=repo_info_dicts,
- shed_tool_conf=shed_tool_conf,
- includes_tools=includes_tools,
- includes_tool_dependencies=includes_tool_dependencies,
- install_tool_dependencies_check_box=install_tool_dependencies_check_box,
- shed_tool_conf_select_field=shed_tool_conf_select_field,
- tool_panel_section_select_field=tool_panel_section_select_field,
- new_tool_panel_section=new_tool_panel_section,
- readme_text=readme_text,
- message=message,
- status=status )
- @web.expose
- @web.require_admin
def install_tool_dependencies( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
@@ -776,8 +588,7 @@
@web.require_admin
def install_tool_shed_repositories( self, trans, tool_shed_repositories, reinstalling=False, **kwd ):
"""Install specified tool shed repositories."""
- encoded_repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] )
- repo_info_dicts = [ tool_shed_decode( repo_info_dict ) for repo_info_dict in encoded_repo_info_dicts ]
+ repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] )
tool_path = kwd[ 'tool_path' ]
includes_tool_dependencies = util.string_as_bool( kwd[ 'includes_tool_dependencies' ] )
install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
@@ -1151,6 +962,207 @@
return open_repository_files_folder( trans, folder_path )
@web.expose
@web.require_admin
+ def prepare_for_install( self, trans, **kwd ):
+ if not trans.app.toolbox.shed_tool_confs:
+ message = 'The <b>tool_config_file</b> setting in <b>universe_wsgi.ini</b> must include at least one shed tool configuration file name with a '
+ message += '<b><toolbox></b> tag that includes a <b>tool_path</b> attribute value which is a directory relative to the Galaxy installation '
+ message += 'directory in order to automatically install tools from a Galaxy tool shed (e.g., the file name <b>shed_tool_conf.xml</b> whose '
+ message += '<b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the '
+ message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Automatic_installation_of_Galaxy_to..." '
+ message += 'target="_blank">Automatic installation of Galaxy tool shed repository tools into a local Galaxy instance</a> section of the '
+ message += '<a href="http://wiki.g2.bx.psu.edu/Tool%20Shed" target="_blank">Galaxy tool shed wiki</a> for all of the details.'
+ return trans.show_error_message( message )
+ message = kwd.get( 'message', '' )
+ status = kwd.get( 'status', 'done' )
+ includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) )
+ tool_shed_url = kwd[ 'tool_shed_url' ]
+ # Every repository will be installed into the same tool panel section or all will be installed outside of any sections.
+ new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' )
+ tool_panel_section = kwd.get( 'tool_panel_section', '' )
+ # One or more repositories may include tools, but not necessarily all of them.
+ includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) )
+ includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) )
+ install_tool_dependencies = kwd.get( 'install_tool_dependencies', '' )
+ encoded_repo_info_dicts = util.listify( kwd.get( 'encoded_repo_info_dicts', None ) )
+ if not encoded_repo_info_dicts:
+ # The request originated in the tool shed.
+ repository_ids = kwd.get( 'repository_ids', None )
+ changeset_revisions = kwd.get( 'changeset_revisions', None )
+ # Get the information necessary to install each repository.
+ url = '%srepository/get_repository_information?repository_ids=%s&changeset_revisions=%s&webapp=galaxy' % ( tool_shed_url, repository_ids, changeset_revisions )
+ response = urllib2.urlopen( url )
+ raw_text = response.read()
+ response.close()
+ repo_information_dict = from_json_string( raw_text )
+ includes_tools = util.string_as_bool( repo_information_dict[ 'includes_tools' ] )
+ includes_tool_dependencies = util.string_as_bool( repo_information_dict[ 'includes_tool_dependencies' ] )
+ encoded_repo_info_dicts = util.listify( repo_information_dict[ 'repo_info_dicts' ] )
+ repo_info_dicts = [ tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ]
+ if not includes_tools or ( includes_tools and kwd.get( 'select_tool_panel_section_button', False ) ):
+ if includes_tools:
+ install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies )
+ shed_tool_conf = kwd[ 'shed_tool_conf' ]
+ else:
+ install_tool_dependencies = False
+ # If installing a repository that includes no tools, get the relative tool_path from the file to which the
+ # migrated_tools_config setting points.
+ shed_tool_conf = trans.app.config.migrated_tools_config
+ # Get the tool path by searching the list of shed_tool_confs for the dictionary that contains the information about shed_tool_conf.
+ for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs:
+ config_filename = shed_tool_conf_dict[ 'config_filename' ]
+ if config_filename == shed_tool_conf:
+ tool_path = shed_tool_conf_dict[ 'tool_path' ]
+ break
+ else:
+ file_name = strip_path( config_filename )
+ if file_name == shed_tool_conf:
+ tool_path = shed_tool_conf_dict[ 'tool_path' ]
+ break
+ # Make sure all tool_shed_repository records exist.
+ created_or_updated_tool_shed_repositories = []
+ # Repositories will be filtered (e.g., if already installed, etc), so filter the associated repo_info_dicts accordingly.
+ filtered_repo_info_dicts = []
+ for repo_info_dict in repo_info_dicts:
+ for name, repo_info_tuple in repo_info_dict.items():
+ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
+ clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, changeset_revision ) )
+ relative_install_dir = os.path.join( clone_dir, name )
+ owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) )
+ # Make sure the repository was not already installed.
+ installed_tool_shed_repository, installed_changeset_revision = self.repository_was_previously_installed( trans,
+ tool_shed_url,
+ name,
+ repo_info_tuple,
+ clone_dir )
+ if installed_tool_shed_repository:
+ message += "The tool shed repository <b>%s</b> with owner <b>%s</b> and changeset revision <b>%s</b> " % ( name, owner, changeset_revision )
+ if installed_changeset_revision != changeset_revision:
+ message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision
+ else:
+ message += "was previously installed. "
+ if installed_tool_shed_repository.uninstalled:
+ message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. "
+ elif installed_tool_shed_repository.deleted:
+ message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. "
+ if installed_changeset_revision != changeset_revision:
+ message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's "
+ message += "<b>Repository Actions</b> pop-up menu. "
+ status = 'error'
+ if len( repo_info_dicts ) == 1:
+ new_kwd = dict( message=message, status=status )
+ return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+ action='browse_repositories',
+ **new_kwd ) )
+ else:
+ print "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name
+ tool_shed_repository = create_or_update_tool_shed_repository( app=trans.app,
+ name=name,
+ description=description,
+ installed_changeset_revision=changeset_revision,
+ ctx_rev=ctx_rev,
+ repository_clone_url=repository_clone_url,
+ metadata_dict={},
+ status=trans.model.ToolShedRepository.installation_status.NEW,
+ current_changeset_revision=changeset_revision,
+ owner=owner,
+ dist_to_shed=False )
+ created_or_updated_tool_shed_repositories.append( tool_shed_repository )
+ filtered_repo_info_dicts.append( repo_info_dict )
+ if created_or_updated_tool_shed_repositories:
+ if includes_tools and ( new_tool_panel_section or tool_panel_section ):
+ if new_tool_panel_section:
+ section_id = new_tool_panel_section.lower().replace( ' ', '_' )
+ tool_panel_section_key = 'section_%s' % str( 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
+ log.debug( "Appending to tool panel section: %s" % new_tool_panel_section )
+ tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ]
+ else:
+ # Appending a new section to trans.app.toolbox.tool_panel
+ log.debug( "Loading new tool panel section: %s" % new_tool_panel_section )
+ elem = Element( 'section' )
+ elem.attrib[ 'name' ] = new_tool_panel_section
+ elem.attrib[ 'id' ] = section_id
+ elem.attrib[ 'version' ] = ''
+ tool_section = tools.ToolSection( elem )
+ trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section
+ else:
+ tool_panel_section_key = 'section_%s' % tool_panel_section
+ tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ]
+ else:
+ tool_panel_section_key = None
+ tool_section = None
+ tsrids_list = [ trans.security.encode_id( tsr.id ) for tsr in created_or_updated_tool_shed_repositories ]
+ new_kwd = dict( includes_tools=includes_tools,
+ includes_tool_dependencies=includes_tool_dependencies,
+ install_tool_dependencies=install_tool_dependencies,
+ message=message,
+ repo_info_dicts=filtered_repo_info_dicts,
+ shed_tool_conf=shed_tool_conf,
+ status=status,
+ tool_path=tool_path,
+ tool_panel_section_key=tool_panel_section_key,
+ tool_shed_repository_ids=tsrids_list,
+ tool_shed_url=tool_shed_url )
+ encoded_kwd = tool_shed_encode( new_kwd )
+ tsrids_str = ','.join( tsrids_list )
+ return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+ action='initiate_repository_installation',
+ shed_repository_ids=tsrids_str,
+ encoded_kwd=encoded_kwd,
+ reinstalling=False ) )
+ else:
+ kwd[ 'message' ] = message
+ kwd[ 'status' ] = status
+ return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+ action='manage_repositories',
+ **kwd ) )
+ if len( trans.app.toolbox.shed_tool_confs ) > 1:
+ shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans )
+ shed_tool_conf = None
+ else:
+ shed_tool_conf_dict = trans.app.toolbox.shed_tool_confs[0]
+ shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ]
+ shed_tool_conf = shed_tool_conf.replace( './', '', 1 )
+ shed_tool_conf_select_field = None
+ tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
+ if includes_tools and len( repo_info_dicts ) == 1:
+ # If we're installing a single repository, see if it contains a readme file tha twe can display.
+ repo_info_dict = repo_info_dicts[ 0 ]
+ name = repo_info_dict.keys()[ 0 ]
+ repo_info_tuple = repo_info_dict[ name ]
+ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
+ url = '%srepository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy&no_reset=true' % \
+ ( tool_shed_url, name, repository_owner, changeset_revision )
+ response = urllib2.urlopen( url )
+ raw_text = response.read()
+ response.close()
+ readme_text = ''
+ for i, line in enumerate( raw_text ):
+ readme_text = '%s%s' % ( readme_text, to_html_str( line ) )
+ if len( readme_text ) > MAX_CONTENT_SIZE:
+ large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE )
+ readme_text = '%s%s' % ( readme_text, to_html_str( large_str ) )
+ break
+ else:
+ readme_text = ''
+ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=True )
+ return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako',
+ encoded_repo_info_dicts=encoded_repo_info_dicts,
+ includes_tools=includes_tools,
+ includes_tool_dependencies=includes_tool_dependencies,
+ install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+ new_tool_panel_section=new_tool_panel_section,
+ repo_info_dicts=repo_info_dicts,
+ shed_tool_conf=shed_tool_conf,
+ shed_tool_conf_select_field=shed_tool_conf_select_field,
+ tool_panel_section_select_field=tool_panel_section_select_field,
+ tool_shed_url=kwd[ 'tool_shed_url' ],
+ readme_text=readme_text,
+ message=message,
+ status=status )
+ @web.expose
+ @web.require_admin
def reinstall_repository( self, trans, **kwd ):
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
diff -r c04a803228753159987fbed332398aff5df17c15 -r ee9cd81ccce258a973c53f62489e54630d5d3fad lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1035,6 +1035,37 @@
trans.response.headers['Pragma'] = 'no-cache'
trans.response.headers['Expires'] = '0'
return get_repository_file_contents( file_path )
+ @web.json
+ def get_repository_information( self, trans, repository_ids, changeset_revisions, **kwd ):
+ """
+ Generate a list of dictionaries, each of which contains the information about a repository that will be necessary for installing
+ it into a local Galaxy instance.
+ """
+ includes_tools = False
+ includes_tool_dependencies = False
+ repo_info_dicts = []
+ for repository_id, changeset_revision in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ):
+ repository_clone_url = generate_clone_url( trans, repository_id )
+ repository = get_repository( trans, repository_id )
+ repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
+ metadata = repository_metadata.metadata
+ if not includes_tools and 'tools' in metadata:
+ includes_tools = True
+ if not includes_tool_dependencies and 'tool_dependencies' in metadata:
+ includes_tool_dependencies = True
+ repo_dir = repository.repo_path
+ repo = hg.repository( get_configured_ui(), repo_dir )
+ ctx = get_changectx_for_changeset( repo, changeset_revision )
+ repo_info_dict = {}
+ repo_info_dict[ repository.name ] = ( repository.description,
+ repository_clone_url,
+ changeset_revision,
+ str( ctx.rev() ),
+ repository.user.username,
+ metadata.get( 'tool_dependencies', None ) )
+ encoded_repo_info_dict = tool_shed_encode( repo_info_dict )
+ repo_info_dicts.append( encoded_repo_info_dict )
+ return dict( includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies, repo_info_dicts=repo_info_dicts )
@web.expose
def get_readme( self, trans, **kwd ):
"""If the received changeset_revision includes a file named readme (case ignored), return it's contents."""
@@ -1218,45 +1249,13 @@
status=status )
@web.expose
def install_repositories_by_revision( self, trans, repository_ids, changeset_revisions, **kwd ):
- """Install a list of repositories into a local Galaxy instance by a specified changeset revision for each."""
- params = util.Params( kwd )
- message = util.restore_text( params.get( 'message', '' ) )
- status = params.get( 'status', 'done' )
- webapp = get_webapp( trans, **kwd )
+ """Send the list of repository_ids and changeset_revisions to Galaxy so it can begin the installation process."""
galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
- repo_info_dicts = []
- includes_tools = False
- includes_tool_dependencies = False
- for repository_id, changeset_revision in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ):
- repository_clone_url = generate_clone_url( trans, repository_id )
- repository = get_repository( trans, repository_id )
- #changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
- repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
- metadata = repository_metadata.metadata
- # Tell the caller if the repository includes Galaxy tools so the page enabling selection of the tool panel section can be displayed.
- if not includes_tools and 'tools' in metadata:
- includes_tools = True
- if not includes_tool_dependencies and 'tool_dependencies' in metadata:
- includes_tool_dependencies = True
- # Get the changelog rev for this changeset_revision.
- repo_dir = repository.repo_path
- repo = hg.repository( get_configured_ui(), repo_dir )
- ctx = get_changectx_for_changeset( repo, changeset_revision )
- repo_info_dict = {}
- repo_info_dict[ repository.name ] = ( repository.description,
- repository_clone_url,
- changeset_revision,
- str( ctx.rev() ),
- repository.user.username,
- metadata.get( 'tool_dependencies', None ) )
- repo_info_dicts.append( tool_shed_encode( repo_info_dict ) )
- encoded_repo_info_dicts = ','.join( repo_info_dicts )
# Redirect back to local Galaxy to perform install.
- url = '%sadmin_toolshed/install_repository' % galaxy_url
+ url = '%sadmin_toolshed/prepare_for_install' % galaxy_url
url += '?tool_shed_url=%s' % url_for( '/', qualified=True )
- url += '&repo_info_dicts=%s' % encoded_repo_info_dicts
- url += '&includes_tools=%s' % includes_tools
- url += '&includes_tool_dependencies=%s' % includes_tool_dependencies
+ url += '&repository_ids=%s' % ','.join( repository_ids )
+ url += '&changeset_revisions=%s' % ','.join( changeset_revisions )
return trans.response.send_redirect( url )
@web.expose
def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
diff -r c04a803228753159987fbed332398aff5df17c15 -r ee9cd81ccce258a973c53f62489e54630d5d3fad templates/admin/tool_shed_repository/select_tool_panel_section.mako
--- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako
+++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
@@ -29,7 +29,7 @@
<div class="toolFormTitle">Choose the tool panel section to contain the installed tools (optional)</div>
%endif
<div class="toolFormBody">
- <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='install_repository', tool_shed_url=tool_shed_url, repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies )}" method="post" >
+ <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies )}" method="post" ><div style="clear: both"></div>
%if includes_tool_dependencies:
${render_tool_dependency_section( install_tool_dependencies_check_box, repo_info_dicts )}
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
9 years, 4 months
- 1
- 0
commit/galaxy-central: greg: Fix for rendering workflows icontained in repositories n the tool shed.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/c04a80322875/
changeset: c04a80322875
user: greg
date: 2012-07-06 03:31:52
summary: Fix for rendering workflows icontained in repositories n the tool shed.
affected #: 1 file
diff -r b9804f980783c4a014a66f7cf45979ae290e71f0 -r c04a803228753159987fbed332398aff5df17c15 templates/webapps/community/repository/common.mako
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -84,7 +84,7 @@
</%def><%def name="render_repository_items( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )">
- <% from galaxy.tool_shed.encoding_util import tool_shed_decode %>
+ <% from galaxy.tool_shed.encoding_util import tool_shed_encode %>
%if metadata or can_set_metadata:
<p/><div class="toolForm">
@@ -236,7 +236,7 @@
%><tr><td>
- <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_decode( workflow_name ), webapp=webapp )}">${workflow_name}</a>
+ <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ), webapp=webapp )}">${workflow_name}</a></td><td>
%if steps:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
9 years, 4 months
- 1
- 0
commit/galaxy-central: greg: Fixes for simultaneously installing multiple tool shed repositories into a local Galaxy instance, and fixes for installing repositories retrieved from searches in the tool shed.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/b9804f980783/
changeset: b9804f980783
user: greg
date: 2012-07-05 23:44:01
summary: Fixes for simultaneously installing multiple tool shed repositories into a local Galaxy instance, and fixes for installing repositories retrieved from searches in the tool shed.
affected #: 13 files
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 lib/galaxy/web/controllers/admin_toolshed.py
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -558,21 +558,15 @@
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
tool_shed_url = kwd[ 'tool_shed_url' ]
+ # The value of repo_info_dicts is a list of one or more dictionaries, each associated with a tool shed repository that will be installed.
+ encoded_repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] )
+ repo_info_dicts = [ tool_shed_decode( repo_info_dict ) for repo_info_dict in encoded_repo_info_dicts ]
+ # Every repository will be installed into the same tool panel section or all will be installed outside of any sections.
new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' )
tool_panel_section = kwd.get( 'tool_panel_section', '' )
+ # One or more repositories may include tools, but not necessarily all of them.
includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) )
includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) )
- if includes_tool_dependencies:
- dict_with_tool_dependencies = tool_shed_decode( kwd[ 'repo_info_dict' ] )
- # The repo_info_dict includes tool dependencies which we need to display so the user knows what will be installed.
- repo_info_dict = {}
- for name, repo_info_tuple in dict_with_tool_dependencies.items():
- description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
- # Create a new repo_info_dict by eliminating tool_dependencies from the repo_info_tuple.
- repo_info_dict[ name ] = ( description, repository_clone_url, changeset_revision, ctx_rev )
- else:
- dict_with_tool_dependencies = {}
- repo_info_dict = tool_shed_decode( kwd[ 'repo_info_dict' ] )
install_tool_dependencies = kwd.get( 'install_tool_dependencies', '' )
tool_section = None
if not includes_tools or ( includes_tools and kwd.get( 'select_tool_panel_section_button', False ) ):
@@ -597,50 +591,51 @@
break
# Make sure all tool_shed_repository records exist.
created_or_updated_tool_shed_repositories = []
- for name, repo_info_tuple in repo_info_dict.items():
- description, repository_clone_url, changeset_revision, ctx_rev = repo_info_tuple
- clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, changeset_revision ) )
- relative_install_dir = os.path.join( clone_dir, name )
- owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) )
- # Make sure the repository was not already installed.
- installed_tool_shed_repository, installed_changeset_revision = self.repository_was_previously_installed( trans,
- tool_shed_url,
- name,
- repo_info_tuple,
- clone_dir )
- if installed_tool_shed_repository:
- message = "The tool shed repository <b>%s</b> with owner <b>%s</b> and changeset revision <b>%s</b> " % ( name, owner, changeset_revision )
- if installed_changeset_revision != changeset_revision:
- message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision
+ for repo_info_dict in repo_info_dicts:
+ for name, repo_info_tuple in repo_info_dict.items():
+ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
+ clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, changeset_revision ) )
+ relative_install_dir = os.path.join( clone_dir, name )
+ owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) )
+ # Make sure the repository was not already installed.
+ installed_tool_shed_repository, installed_changeset_revision = self.repository_was_previously_installed( trans,
+ tool_shed_url,
+ name,
+ repo_info_tuple,
+ clone_dir )
+ if installed_tool_shed_repository:
+ message += "The tool shed repository <b>%s</b> with owner <b>%s</b> and changeset revision <b>%s</b> " % ( name, owner, changeset_revision )
+ if installed_changeset_revision != changeset_revision:
+ message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision
+ else:
+ message += "was previously installed. "
+ if installed_tool_shed_repository.uninstalled:
+ message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. "
+ elif installed_tool_shed_repository.deleted:
+ message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. "
+ if installed_changeset_revision != changeset_revision:
+ message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's "
+ message += "<b>Repository Actions</b> pop-up menu. "
+ status = 'error'
+ if len( repo_info_dicts ) == 1:
+ new_kwd = dict( message=message, status=status )
+ return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+ action='browse_repositories',
+ **new_kwd ) )
else:
- message += "was previously installed. "
- if installed_tool_shed_repository.uninstalled:
- message += "The repository has been uninstalled, however, so reinstall the original repository instead of installing it again. "
- elif installed_tool_shed_repository.deleted:
- message += "The repository has been deactivated, however, so activate the original repository instead of installing it again. "
- if installed_changeset_revision != changeset_revision:
- message += "You can get the latest updates for the repository using the <b>Get updates</b> option from the repository's "
- message += "<b>Repository Actions</b> pop-up menu. "
- status = 'error'
- if len( repo_info_dict ) == 1:
- new_kwd = dict( message=message, status=status )
- return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
- action='browse_repositories',
- **new_kwd ) )
- else:
- print "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name
- tool_shed_repository = create_or_update_tool_shed_repository( app=trans.app,
- name=name,
- description=description,
- installed_changeset_revision=changeset_revision,
- ctx_rev=ctx_rev,
- repository_clone_url=repository_clone_url,
- metadata_dict={},
- status=trans.model.ToolShedRepository.installation_status.NEW,
- current_changeset_revision=changeset_revision,
- owner=owner,
- dist_to_shed=False )
- created_or_updated_tool_shed_repositories.append( tool_shed_repository )
+ print "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name
+ tool_shed_repository = create_or_update_tool_shed_repository( app=trans.app,
+ name=name,
+ description=description,
+ installed_changeset_revision=changeset_revision,
+ ctx_rev=ctx_rev,
+ repository_clone_url=repository_clone_url,
+ metadata_dict={},
+ status=trans.model.ToolShedRepository.installation_status.NEW,
+ current_changeset_revision=changeset_revision,
+ owner=owner,
+ dist_to_shed=False )
+ created_or_updated_tool_shed_repositories.append( tool_shed_repository )
if created_or_updated_tool_shed_repositories:
if includes_tools and ( new_tool_panel_section or tool_panel_section ):
if new_tool_panel_section:
@@ -669,7 +664,7 @@
new_kwd = dict( includes_tool_dependencies=kwd.get( 'includes_tool_dependencies', False ),
includes_tools=kwd.get( 'includes_tools', False ),
install_tool_dependencies=install_tool_dependencies,
- repo_info_dict=kwd[ 'repo_info_dict' ],
+ repo_info_dicts=kwd[ 'repo_info_dicts' ],
message=message,
new_tool_panel_section=kwd.get( 'new_tool_panel_section', '' ),
shed_tool_conf=kwd[ 'shed_tool_conf' ],
@@ -701,12 +696,12 @@
shed_tool_conf = shed_tool_conf.replace( './', '', 1 )
shed_tool_conf_select_field = None
tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
- if includes_tools and len( repo_info_dict ) == 1:
+ if includes_tools and len( repo_info_dicts ) == 1:
# If we're installing a single repository that contains a readme file, get it's contents to display.
+ repo_info_dict = repo_info_dicts[ 0 ]
name = repo_info_dict.keys()[ 0 ]
repo_info_tuple = repo_info_dict[ name ]
- description, repository_clone_url, changeset_revision, ctx_rev = repo_info_tuple
- repository_owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) )
+ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
url = '%srepository/get_readme?name=%s&owner=%s&changeset_revision=%s&webapp=galaxy&no_reset=true' % \
( tool_shed_url, name, repository_owner, changeset_revision )
response = urllib2.urlopen( url )
@@ -724,8 +719,8 @@
install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=True )
return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako',
tool_shed_url=tool_shed_url,
- repo_info_dict=kwd[ 'repo_info_dict' ],
- dict_with_tool_dependencies=dict_with_tool_dependencies,
+ encoded_repo_info_dicts=kwd[ 'repo_info_dicts' ],
+ repo_info_dicts=repo_info_dicts,
shed_tool_conf=shed_tool_conf,
includes_tools=includes_tools,
includes_tool_dependencies=includes_tool_dependencies,
@@ -781,7 +776,8 @@
@web.require_admin
def install_tool_shed_repositories( self, trans, tool_shed_repositories, reinstalling=False, **kwd ):
"""Install specified tool shed repositories."""
- repo_info_dict = tool_shed_decode( kwd[ 'repo_info_dict' ] )
+ encoded_repo_info_dicts = util.listify( kwd[ 'repo_info_dicts' ] )
+ repo_info_dicts = [ tool_shed_decode( repo_info_dict ) for repo_info_dict in encoded_repo_info_dicts ]
tool_path = kwd[ 'tool_path' ]
includes_tool_dependencies = util.string_as_bool( kwd[ 'includes_tool_dependencies' ] )
install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
@@ -790,14 +786,11 @@
tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ]
else:
tool_section = None
- for tool_shed_repository in tool_shed_repositories:
+ for tool_shed_repository, repo_info_dict in zip( tool_shed_repositories, repo_info_dicts ):
# Clone each repository to the configured location.
update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.CLONING )
repo_info_tuple = repo_info_dict[ tool_shed_repository.name ]
- if includes_tool_dependencies and not reinstalling:
- description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
- else:
- description, repository_clone_url, changeset_revision, ctx_rev = repo_info_tuple
+ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) )
relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name )
clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev )
@@ -858,38 +851,38 @@
shutil.rmtree( work_dir )
except:
pass
- if 'datatypes' in metadata:
- update_tool_shed_repository_status( trans.app,
- tool_shed_repository,
- trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES )
- work_dir = make_tmp_directory()
- datatypes_config = get_config_from_repository( trans.app,
- 'datatypes_conf.xml',
- tool_shed_repository,
- tool_shed_repository.installed_changeset_revision,
- work_dir )
- # Load proprietary data types required by tools.
- converter_path, display_path = alter_config_and_load_prorietary_datatypes( trans.app, datatypes_config, relative_install_dir, override=False )
- if converter_path or display_path:
- # Create a dictionary of tool shed repository related information.
- repository_dict = create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed,
- name=tool_shed_repository.name,
- owner=tool_shed_repository.owner,
- installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
- tool_dicts=metadata.get( 'tools', [] ),
- converter_path=converter_path,
- display_path=display_path )
- if converter_path:
- # Load proprietary datatype converters
- trans.app.datatypes_registry.load_datatype_converters( trans.app.toolbox, installed_repository_dict=repository_dict )
- if display_path:
- # Load proprietary datatype display applications
- trans.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
- try:
- shutil.rmtree( work_dir )
- except:
- pass
- update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLED )
+ if 'datatypes' in metadata:
+ update_tool_shed_repository_status( trans.app,
+ tool_shed_repository,
+ trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES )
+ work_dir = make_tmp_directory()
+ datatypes_config = get_config_from_repository( trans.app,
+ 'datatypes_conf.xml',
+ tool_shed_repository,
+ tool_shed_repository.installed_changeset_revision,
+ work_dir )
+ # Load proprietary data types required by tools.
+ converter_path, display_path = alter_config_and_load_prorietary_datatypes( trans.app, datatypes_config, relative_install_dir, override=False )
+ if converter_path or display_path:
+ # Create a dictionary of tool shed repository related information.
+ repository_dict = create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed,
+ name=tool_shed_repository.name,
+ owner=tool_shed_repository.owner,
+ installed_changeset_revision=tool_shed_repository.installed_changeset_revision,
+ tool_dicts=metadata.get( 'tools', [] ),
+ converter_path=converter_path,
+ display_path=display_path )
+ if converter_path:
+ # Load proprietary datatype converters
+ trans.app.datatypes_registry.load_datatype_converters( trans.app.toolbox, installed_repository_dict=repository_dict )
+ if display_path:
+ # Load proprietary datatype display applications
+ trans.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict )
+ try:
+ shutil.rmtree( work_dir )
+ except:
+ pass
+ update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLED )
tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ]
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
action='monitor_repository_installation',
@@ -1241,7 +1234,7 @@
new_kwd = dict( includes_tool_dependencies=tool_shed_repository.includes_tool_dependencies,
includes_tools=tool_shed_repository.includes_tools,
install_tool_dependencies=install_tool_dependencies,
- repo_info_dict=kwd[ 'repo_info_dict' ],
+ repo_info_dicts=kwd[ 'repo_info_dict' ],
message=message,
new_tool_panel_section=new_tool_panel_section,
shed_tool_conf=shed_tool_conf,
@@ -1282,8 +1275,7 @@
# Handle case where the repository was previously installed using an older changeset_revsion, but later the repository was updated
# in the tool shed and now we're trying to install the latest changeset revision of the same repository instead of updating the one
# that was previously installed. We'll look in the database instead of on disk since the repository may be uninstalled.
- description, repository_clone_url, changeset_revision, ctx_rev = repo_info_tuple
- repository_owner = get_repository_owner( clean_repository_clone_url( repository_clone_url ) )
+ description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple
tool_shed = get_tool_shed_from_clone_url( repository_clone_url )
# Get all previous change set revisions from the tool shed for the repository back to, but excluding, the previous valid changeset
# revision to see if it was previously installed using one of them.
@@ -1309,22 +1301,16 @@
def reselect_tool_panel_section( self, trans, **kwd ):
repository = get_repository( trans, kwd[ 'id' ] )
metadata = repository.metadata
- # Populate repo_info_dict.
tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
ctx_rev = get_ctx_rev( tool_shed_url, repository.name, repository.owner, repository.installed_changeset_revision )
repository_clone_url = generate_clone_url( trans, repository )
repo_info_dict = {}
- repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, repository.installed_changeset_revision, ctx_rev )
- dict_with_tool_dependencies = {}
- includes_tool_dependencies = repository.includes_tool_dependencies
- if includes_tool_dependencies:
- # Populate dict_with_tool_dependencies.
- dict_with_tool_dependencies[ repository.name ] = ( repository.description,
- repository_clone_url,
- repository.installed_changeset_revision,
- ctx_rev,
- repository.owner,
- metadata[ 'tool_dependencies' ] )
+ repo_info_dict[ repository.name ] = ( repository.description,
+ repository_clone_url,
+ repository.installed_changeset_revision,
+ ctx_rev,
+ repository.owner,
+ metadata.get( 'tool_dependencies', None ) )
# Get the location in the tool panel in which the tool was originally loaded.
if 'tool_panel_section' in metadata:
tool_panel_dict = metadata[ 'tool_panel_section' ]
@@ -1360,7 +1346,6 @@
install_tool_dependencies_check_box=install_tool_dependencies_check_box,
tool_panel_section_select_field=tool_panel_section_select_field,
repo_info_dict=tool_shed_encode( repo_info_dict ),
- dict_with_tool_dependencies=dict_with_tool_dependencies,
includes_tool_dependencies=includes_tool_dependencies,
message=message,
status=status )
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -381,27 +381,6 @@
repository_metadata.downloadable = changeset_is_downloadable( metadata_dict )
trans.sa_session.add( repository_metadata )
trans.sa_session.flush()
-def decode( value ):
- # Extract and verify hash
- a, b = value.split( ":" )
- value = binascii.unhexlify( b )
- test = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
- assert a == test
- # Restore from string
- try:
- values = json_fix( simplejson.loads( value ) )
- except Exception, e:
- # We do not have a json string
- values = value
- return values
-def encode( val ):
- if isinstance( val, dict ):
- value = simplejson.dumps( val )
- else:
- value = val
- a = hmac_new( 'ToolShedAndGalaxyMustHaveThisSameKey', value )
- b = binascii.hexlify( value )
- return "%s:%s" % ( a, b )
def generate_clone_url( trans, repository_id ):
"""Generate the URL for cloning a repository."""
repository = get_repository( trans, repository_id )
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -819,13 +819,16 @@
trans.sa_session.flush()
download_url = '/repos/%s/%s/archive/%s' % ( repository.user.username, repository.name, file_type_str )
return trans.response.send_redirect( download_url )
- def __encode_repo_info_dict( self, trans, webapp, repository_metadata_ids ):
+ def __encode_repo_info_dict( self, trans, repository_metadata_ids ):
repo_info_dict = {}
includes_tools = False
- for repository_metadata_id in repository_metadata_ids:
+ includes_tool_dependencies = False
+ for repository_metadata_id in util.listify( repository_metadata_ids ):
repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
if not includes_tools and 'tools' in repository_metadata.metadata:
includes_tools = True
+ if not includes_tool_dependencies and 'tool_dependencies' in repository_metadata.metadata:
+ includes_tool_dependencies = True
repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) )
# Get the changelog rev for this changeset_revision.
repo_dir = repository.repo_path
@@ -834,8 +837,11 @@
ctx = get_changectx_for_changeset( repo, changeset_revision )
repository_id = trans.security.encode_id( repository.id )
repository_clone_url = generate_clone_url( trans, repository_id )
- repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision, str( ctx.rev() ) )
- return encode( repo_info_dict ), includes_tools
+ if includes_tool_dependencies:
+ repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision, str( ctx.rev() ) )
+ else:
+ repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision, str( ctx.rev() ) )
+ return tool_shed_encode( repo_info_dict ), includes_tools, includes_tool_dependencies
@web.expose
def find_tools( self, trans, **kwd ):
params = util.Params( kwd )
@@ -865,11 +871,17 @@
action=a,
**kwd ) )
if operation == "install":
- galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
- encoded_repo_info_dict, includes_tools = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
- url = '%sadmin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s&includes_tools=%s' % \
- ( galaxy_url, url_for( '/', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) )
- return trans.response.send_redirect( url )
+ # We've received a list of RepositoryMetadata ids, so we need to build a list of associated Repository ids.
+ encoded_repository_ids = []
+ changeset_revisions = []
+ for repository_metadata_id in util.listify( item_id ):
+ repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id )
+ encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) )
+ changeset_revisions.append( repository_metadata.changeset_revision )
+ return trans.response.send_redirect( web.url_for( controller='repository',
+ action='install_repositories_by_revision',
+ repository_ids=encoded_repository_ids,
+ changeset_revisions=changeset_revisions ) )
else:
# This can only occur when there is a multi-select grid with check boxes and an operation,
# and the user clicked the operation button without checking any of the check boxes.
@@ -945,11 +957,17 @@
action=a,
**kwd ) )
if operation == "install":
- galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
- encoded_repo_info_dict, includes_tools = self.__encode_repo_info_dict( trans, webapp, util.listify( item_id ) )
- url = '%sadmin_toolshed/install_repository?tool_shed_url=%s&webapp=%s&repo_info_dict=%s&includes_tools=%s' % \
- ( galaxy_url, url_for( '/', qualified=True ), webapp, encoded_repo_info_dict, str( includes_tools ) )
- return trans.response.send_redirect( url )
+ # We've received a list of RepositoryMetadata ids, so we need to build a list of associated Repository ids.
+ encoded_repository_ids = []
+ changeset_revisions = []
+ for repository_metadata_id in util.listify( item_id ):
+ repository_metadata = get_repository_metadata_by_id( trans, item_id )
+ encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) )
+ changeset_revisions.append( repository_metadata.changeset_revision )
+ return trans.response.send_redirect( web.url_for( controller='repository',
+ action='install_repositories_by_revision',
+ repository_ids=encoded_repository_ids,
+ changeset_revisions=changeset_revisions ) )
else:
# This can only occur when there is a multi-select grid with check boxes and an operation,
# and the user clicked the operation button without checking any of the check boxes.
@@ -1199,41 +1217,46 @@
message=message,
status=status )
@web.expose
- def install_repository_revision( self, trans, repository_id, **kwd ):
+ def install_repositories_by_revision( self, trans, repository_ids, changeset_revisions, **kwd ):
+ """Install a list of repositories into a local Galaxy instance by a specified changeset revision for each."""
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
webapp = get_webapp( trans, **kwd )
galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
- repository_clone_url = generate_clone_url( trans, repository_id )
- repository = get_repository( trans, repository_id )
- changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
- repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
- metadata = repository_metadata.metadata
- # Tell the caller if the repository includes Galaxy tools so the page enabling selection of the tool panel section can be displayed.
- includes_tools = 'tools' in metadata
- includes_tool_dependencies = 'tool_dependencies' in metadata
- # Get the changelog rev for this changeset_revision.
- repo_dir = repository.repo_path
- repo = hg.repository( get_configured_ui(), repo_dir )
- ctx = get_changectx_for_changeset( repo, changeset_revision )
- repo_info_dict = {}
- if includes_tool_dependencies:
+ repo_info_dicts = []
+ includes_tools = False
+ includes_tool_dependencies = False
+ for repository_id, changeset_revision in zip( util.listify( repository_ids ), util.listify( changeset_revisions ) ):
+ repository_clone_url = generate_clone_url( trans, repository_id )
+ repository = get_repository( trans, repository_id )
+ #changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
+ repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
+ metadata = repository_metadata.metadata
+ # Tell the caller if the repository includes Galaxy tools so the page enabling selection of the tool panel section can be displayed.
+ if not includes_tools and 'tools' in metadata:
+ includes_tools = True
+ if not includes_tool_dependencies and 'tool_dependencies' in metadata:
+ includes_tool_dependencies = True
+ # Get the changelog rev for this changeset_revision.
+ repo_dir = repository.repo_path
+ repo = hg.repository( get_configured_ui(), repo_dir )
+ ctx = get_changectx_for_changeset( repo, changeset_revision )
+ repo_info_dict = {}
repo_info_dict[ repository.name ] = ( repository.description,
repository_clone_url,
changeset_revision,
str( ctx.rev() ),
repository.user.username,
- metadata[ 'tool_dependencies' ] )
- else:
- repo_info_dict[ repository.name ] = ( repository.description,
- repository_clone_url,
- changeset_revision,
- str( ctx.rev() ) )
- encoded_repo_info_dict = encode( repo_info_dict )
+ metadata.get( 'tool_dependencies', None ) )
+ repo_info_dicts.append( tool_shed_encode( repo_info_dict ) )
+ encoded_repo_info_dicts = ','.join( repo_info_dicts )
# Redirect back to local Galaxy to perform install.
- url = '%sadmin_toolshed/install_repository?tool_shed_url=%s&repo_info_dict=%s&includes_tools=%s&includes_tool_dependencies=%s' % \
- ( galaxy_url, url_for( '/', qualified=True ), encoded_repo_info_dict, str( includes_tools ), str( includes_tool_dependencies ) )
+ url = '%sadmin_toolshed/install_repository' % galaxy_url
+ url += '?tool_shed_url=%s' % url_for( '/', qualified=True )
+ url += '&repo_info_dicts=%s' % encoded_repo_info_dicts
+ url += '&includes_tools=%s' % includes_tools
+ url += '&includes_tool_dependencies=%s' % includes_tool_dependencies
return trans.response.send_redirect( url )
@web.expose
def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ):
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 lib/galaxy/webapps/community/controllers/workflow.py
--- a/lib/galaxy/webapps/community/controllers/workflow.py
+++ b/lib/galaxy/webapps/community/controllers/workflow.py
@@ -10,6 +10,7 @@
from galaxy.web.controllers.workflow import attach_ordered_steps
from galaxy.model.orm import *
from common import *
+from galaxy.tool_shed.encoding_util import *
class RepoInputDataModule( InputDataModule ):
@@ -139,7 +140,7 @@
repository_metadata_id = kwd.get( 'repository_metadata_id', '' )
workflow_name = kwd.get( 'workflow_name', '' )
if workflow_name:
- workflow_name = decode( workflow_name )
+ workflow_name = tool_shed_decode( workflow_name )
webapp = kwd.get( 'webapp', 'community' )
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
@@ -159,7 +160,7 @@
repository_id = trans.security.encode_id( repository_metadata.repository_id )
changeset_revision = repository_metadata.changeset_revision
metadata = repository_metadata.metadata
- workflow_name = decode( workflow_name )
+ workflow_name = tool_shed_decode( workflow_name )
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
for workflow_tup in metadata[ 'workflows' ]:
@@ -385,7 +386,7 @@
repository_metadata_id = kwd.get( 'repository_metadata_id', '' )
workflow_name = kwd.get( 'workflow_name', '' )
if workflow_name:
- workflow_name = decode( workflow_name )
+ workflow_name = tool_shed_decode( workflow_name )
webapp = kwd.get( 'webapp', 'community' )
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
@@ -403,7 +404,7 @@
return open( tmp_fname )
galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
url = '%sworkflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s&webapp=%s' % \
- ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, encode( workflow_name ), webapp )
+ ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, tool_shed_encode( workflow_name ), webapp )
return trans.response.send_redirect( url )
return trans.response.send_redirect( web.url_for( controller='workflow',
action='view_workflow',
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 templates/admin/tool_shed_repository/common.mako
--- a/templates/admin/tool_shed_repository/common.mako
+++ b/templates/admin/tool_shed_repository/common.mako
@@ -67,7 +67,7 @@
</script></%def>
-<%def name="render_tool_dependency_section( install_tool_dependencies_check_box, dict_with_tool_dependencies )">
+<%def name="render_tool_dependency_section( install_tool_dependencies_check_box, repo_info_dicts )"><% import os %><div class="form-row"><div class="toolParamHelp" style="clear: both;">
@@ -100,32 +100,36 @@
<th>Type</th><th>Install directory</th></tr>
- %for repository_name, repo_info_tuple in dict_with_tool_dependencies.items():
- <% description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple %>
- %for dependency_key, requirements_dict in tool_dependencies.items():
- <%
- name = requirements_dict[ 'name' ]
- version = requirements_dict[ 'version' ]
- type = requirements_dict[ 'type' ]
- install_dir = os.path.join( trans.app.config.tool_dependency_dir,
- name,
- version,
- repository_owner,
- repository_name,
- changeset_revision )
- tool_dependency_readme_text = requirements_dict.get( 'readme', None )
- %>
- %if not os.path.exists( install_dir ):
- <tr>
- <td>${name}</td>
- <td>${version}</td>
- <td>${type}</td>
- <td>${install_dir}</td>
- </tr>
- %if tool_dependency_readme_text:
- <tr><td colspan="4" bgcolor="#FFFFCC">${name} ${version} requirements and installation information</td></tr>
- <tr><td colspan="4"><pre>${tool_dependency_readme_text}</pre></td></tr>
- %endif
+ %for repo_info_dict in repo_info_dicts:
+ %for repository_name, repo_info_tuple in repo_info_dict.items():
+ <% description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple %>
+ %if tool_dependencies:
+ %for dependency_key, requirements_dict in tool_dependencies.items():
+ <%
+ name = requirements_dict[ 'name' ]
+ version = requirements_dict[ 'version' ]
+ type = requirements_dict[ 'type' ]
+ install_dir = os.path.join( trans.app.config.tool_dependency_dir,
+ name,
+ version,
+ repository_owner,
+ repository_name,
+ changeset_revision )
+ tool_dependency_readme_text = requirements_dict.get( 'readme', None )
+ %>
+ %if not os.path.exists( install_dir ):
+ <tr>
+ <td>${name}</td>
+ <td>${version}</td>
+ <td>${type}</td>
+ <td>${install_dir}</td>
+ </tr>
+ %if tool_dependency_readme_text:
+ <tr><td colspan="4" bgcolor="#FFFFCC">${name} ${version} requirements and installation information</td></tr>
+ <tr><td colspan="4"><pre>${tool_dependency_readme_text}</pre></td></tr>
+ %endif
+ %endif
+ %endfor
%endif
%endfor
%endfor
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
--- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
+++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako
@@ -12,7 +12,7 @@
<form name="reselect_tool_panel_section" id="reselect_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='reinstall_repository', id=trans.security.encode_id( repository.id ), repo_info_dict=repo_info_dict )}" method="post" ><div style="clear: both"></div>
%if includes_tool_dependencies:
- ${render_tool_dependency_section( install_tool_dependencies_check_box, dict_with_tool_dependencies )}
+ ${render_tool_dependency_section( install_tool_dependencies_check_box, [ repo_info_dict ] )}
%endif
<div style="clear: both"></div><div class="form-row">
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 templates/admin/tool_shed_repository/select_tool_panel_section.mako
--- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako
+++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
@@ -23,19 +23,23 @@
<br/><div class="toolForm">
- <div class="toolFormTitle">Confirm tool dependency installation</div>
+ %if includes_tool_dependencies:
+ <div class="toolFormTitle">Confirm tool dependency installation</div>
+ %else:
+ <div class="toolFormTitle">Choose the tool panel section to contain the installed tools (optional)</div>
+ %endif
<div class="toolFormBody">
- <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='install_repository', tool_shed_url=tool_shed_url, repo_info_dict=repo_info_dict, includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies )}" method="post" >
+ <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='install_repository', tool_shed_url=tool_shed_url, repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies )}" method="post" ><div style="clear: both"></div>
%if includes_tool_dependencies:
- ${render_tool_dependency_section( install_tool_dependencies_check_box, dict_with_tool_dependencies )}
+ ${render_tool_dependency_section( install_tool_dependencies_check_box, repo_info_dicts )}
+ <div style="clear: both"></div>
+ <div class="form-row">
+ <table class="colored" width="100%">
+ <th bgcolor="#EBD9B2">Choose the tool panel section to contain the installed tools (optional)</th>
+ </table>
+ </div>
%endif
- <div style="clear: both"></div>
- <div class="form-row">
- <table class="colored" width="100%">
- <th bgcolor="#EBD9B2">Choose the tool panel section to contain the installed tools (optional)</th>
- </table>
- </div>
%if shed_tool_conf_select_field:
<div class="form-row"><label>Shed tool configuration file:</label>
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 templates/webapps/community/repository/common.mako
--- a/templates/webapps/community/repository/common.mako
+++ b/templates/webapps/community/repository/common.mako
@@ -84,7 +84,7 @@
</%def><%def name="render_repository_items( repository_metadata_id, metadata, can_set_metadata=False, webapp='community' )">
- <% from galaxy.webapps.community.controllers.common import encode, decode %>
+ <% from galaxy.tool_shed.encoding_util import tool_shed_decode %>
%if metadata or can_set_metadata:
<p/><div class="toolForm">
@@ -236,7 +236,7 @@
%><tr><td>
- <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp )}">${workflow_name}</a>
+ <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_decode( workflow_name ), webapp=webapp )}">${workflow_name}</a></td><td>
%if steps:
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 templates/webapps/community/repository/preview_tools_in_changeset.mako
--- a/templates/webapps/community/repository/preview_tools_in_changeset.mako
+++ b/templates/webapps/community/repository/preview_tools_in_changeset.mako
@@ -64,7 +64,7 @@
<br/><br/><ul class="manage-table-actions">
- <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li>
+ <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 templates/webapps/community/repository/tool_form.mako
--- a/templates/webapps/community/repository/tool_form.mako
+++ b/templates/webapps/community/repository/tool_form.mako
@@ -123,7 +123,7 @@
%if webapp == 'galaxy':
<li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup">
- <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li>
+ <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li><li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Browse repository</a></li></div><li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 templates/webapps/community/repository/view_repository.mako
--- a/templates/webapps/community/repository/view_repository.mako
+++ b/templates/webapps/community/repository/view_repository.mako
@@ -94,7 +94,7 @@
</div>
%endif
%else:
- <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li>
+ <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="repository-${repository.id}-popup"><a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_repositories', webapp=webapp )}">Browse valid repositories</a>
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 templates/webapps/community/repository/view_tool_metadata.mako
--- a/templates/webapps/community/repository/view_tool_metadata.mako
+++ b/templates/webapps/community/repository/view_tool_metadata.mako
@@ -36,7 +36,7 @@
%if webapp == 'galaxy':
<li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup">
- <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install to local Galaxy</a></li>
+ <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install to local Galaxy</a></li><li><a class="action-button" href="${h.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Browse repository</a></li></div><li><a class="action-button" id="tool_shed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li>
diff -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 -r b9804f980783c4a014a66f7cf45979ae290e71f0 templates/webapps/community/repository/view_workflow.mako
--- a/templates/webapps/community/repository/view_workflow.mako
+++ b/templates/webapps/community/repository/view_workflow.mako
@@ -5,7 +5,7 @@
<%
from galaxy.web.framework.helpers import time_ago
- from galaxy.webapps.community.controllers.common import encode
+ from galaxy.tool_shed.encoding_util import tool_shed_encode
in_tool_shed = webapp == 'community'
is_admin = trans.user_is_admin()
@@ -34,7 +34,7 @@
<%inherit file="${inherit(context)}"/><%def name="render_workflow( repository_metadata_id, workflow_name, webapp )">
- <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp ) %>
+ <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ), webapp=webapp ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def>
@@ -76,8 +76,8 @@
%else:
<li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup">
- <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=encode( workflow_name ), webapp=webapp )}">Import workflow to local Galaxy</a></li>
- <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repository_revision', repository_id=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revision=changeset_revision )}">Install repository to local Galaxy</a></li>
+ <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ), webapp=webapp )}">Import workflow to local Galaxy</a></li>
+ <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), webapp=webapp, changeset_revisions=changeset_revision )}">Install repository to local Galaxy</a></li></div><li><a class="action-button" id="toolshed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li><div popupmenu="toolshed-${repository.id}-popup">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Look for the webapp setting in the request's environ if it is not included in the request's parameters.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/98204b9f4f80/
changeset: 98204b9f4f80
user: greg
date: 2012-07-05 19:54:31
summary: Look for the webapp setting in the request's environ if it is not included in the request's parameters.
affected #: 11 files
diff -r e7e59c068d7002e48eebb9dc6f34721fb7456fb5 -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -1552,7 +1552,7 @@
@web.expose
@web.require_admin
def index( self, trans, **kwd ):
- webapp = kwd.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
if webapp == 'galaxy':
@@ -1572,7 +1572,7 @@
@web.expose
@web.require_admin
def center( self, trans, **kwd ):
- webapp = kwd.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
if webapp == 'galaxy':
@@ -1629,7 +1629,7 @@
@web.require_admin
def create_role( self, trans, **kwd ):
params = util.Params( kwd )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
name = util.restore_text( params.get( 'name', '' ) )
@@ -1706,7 +1706,7 @@
@web.require_admin
def rename_role( self, trans, **kwd ):
params = util.Params( kwd )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
id = params.get( 'id', None )
@@ -1751,7 +1751,7 @@
@web.require_admin
def manage_users_and_groups_for_role( self, trans, **kwd ):
params = util.Params( kwd )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
id = params.get( 'id', None )
@@ -1846,7 +1846,7 @@
@web.require_admin
def mark_role_deleted( self, trans, **kwd ):
params = util.Params( kwd )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
id = kwd.get( 'id', None )
if not id:
message = "No role ids received for deleting"
@@ -1872,7 +1872,7 @@
@web.require_admin
def undelete_role( self, trans, **kwd ):
params = util.Params( kwd )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
id = kwd.get( 'id', None )
if not id:
message = "No role ids received for undeleting"
@@ -1915,7 +1915,7 @@
# - GroupRoleAssociations where role_id == Role.id
# - DatasetPermissionss where role_id == Role.id
params = util.Params( kwd )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
id = kwd.get( 'id', None )
if not id:
message = "No role ids received for purging"
@@ -1988,7 +1988,7 @@
@web.require_admin
def rename_group( self, trans, **kwd ):
params = util.Params( kwd )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
id = params.get( 'id', None )
@@ -2031,7 +2031,7 @@
@web.require_admin
def manage_users_and_roles_for_group( self, trans, **kwd ):
params = util.Params( kwd )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
group = get_group( trans, params.id )
@@ -2078,7 +2078,7 @@
@web.require_admin
def create_group( self, trans, **kwd ):
params = util.Params( kwd )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
name = util.restore_text( params.get( 'name', '' ) )
@@ -2156,7 +2156,7 @@
@web.require_admin
def mark_group_deleted( self, trans, **kwd ):
params = util.Params( kwd )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
id = params.get( 'id', None )
if not id:
message = "No group ids received for marking deleted"
@@ -2182,7 +2182,7 @@
@web.require_admin
def undelete_group( self, trans, **kwd ):
params = util.Params( kwd )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
id = kwd.get( 'id', None )
if not id:
message = "No group ids received for undeleting"
@@ -2220,7 +2220,7 @@
# This method should only be called for a Group that has previously been deleted.
# Purging a deleted Group simply deletes all UserGroupAssociations and GroupRoleAssociations.
params = util.Params( kwd )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
id = kwd.get( 'id', None )
if not id:
message = "No group ids received for purging"
@@ -2259,7 +2259,7 @@
@web.expose
@web.require_admin
def create_new_user( self, trans, **kwd ):
- webapp = kwd.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
return trans.response.send_redirect( web.url_for( controller='user',
action='create',
cntrller='admin',
@@ -2267,7 +2267,7 @@
@web.expose
@web.require_admin
def reset_user_password( self, trans, **kwd ):
- webapp = kwd.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
user_id = kwd.get( 'id', None )
if not user_id:
message = "No users received for resetting passwords."
@@ -2316,7 +2316,7 @@
@web.expose
@web.require_admin
def mark_user_deleted( self, trans, **kwd ):
- webapp = kwd.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
id = kwd.get( 'id', None )
if not id:
message = "No user ids received for deleting"
@@ -2341,7 +2341,7 @@
@web.expose
@web.require_admin
def undelete_user( self, trans, **kwd ):
- webapp = kwd.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
id = kwd.get( 'id', None )
if not id:
message = "No user ids received for undeleting"
@@ -2388,7 +2388,7 @@
# - UserRoleAssociation where user_id == User.id EXCEPT FOR THE PRIVATE ROLE
# - UserAddress where user_id == User.id
# Purging Histories and Datasets must be handled via the cleanup_datasets.py script
- webapp = kwd.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
id = kwd.get( 'id', None )
if not id:
message = "No user ids received for purging"
@@ -2493,7 +2493,7 @@
@web.expose
@web.require_admin
def manage_roles_and_groups_for_user( self, trans, **kwd ):
- webapp = kwd.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
user_id = kwd.get( 'id', None )
message = ''
status = ''
@@ -2714,3 +2714,11 @@
id = trans.security.decode_id( id )
quota = trans.sa_session.query( trans.model.Quota ).get( id )
return quota
+def get_webapp( trans, **kwd ):
+ """Get the value of the webapp, can be one of 'community', 'galaxy', 'reports', 'demo_sequencer'."""
+ if 'webapp' in kwd:
+ return kwd[ 'webapp' ]
+ if 'webapp' in trans.environ:
+ return trans.environ[ 'webapp' ]
+ # The default is galaxy.
+ return 'galaxy'
diff -r e7e59c068d7002e48eebb9dc6f34721fb7456fb5 -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 lib/galaxy/web/controllers/admin.py
--- a/lib/galaxy/web/controllers/admin.py
+++ b/lib/galaxy/web/controllers/admin.py
@@ -51,7 +51,6 @@
return 'never'
# Grid definition
- webapp = "galaxy"
title = "Users"
model_class = model.User
template='/admin/user/grid.mako'
@@ -136,7 +135,6 @@
return 0
# Grid definition
- webapp = "galaxy"
title = "Roles"
model_class = model.Role
template='/admin/dataset_security/role/grid.mako'
@@ -220,7 +218,6 @@
return 0
# Grid definition
- webapp = "galaxy"
title = "Groups"
model_class = model.Group
template='/admin/dataset_security/group/grid.mako'
@@ -302,7 +299,6 @@
return 0
# Grid definition
- webapp = "galaxy"
title = "Quotas"
model_class = model.Quota
template='/admin/quota/grid.mako'
diff -r e7e59c068d7002e48eebb9dc6f34721fb7456fb5 -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 lib/galaxy/web/controllers/admin_toolshed.py
--- a/lib/galaxy/web/controllers/admin_toolshed.py
+++ b/lib/galaxy/web/controllers/admin_toolshed.py
@@ -147,7 +147,6 @@
( bgcolor, trans.security.encode_id( tool_shed_repository.id ), status_label )
return rval
- webapp = "galaxy"
title = "Monitor installing tool shed repositories"
template = "admin/tool_shed_repository/repository_installation_grid.mako"
model_class = model.ToolShedRepository
@@ -230,7 +229,6 @@
( bgcolor, trans.security.encode_id( tool_dependency.id ), tool_dependency.status )
return rval
- webapp = "galaxy"
title = "Tool Dependencies"
template = "admin/tool_shed_repository/tool_dependencies_grid.mako"
model_class = model.ToolDependency
@@ -1516,7 +1514,7 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
repository = get_repository( trans, repository_id )
metadata = {}
tool = None
diff -r e7e59c068d7002e48eebb9dc6f34721fb7456fb5 -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 lib/galaxy/web/controllers/external_service.py
--- a/lib/galaxy/web/controllers/external_service.py
+++ b/lib/galaxy/web/controllers/external_service.py
@@ -21,7 +21,6 @@
return 'Error in loading external_service type: %s' % external_service.external_service_type_id
# Grid definition
- webapp = "galaxy"
title = "External Services"
template = "admin/external_service/grid.mako"
model_class = model.ExternalService
diff -r e7e59c068d7002e48eebb9dc6f34721fb7456fb5 -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 lib/galaxy/web/controllers/request_type.py
--- a/lib/galaxy/web/controllers/request_type.py
+++ b/lib/galaxy/web/controllers/request_type.py
@@ -28,7 +28,6 @@
return len( request_type.external_services )
return 'No external service assigned'
# Grid definition
- webapp = "galaxy"
title = "Request Types"
template = "admin/request_type/grid.mako"
model_class = model.RequestType
diff -r e7e59c068d7002e48eebb9dc6f34721fb7456fb5 -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 lib/galaxy/web/controllers/requests_admin.py
--- a/lib/galaxy/web/controllers/requests_admin.py
+++ b/lib/galaxy/web/controllers/requests_admin.py
@@ -47,7 +47,6 @@
except:
return 'None'
# Grid definition
- webapp = "galaxy"
title = "Sample Datasets"
template = "admin/requests/sample_datasets_grid.mako"
model_class = model.SampleDataset
diff -r e7e59c068d7002e48eebb9dc6f34721fb7456fb5 -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 lib/galaxy/web/controllers/user.py
--- a/lib/galaxy/web/controllers/user.py
+++ b/lib/galaxy/web/controllers/user.py
@@ -514,7 +514,7 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
use_panels = util.string_as_bool( kwd.get( 'use_panels', True ) )
email = util.restore_text( params.get( 'email', '' ) )
# Do not sanitize passwords, so take from kwd
@@ -597,7 +597,7 @@
email = util.restore_text( kwd.get( 'email', '' ) )
password = kwd.get( 'password', '' )
username = util.restore_text( kwd.get( 'username', '' ) )
- webapp = kwd.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
status = kwd.get( 'status', 'done' )
is_admin = cntrller == 'admin' and trans.user_is_admin()
user = trans.app.model.User( email=email )
@@ -694,7 +694,7 @@
user = trans.user
if not user:
raise AssertionError, "The user id (%s) is not valid" % str( user_id )
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
email = util.restore_text( params.get( 'email', user.email ) )
# Do not sanitize passwords, so take from kwd
# instead of params ( which were sanitized )
@@ -759,7 +759,7 @@
def edit_username( self, trans, cntrller, **kwd ):
params = util.Params( kwd )
is_admin = cntrller == 'admin' and trans.user_is_admin()
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
user_id = params.get( 'user_id', None )
@@ -789,7 +789,7 @@
def edit_info( self, trans, cntrller, **kwd ):
params = util.Params( kwd )
is_admin = cntrller == 'admin' and trans.user_is_admin()
- webapp = params.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
user_id = params.get( 'user_id', None )
diff -r e7e59c068d7002e48eebb9dc6f34721fb7456fb5 -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 lib/galaxy/web/controllers/workflow.py
--- a/lib/galaxy/web/controllers/workflow.py
+++ b/lib/galaxy/web/controllers/workflow.py
@@ -1033,7 +1033,7 @@
"""
url = kwd.get( 'url', '' )
workflow_text = kwd.get( 'workflow_text', '' )
- webapp = kwd.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwd )
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
import_button = kwd.get( 'import_button', False )
diff -r e7e59c068d7002e48eebb9dc6f34721fb7456fb5 -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 lib/galaxy/web/framework/helpers/grids.py
--- a/lib/galaxy/web/framework/helpers/grids.py
+++ b/lib/galaxy/web/framework/helpers/grids.py
@@ -53,7 +53,7 @@
def __call__( self, trans, **kwargs ):
# Get basics.
- webapp = kwargs.get( 'webapp', 'galaxy' )
+ webapp = get_webapp( trans, **kwargs )
status = kwargs.get( 'status', None )
message = kwargs.get( 'message', None )
# Build a base filter and sort key that is the combination of the saved state and defaults.
diff -r e7e59c068d7002e48eebb9dc6f34721fb7456fb5 -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 lib/galaxy/webapps/community/controllers/admin.py
--- a/lib/galaxy/webapps/community/controllers/admin.py
+++ b/lib/galaxy/webapps/community/controllers/admin.py
@@ -60,7 +60,6 @@
return query.filter( and_( model.Tool.table.c.user_id == model.User.table.c.id,
model.User.table.c.email == column_filter ) )
# Grid definition
- webapp = "community"
title = "Users"
model_class = model.User
template='/admin/user/grid.mako'
@@ -148,7 +147,6 @@
return 0
# Grid definition
- webapp = "community"
title = "Roles"
model_class = model.Role
template='/admin/dataset_security/role/grid.mako'
@@ -235,7 +233,6 @@
return 0
# Grid definition
- webapp = "community"
title = "Groups"
model_class = model.Group
template='/admin/dataset_security/group/grid.mako'
diff -r e7e59c068d7002e48eebb9dc6f34721fb7456fb5 -r 98204b9f4f806c15fa52fd728b5dacbc64f5eeb1 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -40,7 +40,6 @@
return 0
# Grid definition
- webapp = "community"
title = "Categories"
model_class = model.Category
template='/webapps/community/category/grid.mako'
@@ -377,7 +376,7 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
cntrller = params.get( 'cntrller', 'repository' )
is_admin = trans.user_is_admin()
invalid_tools_dict = odict()
@@ -495,7 +494,7 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) )
repository = get_repository( trans, id )
repo = hg.repository( get_configured_ui(), repository.repo_path )
@@ -511,7 +510,7 @@
status=status )
@web.expose
def browse_valid_repositories( self, trans, **kwd ):
- webapp = kwd.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
galaxy_url = kwd.get( 'galaxy_url', None )
if galaxy_url:
trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
@@ -596,7 +595,7 @@
name = params.get( 'name', None )
owner = params.get( 'owner', None )
changeset_revision = params.get( 'changeset_revision', None )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
repository = get_repository_by_name_and_owner( trans, name, owner )
repo_dir = repository.repo_path
repo = hg.repository( get_configured_ui(), repo_dir )
@@ -769,7 +768,7 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
repository = get_repository( trans, repository_id )
tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config )
tool_state = self.__new_state( trans )
@@ -842,7 +841,7 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
galaxy_url = kwd.get( 'galaxy_url', None )
if galaxy_url:
trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
@@ -922,7 +921,7 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
galaxy_url = kwd.get( 'galaxy_url', None )
if galaxy_url:
trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' )
@@ -1050,7 +1049,7 @@
name = params.get( 'name', None )
owner = params.get( 'owner', None )
changeset_revision = params.get( 'changeset_revision', None )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
repository = get_repository_by_name_and_owner( trans, name, owner )
for downloadable_revision in repository.downloadable_revisions:
if downloadable_revision.changeset_revision == changeset_revision:
@@ -1204,7 +1203,7 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' )
repository_clone_url = generate_clone_url( trans, repository_id )
repository = get_repository( trans, repository_id )
@@ -1241,7 +1240,7 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'error' )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
repository = get_repository( trans, repository_id )
repo_dir = repository.repo_path
repo = hg.repository( get_configured_ui(), repo_dir )
@@ -1537,7 +1536,7 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
repository = get_repository( trans, repository_id )
changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision )
@@ -1999,7 +1998,7 @@
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
repository = get_repository( trans, id )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
repo = hg.repository( get_configured_ui(), repository.repo_path )
avg_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, repository, webapp_model=trans.model )
changeset_revision = util.restore_text( params.get( 'changeset_revision', repository.tip ) )
@@ -2068,7 +2067,7 @@
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
- webapp = params.get( 'webapp', 'community' )
+ webapp = get_webapp( trans, **kwd )
repository = get_repository( trans, repository_id )
metadata = {}
tool = None
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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9 years, 5 months
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commit/galaxy-central: jgoecks: Hacks to get trackster navigation controls to display in embedded visualizations.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/e7e59c068d70/
changeset: e7e59c068d70
user: jgoecks
date: 2012-07-05 18:03:32
summary: Hacks to get trackster navigation controls to display in embedded visualizations.
affected #: 1 file
diff -r 0ffcc91708233cc087d9996235f0917b377cfe8a -r e7e59c068d7002e48eebb9dc6f34721fb7456fb5 templates/page/display.mako
--- a/templates/page/display.mako
+++ b/templates/page/display.mako
@@ -112,6 +112,13 @@
width: 25%;
padding: 0.2em 0.8em;
}
+ ## HACKs to get Trackster navigation controls to display.
+ .embedded-item .trackster-nav-container {
+ height: inherit;
+ }
+ .embedded-item .trackster-nav {
+ position: inherit;
+ }
</style></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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- 1
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commit/galaxy-central: greg: Refine the definition of changeset revisions that can be automatically installed into a local Galaxy instance.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/0ffcc9170823/
changeset: 0ffcc9170823
user: greg
date: 2012-07-05 17:55:10
summary: Refine the definition of changeset revisions that can be automatically installed into a local Galaxy instance.
affected #: 7 files
diff -r eff8b196858c1ff5a6227bd750a06ea924f8530c -r 0ffcc91708233cc087d9996235f0917b377cfe8a lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -76,8 +76,9 @@
processed_invalid_tool_configs = []
processed_relative_workflow_paths = []
processed_datatypes = []
- for downloadable_revision in repository.downloadable_revisions:
- metadata = downloadable_revision.metadata
+ # A repository's metadata_revisions are those that ignore the value of the repository_metadata.downloadable column.
+ for metadata_revision in repository.metadata_revisions:
+ metadata = metadata_revision.metadata
if 'tools' in metadata:
tool_dicts = metadata[ 'tools' ]
for tool_dict in tool_dicts:
@@ -1461,7 +1462,7 @@
"""
# To set excluded_lower_bounds_changeset_revision, calling methods should do the following, where the value of changeset_revision
# is a downloadable changeset_revision.
- # excluded_lower_bounds_changeset_revision = get_previous_valid_changset_revision( repository, repo, changeset_revision )
+ # excluded_lower_bounds_changeset_revision = get_previous_downloadable_changset_revision( repository, repo, changeset_revision )
if excluded_lower_bounds_changeset_revision == INITIAL_CHANGELOG_HASH:
appending_started = True
else:
diff -r eff8b196858c1ff5a6227bd750a06ea924f8530c -r 0ffcc91708233cc087d9996235f0917b377cfe8a lib/galaxy/webapps/community/controllers/common.py
--- a/lib/galaxy/webapps/community/controllers/common.py
+++ b/lib/galaxy/webapps/community/controllers/common.py
@@ -134,10 +134,7 @@
trans.sa_session.add( repository_metadata )
trans.sa_session.flush()
def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True ):
- """
- Build a SelectField whose options are the changeset_revision
- strings of all downloadable_revisions of the received repository.
- """
+ """Build a SelectField whose options are the changeset_rev strings of all downloadable revisions of the received repository."""
repo = hg.repository( get_configured_ui(), repository.repo_path )
options = []
changeset_tups = []
@@ -169,6 +166,10 @@
selected = selected_value and option_tup[1] == selected_value
select_field.add_option( option_tup[0], option_tup[1], selected=selected )
return select_field
+def changeset_is_downloadable( metadata_dict ):
+ # A RepositoryMetadata record will be created if metadata_dict includes only invalid stuff like 'invalid_tools', but in this case
+ # it won't be downloadable.
+ return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict
def changeset_is_malicious( trans, id, changeset_revision, **kwd ):
"""Check the malicious flag in repository metadata for a specified change set"""
repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
@@ -374,15 +375,12 @@
def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ):
repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
if repository_metadata:
- # Update RepositoryMetadata.metadata.
repository_metadata.metadata = metadata_dict
- trans.sa_session.add( repository_metadata )
- trans.sa_session.flush()
else:
- # Create a new repository_metadata table row.
repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict )
- trans.sa_session.add( repository_metadata )
- trans.sa_session.flush()
+ repository_metadata.downloadable = changeset_is_downloadable( metadata_dict )
+ trans.sa_session.add( repository_metadata )
+ trans.sa_session.flush()
def decode( value ):
# Extract and verify hash
a, b = value.split( ":" )
@@ -605,7 +603,7 @@
if parent_id is None:
# The tool did not change through all of the changeset revisions.
return old_id
-def get_previous_valid_changset_revision( repository, repo, before_changeset_revision ):
+def get_previous_downloadable_changset_revision( repository, repo, before_changeset_revision ):
"""
Return the downloadable changeset_revision in the repository changelog just prior to the changeset to which before_changeset_revision
refers. If there isn't one, return the hash value of an empty repository changlog, INITIAL_CHANGELOG_HASH.
@@ -1087,12 +1085,9 @@
# Update the last saved repository_metadata table row.
repository_metadata.changeset_revision = changeset_revision
repository_metadata.metadata = metadata_dict
+ repository_metadata.downloadable = changeset_is_downloadable( metadata_dict )
trans.sa_session.add( repository_metadata )
- try:
- trans.sa_session.flush()
- except TypeError, e:
- message = "Unable to save metadata for this repository probably due to a tool config file that doesn't conform to the Cheetah template syntax."
- status = 'error'
+ trans.sa_session.flush()
else:
# There are no tools in the repository, and we're setting metadata on the repository tip.
repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict )
@@ -1102,6 +1097,7 @@
# We're re-generating metadata for an old repository revision.
repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision )
repository_metadata.metadata = metadata_dict
+ repository_metadata.downloadable = changeset_is_downloadable( metadata_dict )
trans.sa_session.add( repository_metadata )
trans.sa_session.flush()
elif updating_tip and len( repo ) == 1 and not invalid_files:
diff -r eff8b196858c1ff5a6227bd750a06ea924f8530c -r 0ffcc91708233cc087d9996235f0917b377cfe8a lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -75,10 +75,7 @@
def __init__( self, col_name ):
grids.GridColumn.__init__( self, col_name )
def get_value( self, trans, grid, repository ):
- """
- Display a SelectField whose options are the changeset_revision
- strings of all downloadable_revisions of this repository.
- """
+ """Display a SelectField whose options are the changeset_revision strings of all downloadable_revisions of this repository."""
select_field = build_changeset_revision_select_field( trans, repository )
if len( select_field.options ) > 1:
return select_field.get_html()
@@ -245,22 +242,10 @@
filterable="standard" ) )
operations = []
def build_initial_query( self, trans, **kwd ):
- # The clause_list approach is to filter out those repositories that include metadata, but only because they contain 'invalid_tools' in
- # the metadata (i.e., they don't have valid tools, datatypes or workflows). Is there a better approach?
- clause_list = []
- for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \
- .filter( trans.model.RepositoryMetadata.table.c.malicious == False ):
- metadata = repository_metadata.metadata
- if 'datatypes' in metadata or'tools' in metadata or 'workflows' in metadata:
- clause_list.append( trans.model.RepositoryMetadata.table.c.id == repository_metadata.id )
- if clause_list:
- return trans.sa_session.query( self.model_class ) \
- .join( model.RepositoryMetadata.table ) \
- .join( model.User.table ) \
- .filter( or_( *clause_list ) )
return trans.sa_session.query( self.model_class ) \
.join( model.RepositoryMetadata.table ) \
- .join( model.User.table )
+ .join( model.User.table ) \
+ .filter( model.RepositoryMetadata.table.c.downloadable == True )
class MatchedRepositoryListGrid( grids.Grid ):
class NameColumn( grids.TextColumn ):
@@ -400,7 +385,8 @@
for repository in trans.sa_session.query( trans.model.Repository ) \
.filter( trans.model.Repository.table.c.deleted == False ) \
.order_by( trans.model.Repository.table.c.name ):
- for downloadable_revision in repository.downloadable_revisions:
+ # A repository's metadata_revisions are those that ignore the value of the repository_metadata.downloadable column.
+ for downloadable_revision in repository.metadata_revisions:
metadata = downloadable_revision.metadata
invalid_tools = metadata.get( 'invalid_tools', [] )
for invalid_tool_config in invalid_tools:
@@ -410,7 +396,7 @@
.filter( and_( trans.model.Repository.table.c.deleted == False,
trans.model.Repository.table.c.user_id == trans.user.id ) ) \
.order_by( trans.model.Repository.table.c.name ):
- for downloadable_revision in repository.downloadable_revisions:
+ for downloadable_revision in repository.metadata_revisions:
metadata = downloadable_revision.metadata
invalid_tools = metadata.get( 'invalid_tools', [] )
for invalid_tool_config in invalid_tools:
@@ -1595,7 +1581,7 @@
repo_dir = repository.repo_path
repo = hg.repository( get_configured_ui(), repo_dir )
# Get the lower bound changeset revision
- lower_bound_changeset_revision = get_previous_valid_changset_revision( repository, repo, changeset_revision )
+ lower_bound_changeset_revision = get_previous_downloadable_changset_revision( repository, repo, changeset_revision )
# Build the list of changeset revision hashes.
changeset_hashes = []
for changeset in reversed_lower_upper_bounded_changelog( repo, lower_bound_changeset_revision, changeset_revision ):
diff -r eff8b196858c1ff5a6227bd750a06ea924f8530c -r 0ffcc91708233cc087d9996235f0917b377cfe8a lib/galaxy/webapps/community/controllers/upload.py
--- a/lib/galaxy/webapps/community/controllers/upload.py
+++ b/lib/galaxy/webapps/community/controllers/upload.py
@@ -130,9 +130,6 @@
error, error_message = handle_sample_tool_data_table_conf_file( trans.app, full_path )
if error:
message = '%s<br/>%s' % ( message, error_message )
- #if full_path.endswith( '.loc.sample' ):
- # # Handle the special case where a xxx.loc.sample file is being uploaded by copying it to ~/tool-data/xxx.loc.
- # copy_sample_file( trans.app, full_path )
# See if the content of the change set was valid.
admin_only = len( repository.downloadable_revisions ) != 1
handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only )
@@ -272,7 +269,6 @@
if error:
return False, message, files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed
commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message )
- # See if the content of the change set was valid.
admin_only = len( repository.downloadable_revisions ) != 1
handle_email_alerts( trans, repository, content_alert_str=content_alert_str, new_repo_alert=new_repo_alert, admin_only=admin_only )
return True, '', files_to_remove, content_alert_str, undesirable_dirs_removed, undesirable_files_removed
diff -r eff8b196858c1ff5a6227bd750a06ea924f8530c -r 0ffcc91708233cc087d9996235f0917b377cfe8a lib/galaxy/webapps/community/model/mapping.py
--- a/lib/galaxy/webapps/community/model/mapping.py
+++ b/lib/galaxy/webapps/community/model/mapping.py
@@ -121,7 +121,8 @@
Column( "changeset_revision", TrimmedString( 255 ), index=True ),
Column( "metadata", JSONType, nullable=True ),
Column( "tool_versions", JSONType, nullable=True ),
- Column( "malicious", Boolean, default=False ) )
+ Column( "malicious", Boolean, default=False ),
+ Column( "downloadable", Boolean, default=True ) )
RepositoryRatingAssociation.table = Table( "repository_rating_association", metadata,
Column( "id", Integer, primary_key=True ),
@@ -196,7 +197,11 @@
categories=relation( RepositoryCategoryAssociation ),
ratings=relation( RepositoryRatingAssociation, order_by=desc( RepositoryRatingAssociation.table.c.update_time ), backref="repositories" ),
user=relation( User.mapper ),
- downloadable_revisions=relation( RepositoryMetadata, order_by=desc( RepositoryMetadata.table.c.update_time ) ) ) )
+ downloadable_revisions=relation( RepositoryMetadata,
+ primaryjoin=( ( Repository.table.c.id == RepositoryMetadata.table.c.repository_id ) & ( RepositoryMetadata.table.c.downloadable == True ) ),
+ order_by=desc( RepositoryMetadata.table.c.update_time ) ),
+ metadata_revisions=relation( RepositoryMetadata,
+ order_by=desc( RepositoryMetadata.table.c.update_time ) ) ) )
assign_mapper( context, RepositoryMetadata, RepositoryMetadata.table,
properties=dict( repository=relation( Repository ) ) )
diff -r eff8b196858c1ff5a6227bd750a06ea924f8530c -r 0ffcc91708233cc087d9996235f0917b377cfe8a lib/galaxy/webapps/community/model/migrate/check.py
--- a/lib/galaxy/webapps/community/model/migrate/check.py
+++ b/lib/galaxy/webapps/community/model/migrate/check.py
@@ -77,8 +77,10 @@
# Verify that the code and the DB are in sync
db_schema = schema.ControlledSchema( engine, migrate_repository )
if migrate_repository.versions.latest != db_schema.version:
- raise Exception( "Your database has version '%d' but this code expects version '%d'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'."
- % ( db_schema.version, migrate_repository.versions.latest ) )
+ exception_msg = "Your database has version '%d' but this code expects version '%d'. " % ( db_schema.version, migrate_repository.versions.latest )
+ exception_msg += "Back up your database and then migrate the schema by running the following from your Galaxy installation directory:"
+ exception_msg += "\n\nsh manage_db.sh upgrade community\n"
+ raise Exception( exception_msg )
else:
log.info( "At database version %d" % db_schema.version )
diff -r eff8b196858c1ff5a6227bd750a06ea924f8530c -r 0ffcc91708233cc087d9996235f0917b377cfe8a lib/galaxy/webapps/community/model/migrate/versions/0012_add_downloadable_column.py
--- /dev/null
+++ b/lib/galaxy/webapps/community/model/migrate/versions/0012_add_downloadable_column.py
@@ -0,0 +1,48 @@
+"""
+Migration script to add the downloadable column to the repository_metadata table.
+"""
+
+from sqlalchemy import *
+from sqlalchemy.orm import *
+from migrate import *
+from migrate.changeset import *
+
+import sys, logging
+log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
+
+metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
+
+def upgrade():
+ print __doc__
+ metadata.reflect()
+ # Create and initialize imported column in job table.
+ RepositoryMetadata_table = Table( "repository_metadata", metadata, autoload=True )
+ c = Column( "downloadable", Boolean, default=True )
+ try:
+ # Create
+ c.create( RepositoryMetadata_table )
+ assert c is RepositoryMetadata_table.c.downloadable
+ # Initialize.
+ if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite':
+ default_true = "1"
+ elif migrate_engine.name == 'postgres':
+ default_true = "true"
+ db_session.execute( "UPDATE repository_metadata SET downloadable=%s" % default_true )
+ except Exception, e:
+ print "Adding downloadable column to the repository_metadata table failed: %s" % str( e )
+
+def downgrade():
+ metadata.reflect()
+ # Drop downloadable column from repository_metadata table.
+ RepositoryMetadata_table = Table( "repository_metadata", metadata, autoload=True )
+ try:
+ RepositoryMetadata_table.c.downloadable.drop()
+ except Exception, e:
+ print "Dropping column downloadable from the repository_metadata table failed: %s" % str( e )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: jgoecks: Add introductory help text for paramamonster.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/eff8b196858c/
changeset: eff8b196858c
user: jgoecks
date: 2012-07-05 17:26:24
summary: Add introductory help text for paramamonster.
affected #: 3 files
diff -r 202c6a7dae95450eb9781c8df6fdc0c2795b6968 -r eff8b196858c1ff5a6227bd750a06ea924f8530c static/scripts/packed/viz/paramamonster.js
--- a/static/scripts/packed/viz/paramamonster.js
+++ b/static/scripts/packed/viz/paramamonster.js
@@ -1,1 +1,1 @@
-var ToolInputsSettings=Backbone.Model.extend({defaults:{inputs:null,values:null}});var ToolParameterTree=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(b){var a=this;this.get("tool").get("inputs").each(function(c){if(!c.get_samples()){return}c.on("change:min change:max change:num_samples",function(d){if(d.get("in_ptree")){a.set_tree_data()}},a);c.on("change:in_ptree",function(d){if(d.get("in_ptree")){a.add_param(d)}else{a.remove_param(d)}a.set_tree_data()},a)});if(b.config){_.each(b.config,function(d){var c=a.get("tool").get("inputs").find(function(e){return e.get("name")===d.name});a.add_param(c);c.set(d)})}},add_param:function(a){if(a.get("ptree_index")){return}a.set("in_ptree",true);a.set("ptree_index",this.get_tree_params().length)},remove_param:function(a){a.set("in_ptree",false);a.set("ptree_index",null);_(this.get_tree_params()).each(function(b,c){b.set("ptree_index",c+1)})},set_tree_data:function(){var b=_.map(this.get_tree_params(),function(d){return{param:d,samples:d.get_samples()}});var a=0,c=function(g,d){var i=g[d],h=i.param,f=h.get("label"),e=i.samples;if(g.length-1===d){return _.map(e,function(j){return{id:a++,name:j,param:h,value:j}})}return _.map(e,function(j){return{id:a++,name:j,param:h,value:j,children:c(g,d+1)}})};this.set("tree_data",{name:"Root",id:a++,children:(b.length!==0?c(b,0):null)})},get_tree_params:function(){return _(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(a){return a.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(a,b){return a*b.get_samples().length},1)},get_node_settings:function(e){var c=this.get("tool").get_inputs_dict();var f=e.parent;if(f){while(f.depth!==0){c[f.param.get("name")]=f.value;f=f.parent}}var a=this,b=function(h,g){if(h.param){g[h.param.get("name")]=h.value}if(!h.children){return new ToolInputsSettings({inputs:a.get("tool").get("inputs"),values:g})}else{return _.flatten(_.map(h.children,function(i){return b(i,_.clone(g))}))}},d=b(e,c);if(!_.isArray(d)){d=[d]}return d},get_connected_nodes:function(c){var d=function(e){if(!e.children){return e}else{return _.flatten([e,_.map(e.children,function(f){return d(f)})])}};var b=[],a=c.parent;while(a){b.push(a);a=a.parent}return _.flatten([b,d(c)])},get_leaf:function(b){var c=this.get("tree_data"),a=function(d){return _.find(d,function(e){return b[e.param.get("name")]===e.value})};while(c.children){c=a(c.children)}return c},toJSON:function(){return this.get_tree_params().map(function(a){return{name:a.get("name"),min:a.get("min"),max:a.get("max"),num_samples:a.get("num_samples")}})}});var ParamaMonsterTrack=Backbone.RelationalModel.extend({defaults:{track:null,settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"}],initialize:function(a){if(a.track){var b=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},a.track);delete b.mode;this.set("track",object_from_template(b,{},null))}},same_settings:function(a){var b=this.get("settings"),c=a.get("settings");for(var d in b){if(!c[d]||b[d]!==c[d]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var TrackCollection=Backbone.Collection.extend({model:ParamaMonsterTrack});var ParamaMonsterVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:"Dataset"},{type:Backbone.HasOne,key:"tool",relatedModel:"Tool"},{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"},{type:Backbone.HasMany,key:"tracks",relatedModel:"ParamaMonsterTrack"}],initialize:function(a){var b=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",b);this.set("parameter_tree",new ToolParameterTree({tool:b,config:a.tree_config}))},add_placeholder:function(a){this.get("tracks").add(new PlaceholderTrack(a))},add_track:function(a){this.get("tracks").add(a)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"paramamonster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var ParamaMonsterTrackView=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(a){this.canvas_manager=a.canvas_manager;this.render();this.model.on("change:track",this.draw_tiles,this)},render:function(){var f=this.model.get("settings"),b=f.get("values"),d=$("<td/>").addClass("settings").appendTo(this.$el),c=$("<div/>").addClass("track-info").hide().appendTo(d);c.append($("<div/>").css("font-weight","bold").text("Track Settings"));f.get("inputs").each(function(h){c.append(h.get("label")+": "+b[h.get("name")]+"<br/>")});var a=this,g=$("<button/>").appendTo(c).text("Run on complete dataset").click(function(){c.toggle();a.trigger("run_on_dataset",f)});var e=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){c.toggle()},tipsy_config:{gravity:"s"}},{title:"Remove",icon_class:"cross-circle",on_click:function(){a.$el.remove();$(".tipsy").remove()}}]);d.prepend(e.$el);this.model.get("regions").each(function(){a.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var b=this,a=this.model.get("track"),d=this.model.get("regions"),c=this.$el.find("td.tile");$.when(a.data_manager.data_is_ready()).then(function(e){d.each(function(h,g){var f=h.length()/b.TILE_LEN,j=1/f,i="Pack";$.when(a.data_manager.get_data(h,i,f,{})).then(function(l){var k=b.canvas_manager.new_canvas();k.width=b.TILE_LEN;k.height=a.get_canvas_height(l,i,j,k.width);a.draw_tile(l,k.getContext("2d"),i,f,h,j);$(c[g]).empty().append(k)})})})}});var ToolInputValOrSweepView=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(a){this.$el=a.tool_row;this.render()},render:function(){var b=this.model,f=b.get("type"),h=this.$el.find(".form-row-input"),d=null;h.find(":input").change(function(){b.set("value",$(this).val())});if(f==="number"){d=$(_.template(this.number_input_template,this.model.toJSON()))}else{if(f==="select"){var c=_.map(this.$el.find("select option"),function(i){return $(i).val()}),e=c.join(", ");d=$(_.template(this.select_input_template,{options:e}))}}d.insertAfter(h);var a=this,g=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){b.set("in_ptree",true);h.hide();d.show();$(this).hide();a.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){b.set("in_ptree",false);d.hide();h.show();$(this).hide();a.$el.find(".icon-button.plus-button").show()}}],{tipsy_config:{gravity:"s"}});this.$el.prepend(g.$el);if(b.get("in_ptree")){h.hide();a.$el.find(".icon-button.plus-button").hide()}else{a.$el.find(".icon-button.toggle").hide();d.hide()}_.each(["min","max","num_samples"],function(i){d.find("."+i).change(function(){b.set(i,parseFloat($(this).val()))})})}});var ToolParameterTreeDesignView=Backbone.View.extend({className:"tree-design",initialize:function(a){this.render()},render:function(){var c=new ToolFormView({model:this.model.get("tool")});c.render();this.$el.append(c.$el);var b=this,a=b.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(d){var e=new ToolInputValOrSweepView({model:a.at(d),tool_row:$(this)})})}});var ToolParameterTreeView=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(a){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var i=this.model.get_tree_params();if(!i.length){return}this.width=100*(2+i.length);this.height=15*this.model.get_num_leaves();var h=this;var g=d3.layout.cluster().size([this.height,this.width-160]);var c=d3.svg.diagonal().projection(function(j){return[j.y,j.x]});var a=g.nodes(this.model.get("tree_data"));var d=_.uniq(_.pluck(a,"y"));_.each(i,function(l,k){var j=d[k+1];h.$el.append($("<div>").addClass("label").text(l.get("label")).css("left",j+250))});var b=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+20).append("g").attr("transform","translate(40, 10)");var f=b.selectAll("path.link").data(g.links(a)).enter().append("path").attr("class","link").attr("d",c);var e=b.selectAll("g.node").data(a).enter().append("g").attr("class","node").attr("transform",function(j){return"translate("+j.y+","+j.x+")"}).on("mouseover",function(k){var j=_.pluck(h.model.get_connected_nodes(k),"id");e.filter(function(l){return _.find(j,function(m){return m===l.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){e.style("fill","#000")});e.append("circle").attr("r",9);e.append("text").attr("dx",function(j){return j.children?-12:12}).attr("dy",3).attr("text-anchor",function(j){return j.children?"end":"start"}).text(function(j){return j.name})}});var ParamaMonsterVisualizationView=Backbone.View.extend({className:"paramamonster",initialize:function(b){this.canvas_manager=new CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new ToolParameterTreeView({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var a=this;this.model.get("tracks").each(function(c){c.get("track").view=a})},render:function(){var d=new ToolParameterTreeDesignView({model:this.model.get("parameter_tree")});$("#left").append(d.$el);var a=this,e=a.model.get("regions"),b=$("<tr/>").appendTo(this.track_collection_container);e.each(function(f){b.append($("<th>").text(f.toString()))});b.children().first().attr("colspan",2);var c=$("<div>").addClass("tiles");$("#right").append(c.append(this.track_collection_container));a.model.get("tracks").each(function(f){a.add_track(f)});this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks()},run_tool_on_dataset:function(b){var a=this.model.get("tool"),d=a.get("name"),c=this.model.get("dataset");a.set_input_values(b.get("values"));$.when(a.rerun(c)).then(function(e){});show_modal("Running "+d+" on complete dataset",d+" is running on dataset '"+c.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(d){var b=this,c=this.model.get("parameter_tree");b.model.add_track(d);var a=new ParamaMonsterTrackView({model:d,canvas_manager:b.canvas_manager});a.on("run_on_dataset",b.run_tool_on_dataset,b);b.track_collection_container.append(a.$el);a.$el.hover(function(){var f=c.get_leaf(d.get("settings").get("values"));var e=_.pluck(c.get_connected_nodes(f),"id");d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(g){return _.find(e,function(h){return h===g.id})!==undefined}).style("fill","#f00")},function(){d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return d},handle_node_clicks:function(){var a=this,b=this.model.get("parameter_tree"),d=this.model.get("regions"),c=d3.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");c.on("click",function(k,g){var f=a.model.get("tool"),j=a.model.get("dataset"),h=b.get_node_settings(k),e=$.Deferred();if(h.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+a.model.get("tool").get("name")+" with "+h.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();e.resolve(false)}})}else{e.resolve(true)}$.when(e).then(function(i){if(!i){return}var l=_.map(h,function(m){var n=new ParamaMonsterTrack({settings:m,regions:d});a.add_track(n);return n});_.each(l,function(n,m){setTimeout(function(){f.set_input_values(n.get("settings").get("values"));$.when(f.rerun(j,d)).then(function(p){var q=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},p.first().get("track_config")),o=object_from_template(q,a,null);n.set("track",o)})},m*10000)})})})}});
\ No newline at end of file
+var ToolInputsSettings=Backbone.Model.extend({defaults:{inputs:null,values:null}});var ToolParameterTree=Backbone.RelationalModel.extend({defaults:{tool:null,tree_data:null},initialize:function(b){var a=this;this.get("tool").get("inputs").each(function(c){if(!c.get_samples()){return}c.on("change:min change:max change:num_samples",function(d){if(d.get("in_ptree")){a.set_tree_data()}},a);c.on("change:in_ptree",function(d){if(d.get("in_ptree")){a.add_param(d)}else{a.remove_param(d)}a.set_tree_data()},a)});if(b.config){_.each(b.config,function(d){var c=a.get("tool").get("inputs").find(function(e){return e.get("name")===d.name});a.add_param(c);c.set(d)})}},add_param:function(a){if(a.get("ptree_index")){return}a.set("in_ptree",true);a.set("ptree_index",this.get_tree_params().length)},remove_param:function(a){a.set("in_ptree",false);a.set("ptree_index",null);_(this.get_tree_params()).each(function(b,c){b.set("ptree_index",c+1)})},set_tree_data:function(){var b=_.map(this.get_tree_params(),function(d){return{param:d,samples:d.get_samples()}});var a=0,c=function(g,d){var i=g[d],h=i.param,f=h.get("label"),e=i.samples;if(g.length-1===d){return _.map(e,function(j){return{id:a++,name:j,param:h,value:j}})}return _.map(e,function(j){return{id:a++,name:j,param:h,value:j,children:c(g,d+1)}})};this.set("tree_data",{name:"Root",id:a++,children:(b.length!==0?c(b,0):null)})},get_tree_params:function(){return _(this.get("tool").get("inputs").where({in_ptree:true})).sortBy(function(a){return a.get("ptree_index")})},get_num_leaves:function(){return this.get_tree_params().reduce(function(a,b){return a*b.get_samples().length},1)},get_node_settings:function(e){var c=this.get("tool").get_inputs_dict();var f=e.parent;if(f){while(f.depth!==0){c[f.param.get("name")]=f.value;f=f.parent}}var a=this,b=function(h,g){if(h.param){g[h.param.get("name")]=h.value}if(!h.children){return new ToolInputsSettings({inputs:a.get("tool").get("inputs"),values:g})}else{return _.flatten(_.map(h.children,function(i){return b(i,_.clone(g))}))}},d=b(e,c);if(!_.isArray(d)){d=[d]}return d},get_connected_nodes:function(c){var d=function(e){if(!e.children){return e}else{return _.flatten([e,_.map(e.children,function(f){return d(f)})])}};var b=[],a=c.parent;while(a){b.push(a);a=a.parent}return _.flatten([b,d(c)])},get_leaf:function(b){var c=this.get("tree_data"),a=function(d){return _.find(d,function(e){return b[e.param.get("name")]===e.value})};while(c.children){c=a(c.children)}return c},toJSON:function(){return this.get_tree_params().map(function(a){return{name:a.get("name"),min:a.get("min"),max:a.get("max"),num_samples:a.get("num_samples")}})}});var ParamaMonsterTrack=Backbone.RelationalModel.extend({defaults:{track:null,settings:null,regions:null},relations:[{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"}],initialize:function(a){if(a.track){var b=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},a.track);delete b.mode;this.set("track",object_from_template(b,{},null))}},same_settings:function(a){var b=this.get("settings"),c=a.get("settings");for(var d in b){if(!c[d]||b[d]!==c[d]){return false}}return true},toJSON:function(){return{track:this.get("track").to_dict(),settings:this.get("settings"),regions:this.get("regions")}}});var TrackCollection=Backbone.Collection.extend({model:ParamaMonsterTrack});var ParamaMonsterVisualization=Visualization.extend({defaults:_.extend({},Visualization.prototype.defaults,{dataset:null,tool:null,parameter_tree:null,regions:null,tracks:null}),relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:"Dataset"},{type:Backbone.HasOne,key:"tool",relatedModel:"Tool"},{type:Backbone.HasMany,key:"regions",relatedModel:"GenomeRegion"},{type:Backbone.HasMany,key:"tracks",relatedModel:"ParamaMonsterTrack"}],initialize:function(a){var b=this.get("tool").copy(true);this.set("tool_with_samplable_inputs",b);this.set("parameter_tree",new ToolParameterTree({tool:b,config:a.tree_config}))},add_placeholder:function(a){this.get("tracks").add(new PlaceholderTrack(a))},add_track:function(a){this.get("tracks").add(a)},toJSON:function(){return{id:this.get("id"),title:"Parameter exploration for dataset '"+this.get("dataset").get("name")+"'",type:"paramamonster",dataset_id:this.get("dataset").id,tool_id:this.get("tool").id,regions:this.get("regions").toJSON(),tree_config:this.get("parameter_tree").toJSON(),tracks:this.get("tracks").toJSON()}}});var ParamaMonsterTrackView=Backbone.View.extend({tagName:"tr",TILE_LEN:250,initialize:function(a){this.canvas_manager=a.canvas_manager;this.render();this.model.on("change:track",this.draw_tiles,this)},render:function(){var f=this.model.get("settings"),b=f.get("values"),d=$("<td/>").addClass("settings").appendTo(this.$el),c=$("<div/>").addClass("track-info").hide().appendTo(d);c.append($("<div/>").css("font-weight","bold").text("Track Settings"));f.get("inputs").each(function(h){c.append(h.get("label")+": "+b[h.get("name")]+"<br/>")});var a=this,g=$("<button/>").appendTo(c).text("Run on complete dataset").click(function(){c.toggle();a.trigger("run_on_dataset",f)});var e=create_icon_buttons_menu([{title:"Settings",icon_class:"gear track-settings",on_click:function(){c.toggle()},tipsy_config:{gravity:"s"}},{title:"Remove",icon_class:"cross-circle",on_click:function(){a.$el.remove();$(".tipsy").remove()}}]);d.prepend(e.$el);this.model.get("regions").each(function(){a.$el.append($("<td/>").addClass("tile").html($("<img/>").attr("src",galaxy_paths.get("image_path")+"/loading_large_white_bg.gif")))});if(this.model.get("track")){this.draw_tiles()}},draw_tiles:function(){var b=this,a=this.model.get("track"),d=this.model.get("regions"),c=this.$el.find("td.tile");$.when(a.data_manager.data_is_ready()).then(function(e){d.each(function(h,g){var f=h.length()/b.TILE_LEN,j=1/f,i="Pack";$.when(a.data_manager.get_data(h,i,f,{})).then(function(l){var k=b.canvas_manager.new_canvas();k.width=b.TILE_LEN;k.height=a.get_canvas_height(l,i,j,k.width);a.draw_tile(l,k.getContext("2d"),i,f,h,j);$(c[g]).empty().append(k)})})})}});var ToolInputValOrSweepView=Backbone.View.extend({number_input_template:'<div class="form-row-input sweep"><input class="min" type="text" size="6" value="<%= min %>"> - <input class="max" type="text" size="6" value="<%= max %>"> samples: <input class="num_samples" type="text" size="1" value="<%= num_samples %>"></div>',select_input_template:'<div class="form-row-input sweep"><%= options %></div>',initialize:function(a){this.$el=a.tool_row;this.render()},render:function(){var b=this.model,f=b.get("type"),h=this.$el.find(".form-row-input"),d=null;h.find(":input").change(function(){b.set("value",$(this).val())});if(f==="number"){d=$(_.template(this.number_input_template,this.model.toJSON()))}else{if(f==="select"){var c=_.map(this.$el.find("select option"),function(i){return $(i).val()}),e=c.join(", ");d=$(_.template(this.select_input_template,{options:e}))}}d.insertAfter(h);var a=this,g=create_icon_buttons_menu([{title:"Add parameter to tree",icon_class:"plus-button",on_click:function(){b.set("in_ptree",true);h.hide();d.show();$(this).hide();a.$el.find(".icon-button.toggle").show()}},{title:"Remove parameter from tree",icon_class:"toggle",on_click:function(){b.set("in_ptree",false);d.hide();h.show();$(this).hide();a.$el.find(".icon-button.plus-button").show()}}],{tipsy_config:{gravity:"s"}});this.$el.prepend(g.$el);if(b.get("in_ptree")){h.hide();a.$el.find(".icon-button.plus-button").hide()}else{a.$el.find(".icon-button.toggle").hide();d.hide()}_.each(["min","max","num_samples"],function(i){d.find("."+i).change(function(){b.set(i,parseFloat($(this).val()))})})}});var ToolParameterTreeDesignView=Backbone.View.extend({className:"tree-design",initialize:function(a){this.render()},render:function(){var c=new ToolFormView({model:this.model.get("tool")});c.render();this.$el.append(c.$el);var b=this,a=b.model.get("tool").get("inputs");this.$el.find(".form-row").not(".form-actions").each(function(d){var e=new ToolInputValOrSweepView({model:a.at(d),tool_row:$(this)})})}});var ToolParameterTreeView=Backbone.View.extend({className:"tool-parameter-tree",initialize:function(a){this.model.on("change:tree_data",this.render,this)},render:function(){this.$el.children().remove();var i=this.model.get_tree_params();if(!i.length){return}this.width=100*(2+i.length);this.height=15*this.model.get_num_leaves();var h=this;var g=d3.layout.cluster().size([this.height,this.width-160]);var c=d3.svg.diagonal().projection(function(j){return[j.y,j.x]});var a=g.nodes(this.model.get("tree_data"));var d=_.uniq(_.pluck(a,"y"));_.each(i,function(l,k){var j=d[k+1],m=$("#center").position().left;h.$el.append($("<div>").addClass("label").text(l.get("label")).css("left",j+m))});var b=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height+20).append("g").attr("transform","translate(40, 10)");var f=b.selectAll("path.link").data(g.links(a)).enter().append("path").attr("class","link").attr("d",c);var e=b.selectAll("g.node").data(a).enter().append("g").attr("class","node").attr("transform",function(j){return"translate("+j.y+","+j.x+")"}).on("mouseover",function(k){var j=_.pluck(h.model.get_connected_nodes(k),"id");e.filter(function(l){return _.find(j,function(m){return m===l.id})!==undefined}).style("fill","#f00")}).on("mouseout",function(){e.style("fill","#000")});e.append("circle").attr("r",9);e.append("text").attr("dx",function(j){return j.children?-12:12}).attr("dy",3).attr("text-anchor",function(j){return j.children?"end":"start"}).text(function(j){return j.name})}});var ParamaMonsterVisualizationView=Backbone.View.extend({className:"paramamonster",helpText:"<div><h4>Getting Started</h4><ol><li>Create a parameter tree by using the icons next to the tool's parameter names to add or remove parameters.<li>Adjust the tree by using parameter inputs to select min, max, and number of samples<li>Run the tool with different settings by clicking on tree nodes</ol></div>",initialize:function(b){this.canvas_manager=new CanvasManager(this.$el.parents("body"));this.tool_param_tree_view=new ToolParameterTreeView({model:this.model.get("parameter_tree")});this.track_collection_container=$("<table/>").addClass("tracks");this.model.get("parameter_tree").on("change:tree_data",this.handle_node_clicks,this);var a=this;this.model.get("tracks").each(function(c){c.get("track").view=a})},render:function(){var f=new ToolParameterTreeDesignView({model:this.model.get("parameter_tree")});$("#left").append(f.$el);var b=this,g=b.model.get("regions"),c=$("<tr/>").appendTo(this.track_collection_container);g.each(function(h){c.append($("<th>").text(h.toString()))});c.children().first().attr("colspan",2);var e=$("<div>").addClass("tiles");$("#right").append(e.append(this.track_collection_container));b.model.get("tracks").each(function(h){b.add_track(h)});var d=$(this.helpText).addClass("help"),a=create_icon_buttons_menu([{title:"Close",icon_class:"cross-circle",on_click:function(){$(".tipsy").remove();d.remove()},tipsy_config:{gravity:"s"}}]);d.prepend(a.$el.css("float","right"));$("#center").append(d);this.tool_param_tree_view.render();$("#center").append(this.tool_param_tree_view.$el);this.handle_node_clicks()},run_tool_on_dataset:function(b){var a=this.model.get("tool"),d=a.get("name"),c=this.model.get("dataset");a.set_input_values(b.get("values"));$.when(a.rerun(c)).then(function(e){});show_modal("Running "+d+" on complete dataset",d+" is running on dataset '"+c.get("name")+"'. Outputs are in the dataset's history.",{Ok:function(){hide_modal()}})},add_track:function(d){var b=this,c=this.model.get("parameter_tree");b.model.add_track(d);var a=new ParamaMonsterTrackView({model:d,canvas_manager:b.canvas_manager});a.on("run_on_dataset",b.run_tool_on_dataset,b);b.track_collection_container.append(a.$el);a.$el.hover(function(){var f=c.get_leaf(d.get("settings").get("values"));var e=_.pluck(c.get_connected_nodes(f),"id");d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").filter(function(g){return _.find(e,function(h){return h===g.id})!==undefined}).style("fill","#f00")},function(){d3.select(b.tool_param_tree_view.$el[0]).selectAll("g.node").style("fill","#000")});return d},handle_node_clicks:function(){var a=this,b=this.model.get("parameter_tree"),d=this.model.get("regions"),c=d3.select(this.tool_param_tree_view.$el[0]).selectAll("g.node");c.on("click",function(k,g){var f=a.model.get("tool"),j=a.model.get("dataset"),h=b.get_node_settings(k),e=$.Deferred();if(h.length>=10){show_modal("Whoa there cowboy!","You clicked on a node to try "+a.model.get("tool").get("name")+" with "+h.length+" different combinations of settings. You can only run 10 jobs at a time.",{Ok:function(){hide_modal();e.resolve(false)}})}else{e.resolve(true)}$.when(e).then(function(i){if(!i){return}var l=_.map(h,function(m){var n=new ParamaMonsterTrack({settings:m,regions:d});a.add_track(n);return n});_.each(l,function(n,m){setTimeout(function(){f.set_input_values(n.get("settings").get("values"));$.when(f.rerun(j,d)).then(function(p){var q=_.extend({data_url:galaxy_paths.get("raw_data_url"),converted_datasets_state_url:galaxy_paths.get("dataset_state_url")},p.first().get("track_config")),o=object_from_template(q,a,null);n.set("track",o)})},m*10000)})})})}});
\ No newline at end of file
diff -r 202c6a7dae95450eb9781c8df6fdc0c2795b6968 -r eff8b196858c1ff5a6227bd750a06ea924f8530c static/scripts/viz/paramamonster.js
--- a/static/scripts/viz/paramamonster.js
+++ b/static/scripts/viz/paramamonster.js
@@ -626,11 +626,11 @@
// Setup and add labels for tree levels.
var param_depths = _.uniq(_.pluck(nodes, "y"));
_.each(tree_params, function(param, index) {
- var x = param_depths[index+1];
+ var x = param_depths[index+1],
+ center_left = $('#center').position().left;
self.$el.append( $('<div>').addClass('label')
.text(param.get('label'))
- // HACK: add 250 b/c in center panel.
- .css('left', x + 250) );
+ .css('left', x + center_left) );
});
// Set up vis element.
@@ -681,6 +681,13 @@
*/
var ParamaMonsterVisualizationView = Backbone.View.extend({
className: 'paramamonster',
+
+ helpText:
+ '<div><h4>Getting Started</h4>' +
+ '<ol><li>Create a parameter tree by using the icons next to the tool\'s parameter names to add or remove parameters.' +
+ '<li>Adjust the tree by using parameter inputs to select min, max, and number of samples' +
+ '<li>Run the tool with different settings by clicking on tree nodes' +
+ '</ol></div>',
initialize: function(options) {
this.canvas_manager = new CanvasManager(this.$el.parents('body'));
@@ -722,7 +729,26 @@
self.add_track(track);
});
- // Render tool parameter tree in center panel.
+ // -- Render help and tool parameter tree in center panel. --
+
+ // Help includes text and a close button.
+ var help_div = $(this.helpText).addClass('help'),
+ close_button = create_icon_buttons_menu([
+ {
+ title: 'Close',
+ icon_class: 'cross-circle',
+ on_click: function() {
+ $('.tipsy').remove();
+ help_div.remove();
+ },
+ tipsy_config: { gravity: 's' }
+ }
+ ]);
+
+ help_div.prepend(close_button.$el.css('float', 'right'));
+ $('#center').append(help_div);
+
+ // Parameter tree:
this.tool_param_tree_view.render();
$('#center').append(this.tool_param_tree_view.$el);
diff -r 202c6a7dae95450eb9781c8df6fdc0c2795b6968 -r eff8b196858c1ff5a6227bd750a06ea924f8530c templates/visualization/paramamonster.mako
--- a/templates/visualization/paramamonster.mako
+++ b/templates/visualization/paramamonster.mako
@@ -12,9 +12,6 @@
<%def name="stylesheets()">
${parent.stylesheets()}
<style>
- div#center {
- overflow: auto;
- }
.link {
fill: none;
stroke: #ccc;
@@ -84,6 +81,7 @@
#center {
left: 300px;
right: 600px;
+ overflow: auto;
}
#right {
width: 600px;
@@ -96,6 +94,12 @@
left: 0;
right: 0;
}
+ .help {
+ border-radius: 15px;
+ border: solid 1px #CCC;
+ padding: 0px 2px;
+ margin: 10px;
+ }
</style></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: inithello: Cleaned up code, added searchable list of NCBI builds.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/202c6a7dae95/
changeset: 202c6a7dae95
user: inithello
date: 2012-07-05 15:56:54
summary: Cleaned up code, added searchable list of NCBI builds.
affected #: 12 files
Diff too large to display.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Make sure there is an entry for the main public Galaxy tool shed in the tool_sheds_conf.xml file when attempting to determine if tools migrated from the distribution to the tool shed are missing and need to be installed.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/d9c384f7a754/
changeset: d9c384f7a754
user: greg
date: 2012-07-05 15:42:11
summary: Make sure there is an entry for the main public Galaxy tool shed in the tool_sheds_conf.xml file when attempting to determine if tools migrated from the distribution to the tool shed are missing and need to be installed.
affected #: 1 file
diff -r 456f11df0b53897086257b952457d615b3942539 -r d9c384f7a75435173817754300f8e7bef12d8840 lib/galaxy/tool_shed/migrate/common.py
--- a/lib/galaxy/tool_shed/migrate/common.py
+++ b/lib/galaxy/tool_shed/migrate/common.py
@@ -21,39 +21,44 @@
root = tree.getroot()
tool_shed = root.get( 'name' )
tool_shed_url = get_tool_shed_url_from_tools_xml_file_path( app, tool_shed )
- for elem in root:
- if elem.tag == 'repository':
- tool_dependencies = []
- tool_dependencies_dict = {}
- repository_name = elem.get( 'name' )
- changeset_revision = elem.get( 'changeset_revision' )
- url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&webapp=install_manager&no_reset=true' % \
- ( tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision )
- response = urllib2.urlopen( url )
- text = response.read()
- response.close()
- if text:
- tool_dependencies_dict = tool_shed_decode( text )
- for dependency_key, requirements_dict in tool_dependencies_dict.items():
- tool_dependency_name = requirements_dict[ 'name' ]
- tool_dependency_version = requirements_dict[ 'version' ]
- tool_dependency_type = requirements_dict[ 'type' ]
- tool_dependency_readme = requirements_dict.get( 'readme', '' )
- tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) )
- for tool_elem in elem.findall( 'tool' ):
- migrated_tool_configs_dict[ tool_elem.get( 'file' ) ] = tool_dependencies
- # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names.
- missing_tool_configs_dict = odict()
- for tool_panel_config in tool_panel_configs:
- tree = util.parse_xml( tool_panel_config )
- root = tree.getroot()
+ if tool_shed_url:
for elem in root:
- if elem.tag == 'tool':
- missing_tool_configs_dict = check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict )
- elif elem.tag == 'section':
- for section_elem in elem:
- if section_elem.tag == 'tool':
- missing_tool_configs_dict = check_tool_tag_set( section_elem, migrated_tool_configs_dict, missing_tool_configs_dict )
+ if elem.tag == 'repository':
+ tool_dependencies = []
+ tool_dependencies_dict = {}
+ repository_name = elem.get( 'name' )
+ changeset_revision = elem.get( 'changeset_revision' )
+ url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&webapp=install_manager&no_reset=true' % \
+ ( tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision )
+ response = urllib2.urlopen( url )
+ text = response.read()
+ response.close()
+ if text:
+ tool_dependencies_dict = tool_shed_decode( text )
+ for dependency_key, requirements_dict in tool_dependencies_dict.items():
+ tool_dependency_name = requirements_dict[ 'name' ]
+ tool_dependency_version = requirements_dict[ 'version' ]
+ tool_dependency_type = requirements_dict[ 'type' ]
+ tool_dependency_readme = requirements_dict.get( 'readme', '' )
+ tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) )
+ for tool_elem in elem.findall( 'tool' ):
+ migrated_tool_configs_dict[ tool_elem.get( 'file' ) ] = tool_dependencies
+ # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names.
+ missing_tool_configs_dict = odict()
+ for tool_panel_config in tool_panel_configs:
+ tree = util.parse_xml( tool_panel_config )
+ root = tree.getroot()
+ for elem in root:
+ if elem.tag == 'tool':
+ missing_tool_configs_dict = check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict )
+ elif elem.tag == 'section':
+ for section_elem in elem:
+ if section_elem.tag == 'tool':
+ missing_tool_configs_dict = check_tool_tag_set( section_elem, migrated_tool_configs_dict, missing_tool_configs_dict )
+ else:
+ exception_msg = '\n\nThe entry for the main Galaxy tool shed at %s is missing from the %s file. ' % ( tool_shed, app.config.tool_sheds_config )
+ exception_msg += 'The entry for this tool shed must always be available in this file, so re-add it before attempting to start your Galaxy server.\n'
+ raise Exception( exception_msg )
return missing_tool_configs_dict
def check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ):
file_path = elem.get( 'file', None )
@@ -76,8 +81,9 @@
config_filenames.append( config_filename )
return config_filenames
def get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ):
+ search_str = '://%s' % tool_shed
for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items():
- if shed_url.find( tool_shed ) >= 0:
+ if shed_url.find( search_str ) >= 0:
if shed_url.endswith( '/' ):
shed_url = shed_url.rstrip( '/' )
return shed_url
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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9 years, 5 months
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commit/galaxy-central: jgoecks: Make bookmarks available in shared Trackster visualizations.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/456f11df0b53/
changeset: 456f11df0b53
user: jgoecks
date: 2012-07-05 15:31:19
summary: Make bookmarks available in shared Trackster visualizations.
affected #: 6 files
diff -r 6face40d68836de96bf92d46c0d6e6bf32cdb616 -r 456f11df0b53897086257b952457d615b3942539 static/scripts/packed/viz/trackster_ui.js
--- a/static/scripts/packed/viz/trackster_ui.js
+++ b/static/scripts/packed/viz/trackster_ui.js
@@ -1,1 +1,1 @@
-var add_bookmark=function(d,b){var f=$("#bookmarks-container"),h=$("<div/>").addClass("bookmark").appendTo(f),g=$("<div/>").addClass("delete-icon-container").appendTo(h).click(function(){h.slideUp("fast");h.remove();view.has_changes=true;return false}),a=$("<a href=''/>").addClass("icon-button delete").appendTo(g),i=$("<div/>").addClass("position").appendTo(h),e=$("<a href=''/>").text(d).appendTo(i).click(function(){view.go_to(d);return false}),c=$("<div/>").text(b).make_text_editable({num_rows:3,use_textarea:true,help_text:"Set bookmark note"}).addClass("annotation").appendTo(h);view.has_changes=true;return h};var object_from_template=function(c,b,a){if("copy" in c){return c.copy(a)}else{var d=c.obj_type;if(!d){d=c.track_type}return new addable_objects[d](b,a,c)}};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,CompositeTrack:CompositeTrack,DrawableGroup:DrawableGroup};var create_visualization=function(c,a,b,d){view=new View(c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var n=a.chrom,e=a.start,k=a.end,g=a.overview;if(n&&(e!==undefined)&&k){view.change_chrom(n,e,k)}}if(b){var h,f,j;for(var l=0;l<b.length;l++){view.add_drawable(object_from_template(b[l],view,view))}}view.update_intro_div();var o;for(var l=0;l<view.drawables.length;l++){if(view.drawables[l].name===g){view.set_overview(view.drawables[l]);break}}if(d){var m;for(var l=0;l<d.length;l++){m=d[l];add_bookmark(m.position,m.annotation)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()-20);break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()+20);break}})};
\ No newline at end of file
+var add_bookmark=function(e,c,a){var g=$("#bookmarks-container"),i=$("<div/>").addClass("bookmark").appendTo(g);var j=$("<div/>").addClass("position").appendTo(i),f=$("<a href=''/>").text(e).appendTo(j).click(function(){view.go_to(e);return false}),d=$("<div/>").text(c).appendTo(i);if(a){var h=$("<div/>").addClass("delete-icon-container").prependTo(i).click(function(){i.slideUp("fast");i.remove();view.has_changes=true;return false}),b=$("<a href=''/>").addClass("icon-button delete").appendTo(h);d.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return i};var object_from_template=function(c,b,a){if("copy" in c){return c.copy(a)}else{var d=c.obj_type;if(!d){d=c.track_type}return new addable_objects[d](b,a,c)}};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,CompositeTrack:CompositeTrack,DrawableGroup:DrawableGroup};var create_visualization=function(d,a,c,e,b){view=new View(d);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var o=a.chrom,f=a.start,l=a.end,h=a.overview;if(o&&(f!==undefined)&&l){view.change_chrom(o,f,l)}}if(c){var j,g,k;for(var m=0;m<c.length;m++){view.add_drawable(object_from_template(c[m],view,view))}}view.update_intro_div();var p;for(var m=0;m<view.drawables.length;m++){if(view.drawables[m].name===h){view.set_overview(view.drawables[m]);break}}if(e){var n;for(var m=0;m<e.length;m++){n=e[m];add_bookmark(n.position,n.annotation,b)}}view.has_changes=false});return view};var init_keyboard_nav=function(a){$(document).keydown(function(b){if($(b.srcElement).is(":input")){return}switch(b.which){case 37:a.move_fraction(0.25);break;case 38:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()-20);break;case 39:a.move_fraction(-0.25);break;case 40:var c=Math.round(a.viewport_container.height()/15);a.viewport_container.scrollTop(a.viewport_container.scrollTop()+20);break}})};
\ No newline at end of file
diff -r 6face40d68836de96bf92d46c0d6e6bf32cdb616 -r 456f11df0b53897086257b952457d615b3942539 static/scripts/packed/viz/visualization.js
--- a/static/scripts/packed/viz/visualization.js
+++ b/static/scripts/packed/viz/visualization.js
@@ -1,1 +1,1 @@
-var ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});var CanvasManager=function(a){this.default_font=a!==undefined?a:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};_.extend(CanvasManager.prototype,{load_pattern:function(a,e){var b=this.patterns,c=this.dummy_context,d=new Image();d.src=galaxy_paths.attributes.image_path+e;d.onload=function(){b[a]=c.createPattern(d,"repeat")}},get_pattern:function(a){return this.patterns[a]},new_canvas:function(){var a=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(a)}a.manager=this;return a}});var Cache=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(a){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,a=d.indexOf(b);if(a!==-1){if(c[b].stale){d.splice(a,1);delete c[b]}else{this.move_key_to_end(b,a)}}return c[b]},set_elt:function(b,d){var e=this.attributes.obj_cache,f=this.attributes.key_ary,c=this.attributes.num_elements;if(!e[b]){if(f.length>=c){var a=f.shift();delete e[a]}f.push(b)}e[b]=d;return d},move_key_to_end:function(b,a){this.attributes.key_ary.splice(a,1);this.attributes.key_ary.push(b)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var GenomeDataManager=Cache.extend({defaults:_.extend({},Cache.prototype.defaults,{dataset:null,filters_manager:null,data_url:null,dataset_state_url:null,data_mode_compatible:function(a,b){return true},can_subset:function(a){return false}}),data_is_ready:function(){var c=this.get("dataset"),b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.get("dataset_state_url"),data:{dataset_id:c.id,hda_ldda:c.get("hda_ldda")},dataType:"json"},interval:5000,success_fn:function(d){return d!=="pending"}});$.when(a.go()).then(function(d){b.resolve(d==="ok"||d==="data")});return b},load_data:function(h,g,b,f){var d={chrom:h.get("chrom"),low:h.get("start"),high:h.get("end"),mode:g,resolution:b};dataset=this.get("dataset");if(dataset){d.dataset_id=dataset.id;d.hda_ldda=dataset.get("hda_ldda")}$.extend(d,f);var j=this.get("filters_manager");if(j){var k=[];var a=j.filters;for(var e=0;e<a.length;e++){k.push(a[e].name)}d.filter_cols=JSON.stringify(k)}var c=this;return $.getJSON(this.get("data_url"),d,function(i){c.set_data(h,i)})},get_data:function(g,f,c,e){var h=this.get_elt(g);if(h&&(is_deferred(h)||this.get("data_mode_compatible")(h,f))){return h}var j=this.get("key_ary"),b=this.get("obj_cache"),k,a;for(var d=0;d<j.length;d++){k=j[d];a=new GenomeRegion({from_str:k});if(a.contains(g)){h=b[k];if(is_deferred(h)||(this.get("data_mode_compatible")(h,f)&&this.get("can_subset")(h))){this.move_key_to_end(k,d);return h}}}h=this.load_data(g,f,c,e);this.set_data(g,h);return h},set_data:function(b,a){this.set_elt(b,a)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(i,h,d,g,e){var k=this.get_elt(i);if(!(k&&this.get("data_mode_compatible")(k,h))){console.log("ERROR: no current data for: ",dataset,i.toString(),h,d,g);return}k.stale=true;var c=i.get("start");if(e===this.DEEP_DATA_REQ){$.extend(g,{start_val:k.data.length+1})}else{if(e===this.BROAD_DATA_REQ){c=(k.max_high?k.max_high:k.data[k.data.length-1][2])+1}}var j=i.copy().set("start",c);var b=this,f=this.load_data(j,h,d,g),a=$.Deferred();this.set_data(i,a);$.when(f).then(function(l){if(l.data){l.data=k.data.concat(l.data);if(l.max_low){l.max_low=k.max_low}if(l.message){l.message=l.message.replace(/[0-9]+/,l.data.length)}}b.set_data(i,l);a.resolve(l)});return a},get_elt:function(a){return Cache.prototype.get_elt.call(this,a.toString())},set_elt:function(b,a){return Cache.prototype.set_elt.call(this,b.toString(),a)}});var ReferenceTrackDataManager=GenomeDataManager.extend({load_data:function(a,d,e,b,c){if(b>1){return{data:null}}return GenomeDataManager.prototype.load_data.call(this,a,d,e,b,c)}});var Genome=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var GenomeRegion=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(b){if(b.from_str){var d=b.from_str.split(":"),c=d[0],a=d[1].split("-");this.set({chrom:c,start:parseInt(a[0],10),end:parseInt(a[1],10)})}},copy:function(){return new GenomeRegion({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(h){var b=this.get("chrom"),g=h.get("chrom"),f=this.get("start"),d=h.get("start"),e=this.get("end"),c=h.get("end"),a;if(b&&g&&b!==g){return this.get("DIF_CHROMS")}if(f<d){if(e<d){a=this.get("BEFORE")}else{if(e<=c){a=this.get("OVERLAP_START")}else{a=this.get("CONTAINS")}}}else{if(f>c){a=this.get("AFTER")}else{if(e<=c){a=this.get("CONTAINED_BY")}else{a=this.get("OVERLAP_END")}}}return a},contains:function(a){return this.compute_overlap(a)===this.get("CONTAINS")},overlaps:function(a){return _.intersection([this.compute_overlap(a)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var GenomeRegionCollection=Backbone.Collection.extend({model:GenomeRegion});var BrowserBookmark=Backbone.Model.extend({defaults:{region:null,note:""}});var BrowserBookmarks=Backbone.Collection.extend({model:BrowserBookmark});var Visualization=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",datasets:[]},url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var TracksterVisualization=Visualization.extend({defaults:{bookmarks:[],viewport:{}}});var CircsterVisualization=Visualization.extend({});var HistogramDataset=Backbone.Model.extend({initialize:function(a){this.attributes.data=a;this.attributes.max=_.max(a,function(b){if(!b||typeof b==="string"){return 0}return b[1]})[1]}});var TrackConfig=Backbone.Model.extend({});var CircsterHistogramDatasetLayout=Backbone.Model.extend({chroms_layout:function(){var b=this.attributes.genome.get_chroms_info(),d=d3.layout.pie().value(function(f){return f.len}).sort(null),e=d(b),a=this.attributes.total_gap/b.length,c=_.map(e,function(h,g){var f=h.endAngle-a;h.endAngle=(f>h.startAngle?f:h.startAngle);return h});return c},chrom_data_layout:function(j,b,g,f,h){if(!b||typeof b==="string"){return null}var d=b[0],i=b[3],c=d3.scale.linear().domain([0,h]).range([g,f]),e=d3.layout.pie().value(function(k){return i}).startAngle(j.startAngle).endAngle(j.endAngle),a=e(d);_.each(d,function(k,l){a[l].outerRadius=c(k[1])});return a}});var CircsterView=Backbone.View.extend({className:"circster",initialize:function(a){this.width=a.width;this.height=a.height;this.total_gap=a.total_gap;this.genome=a.genome;this.dataset=a.dataset;this.radius_start=a.radius_start;this.dataset_arc_height=a.dataset_arc_height},render:function(){var d=this.radius_start,e=this.dataset_arc_height,j=new CircsterHistogramDatasetLayout({genome:this.genome,total_gap:this.total_gap}),i=j.chroms_layout(),g=_.zip(i,this.dataset.attributes.data),h=this.dataset.attributes.max,b=_.map(g,function(m){var n=m[0],l=m[1];return j.chrom_data_layout(n,l,d,d+e,h)});var c=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height).append("g").attr("transform","translate("+this.width/2+","+this.height/2+")");var k=c.append("g").attr("id","inner-arc"),f=d3.svg.arc().innerRadius(d).outerRadius(d+e),a=k.selectAll("#inner-arc>path").data(i).enter().append("path").attr("d",f).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(l){return l.data.chrom});_.each(b,function(l){if(!l){return}var o=c.append("g"),n=d3.svg.arc().innerRadius(d),m=o.selectAll("path").data(l).enter().append("path").attr("d",n).style("stroke","red").style("fill","red")})}});var TrackBrowserRouter=Backbone.Router.extend({initialize:function(b){this.view=b.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var a=this;a.view.on("navigate",function(c){a.navigate(c)})},change_location:function(a){this.view.go_to(a)}});var add_datasets=function(a,c,b){$.ajax({url:a,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(d){show_modal("Select datasets for new tracks",d,{Cancel:function(){hide_modal()},Add:function(){var e=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var f,g=$(this).val();if($(this).attr("name")==="id"){f={hda_id:g}}else{f={ldda_id:g}}e[e.length]=$.ajax({url:c,data:f,dataType:"json"})});$.when.apply($,e).then(function(){var f=(arguments[0] instanceof Array?$.map(arguments,function(g){return g[0]}):[arguments[0]]);b(f)});hide_modal()}})}})};
\ No newline at end of file
+var ServerStateDeferred=Backbone.Model.extend({defaults:{ajax_settings:{},interval:1000,success_fn:function(a){return true}},go:function(){var d=$.Deferred(),c=this,f=c.get("ajax_settings"),e=c.get("success_fn"),b=c.get("interval"),a=function(){$.ajax(f).success(function(g){if(e(g)){d.resolve(g)}else{setTimeout(a,b)}})};a();return d}});var CanvasManager=function(a){this.default_font=a!==undefined?a:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};_.extend(CanvasManager.prototype,{load_pattern:function(a,e){var b=this.patterns,c=this.dummy_context,d=new Image();d.src=galaxy_paths.attributes.image_path+e;d.onload=function(){b[a]=c.createPattern(d,"repeat")}},get_pattern:function(a){return this.patterns[a]},new_canvas:function(){var a=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(a)}a.manager=this;return a}});var Cache=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(a){this.clear()},get_elt:function(b){var c=this.attributes.obj_cache,d=this.attributes.key_ary,a=d.indexOf(b);if(a!==-1){if(c[b].stale){d.splice(a,1);delete c[b]}else{this.move_key_to_end(b,a)}}return c[b]},set_elt:function(b,d){var e=this.attributes.obj_cache,f=this.attributes.key_ary,c=this.attributes.num_elements;if(!e[b]){if(f.length>=c){var a=f.shift();delete e[a]}f.push(b)}e[b]=d;return d},move_key_to_end:function(b,a){this.attributes.key_ary.splice(a,1);this.attributes.key_ary.push(b)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var GenomeDataManager=Cache.extend({defaults:_.extend({},Cache.prototype.defaults,{dataset:null,filters_manager:null,data_url:null,dataset_state_url:null,data_mode_compatible:function(a,b){return true},can_subset:function(a){return false}}),data_is_ready:function(){var c=this.get("dataset"),b=$.Deferred(),a=new ServerStateDeferred({ajax_settings:{url:this.get("dataset_state_url"),data:{dataset_id:c.id,hda_ldda:c.get("hda_ldda")},dataType:"json"},interval:5000,success_fn:function(d){return d!=="pending"}});$.when(a.go()).then(function(d){b.resolve(d==="ok"||d==="data")});return b},load_data:function(h,g,b,f){var d={chrom:h.get("chrom"),low:h.get("start"),high:h.get("end"),mode:g,resolution:b};dataset=this.get("dataset");if(dataset){d.dataset_id=dataset.id;d.hda_ldda=dataset.get("hda_ldda")}$.extend(d,f);var j=this.get("filters_manager");if(j){var k=[];var a=j.filters;for(var e=0;e<a.length;e++){k.push(a[e].name)}d.filter_cols=JSON.stringify(k)}var c=this;return $.getJSON(this.get("data_url"),d,function(i){c.set_data(h,i)})},get_data:function(g,f,c,e){var h=this.get_elt(g);if(h&&(is_deferred(h)||this.get("data_mode_compatible")(h,f))){return h}var j=this.get("key_ary"),b=this.get("obj_cache"),k,a;for(var d=0;d<j.length;d++){k=j[d];a=new GenomeRegion({from_str:k});if(a.contains(g)){h=b[k];if(is_deferred(h)||(this.get("data_mode_compatible")(h,f)&&this.get("can_subset")(h))){this.move_key_to_end(k,d);return h}}}h=this.load_data(g,f,c,e);this.set_data(g,h);return h},set_data:function(b,a){this.set_elt(b,a)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(i,h,d,g,e){var k=this.get_elt(i);if(!(k&&this.get("data_mode_compatible")(k,h))){console.log("ERROR: no current data for: ",dataset,i.toString(),h,d,g);return}k.stale=true;var c=i.get("start");if(e===this.DEEP_DATA_REQ){$.extend(g,{start_val:k.data.length+1})}else{if(e===this.BROAD_DATA_REQ){c=(k.max_high?k.max_high:k.data[k.data.length-1][2])+1}}var j=i.copy().set("start",c);var b=this,f=this.load_data(j,h,d,g),a=$.Deferred();this.set_data(i,a);$.when(f).then(function(l){if(l.data){l.data=k.data.concat(l.data);if(l.max_low){l.max_low=k.max_low}if(l.message){l.message=l.message.replace(/[0-9]+/,l.data.length)}}b.set_data(i,l);a.resolve(l)});return a},get_elt:function(a){return Cache.prototype.get_elt.call(this,a.toString())},set_elt:function(b,a){return Cache.prototype.set_elt.call(this,b.toString(),a)}});var ReferenceTrackDataManager=GenomeDataManager.extend({load_data:function(a,d,e,b,c){if(b>1){return{data:null}}return GenomeDataManager.prototype.load_data.call(this,a,d,e,b,c)}});var Genome=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info}});var GenomeRegion=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006},initialize:function(b){if(b.from_str){var d=b.from_str.split(":"),c=d[0],a=d[1].split("-");this.set({chrom:c,start:parseInt(a[0],10),end:parseInt(a[1],10)})}},copy:function(){return new GenomeRegion({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(h){var b=this.get("chrom"),g=h.get("chrom"),f=this.get("start"),d=h.get("start"),e=this.get("end"),c=h.get("end"),a;if(b&&g&&b!==g){return this.get("DIF_CHROMS")}if(f<d){if(e<d){a=this.get("BEFORE")}else{if(e<=c){a=this.get("OVERLAP_START")}else{a=this.get("CONTAINS")}}}else{if(f>c){a=this.get("AFTER")}else{if(e<=c){a=this.get("CONTAINED_BY")}else{a=this.get("OVERLAP_END")}}}return a},contains:function(a){return this.compute_overlap(a)===this.get("CONTAINS")},overlaps:function(a){return _.intersection([this.compute_overlap(a)],[this.get("DIF_CHROMS"),this.get("BEFORE"),this.get("AFTER")]).length===0}});var GenomeRegionCollection=Backbone.Collection.extend({model:GenomeRegion});var BrowserBookmark=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:"GenomeRegion"}]});var BrowserBookmarkCollection=Backbone.Collection.extend({model:BrowserBookmark});var Visualization=Backbone.RelationalModel.extend({defaults:{id:"",title:"",type:"",dbkey:"",datasets:[]},url:function(){return galaxy_paths.get("visualization_url")},save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var TracksterVisualization=Visualization.extend({defaults:{bookmarks:[],viewport:{}}});var CircsterVisualization=Visualization.extend({});var HistogramDataset=Backbone.Model.extend({initialize:function(a){this.attributes.data=a;this.attributes.max=_.max(a,function(b){if(!b||typeof b==="string"){return 0}return b[1]})[1]}});var TrackConfig=Backbone.Model.extend({});var CircsterHistogramDatasetLayout=Backbone.Model.extend({chroms_layout:function(){var b=this.attributes.genome.get_chroms_info(),d=d3.layout.pie().value(function(f){return f.len}).sort(null),e=d(b),a=this.attributes.total_gap/b.length,c=_.map(e,function(h,g){var f=h.endAngle-a;h.endAngle=(f>h.startAngle?f:h.startAngle);return h});return c},chrom_data_layout:function(j,b,g,f,h){if(!b||typeof b==="string"){return null}var d=b[0],i=b[3],c=d3.scale.linear().domain([0,h]).range([g,f]),e=d3.layout.pie().value(function(k){return i}).startAngle(j.startAngle).endAngle(j.endAngle),a=e(d);_.each(d,function(k,l){a[l].outerRadius=c(k[1])});return a}});var CircsterView=Backbone.View.extend({className:"circster",initialize:function(a){this.width=a.width;this.height=a.height;this.total_gap=a.total_gap;this.genome=a.genome;this.dataset=a.dataset;this.radius_start=a.radius_start;this.dataset_arc_height=a.dataset_arc_height},render:function(){var d=this.radius_start,e=this.dataset_arc_height,j=new CircsterHistogramDatasetLayout({genome:this.genome,total_gap:this.total_gap}),i=j.chroms_layout(),g=_.zip(i,this.dataset.attributes.data),h=this.dataset.attributes.max,b=_.map(g,function(m){var n=m[0],l=m[1];return j.chrom_data_layout(n,l,d,d+e,h)});var c=d3.select(this.$el[0]).append("svg").attr("width",this.width).attr("height",this.height).append("g").attr("transform","translate("+this.width/2+","+this.height/2+")");var k=c.append("g").attr("id","inner-arc"),f=d3.svg.arc().innerRadius(d).outerRadius(d+e),a=k.selectAll("#inner-arc>path").data(i).enter().append("path").attr("d",f).style("stroke","#ccc").style("fill","#ccc").append("title").text(function(l){return l.data.chrom});_.each(b,function(l){if(!l){return}var o=c.append("g"),n=d3.svg.arc().innerRadius(d),m=o.selectAll("path").data(l).enter().append("path").attr("d",n).style("stroke","red").style("fill","red")})}});var TrackBrowserRouter=Backbone.Router.extend({initialize:function(b){this.view=b.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var a=this;a.view.on("navigate",function(c){a.navigate(c)})},change_location:function(a){this.view.go_to(a)}});var add_datasets=function(a,c,b){$.ajax({url:a,data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(d){show_modal("Select datasets for new tracks",d,{Cancel:function(){hide_modal()},Add:function(){var e=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var f,g=$(this).val();if($(this).attr("name")==="id"){f={hda_id:g}}else{f={ldda_id:g}}e[e.length]=$.ajax({url:c,data:f,dataType:"json"})});$.when.apply($,e).then(function(){var f=(arguments[0] instanceof Array?$.map(arguments,function(g){return g[0]}):[arguments[0]]);b(f)});hide_modal()}})}})};
\ No newline at end of file
diff -r 6face40d68836de96bf92d46c0d6e6bf32cdb616 -r 456f11df0b53897086257b952457d615b3942539 static/scripts/viz/trackster_ui.js
--- a/static/scripts/viz/trackster_ui.js
+++ b/static/scripts/viz/trackster_ui.js
@@ -5,29 +5,35 @@
/**
* Add bookmark.
*/
-var add_bookmark = function(position, annotation) {
- var
- bookmarks_container = $("#bookmarks-container"),
- new_bookmark = $("<div/>").addClass("bookmark").appendTo(bookmarks_container),
- delete_icon_container = $("<div/>").addClass("delete-icon-container").appendTo(new_bookmark).click(function (){
- // Remove bookmark.
- new_bookmark.slideUp("fast");
- new_bookmark.remove();
- view.has_changes = true;
- return false;
- }),
- delete_icon = $("<a href=''/>").addClass("icon-button delete").appendTo(delete_icon_container),
- position_div = $("<div/>").addClass("position").appendTo(new_bookmark),
+var add_bookmark = function(position, annotation, editable) {
+ // Create HTML.
+ var bookmarks_container = $("#bookmarks-container"),
+ new_bookmark = $("<div/>").addClass("bookmark").appendTo(bookmarks_container);
+
+ var position_div = $("<div/>").addClass("position").appendTo(new_bookmark),
position_link = $("<a href=''/>").text(position).appendTo(position_div).click(function() {
view.go_to(position);
return false;
}),
- annotation_div = $("<div/>").text(annotation).make_text_editable({
+ annotation_div = $("<div/>").text(annotation).appendTo(new_bookmark);
+
+ // If editable, enable bookmark deletion and annotation editing.
+ if (editable) {
+ var delete_icon_container = $("<div/>").addClass("delete-icon-container").prependTo(new_bookmark).click(function (){
+ // Remove bookmark.
+ new_bookmark.slideUp("fast");
+ new_bookmark.remove();
+ view.has_changes = true;
+ return false;
+ }),
+ delete_icon = $("<a href=''/>").addClass("icon-button delete").appendTo(delete_icon_container);
+ annotation_div.make_text_editable({
num_rows: 3,
use_textarea: true,
- help_text: "Set bookmark note"
- }).addClass("annotation").appendTo(new_bookmark);
-
+ help_text: "Edit bookmark note"
+ }).addClass("annotation");
+ }
+
view.has_changes = true;
return new_bookmark;
};
@@ -67,7 +73,7 @@
/**
* Create a complete Trackster visualization. Returns view.
*/
-var create_visualization = function(view_config, viewport_config, drawables_config, bookmarks_config) {
+var create_visualization = function(view_config, viewport_config, drawables_config, bookmarks_config, editable) {
// Create view.
view = new View(view_config);
@@ -114,7 +120,7 @@
var bookmark;
for (var i = 0; i < bookmarks_config.length; i++) {
bookmark = bookmarks_config[i];
- add_bookmark(bookmark['position'], bookmark['annotation']);
+ add_bookmark(bookmark['position'], bookmark['annotation'], editable);
}
}
diff -r 6face40d68836de96bf92d46c0d6e6bf32cdb616 -r 456f11df0b53897086257b952457d615b3942539 static/scripts/viz/visualization.js
--- a/static/scripts/viz/visualization.js
+++ b/static/scripts/viz/visualization.js
@@ -526,17 +526,25 @@
/**
* A genome browser bookmark.
*/
-var BrowserBookmark = Backbone.Model.extend({
+var BrowserBookmark = Backbone.RelationalModel.extend({
defaults: {
region: null,
- note: ""
- }
+ note: ''
+ },
+
+ relations: [
+ {
+ type: Backbone.HasOne,
+ key: 'region',
+ relatedModel: 'GenomeRegion'
+ }
+ ]
});
/**
* Bookmarks collection.
*/
-var BrowserBookmarks = Backbone.Collection.extend({
+var BrowserBookmarkCollection = Backbone.Collection.extend({
model: BrowserBookmark
});
diff -r 6face40d68836de96bf92d46c0d6e6bf32cdb616 -r 456f11df0b53897086257b952457d615b3942539 templates/tracks/browser.mako
--- a/templates/tracks/browser.mako
+++ b/templates/tracks/browser.mako
@@ -178,7 +178,8 @@
},
JSON.parse('${ h.to_json_string( config.get( 'viewport', dict() ) ) }'),
JSON.parse('${ h.to_json_string( config['tracks'] ).replace("'", "\\'") }'),
- JSON.parse('${ h.to_json_string( config['bookmarks'] ) }')
+ JSON.parse('${ h.to_json_string( config['bookmarks'] ) }'),
+ true
);
init_editor();
set_up_router({view: view});
@@ -239,7 +240,7 @@
// Add new bookmark.
var position = view.chrom + ":" + view.low + "-" + view.high,
annotation = "Bookmark description";
- return add_bookmark(position, annotation);
+ return add_bookmark(position, annotation, true);
});
// make_popupmenu( $("#bookmarks-more-button"), {
diff -r 6face40d68836de96bf92d46c0d6e6bf32cdb616 -r 456f11df0b53897086257b952457d615b3942539 templates/visualization/display.mako
--- a/templates/visualization/display.mako
+++ b/templates/visualization/display.mako
@@ -3,6 +3,16 @@
<%def name="javascripts()"><% config = item_data %>
${parent.javascripts()}
+
+ <script type='text/javascript'>
+ $(function() {
+ // HACK: add bookmarks container and header.
+ $('#right > .unified-panel-body > div').append(
+ $('<div/>').attr('id', 'bookmarks-container')
+ .append( $('<h4/>').text('Bookmarks') )
+ );
+ });
+ </script><!--[if lt IE 9]><script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script>
@@ -12,30 +22,16 @@
<%def name="stylesheets()">
${parent.stylesheets()}
- ## For page:
+ ## Style changes needed for display.
<style type="text/css">
.page-body {
padding: 0px;
}
- </style>
-
- <style type="text/css">
- #browser-container {
- overflow: none;
+ #bookmarks-container {
+ padding-left: 10px;
}
- .nav-container {
- width: 100%;
- ## Overriding styles from trackster.css to push nav up into title bar
- height: 0;
- text-align: center;
- }
- .nav {
- ## Overriding styles from trackster.css to push nav up into title bar
- position: relative;
- display: inline-block;
- top: -2em;
- background: transparent;
- border: none;
+ .bookmark {
+ margin: 0em;
}
</style></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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