| %s.%s | ' % ( str( i+1 ), name ) ) - if dataset.metadata.columns - len( self.column_names ) > 0: - for i in range( len( self.column_names ), dataset.metadata.columns ): - out.append( '%s | ' % str( i+1 ) ) - out.append( '
|---|
| %s.Chrom | ' % i ) - elif i == dataset.metadata.startCol: - out.append( '%s.Start | ' % i ) - elif i == dataset.metadata.endCol: - out.append( '%s.End | ' % i ) - elif dataset.metadata.strandCol and i == dataset.metadata.strandCol: - out.append( '%s.Strand | ' % i ) - elif dataset.metadata.nameCol and i == dataset.metadata.nameCol: - out.append( '%s.Name | ' % i ) - else: - out.append( '%s | ' % i ) - out.append('
|---|
| %s.%s | ' % ( str( i+1 ), name ) ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '
|---|
| %s | ' % str( i ) ) - out.append( '
|---|
| %s.%s | ' % ( str( i+1 ), name ) ) - # This data type requires at least 24 columns in the data - if dataset.metadata.columns - len( self.column_names ) > 0: - for i in range( len( self.column_names ), dataset.metadata.columns ): - out.append( '%s | ' % str( i+1 ) ) - out.append( '
|---|
| %s.%s | ' % ( str( i+1 ), name ) ) - # This data type requires at least 11 columns in the data - if dataset.metadata.columns - len( self.column_names ) > 0: - for i in range( len( self.column_names ), dataset.metadata.columns ): - out.append( '%s | ' % str( i+1 ) ) - out.append( '
|---|
| %s.Chrom | ' % i ) - elif i == dataset.metadata.startCol: - out.append( '%s.Start | ' % i ) - elif i == dataset.metadata.baseCol: - out.append( '%s.Base | ' % i ) - else: - out.append( '%s | ' % i ) - out.append('
|---|
| %s.%s | ' % ( str( i+1 ), name ) ) - out.append( self.make_html_peek_rows( dataset, skipchars=skipchars ) ) - out.append( '
|---|
%s
' % tool_shed_repository.name
+ return tool_shed_repository.name
+ class DescriptionColumn( grids.TextColumn ):
+ def get_value( self, trans, grid, tool_shed_repository ):
+ return tool_shed_repository.description
+ class OwnerColumn( grids.TextColumn ):
+ def get_value( self, trans, grid, tool_shed_repository ):
+ return tool_shed_repository.owner
+ class RevisionColumn( grids.TextColumn ):
+ def get_value( self, trans, grid, tool_shed_repository ):
+ return tool_shed_repository.changeset_revision
+ class ToolShedColumn( grids.TextColumn ):
+ def get_value( self, trans, grid, tool_shed_repository ):
+ return tool_shed_repository.tool_shed
+ # Grid definition
+ title = "Installed tool shed repositories"
+ model_class = model.ToolShedRepository
+ template='/admin/tool_shed_repository/grid.mako'
+ default_sort_key = "name"
+ columns = [
+ NameColumn( "Name",
+ key="name",
+ link=( lambda item: dict( operation="manage_repository", id=item.id, webapp="galaxy" ) ),
+ attach_popup=True ),
+ DescriptionColumn( "Description" ),
+ OwnerColumn( "Owner" ),
+ RevisionColumn( "Revision" ),
+ ToolShedColumn( "Tool shed" ),
+ # Columns that are valid for filtering but are not visible.
+ grids.DeletedColumn( "Deleted",
+ key="deleted",
+ visible=False,
+ filterable="advanced" )
+ ]
+ columns.append( grids.MulticolFilterColumn( "Search repository name",
+ cols_to_filter=[ columns[0] ],
+ key="free-text-search",
+ visible=False,
+ filterable="standard" ) )
+ global_actions = [
+ grids.GridAction( "View tool id guid map", dict( controller='admin_toolshed', action='browse_tool_id_guid_map' ) )
+ ]
+ operations = [ grids.GridOperation( "Get updates",
+ allow_multiple=False,
+ condition=( lambda item: not item.deleted ),
+ async_compatible=False ) ]
+ standard_filters = []
+ default_filter = dict( deleted="False" )
+ num_rows_per_page = 50
+ preserve_state = False
+ use_paging = True
+ def build_initial_query( self, trans, **kwd ):
+ return trans.sa_session.query( self.model_class ) \
+ .filter( self.model_class.table.c.deleted == False )
+
+class AdminToolshed( AdminGalaxy ):
+
+ repository_list_grid = RepositoryListGrid()
+ tool_id_guid_map_grid = ToolIdGuidMapGrid()
+
+ @web.expose
+ @web.require_admin
+ def browse_tool_id_guid_map( self, trans, **kwd ):
+ return self.tool_id_guid_map_grid( trans, **kwd )
+ @web.expose
+ @web.require_admin
+ def browse_repository( self, trans, **kwd ):
+ params = util.Params( kwd )
+ message = util.restore_text( params.get( 'message', '' ) )
+ status = params.get( 'status', 'done' )
+ repository = get_repository( trans, kwd[ 'id' ] )
+ return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako',
+ repository=repository,
+ message=message,
+ status=status )
+ @web.expose
+ @web.require_admin
+ def browse_repositories( self, trans, **kwd ):
+ if 'operation' in kwd:
+ operation = kwd.pop( 'operation' ).lower()
+ if operation == "manage_repository":
+ return self.manage_repository( trans, **kwd )
+ if operation == "get updates":
+ return self.check_for_updates( trans, **kwd )
+ kwd[ 'message' ] = 'Names of repositories for which updates are available are highlighted in red.'
+ return self.repository_list_grid( trans, **kwd )
+ @web.expose
+ @web.require_admin
+ def browse_tool_sheds( self, trans, **kwd ):
+ params = util.Params( kwd )
+ message = util.restore_text( params.get( 'message', '' ) )
+ status = params.get( 'status', 'done' )
+ return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako',
+ webapp='galaxy',
+ message=message,
+ status='error' )
+ @web.expose
+ @web.require_admin
+ def find_tools_in_tool_shed( self, trans, **kwd ):
+ tool_shed_url = kwd[ 'tool_shed_url' ]
+ galaxy_url = url_for( '', qualified=True )
+ url = '%s/repository/find_tools?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
+ return trans.response.send_redirect( url )
+ @web.expose
+ @web.require_admin
+ def find_workflows_in_tool_shed( self, trans, **kwd ):
+ tool_shed_url = kwd[ 'tool_shed_url' ]
+ galaxy_url = url_for( '', qualified=True )
+ url = '%s/repository/find_workflows?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
+ return trans.response.send_redirect( url )
+ @web.expose
+ @web.require_admin
+ def browse_tool_shed( self, trans, **kwd ):
+ tool_shed_url = kwd[ 'tool_shed_url' ]
+ galaxy_url = url_for( '', qualified=True )
+ url = '%s/repository/browse_valid_repositories?galaxy_url=%s&webapp=galaxy' % ( tool_shed_url, galaxy_url )
+ return trans.response.send_redirect( url )
+ @web.expose
+ @web.require_admin
+ def install_repository( self, trans, **kwd ):
+ if not trans.app.toolbox.shed_tool_confs:
+ message = 'The tool_config_file setting in universe_wsgi.ini must include at least one shed tool configuration file name with a '
+ message += '<toolbox> tag that includes a tool_path 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 shed_tool_conf.xml whose '
+ message += '<toolbox> tag is <toolbox tool_path="../shed_tools">).See the '
+ message += ' 1:
+ shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans )
+ shed_tool_conf = None
+ else:
+ shed_tool_conf = trans.app.toolbox.shed_tool_confs.keys()[0].lstrip( './' )
+ shed_tool_conf_select_field = None
+ tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
+ return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako',
+ tool_shed_url=tool_shed_url,
+ repo_info_dict=repo_info_dict,
+ shed_tool_conf=shed_tool_conf,
+ includes_tools=includes_tools,
+ 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,
+ message=message,
+ status=status )
+ @web.expose
+ @web.require_admin
+ def manage_repository( self, trans, **kwd ):
+ params = util.Params( kwd )
+ message = util.restore_text( params.get( 'message', '' ) )
+ status = params.get( 'status', 'done' )
+ repository = get_repository( trans, kwd[ 'id' ] )
+ description = util.restore_text( params.get( 'description', repository.description ) )
+ tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository )
+ repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) )
+ if params.get( 'edit_repository_button', False ):
+ if description != repository.description:
+ repository.description = description
+ trans.sa_session.add( repository )
+ trans.sa_session.flush()
+ message = "The repository information has been updated."
+ elif params.get( 'set_metadata_button', False ):
+ repository_clone_url = self.__generate_clone_url( trans, repository )
+ metadata_dict = generate_metadata( trans.app.toolbox, relative_install_dir, repository_clone_url )
+ if metadata_dict:
+ repository.metadata = metadata_dict
+ trans.sa_session.add( repository )
+ trans.sa_session.flush()
+ message = "Repository metadata has been reset."
+ return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako',
+ repository=repository,
+ description=description,
+ repo_files_dir=repo_files_dir,
+ message=message,
+ status=status )
+ @web.expose
+ @web.require_admin
+ def check_for_updates( self, trans, **kwd ):
+ # Send a request to the relevant tool shed to see if there are any updates.
+ repository = get_repository( trans, kwd[ 'id' ] )
+ tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository )
+ url = '%s/repository/check_for_updates?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s&webapp=galaxy' % \
+ ( tool_shed_url, url_for( '', qualified=True ), repository.name, repository.owner, repository.changeset_revision )
+ return trans.response.send_redirect( url )
+ @web.expose
+ @web.require_admin
+ def update_to_changeset_revision( self, trans, **kwd ):
+ """Update a cloned repository to the latest revision possible."""
+ params = util.Params( kwd )
+ message = util.restore_text( params.get( 'message', '' ) )
+ status = params.get( 'status', 'done' )
+ tool_shed_url = kwd[ 'tool_shed_url' ]
+ name = params.get( 'name', None )
+ owner = params.get( 'owner', None )
+ changeset_revision = params.get( 'changeset_revision', None )
+ latest_changeset_revision = params.get( 'latest_changeset_revision', None )
+ repository = get_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed_url, name, owner, changeset_revision )
+ if changeset_revision and latest_changeset_revision:
+ if changeset_revision == latest_changeset_revision:
+ message = "The cloned tool shed repository named '%s' is current (there are no updates available)." % name
+ else:
+ current_working_dir = os.getcwd()
+ tool_path, relative_install_dir = self.__get_tool_path_and_relative_install_dir( trans, repository )
+ if relative_install_dir:
+ repo_files_dir = os.path.join( relative_install_dir, name )
+ returncode, tmp_name = pull_repository( current_working_dir, repo_files_dir, name )
+ if returncode == 0:
+ returncode, tmp_name = update_repository( current_working_dir, repo_files_dir, latest_changeset_revision )
+ if returncode == 0:
+ # Update the repository metadata.
+ repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name )
+ metadata_dict = load_repository_contents( app=trans.app,
+ name=name,
+ description=repository.description,
+ owner=owner,
+ changeset_revision=changeset_revision,
+ tool_path=tool_path,
+ repository_clone_url=repository_clone_url,
+ relative_install_dir=relative_install_dir,
+ current_working_dir=current_working_dir,
+ tmp_name=tmp_name,
+ tool_section=None,
+ shed_tool_conf=None,
+ new_install=False )
+ # Update the repository changeset_revision in the database.
+ repository.changeset_revision = latest_changeset_revision
+ repository.update_available = False
+ trans.sa_session.add( repository )
+ trans.sa_session.flush()
+ message = "The cloned repository named '%s' has been updated to change set revision '%s'." % \
+ ( name, latest_changeset_revision )
+ else:
+ tmp_stderr = open( tmp_name, 'rb' )
+ message = tmp_stderr.read()
+ tmp_stderr.close()
+ status = 'error'
+ else:
+ tmp_stderr = open( tmp_name, 'rb' )
+ message = tmp_stderr.read()
+ tmp_stderr.close()
+ status = 'error'
+ else:
+ message = "The directory containing the cloned repository named '%s' cannot be found." % name
+ status = 'error'
+ else:
+ message = "The latest changeset revision could not be retrieved for the repository named '%s'." % name
+ status = 'error'
+ return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
+ action='manage_repository',
+ id=trans.security.encode_id( repository.id ),
+ message=message,
+ status=status ) )
+ @web.expose
+ @web.require_admin
+ def view_tool_metadata( self, trans, repository_id, tool_id, **kwd ):
+ params = util.Params( kwd )
+ message = util.restore_text( params.get( 'message', '' ) )
+ status = params.get( 'status', 'done' )
+ webapp = params.get( 'webapp', 'community' )
+ repository = get_repository( trans, repository_id )
+ metadata = {}
+ tool = None
+ if 'tools' in repository.metadata:
+ for tool_metadata_dict in repository.metadata[ 'tools' ]:
+ if tool_metadata_dict[ 'id' ] == tool_id:
+ metadata = tool_metadata_dict
+ tool = trans.app.toolbox.load_tool( os.path.abspath( metadata[ 'tool_config' ] ) )
+ break
+ return trans.fill_template( "/admin/tool_shed_repository/view_tool_metadata.mako",
+ repository=repository,
+ tool=tool,
+ metadata=metadata,
+ message=message,
+ status=status )
+ def __get_tool_path_and_relative_install_dir( self, trans, repository ):
+ # Return both the tool_path configured in the relative shed_tool_conf and
+ # the relative path to the directory where the repository is installed.
+ tool_shed = clean_tool_shed_url( repository.tool_shed )
+ partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.installed_changeset_revision )
+ # Get the relative tool installation paths from each of the shed tool configs.
+ shed_tool_confs = trans.app.toolbox.shed_tool_confs
+ relative_install_dir = None
+ # The shed_tool_confs dictionary contains { shed_conf_filename : tool_path } pairs.
+ for shed_conf_filename, tool_path in shed_tool_confs.items():
+ relative_install_dir = os.path.join( tool_path, partial_install_dir )
+ if os.path.isdir( relative_install_dir ):
+ break
+ return tool_path, relative_install_dir
+ def __generate_tool_path( self, repository_clone_url, changeset_revision ):
+ """
+ Generate a tool path that guarantees repositories with the same name will always be installed
+ in different directories. The tool path will be of the form:
+ Welcome to Galaxy
-- This installation of Galaxy has been configured such that only users who are logged in may use it.%s + This %s has been configured such that only users who are logged in may use it.%s
""" -require_login_nocreation_template = require_login_template % "" -require_login_creation_template = require_login_template % " If you don't already have an account, you may create one." OPENID_PROVIDERS = { 'Google' : 'https://www.google.com/accounts/o8/id', 'Yahoo!' : 'http://yahoo.com', @@ -368,9 +364,17 @@ class User( BaseUIController, UsesFormDefinitions ): redirect_url = url_for( '/' ) if not user and trans.app.config.require_login: if trans.app.config.allow_user_creation: - header = require_login_creation_template % web.url_for( action='create', cntrller='user' ) + create_account_str = " If you don't already have an account, you may create one." % \ + web.url_for( action='create', cntrller='user', webapp=webapp ) + if webapp == 'galaxy': + header = require_login_template % ( "Galaxy instance", create_account_str ) + else: + header = require_login_template % ( "Galaxy tool shed", create_account_str ) else: - header = require_login_nocreation_template + if webapp == 'galaxy': + header = require_login_template % ( "Galaxy instance", "" ) + else: + header = require_login_template % ( "Galaxy tool shed", "" ) return trans.fill_template( '/user/login.mako', webapp=webapp, email=email, @@ -405,11 +409,12 @@ class User( BaseUIController, UsesFormDefinitions ): status = 'error' else: trans.handle_user_login( user, webapp ) - trans.log_event( "User logged in" ) - message = 'You are now logged in as %s.You can go back to the page you were visiting or go to the home page.' % \ - ( user.email, referer, url_for( '/' ) ) - if trans.app.config.require_login: - message += ' Click here to continue to the home page.' % web.url_for( '/static/welcome.html' ) + if webapp == 'galaxy': + trans.log_event( "User logged in" ) + message = 'You are now logged in as %s.
You can go back to the page you were visiting or go to the home page.' % \ + ( user.email, referer, url_for( '/' ) ) + if trans.app.config.require_login: + message += ' Click here to continue to the home page.' % web.url_for( '/static/welcome.html' ) success = True return ( message, status, user, success ) @web.expose @@ -419,10 +424,10 @@ class User( BaseUIController, UsesFormDefinitions ): refresh_frames = [ 'masthead', 'history', 'tools' ] else: refresh_frames = [ 'masthead', 'history' ] + # Since logging an event requires a session, we'll log prior to ending the session + trans.log_event( "User logged out" ) else: refresh_frames = [ 'masthead' ] - # Since logging an event requires a session, we'll log prior to ending the session - trans.log_event( "User logged out" ) trans.handle_user_logout( logout_all=logout_all ) message = 'You have been logged out.
You can log in again, go back to the page you were visiting or go to the home page.' % \ ( trans.request.referer, url_for( '/' ) ) @@ -471,10 +476,8 @@ class User( BaseUIController, UsesFormDefinitions ): cntrller, subscribe_checked, **kwd ) - if success and not is_admin and webapp != 'galaxy': - # Must be logging into the community space webapp - trans.handle_user_login( user, webapp ) - redirect_url = referer + if webapp == 'community': + redirect_url = url_for( '/' ) if success and not is_admin: # The handle_user_login() method has a call to the history_set_default_permissions() method # (needed when logging in with a history), user needs to have default permissions set before logging in @@ -753,7 +756,7 @@ class User( BaseUIController, UsesFormDefinitions ): password = kwd.get( 'password', '' ) confirm = kwd.get( 'confirm', '' ) ok = True - if not webapp == 'galaxy' and not is_admin: + if not is_admin: # If the current user is changing their own password, validate their current password current = kwd.get( 'current', '' ) if not trans.user.check_password( current ): @@ -768,10 +771,17 @@ class User( BaseUIController, UsesFormDefinitions ): else: # Save new password user.set_password_cleartext( password ) + # Invalidate all other sessions + for other_galaxy_session in trans.sa_session.query( trans.app.model.GalaxySession ) \ + .filter( and_( trans.app.model.GalaxySession.table.c.user_id==trans.user.id, + trans.app.model.GalaxySession.table.c.is_valid==True, + trans.app.model.GalaxySession.table.c.id!=trans.galaxy_session.id ) ): + other_galaxy_session.is_valid = False + trans.sa_session.add( other_galaxy_session ) trans.sa_session.add( user ) trans.sa_session.flush() trans.log_event( "User change password" ) - message = 'The password has been changed.' + message = 'The password has been changed and any other existing Galaxy sessions have been logged out (but jobs in histories in those sessions will not be interrupted).' elif user and params.get( 'edit_user_info_button', False ): # Edit user information - webapp MUST BE 'galaxy' user_type_fd_id = params.get( 'user_type_fd_id', 'none' ) @@ -1188,14 +1198,57 @@ class User( BaseUIController, UsesFormDefinitions ): # Add new custom build. name = kwds.get('name', '') key = kwds.get('key', '') - dataset_id = kwds.get('dataset_id', '') - if not name or not key or not dataset_id: + + # Look for build's chrom info in len_file and len_text. + len_file = kwds.get( 'len_file', None ) + if getattr( len_file, "file", None ): # Check if it's a FieldStorage object + len_text = len_file.file.read() + else: + len_text = kwds.get( 'len_text', None ) + + if not len_text: + # Using FASTA from history. + dataset_id = kwds.get('dataset_id', '') + + if not name or not key or not ( len_text or dataset_id ): message = "You must specify values for all the fields." elif key in dbkeys: message = "There is already a custom build with that key. Delete it first if you want to replace it." else: - dataset_id = trans.security.decode_id( dataset_id ) - dbkeys[key] = { "name": name, "fasta": dataset_id } + # Have everything needed; create new build. + build_dict = { "name": name } + if len_text: + # Create new len file + new_len = trans.app.model.HistoryDatasetAssociation( extension="len", create_dataset=True, sa_session=trans.sa_session ) + trans.sa_session.add( new_len ) + new_len.name = name + new_len.visible = False + new_len.state = trans.app.model.Job.states.OK + new_len.info = "custom build .len file" + trans.sa_session.flush() + counter = 0 + f = open(new_len.file_name, "w") + # LEN files have format: + #
Message: %s" % ( url, str( e ) ) ) - else: - workflow_data = workflow_text - # Convert incoming workflow data from json - try: - data = simplejson.loads( workflow_data ) - except Exception, e: - return trans.show_error_message( "Data at '%s' does not appear to be a Galaxy workflow
Message: %s" % ( url, str( e ) ) ) - - # Create workflow. - workflow = self._workflow_from_dict( trans, data, source="uploaded file" ).latest_workflow - - # Provide user feedback and show workflow list. - if workflow.has_errors: - trans.set_message( "Imported, but some steps in this workflow have validation errors", - type="warning" ) - if workflow.has_cycles: - trans.set_message( "Imported, but this workflow contains cycles", - type="warning" ) - else: - trans.set_message( "Workflow '%s' imported" % workflow.name ) - return self.list( trans ) - + def import_workflow( self, trans, **kwd ): + """ + Import a workflow by reading an url, uploading a file, opening and reading the contents + of a local file, or receiving the textual representation of a workflow via http. + """ + url = kwd.get( 'url', '' ) + workflow_text = kwd.get( 'workflow_text', '' ) + webapp = kwd.get( 'webapp', 'galaxy' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + import_button = kwd.get( 'import_button', False ) + # The following parameters will have values only if the workflow + # id being imported from a Galaxy tool shed repository. + tool_shed_url = kwd.get( 'tool_shed_url', '' ) + repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) + # The workflow_name parameter is in the request only if the import originated + # from a Galaxy tool shed, in which case the value was encoded. + workflow_name = kwd.get( 'workflow_name', '' ) + if workflow_name: + workflow_name = tool_shed_decode( workflow_name ) + # The following parameters will have a value only if the import originated + # from a tool shed repository installed locally. + installed_repository_file = kwd.get( 'installed_repository_file', '' ) + repository_id = kwd.get( 'repository_id', '' ) + if installed_repository_file and not import_button: + workflow_file = open( installed_repository_file, 'rb' ) + workflow_text = workflow_file.read() + workflow_file.close() + import_button = True + if tool_shed_url and not import_button: + # Use urllib (send another request to the tool shed) to retrieve the workflow. + workflow_url = '%s/workflow/import_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&open_for_url=true' % \ + ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp ) + response = urllib2.urlopen( workflow_url ) + workflow_text = response.read() + response.close() + import_button = True + if import_button: + workflow_data = None + if url: + # Load workflow from external URL + # NOTE: blocks the web thread. + try: + workflow_data = urllib2.urlopen( url ).read() + except Exception, e: + message = "Failed to open URL: %s
Exception: %s" % ( url, str( e ) ) + status = 'error' + elif workflow_text: + # This case occurs when the workflow_text was sent via http from the tool shed. + workflow_data = workflow_text + else: + # Load workflow from browsed file. + file_data = kwd.get( 'file_data', '' ) + if file_data in ( '', None ): + message = 'No exported Galaxy workflow files were selected.' + status = 'error' + else: + uploaded_file = file_data.file + uploaded_file_name = uploaded_file.name + uploaded_file_filename = file_data.filename + if os.path.getsize( os.path.abspath( uploaded_file_name ) ) > 0: + # We're reading the file as text so we can re-use the existing code below. + # This may not be ideal... + workflow_data = uploaded_file.read() + else: + message= 'You attempted to upload an empty file.' + status = 'error' + if workflow_data: + # Convert incoming workflow data from json + try: + data = simplejson.loads( workflow_data ) + except Exception, e: + data = None + message = "The data content does not appear to be a Galaxy workflow.
Exception: %s" % str( e ) + status = 'error' + if data: + # Create workflow if possible. If a required tool is not available in the local + # Galaxy instance, the tool information will be available in the step_dict. + workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="uploaded file" ) + workflow = workflow.latest_workflow + # Provide user feedback and show workflow list. + if workflow.has_errors: + message += "Imported, but some steps in this workflow have validation errors. " + status = "error" + if workflow.has_cycles: + message += "Imported, but this workflow contains cycles. " + status = "error" + else: + message += "Workflow %s imported successfully. " % workflow.name + if missing_tool_tups: + if trans.user_is_admin(): + # A required tool is not available in the local Galaxy instance. + # TODO: It would sure be nice to be able to redirect to a mako template here that displays a nice + # page including the links to the configured tool sheds instead of this message, but trying + # to get the panels back is a nightmare since workflow eliminates the Galaxy panels. Someone + # involved in workflow development needs to figure out what it will take to be able to switch + # back and forth between Galaxy (with panels ) and the workflow view (without panels ), having + # the Galaxy panels displayed whenever in Galaxy. + message += "The workflow requires the following tools that are not available in this Galaxy instance." + message += "You can likely install the required tools from one of the Galaxy tool sheds listed below.
" + for shed_name, shed_url in trans.app.tool_shed_registry.tool_sheds.items(): + if shed_url.endswith( '/' ): + shed_url = shed_url.rstrip( '/' ) + url = '%s/repository/find_tools?galaxy_url=%s&webapp=%s' % ( shed_url, url_for( '', qualified=True ), webapp ) + if missing_tool_tups: + url += '&tool_id=' + for missing_tool_tup in missing_tool_tups: + missing_tool_id = missing_tool_tup[0] + url += '%s,' % missing_tool_id + message += '%s
' % ( url, shed_name ) + status = 'error' + if installed_repository_file or tool_shed_url: + # Another Galaxy panels Hack: The request did not originate from the Galaxy + # workflow view, so we don't need to render the Galaxy panels. + action = 'center' + else: + # Another Galaxy panels hack: The request originated from the Galaxy + # workflow view, so we need to render the Galaxy panels. + action = 'index' + return trans.response.send_redirect( web.url_for( controller='admin', + action=action, + webapp='galaxy', + message=message, + status=status ) ) + else: + # TODO: Figure out what to do here... + pass + if tool_shed_url: + # We've received the textual representation of a workflow from a Galaxy tool shed. + message = "Workflow %s imported successfully." % workflow.name + url = '%s/workflow/view_workflow?repository_metadata_id=%s&workflow_name=%s&webapp=%s&message=%s' % \ + ( tool_shed_url, repository_metadata_id, tool_shed_encode( workflow_name ), webapp, message ) + return trans.response.send_redirect( url ) + elif installed_repository_file: + # The workflow was read from a file included with an installed tool shed repository. + message = "Workflow %s imported successfully." % workflow.name + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='browse_repository', + id=repository_id, + message=message, + status=status ) ) + return self.list( trans ) + return trans.fill_template( "workflow/import.mako", + url=url, + message=message, + status=status, + use_panels=True ) @web.json def get_datatypes( self, trans ): ext_to_class_name = dict() @@ -1201,7 +1306,16 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn for job_id in job_ids: assert job_id in jobs_by_id, "Attempt to create workflow with job not connected to current history" job = jobs_by_id[ job_id ] - tool = trans.app.toolbox.tools_by_id[ job.tool_id ] + try: + tool = trans.app.toolbox.tools_by_id[ job.tool_id ] + except KeyError, e: + # Handle the case where the workflow requires a tool not available in the local Galaxy instance. + # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id + # attribute should contain what we're looking for. + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if job.tool_id == available_tool.old_id: + tool = available_tool + break param_values = job.get_param_values( trans.app ) associations = cleanup_param_values( tool.inputs, param_values ) # Doing it this way breaks dynamic parameters, backed out temporarily. @@ -1258,7 +1372,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn ## % ( workflow_name, web.url_for( action='editor', id=trans.security.encode_id(stored.id) ) ) ) @web.expose - def run( self, trans, id, **kwargs ): + def run( self, trans, id, history_id=None, hide_fixed_params=False, **kwargs ): stored = self.get_stored_workflow( trans, id, check_ownership=False ) user = trans.get_user() if stored.user != user: @@ -1279,164 +1393,196 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn errors = {} has_upgrade_messages = False has_errors = False - if kwargs: - # If kwargs were provided, the states for each step should have - # been POSTed - # Get the kwarg keys for data inputs - input_keys = filter(lambda a: a.endswith('|input'), kwargs) - # Example: prefixed='2|input' - # Check if one of them is a list - multiple_input_key = None - multiple_inputs = [None] - for input_key in input_keys: - if isinstance(kwargs[input_key], list): - multiple_input_key = input_key - multiple_inputs = kwargs[input_key] - # List to gather values for the template - invocations=[] - for input_number, single_input in enumerate(multiple_inputs): - # Example: single_input='1', single_input='2', etc... - # 'Fix' the kwargs, to have only the input for this iteration - if multiple_input_key: - kwargs[multiple_input_key] = single_input + saved_history = None + if history_id is not None: + saved_history = trans.get_history(); + try: + decoded_history_id = trans.security.decode_id( history_id ) + history = trans.sa_session.query(trans.app.model.History).get(decoded_history_id) + if history.user != trans.user and not trans.user_is_admin(): + if trans.sa_session.query(trans.app.model.HistoryUserShareAssociation).filter_by(user=trans.user, history=history).count() == 0: + error("History is not owned by or shared with current user") + trans.set_history(history) + except TypeError: + error("Malformed history id ( %s ) specified, unable to decode." % str( history_id )) + except: + error("That history does not exist.") + try: # use a try/finally block to restore the user's current history + if kwargs: + # If kwargs were provided, the states for each step should have + # been POSTed + # Get the kwarg keys for data inputs + input_keys = filter(lambda a: a.endswith('|input'), kwargs) + # Example: prefixed='2|input' + # Check if one of them is a list + multiple_input_key = None + multiple_inputs = [None] + for input_key in input_keys: + if isinstance(kwargs[input_key], list): + multiple_input_key = input_key + multiple_inputs = kwargs[input_key] + # List to gather values for the template + invocations=[] + for input_number, single_input in enumerate(multiple_inputs): + # Example: single_input='1', single_input='2', etc... + # 'Fix' the kwargs, to have only the input for this iteration + if multiple_input_key: + kwargs[multiple_input_key] = single_input + for step in workflow.steps: + step.upgrade_messages = {} + # Connections by input name + step.input_connections_by_name = \ + dict( ( conn.input_name, conn ) for conn in step.input_connections ) + # Extract just the arguments for this step by prefix + p = "%s|" % step.id + l = len(p) + step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) ) + step_errors = None + if step.type == 'tool' or step.type is None: + module = module_factory.from_workflow_step( trans, step ) + # Fix any missing parameters + step.upgrade_messages = module.check_and_update_state() + if step.upgrade_messages: + has_upgrade_messages = True + # Any connected input needs to have value DummyDataset (these + # are not persisted so we need to do it every time) + module.add_dummy_datasets( connections=step.input_connections ) + # Get the tool + tool = module.tool + # Get the state + step.state = state = module.state + # Get old errors + old_errors = state.inputs.pop( "__errors__", {} ) + # Update the state + step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args, + update_only=True, old_errors=old_errors ) + else: + # Fix this for multiple inputs + module = step.module = module_factory.from_workflow_step( trans, step ) + state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) ) + step_errors = module.update_runtime_state( trans, state, step_args ) + if step_errors: + errors[step.id] = state.inputs["__errors__"] = step_errors + if 'run_workflow' in kwargs and not errors: + new_history = None + if 'new_history' in kwargs: + if 'new_history_name' in kwargs and kwargs['new_history_name'] != '': + nh_name = kwargs['new_history_name'] + else: + nh_name = "History from %s workflow" % workflow.name + if multiple_input_key: + nh_name = '%s %d' % (nh_name, input_number + 1) + new_history = trans.app.model.History( user=trans.user, name=nh_name ) + trans.sa_session.add( new_history ) + # Run each step, connecting outputs to inputs + workflow_invocation = model.WorkflowInvocation() + workflow_invocation.workflow = workflow + outputs = odict() + for i, step in enumerate( workflow.steps ): + # Execute module + job = None + if step.type == 'tool' or step.type is None: + try: + tool = trans.app.toolbox.tools_by_id[ step.tool_id ] + except KeyError, e: + # Handle the case where the workflow requires a tool not available in the local Galaxy instance. + # The id value of tools installed from a Galaxy tool shed is a guid, but these tool's old_id + # attribute should contain what we're looking for. + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if step.tool_id == available_tool.old_id: + tool = available_tool + break + input_values = step.state.inputs + # Connect up + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, DataToolParameter ): + if prefixed_name in step.input_connections_by_name: + conn = step.input_connections_by_name[ prefixed_name ] + return outputs[ conn.output_step.id ][ conn.output_name ] + visit_input_values( tool.inputs, step.state.inputs, callback ) + # Execute it + job, out_data = tool.execute( trans, step.state.inputs, history=new_history) + outputs[ step.id ] = out_data + # Create new PJA associations with the created job, to be run on completion. + # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) + # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. + replacement_dict = {} + for k, v in kwargs.iteritems(): + if k.startswith('wf_parm|'): + replacement_dict[k[8:]] = v + for pja in step.post_job_actions: + if pja.action_type in ActionBox.immediate_actions: + ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict) + else: + job.add_post_job_action(pja) + else: + job, out_data = step.module.execute( trans, step.state ) + outputs[ step.id ] = out_data + # Record invocation + workflow_invocation_step = model.WorkflowInvocationStep() + workflow_invocation_step.workflow_invocation = workflow_invocation + workflow_invocation_step.workflow_step = step + workflow_invocation_step.job = job + # All jobs ran sucessfully, so we can save now + trans.sa_session.add( workflow_invocation ) + invocations.append({'outputs': outputs, + 'new_history': new_history}) + trans.sa_session.flush() + if invocations: + return trans.fill_template( "workflow/run_complete.mako", + workflow=stored, + invocations=invocations ) + else: + # Prepare each step + missing_tools = [] for step in workflow.steps: step.upgrade_messages = {} - # Connections by input name - step.input_connections_by_name = \ - dict( ( conn.input_name, conn ) for conn in step.input_connections ) - # Extract just the arguments for this step by prefix - p = "%s|" % step.id - l = len(p) - step_args = dict( ( k[l:], v ) for ( k, v ) in kwargs.iteritems() if k.startswith( p ) ) - step_errors = None + # Contruct modules if step.type == 'tool' or step.type is None: - module = module_factory.from_workflow_step( trans, step ) - # Fix any missing parameters - step.upgrade_messages = module.check_and_update_state() + # Restore the tool state for the step + step.module = module_factory.from_workflow_step( trans, step ) + if not step.module: + if step.tool_id not in missing_tools: + missing_tools.append(step.tool_id) + continue + step.upgrade_messages = step.module.check_and_update_state() if step.upgrade_messages: has_upgrade_messages = True # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) - module.add_dummy_datasets( connections=step.input_connections ) - # Get the tool - tool = module.tool - # Get the state - step.state = state = module.state - # Get old errors - old_errors = state.inputs.pop( "__errors__", {} ) - # Update the state - step_errors = tool.update_state( trans, tool.inputs, step.state.inputs, step_args, - update_only=True, old_errors=old_errors ) + step.module.add_dummy_datasets( connections=step.input_connections ) + # Store state with the step + step.state = step.module.state + # Error dict + if step.tool_errors: + has_errors = True + errors[step.id] = step.tool_errors else: - # Fix this for multiple inputs - module = step.module = module_factory.from_workflow_step( trans, step ) - state = step.state = module.decode_runtime_state( trans, step_args.pop( "tool_state" ) ) - step_errors = module.update_runtime_state( trans, state, step_args ) - if step_errors: - errors[step.id] = state.inputs["__errors__"] = step_errors - if 'run_workflow' in kwargs and not errors: - new_history = None - if 'new_history' in kwargs: - if 'new_history_name' in kwargs and kwargs['new_history_name'] != '': - nh_name = kwargs['new_history_name'] - else: - nh_name = "History from %s workflow" % workflow.name - if multiple_input_key: - nh_name = '%s %d' % (nh_name, input_number + 1) - new_history = trans.app.model.History( user=trans.user, name=nh_name ) - trans.sa_session.add( new_history ) - # Run each step, connecting outputs to inputs - workflow_invocation = model.WorkflowInvocation() - workflow_invocation.workflow = workflow - outputs = odict() - for i, step in enumerate( workflow.steps ): - # Execute module - job = None - if step.type == 'tool' or step.type is None: - tool = trans.app.toolbox.tools_by_id[ step.tool_id ] - input_values = step.state.inputs - # Connect up - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, DataToolParameter ): - if prefixed_name in step.input_connections_by_name: - conn = step.input_connections_by_name[ prefixed_name ] - return outputs[ conn.output_step.id ][ conn.output_name ] - visit_input_values( tool.inputs, step.state.inputs, callback ) - # Execute it - job, out_data = tool.execute( trans, step.state.inputs, history=new_history) - outputs[ step.id ] = out_data - # Create new PJA associations with the created job, to be run on completion. - # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now) - # Pass along replacement dict with the execution of the PJA so we don't have to modify the object. - replacement_dict = {} - for k, v in kwargs.iteritems(): - if k.startswith('wf_parm|'): - replacement_dict[k[8:]] = v - for pja in step.post_job_actions: - if pja.action_type in ActionBox.immediate_actions: - ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict) - else: - job.add_post_job_action(pja) - else: - job, out_data = step.module.execute( trans, step.state ) - outputs[ step.id ] = out_data - # Record invocation - workflow_invocation_step = model.WorkflowInvocationStep() - workflow_invocation_step.workflow_invocation = workflow_invocation - workflow_invocation_step.workflow_step = step - workflow_invocation_step.job = job - # All jobs ran sucessfully, so we can save now - trans.sa_session.add( workflow_invocation ) - invocations.append({'outputs': outputs, - 'new_history': new_history}) - trans.sa_session.flush() - return trans.fill_template( "workflow/run_complete.mako", - workflow=stored, - invocations=invocations ) - else: - # Prepare each step - missing_tools = [] - for step in workflow.steps: - step.upgrade_messages = {} - # Contruct modules - if step.type == 'tool' or step.type is None: - # Restore the tool state for the step - step.module = module_factory.from_workflow_step( trans, step ) - if not step.module: - if step.tool_id not in missing_tools: - missing_tools.append(step.tool_id) - continue - step.upgrade_messages = step.module.check_and_update_state() - if step.upgrade_messages: - has_upgrade_messages = True - # Any connected input needs to have value DummyDataset (these - # are not persisted so we need to do it every time) - step.module.add_dummy_datasets( connections=step.input_connections ) - # Store state with the step - step.state = step.module.state - # Error dict - if step.tool_errors: - has_errors = True - errors[step.id] = step.tool_errors - else: - ## Non-tool specific stuff? - step.module = module_factory.from_workflow_step( trans, step ) - step.state = step.module.get_runtime_state() - # Connections by input name - step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) - if missing_tools: - stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) - return trans.fill_template("workflow/run.mako", steps=[], workflow=stored, missing_tools = missing_tools) - # Render the form - stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) - return trans.fill_template( - "workflow/run.mako", - steps=workflow.steps, - workflow=stored, - has_upgrade_messages=has_upgrade_messages, - errors=errors, - incoming=kwargs ) - + ## Non-tool specific stuff? + step.module = module_factory.from_workflow_step( trans, step ) + step.state = step.module.get_runtime_state() + # Connections by input name + step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) + if missing_tools: + stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) + return trans.fill_template("workflow/run.mako", steps=[], workflow=stored, missing_tools = missing_tools) + # Render the form + stored.annotation = self.get_item_annotation_str( trans.sa_session, trans.user, stored ) + return trans.fill_template( + "workflow/run.mako", + steps=workflow.steps, + workflow=stored, + has_upgrade_messages=has_upgrade_messages, + errors=errors, + incoming=kwargs, + history_id=history_id, + hide_fixed_params=hide_fixed_params, + enable_unique_defaults=trans.app.config.enable_unique_workflow_defaults) + finally: + # restore the active history + if saved_history is not None: + trans.set_history(saved_history) + def get_item( self, trans, id ): return self.get_stored_workflow( trans, id ) @@ -1583,8 +1729,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn step_annotation = self.get_item_annotation_obj(trans.sa_session, trans.user, step ) annotation_str = "" if step_annotation: - annotation_str = step_annotation.annotation - + annotation_str = step_annotation.annotation # Step info step_dict = { 'id': step.order_index, @@ -1598,7 +1743,6 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn ## 'data_outputs': module.get_data_outputs(), 'annotation' : annotation_str } - # Add post-job actions to step dict. if module.type == 'tool': pja_dict = {} @@ -1607,7 +1751,6 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn output_name = pja.output_name, action_arguments = pja.action_arguments ) step_dict[ 'post_job_actions' ] = pja_dict - # Data inputs step_dict['inputs'] = [] if module.type == "data_input": @@ -1625,7 +1768,6 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn for partname, partval in val.items(): if type( partval ) == RuntimeValue: step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) - # User outputs step_dict['user_outputs'] = [] """ @@ -1646,7 +1788,6 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn if type( module ) is ToolModule: for output in module.get_data_outputs(): step_dict['outputs'].append( { 'name' : output['name'], 'type' : output['extensions'][0] } ) - # Connections input_connections = step.input_connections if step.type is None or step.type == 'tool': @@ -1670,7 +1811,6 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn # Add to return value data['steps'][step.order_index] = step_dict return data - def _workflow_from_dict( self, trans, data, source=None ): """ Creates a workflow from a dict. Created workflow is stored in the database and returned. @@ -1692,8 +1832,12 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn # The editor will provide ids for each step that we don't need to save, # but do need to use to make connections steps_by_external_id = {} + # Keep track of tools required by the workflow that are not available in + # the local Galaxy instance. Each tuple in the list of missing_tool_tups + # will be ( tool_id, tool_name, tool_version ). + missing_tool_tups = [] # First pass to build step objects and populate basic values - for key, step_dict in data['steps'].iteritems(): + for key, step_dict in data[ 'steps' ].iteritems(): # Create the model class for the step step = model.WorkflowStep() steps.append( step ) @@ -1701,6 +1845,11 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn # FIXME: Position should be handled inside module step.position = step_dict['position'] module = module_factory.from_dict( trans, step_dict, secure=False ) + if module.type == 'tool' and module.tool is None: + # A required tool is not available in the local Galaxy instance. + missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) + if missing_tool_tup not in missing_tool_tups: + missing_tool_tups.append( missing_tool_tup ) module.save_to_step( step ) if step.tool_errors: workflow.has_errors = True @@ -1739,7 +1888,7 @@ class WorkflowController( BaseUIController, Sharable, UsesStoredWorkflow, UsesAn # Persist trans.sa_session.add( stored ) trans.sa_session.flush() - return stored + return stored, missing_tool_tups ## ---- Utility methods ------------------------------------------------------- diff --git a/lib/galaxy/web/framework/__init__.py b/lib/galaxy/web/framework/__init__.py index fbc1283264d..ed8e9ba4359 100644 --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -404,28 +404,41 @@ class GalaxyWebTransaction( base.DefaultWebTransaction ): # If the old session was invalid, get a new history with our new session if invalidate_existing_session: self.new_history() - def _ensure_logged_in_user( self, environ ): - allowed_paths = ( - url_for( controller='root', action='index' ), - url_for( controller='root', action='tool_menu' ), - url_for( controller='root', action='masthead' ), - url_for( controller='root', action='history' ), - url_for( controller='user', action='login' ), - url_for( controller='user', action='create' ), - url_for( controller='user', action='reset_password' ), - url_for( controller='library', action='browse' ) - ) - display_as = url_for( controller='root', action='display_as' ) - if self.galaxy_session.user is None: - if self.app.config.ucsc_display_sites and self.request.path == display_as: - try: - host = socket.gethostbyaddr( self.environ[ 'REMOTE_ADDR' ] )[0] - except( socket.error, socket.herror, socket.gaierror, socket.timeout ): - host = None - if host in UCSC_SERVERS: - return - if self.request.path not in allowed_paths: - self.response.send_redirect( url_for( controller='root', action='index' ) ) + def _ensure_logged_in_user( self, environ, session_cookie ): + # The value of session_cookie can be one of + # 'galaxysession' or 'galaxycommunitysession' + # Currently this method does nothing unless session_cookie is 'galaxysession' + if session_cookie == 'galaxysession': + # TODO: re-engineer to eliminate the use of allowed_paths + # as maintenance overhead is far too high. + allowed_paths = ( + url_for( controller='root', action='index' ), + url_for( controller='root', action='tool_menu' ), + url_for( controller='root', action='masthead' ), + url_for( controller='root', action='history' ), + url_for( controller='user', action='api_keys' ), + url_for( controller='user', action='create' ), + url_for( controller='user', action='index' ), + url_for( controller='user', action='login' ), + url_for( controller='user', action='logout' ), + url_for( controller='user', action='manage_user_info' ), + url_for( controller='user', action='set_default_permissions' ), + url_for( controller='user', action='reset_password' ), + url_for( controller='library', action='browse' ), + url_for( controller='history', action='list' ), + url_for( controller='dataset', action='list' ) + ) + display_as = url_for( controller='root', action='display_as' ) + if self.galaxy_session.user is None: + if self.app.config.ucsc_display_sites and self.request.path == display_as: + try: + host = socket.gethostbyaddr( self.environ[ 'REMOTE_ADDR' ] )[0] + except( socket.error, socket.herror, socket.gaierror, socket.timeout ): + host = None + if host in UCSC_SERVERS: + return + if self.request.path not in allowed_paths: + self.response.send_redirect( url_for( controller='root', action='index' ) ) def __create_new_session( self, prev_galaxy_session=None, user_for_new_session=None ): """ Create a new GalaxySession for this request, possibly with a connection @@ -857,7 +870,7 @@ class GalaxyWebUITransaction( GalaxyWebTransaction ): if self.app.config.use_remote_user and self.galaxy_session.user.deleted: self.response.send_redirect( url_for( '/static/user_disabled.html' ) ) if self.app.config.require_login: - self._ensure_logged_in_user( environ ) + self._ensure_logged_in_user( environ, session_cookie ) def get_user( self ): """Return the current user if logged in or None.""" return self.galaxy_session.user diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py index 7937406d224..02441e0cbfe 100644 --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -6,9 +6,12 @@ from webhelpers import * from galaxy.util.json import to_json_string from galaxy.util import hash_util from datetime import datetime, timedelta +import time from cgi import escape +server_starttime = int(time.time()) + # If the date is more than one week ago, then display the actual date instead of in words def time_ago( x ): delta = timedelta(weeks=1) @@ -38,20 +41,18 @@ def css( *args ): Take a list of stylesheet names (no extension) and return appropriate string of link tags. - TODO: This has a hardcoded "?v=X" to defeat caching. This should be done - in a better way. + Cache-bust with time that server started running on """ - return "\n".join( [ stylesheet_link_tag( "/static/style/" + name + ".css?v=3" ) for name in args ] ) + return "\n".join( [ stylesheet_link_tag( "/static/style/" + name + ".css?v=%s" % server_starttime ) for name in args ] ) def js( *args ): """ Take a list of javascript names (no extension) and return appropriate string of script tags. - TODO: This has a hardcoded "?v=X" to defeat caching. This should be done - in a better way. + Cache-bust with time that server started running on """ - return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=8" ) for name in args ] ) + return "\n".join( [ javascript_include_tag( "/static/scripts/" + name + ".js?v=%s" % server_starttime ) for name in args ] ) # Hashes diff --git a/lib/galaxy/web/framework/middleware/static.py b/lib/galaxy/web/framework/middleware/static.py index 7fd9467c216..917c371cd7e 100644 --- a/lib/galaxy/web/framework/middleware/static.py +++ b/lib/galaxy/web/framework/middleware/static.py @@ -19,6 +19,12 @@ class CacheableStaticURLParser( StaticURLParser ): def __call__( self, environ, start_response ): path_info = environ.get('PATH_INFO', '') if not path_info: + #See if this is a static file hackishly mapped. + if os.path.exists(self.directory) and os.path.isfile(self.directory): + app = fileapp.FileApp(self.directory) + if self.cache_seconds: + app.cache_control( max_age = int( self.cache_seconds ) ) + return app(environ, start_response) return self.add_slash(environ, start_response) if path_info == '/': # @@: This should obviously be configurable @@ -45,6 +51,6 @@ class CacheableStaticURLParser( StaticURLParser ): if self.cache_seconds: app.cache_control( max_age = int( self.cache_seconds ) ) return app(environ, start_response) - + def make_static( global_conf, document_root, cache_seconds=None ): - return CacheableStaticURLParser( document_root, cache_seconds ) \ No newline at end of file + return CacheableStaticURLParser( document_root, cache_seconds ) diff --git a/lib/galaxy/webapps/community/app.py b/lib/galaxy/webapps/community/app.py index 3f622002751..f01576d8475 100644 --- a/lib/galaxy/webapps/community/app.py +++ b/lib/galaxy/webapps/community/app.py @@ -15,7 +15,9 @@ class UniverseApplication( object ): self.config.check() config.configure_logging( self.config ) # Set up datatypes registry - self.datatypes_registry = galaxy.datatypes.registry.Registry( self.config.root, self.config.datatypes_config ) + self.datatypes_registry = galaxy.datatypes.registry.Registry() + # TODO: Handle datatypes included in repositories - the following will only load datatypes_conf.xml. + self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) # Determine the database url if self.config.database_connection: db_url = self.config.database_connection @@ -35,6 +37,8 @@ class UniverseApplication( object ): self.tag_handler = CommunityTagHandler() # Tool data tables self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path ) + # The tool shed has no toolbox, but this attribute is still required. + self.toolbox = None # Load security policy self.security_agent = self.model.security_agent self.quota_agent = galaxy.quota.NoQuotaAgent( self.model ) diff --git a/lib/galaxy/webapps/community/config.py b/lib/galaxy/webapps/community/config.py index 574aad0cf2c..5a820a18502 100644 --- a/lib/galaxy/webapps/community/config.py +++ b/lib/galaxy/webapps/community/config.py @@ -41,6 +41,7 @@ class Configuration( object ): self.cookie_path = kwargs.get( "cookie_path", "/" ) # web API self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) ) + self.enable_quotas = string_as_bool( kwargs.get( 'enable_quotas', False ) ) self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) @@ -61,6 +62,7 @@ class Configuration( object ): self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) + self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/community" ), self.root ) diff --git a/lib/galaxy/webapps/community/controllers/admin.py b/lib/galaxy/webapps/community/controllers/admin.py index 040f596eaf1..0a7cc687ebb 100644 --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -332,13 +332,13 @@ class RepositoryMetadataListGrid( grids.Grid ): if 'tools' in metadata: metadata_str += 'Tools:
' for tool_metadata_dict in metadata[ 'tools' ]: - metadata_str += '%s %s
' % \ - ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) + metadata_str += '%s %s
' % ( tool_metadata_dict[ 'id' ], + tool_metadata_dict[ 'version' ] ) if 'workflows' in metadata: metadata_str += 'Workflows:
' for workflow_metadata_dict in metadata[ 'workflows' ]: - metadata_str += '%s %s
' % \ - ( workflow_metadata_dict[ 'name' ], workflow_metadata_dict[ 'format-version' ] ) + metadata_str += '%s %s
' % ( workflow_metadata_dict[ 'name' ], + workflow_metadata_dict[ 'format-version' ] ) return metadata_str class MaliciousColumn( grids.BooleanColumn ): def get_value( self, trans, grid, repository_metadata ): @@ -475,6 +475,7 @@ class AdminController( BaseUIController, Admin ): kwd[ 'f-Category.name' ] = category.name elif operation == "receive email alerts": if kwd[ 'id' ]: + kwd[ 'caller' ] = 'browse_repositories' return trans.response.send_redirect( web.url_for( controller='repository', action='set_email_alerts', **kwd ) ) diff --git a/lib/galaxy/webapps/community/controllers/common.py b/lib/galaxy/webapps/community/controllers/common.py index 0cbda2eed7d..9be25a0325e 100644 --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1,8 +1,10 @@ -import os, string, socket, logging +import os, string, socket, logging, simplejson, binascii from time import strftime from datetime import * from galaxy.tools import * from galaxy.util.json import from_json_string, to_json_string +from galaxy.util.hash_util import * +from galaxy.util.shed_util import generate_datatypes_metadata, generate_tool_metadata, generate_workflow_metadata from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -11,6 +13,28 @@ from mercurial import hg, ui, commands log = logging.getLogger( __name__ ) +new_repo_email_alert_template = """ +GALAXY TOOL SHED NEW REPOSITORY ALERT +----------------------------------------------------------------------------- +You received this alert because you registered to receive email when +new repositories were created in the Galaxy tool shed named "${host}". +----------------------------------------------------------------------------- + +Repository name: ${repository_name} +Date content uploaded: ${display_date} +Uploaded by: ${username} + +Revision: ${revision} +Change description: +${description} + +${content_alert_str} + +----------------------------------------------------------------------------- +This change alert was sent from the Galaxy tool shed hosted on the server +"${host}" +""" + email_alert_template = """ GALAXY TOOL SHED REPOSITORY UPDATE ALERT ----------------------------------------------------------------------------- @@ -25,6 +49,8 @@ Revision: ${revision} Change description: ${description} +${content_alert_str} + ----------------------------------------------------------------------------- This change alert was sent from the Galaxy tool shed hosted on the server "${host}" @@ -123,40 +149,8 @@ def get_latest_repository_metadata( trans, id ): .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ .order_by( trans.model.RepositoryMetadata.table.c.id.desc() ) \ .first() -def generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ): - """ - Update the received metadata_dict with changes that have been applied - to the received exported_workflow_dict. Store everything except the - workflow steps in the database. - """ - workflow_dict = { 'a_galaxy_workflow' : exported_workflow_dict[ 'a_galaxy_workflow' ], - 'name' :exported_workflow_dict[ 'name' ], - 'annotation' : exported_workflow_dict[ 'annotation' ], - 'format-version' : exported_workflow_dict[ 'format-version' ] } - if 'workflows' in metadata_dict: - metadata_dict[ 'workflows' ].append( workflow_dict ) - else: - metadata_dict[ 'workflows' ] = [ workflow_dict ] - return metadata_dict -def new_workflow_metadata_required( trans, id, metadata_dict ): - """ - TODO: Currently everything about an exported workflow except the name is hard-coded, so - there's no real way to differentiate versions of exported workflows. If this changes at - some future time, this method should be enhanced accordingly... - """ - if 'workflows' in metadata_dict: - repository_metadata = get_latest_repository_metadata( trans, id ) - if repository_metadata: - if repository_metadata.metadata: - # The repository has metadata, so update the workflows value - no new record is needed. - return False - else: - # There is no saved repository metadata, so we need to create a new repository_metadata table record. - return True - # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table - # record is not needed. - return False def generate_clone_url( trans, repository_id ): + """Generate the URL for cloning a repository.""" repository = get_repository( trans, repository_id ) protocol, base = trans.request.base.split( '://' ) if trans.user: @@ -194,7 +188,7 @@ def check_tool_input_params( trans, name, tool, sample_files, invalid_files ): head, tail = os.path.split( sample_file ) if tail == 'tool_data_table_conf.xml.sample': sample_found = True - error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_file ) + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, sample_file ) if error: can_set_metadata = False invalid_files.append( ( tail, correction_msg ) ) @@ -215,10 +209,11 @@ def check_tool_input_params( trans, name, tool, sample_files, invalid_files ): for sample_file in sample_files: sample_head, sample_tail = os.path.split( sample_file ) if sample_tail == '%s.sample' % index_tail: - copy_sample_loc_file( trans, sample_file ) + copy_sample_loc_file( trans.app, sample_file ) options.index_file = index_tail options.missing_index_file = None - options.tool_data_table.missing_index_file = None + if options.tool_data_table: + options.tool_data_table.missing_index_file = None sample_found = True break if not sample_found: @@ -227,54 +222,6 @@ def check_tool_input_params( trans, name, tool, sample_files, invalid_files ): correction_msg += "Upload a file named %s.sample to the repository to correct this error." % str( index_tail ) invalid_files.append( ( name, correction_msg ) ) return can_set_metadata, invalid_files -def generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ): - """ - Update the received metadata_dict with changes that have been - applied to the received tool. - """ - repository = get_repository( trans, id ) - # Handle tool.requirements. - tool_requirements = [] - for tr in tool.requirements: - name=tr.name - type=tr.type - if type == 'fabfile': - version = None - fabfile = tr.fabfile - method = tr.method - else: - version = tr.version - fabfile = None - method = None - requirement_dict = dict( name=name, - type=type, - version=version, - fabfile=fabfile, - method=method ) - tool_requirements.append( requirement_dict ) - # Handle tool.tests. - tool_tests = [] - if tool.tests: - for ttb in tool.tests: - test_dict = dict( name=ttb.name, - required_files=ttb.required_files, - inputs=ttb.inputs, - outputs=ttb.outputs ) - tool_tests.append( test_dict ) - tool_dict = dict( id=tool.id, - guid = generate_tool_guid( trans, repository, tool ), - name=tool.name, - version=tool.version, - description=tool.description, - version_string_cmd = tool.version_string_cmd, - tool_config=tool_config, - requirements=tool_requirements, - tests=tool_tests ) - if 'tools' in metadata_dict: - metadata_dict[ 'tools' ].append( tool_dict ) - else: - metadata_dict[ 'tools' ] = [ tool_dict ] - return metadata_dict def new_tool_metadata_required( trans, id, metadata_dict ): """ Compare the last saved metadata for each tool in the repository with the new metadata @@ -316,94 +263,158 @@ def new_tool_metadata_required( trans, id, metadata_dict ): # The received metadata_dict includes no metadata for tools, so a new repository_metadata table # record is not needed. return False -def set_repository_metadata( trans, id, changeset_revision, **kwd ): +def new_workflow_metadata_required( trans, id, metadata_dict ): + """ + Currently everything about an exported workflow except the name is hard-coded, so there's + no real way to differentiate versions of exported workflows. If this changes at some future + time, this method should be enhanced accordingly. + """ + if 'workflows' in metadata_dict: + repository_metadata = get_latest_repository_metadata( trans, id ) + if repository_metadata: + if repository_metadata.metadata: + # The repository has metadata, so update the workflows value - no new record is needed. + return False + else: + # There is no saved repository metadata, so we need to create a new repository_metadata table record. + return True + # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table + # record is not needed. + return False +def generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, repo_dir ): + # Browse the repository tip files on disk to generate metadata. This is faster than + # the generate_metadata_for_changeset_revision() method below because fctx.data() does + # not have to be written to disk to load tools. also, since changeset_revision is the + # repository tip, we handle things like .loc.sample files here. + metadata_dict = {} + invalid_files = [] + sample_files = [] + datatypes_config = None + # Find datatypes_conf.xml if it exists. + for root, dirs, files in os.walk( repo_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == 'datatypes_conf.xml': + datatypes_config = os.path.abspath( os.path.join( root, name ) ) + break + if datatypes_config: + metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) + # Find all special .sample files. + for root, dirs, files in os.walk( repo_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name.endswith( '.sample' ): + sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) + # Find all tool configs and exported workflows. + for root, dirs, files in os.walk( repo_dir ): + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: + if '.hg' in dirs: + dirs.remove( '.hg' ) + for name in files: + # Find all tool configs. + if name != 'datatypes_conf.xml' and name.endswith( '.xml' ): + full_path = os.path.abspath( os.path.join( root, name ) ) + try: + tool = load_tool( trans, full_path ) + valid = True + except Exception, e: + valid = False + invalid_files.append( ( name, str( e ) ) ) + if valid and tool is not None: + can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) + if can_set_metadata: + # Update the list of metadata dictionaries for tools in metadata_dict. + tool_config = os.path.join( root, name ) + repository_clone_url = generate_clone_url( trans, id ) + metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) + # Find all exported workflows + elif name.endswith( '.ga' ): + try: + relative_path = os.path.join( root, name ) + # Convert workflow data from json + fp = open( relative_path, 'rb' ) + workflow_text = fp.read() + fp.close() + exported_workflow_dict = from_json_string( workflow_text ) + if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) + except Exception, e: + invalid_files.append( ( name, str( e ) ) ) + return metadata_dict, invalid_files +def generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision, repo_dir ): + # Browse repository files within a change set to generate metadata. + metadata_dict = {} + invalid_files = [] + sample_files = [] + datatypes_config = None + # Find datatypes_conf.xml if it exists. + for filename in ctx: + if filename == 'datatypes_conf.xml': + fctx = ctx[ filename ] + datatypes_config = fctx.data() + break + if datatypes_config: + metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) + # Get all tool config file names from the hgweb url, something like: + # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml + for filename in ctx: + # Find all tool configs. + if filename != 'datatypes_conf.xml' and filename.endswith( '.xml' ): + fctx = ctx[ filename ] + # Write the contents of the old tool config to a temporary file. + # TODO: figure out how to enhance the load_tool method so that a + # temporary disk file is not necessary in order to pass the tool + # config. + fh = tempfile.NamedTemporaryFile( 'w' ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'w' ) + fh.write( fctx.data() ) + fh.close() + try: + tool = load_tool( trans, tmp_filename ) + valid = True + except Exception, e: + invalid_files.append( ( filename, str( e ) ) ) + valid = False + if valid and tool is not None: + # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename + # here is the relative path to the config file within the change set context, something + # like filtering.xml, but when the change set was the repository tip, the value was + # something like database/community_files/000/repo_1/filtering.xml. This shouldn't break + # anything, but may result in a bit of confusion when maintaining the code / data over time. + # IMPORTANT NOTE: Here we are assuming that since the current change set is not the repository + # tip, we do not have to handle any .loc.sample files since they would have been handled previously. + repository_clone_url = generate_clone_url( trans, id ) + metadata_dict = generate_tool_metadata( filename, tool, repository_clone_url, metadata_dict ) + try: + os.unlink( tmp_filename ) + except: + pass + # Find all exported workflows. + elif filename.endswith( '.ga' ): + try: + fctx = ctx[ filename ] + workflow_text = fctx.data() + exported_workflow_dict = from_json_string( workflow_text ) + if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + metadata_dict = generate_workflow_metadata( '', exported_workflow_dict, metadata_dict ) + except Exception, e: + invalid_files.append( ( name, str( e ) ) ) + return metadata_dict, invalid_files +def set_repository_metadata( trans, id, changeset_revision, content_alert_str='', **kwd ): """Set repository metadata""" message = '' status = 'done' repository = get_repository( trans, id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) - invalid_files = [] - sample_files = [] ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) if ctx is not None: - metadata_dict = {} if changeset_revision == repository.tip: - for root, dirs, files in os.walk( repo_dir ): - if not root.find( '.hg' ) >= 0 and not root.find( 'hgrc' ) >= 0: - if '.hg' in dirs: - # Don't visit .hg directories - should be impossible since we don't - # allow uploaded archives that contain .hg dirs, but just in case... - dirs.remove( '.hg' ) - if 'hgrc' in files: - # Don't include hgrc files in commit. - files.remove( 'hgrc' ) - # Find all special .sample files first. - for name in files: - if name.endswith( '.sample' ): - sample_files.append( os.path.abspath( os.path.join( root, name ) ) ) - for name in files: - # Find all tool configs. - if name.endswith( '.xml' ): - try: - full_path = os.path.abspath( os.path.join( root, name ) ) - tool = load_tool( trans, full_path ) - if tool is not None: - can_set_metadata, invalid_files = check_tool_input_params( trans, name, tool, sample_files, invalid_files ) - if can_set_metadata: - # Update the list of metadata dictionaries for tools in metadata_dict. - tool_config = os.path.join( root, name ) - metadata_dict = generate_tool_metadata( trans, id, changeset_revision, tool_config, tool, metadata_dict ) - except Exception, e: - invalid_files.append( ( name, str( e ) ) ) - # Find all exported workflows - elif name.endswith( '.ga' ): - try: - full_path = os.path.abspath( os.path.join( root, name ) ) - # Convert workflow data from json - fp = open( full_path, 'rb' ) - workflow_text = fp.read() - fp.close() - exported_workflow_dict = from_json_string( workflow_text ) - # Update the list of metadata dictionaries for workflows in metadata_dict. - metadata_dict = generate_workflow_metadata( trans, id, changeset_revision, exported_workflow_dict, metadata_dict ) - except Exception, e: - invalid_files.append( ( name, str( e ) ) ) + metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, id, ctx, changeset_revision, repo_dir ) else: - # Find all special .sample files first. - for filename in ctx: - if filename.endswith( '.sample' ): - sample_files.append( os.path.abspath( os.path.join( root, filename ) ) ) - # Get all tool config file names from the hgweb url, something like: - # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml - for filename in ctx: - # Find all tool configs - should not have to update metadata for workflows for now. - if filename.endswith( '.xml' ): - fctx = ctx[ filename ] - # Write the contents of the old tool config to a temporary file. - fh = tempfile.NamedTemporaryFile( 'w' ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'w' ) - fh.write( fctx.data() ) - fh.close() - try: - tool = load_tool( trans, tmp_filename ) - if tool is not None: - can_set_metadata, invalid_files = check_tool_input_params( trans, filename, tool, sample_files, invalid_files ) - if can_set_metadata: - # Update the list of metadata dictionaries for tools in metadata_dict. Note that filename - # here is the relative path to the config file within the change set context, something - # like filtering.xml, but when the change set was the repository tip, the value was - # something like database/community_files/000/repo_1/filtering.xml. This shouldn't break - # anything, but may result in a bit of confusion when maintaining the code / data over time. - metadata_dict = generate_tool_metadata( trans, id, changeset_revision, filename, tool, metadata_dict ) - except Exception, e: - invalid_files.append( ( name, str( e ) ) ) - try: - os.unlink( tmp_filename ) - except: - pass + metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, id, ctx, changeset_revision, repo_dir ) if metadata_dict: if changeset_revision == repository.tip: if new_tool_metadata_required( trans, id, metadata_dict ) or new_workflow_metadata_required( trans, id, metadata_dict ): @@ -411,13 +422,22 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ): repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) trans.sa_session.add( repository_metadata ) trans.sa_session.flush() + # If this is the first record stored for this repository, see if we need to send any email alerts. + if len( repository.downloadable_revisions ) == 1: + handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) else: - # Update the last saved repository_metadata table row. repository_metadata = get_latest_repository_metadata( trans, id ) - repository_metadata.changeset_revision = changeset_revision - repository_metadata.metadata = metadata_dict - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() + if repository_metadata: + # Update the last saved repository_metadata table row. + repository_metadata.changeset_revision = changeset_revision + repository_metadata.metadata = metadata_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() + else: + # There are no tools in the repository, and we're setting metadat on the repository tip. + repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() else: # We're re-generating metadata for an old repository revision. repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) @@ -425,18 +445,20 @@ def set_repository_metadata( trans, id, changeset_revision, **kwd ): trans.sa_session.add( repository_metadata ) trans.sa_session.flush() else: - message = "Change set revision '%s' includes no tools or exported workflows for which metadata can be set." % str( changeset_revision ) + message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( changeset_revision ) + message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." status = "error" else: # change_set is None - message = "Repository does not include change set revision '%s'." % str( changeset_revision ) + message = "This repository does not include revision '%s'." % str( changeset_revision ) status = 'error' if invalid_files: if metadata_dict: - message = "Metadata was defined for some items in change set revision '%s'. " % str( changeset_revision ) + message = "Metadata was defined for some items in revision '%s'. " % str( changeset_revision ) message += "Correct the following problems if necessary and reset metadata.
" else: - message = "Metadata cannot be defined for change set revision '%s'. Correct the following problems and reset metadata.
" % str( changeset_revision ) + message = "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( changeset_revision ) + message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.
" for itc_tup in invalid_files: tool_file, exception_msg = itc_tup if exception_msg.find( 'No such file or directory' ) >= 0: @@ -482,11 +504,31 @@ def get_configured_ui(): def get_user( trans, id ): """Get a user from the database by id""" return trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( id ) ) -def handle_email_alerts( trans, repository ): +def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=False, admin_only=False ): + # There are 2 complementary features that enable a tool shed user to receive email notification: + # 1. Within User Preferences, they can elect to receive email when the first (or first valid) + # change set is produced for a new repository. + # 2. When viewing or managing a repository, they can check the box labeled "Receive email alerts" + # which caused them to receive email alerts when updates to the repository occur. This same feature + # is available on a per-repository basis on the repository grid within the tool shed. + # + # There are currently 4 scenarios for sending email notification when a change is made to a repository: + # 1. An admin user elects to receive email when the first change set is produced for a new repository + # from User Preferences. The change set does not have to include any valid content. This allows for + # the capture of inappropriate content being uploaded to new repositories. + # 2. A regular user elects to receive email when the first valid change set is produced for a new repository + # from User Preferences. This differs from 1 above in that the user will not receive email until a + # change set tha tincludes valid content is produced. + # 3. An admin user checks the "Receive email alerts" check box on the manage repository page. Since the + # user is an admin user, the email will include information about both HTML and image content that was + # included in the change set. + # 4. A regular user checks the "Receive email alerts" check box on the manage repository page. Since the + # user is not an admin user, the email will not include any information about both HTML and image content + # that was included in the change set. repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) smtp_server = trans.app.config.smtp_server - if smtp_server and repository.email_alerts: + if smtp_server and ( new_repo_alert or repository.email_alerts ): # Send email alert to users that want them. if trans.app.config.email_from is not None: email_from = trans.app.config.email_from @@ -503,24 +545,63 @@ def handle_email_alerts( trans, repository ): username = ctx.user().split()[0] except: username = ctx.user() - # Build the email message - body = string.Template( email_alert_template ) \ - .safe_substitute( host=trans.request.host, - repository_name=repository.name, - revision='%s:%s' %( str( ctx.rev() ), ctx ), - display_date=display_date, - description=ctx.description(), - username=username ) + # We'll use 2 template bodies because we only want to send content + # alerts to tool shed admin users. + if new_repo_alert: + template = new_repo_email_alert_template + else: + template = email_alert_template + admin_body = string.Template( template ).safe_substitute( host=trans.request.host, + repository_name=repository.name, + revision='%s:%s' %( str( ctx.rev() ), ctx ), + display_date=display_date, + description=ctx.description(), + username=username, + content_alert_str=content_alert_str ) + body = string.Template( template ).safe_substitute( host=trans.request.host, + repository_name=repository.name, + revision='%s:%s' %( str( ctx.rev() ), ctx ), + display_date=display_date, + description=ctx.description(), + username=username, + content_alert_str='' ) + admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) frm = email_from - subject = "Galaxy tool shed repository update alert" - email_alerts = from_json_string( repository.email_alerts ) + if new_repo_alert: + subject = "New Galaxy tool shed repository alert" + email_alerts = [] + for user in trans.sa_session.query( trans.model.User ) \ + .filter( and_( trans.model.User.table.c.deleted == False, + trans.model.User.table.c.new_repo_alert == True ) ): + if admin_only: + if user.email in admin_users: + email_alerts.append( user.email ) + else: + email_alerts.append( user.email ) + else: + subject = "Galaxy tool shed repository update alert" + email_alerts = from_json_string( repository.email_alerts ) for email in email_alerts: to = email.strip() # Send it try: - util.send_mail( frm, to, subject, body, trans.app.config ) + if to in admin_users: + util.send_mail( frm, to, subject, admin_body, trans.app.config ) + else: + util.send_mail( frm, to, subject, body, trans.app.config ) except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) +def check_file_contents( trans ): + # See if any admin users have chosen to receive email alerts when a repository is updated. + # If so, the file contents of the update must be checked for inappropriate content. + admin_users = trans.app.config.get( "admin_users", "" ).split( "," ) + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( trans.model.Repository.table.c.email_alerts != None ): + email_alerts = from_json_string( repository.email_alerts ) + for user_email in email_alerts: + if user_email in admin_users: + return True + return False def update_for_browsing( trans, repository, current_working_dir, commit_message='' ): # Make a copy of a repository's files for browsing, remove from disk all files that # are not tracked, and commit all added, modified or removed files that have not yet @@ -529,12 +610,10 @@ def update_for_browsing( trans, repository, current_working_dir, commit_message= repo = hg.repository( get_configured_ui(), repo_dir ) # The following will delete the disk copy of only the files in the repository. #os.system( 'hg update -r null > /dev/null 2>&1' ) - repo.ui.pushbuffer() - commands.status( repo.ui, repo, all=True ) - status_and_file_names = repo.ui.popbuffer().strip().split( "\n" ) - # status_and_file_names looks something like: - # ['? README', '? tmap_tool/tmap-0.0.9.tar.gz', '? dna_filtering.py', 'C filtering.py', 'C filtering.xml'] - # The codes used to show the status of files are: + files_to_remove_from_disk = [] + files_to_commit = [] + # We may have files on disk in the repo directory that aren't being tracked, so they must be removed. + # The codes used to show the status of files are as follows. # M = modified # A = added # R = removed @@ -542,37 +621,50 @@ def update_for_browsing( trans, repository, current_working_dir, commit_message= # ! = deleted, but still tracked # ? = not tracked # I = ignored - files_to_remove_from_disk = [] - files_to_commit = [] - for status_and_file_name in status_and_file_names: - if status_and_file_name.startswith( '?' ) or status_and_file_name.startswith( 'I' ): - files_to_remove_from_disk.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) - elif status_and_file_name.startswith( 'M' ) or status_and_file_name.startswith( 'A' ) or status_and_file_name.startswith( 'R' ): - files_to_commit.append( os.path.abspath( os.path.join( repo_dir, status_and_file_name.split()[1] ) ) ) - for full_path in files_to_remove_from_disk: - # We'll remove all files that are not tracked or ignored. - if os.path.isdir( full_path ): - try: - os.rmdir( full_path ) - except OSError, e: - # The directory is not empty - pass - elif os.path.isfile( full_path ): - os.remove( full_path ) - dir = os.path.split( full_path )[0] - try: - os.rmdir( dir ) - except OSError, e: - # The directory is not empty - pass + # We'll use mercurial's purge extension to remove untracked file. Using this extension requires the + # following entry in the repository's hgrc file which was not required for some time, so we'll add it + # if it's missing. + # [extensions] + # hgext.purge= + lines = repo.opener( 'hgrc', 'rb' ).readlines() + if not '[extensions]\n' in lines: + # No extensions have been added at all, so just append to the file. + fp = repo.opener( 'hgrc', 'a' ) + fp.write( '[extensions]\n' ) + fp.write( 'hgext.purge=\n' ) + fp.close() + elif not 'hgext.purge=\n' in lines: + # The file includes and [extensions] section, but we need to add the + # purge extension. + fp = repo.opener( 'hgrc', 'wb' ) + for line in lines: + if line.startswith( '[extensions]' ): + fp.write( line ) + fp.write( 'hgext.purge=\n' ) + else: + fp.write( line ) + fp.close() + cmd = 'hg purge' + os.chdir( repo_dir ) + proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) + return_code = proc.wait() + os.chdir( current_working_dir ) + if return_code != 0: + output = proc.stdout.read( 32768 ) + log.debug( 'hg purge failed in repository directory %s, reason: %s' % ( repo_dir, output ) ) if files_to_commit: if not commit_message: commit_message = 'Committed changes to: %s' % ', '.join( files_to_commit ) repo.dirstate.write() repo.commit( user=trans.user.username, text=commit_message ) + cmd = 'hg update > /dev/null 2>&1' os.chdir( repo_dir ) - os.system( 'hg update > /dev/null 2>&1' ) + proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT ) + return_code = proc.wait() os.chdir( current_working_dir ) + if return_code != 0: + output = proc.stdout.read( 32768 ) + log.debug( 'hg update > /dev/null 2>&1 failed in repository directory %s, reason: %s' % ( repo_dir, output ) ) def load_tool( trans, config_file ): """ Load a single tool from the file named by `config_file` and return @@ -595,6 +687,48 @@ def load_tool( trans, config_file ): ToolClass = Tool return ToolClass( config_file, root, trans.app ) return None +def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ): + repository = get_repository( trans, repository_id ) + repo = hg.repository( get_configured_ui(), repository.repo_path ) + tool = None + message = '' + if changeset_revision == repository.tip: + try: + tool = load_tool( trans, os.path.abspath( tool_config ) ) + except Exception, e: + tool = None + message = "Error loading tool: %s. Clicking Reset metadata may correct this error." % str( e ) + else: + # Get the tool config file name from the hgweb url, something like: + # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml + old_tool_config_file_name = tool_config.split( '/' )[ -1 ] + ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) + fctx = None + for filename in ctx: + filename_head, filename_tail = os.path.split( filename ) + if filename_tail == old_tool_config_file_name: + fctx = ctx[ filename ] + break + if fctx: + # Write the contents of the old tool config to a temporary file. + fh = tempfile.NamedTemporaryFile( 'w' ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'w' ) + fh.write( fctx.data() ) + fh.close() + try: + tool = load_tool( trans, tmp_filename ) + except Exception, e: + tool = None + message = "Error loading tool: %s. Clicking Reset metadata may correct this error." % str( e ) + try: + os.unlink( tmp_filename ) + except: + pass + else: + tool = None + return tool, message 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 @@ -619,3 +753,24 @@ def build_changeset_revision_select_field( trans, repository, selected_value=Non 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 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 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 diff --git a/lib/galaxy/webapps/community/controllers/repository.py b/lib/galaxy/webapps/community/controllers/repository.py index 1a377dcc450..53147bb7853 100644 --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1,4 +1,4 @@ -import os, logging, urllib, ConfigParser, tempfile, shutil +import os, logging, tempfile, shutil from time import strftime from datetime import date, datetime from galaxy import util @@ -182,20 +182,51 @@ class RepositoryListGrid( grids.Grid ): .outerjoin( model.RepositoryCategoryAssociation.table ) \ .outerjoin( model.Category.table ) -class DownloadableRepositoryListGrid( RepositoryListGrid ): +class EmailAlertsRepositoryListGrid( RepositoryListGrid ): + columns = [ + RepositoryListGrid.NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", + id=item.id, + webapp="community" ) ), + attach_popup=False ), + RepositoryListGrid.DescriptionColumn( "Synopsis", + key="description", + attach_popup=False ), + RepositoryListGrid.UserColumn( "Owner", + model_class=model.User, + link=( lambda item: dict( operation="repositories_by_user", id=item.id, webapp="community" ) ), + attach_popup=False, + key="User.username" ), + RepositoryListGrid.EmailAlertsColumn( "Alert", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) + ] + operations = [ grids.GridOperation( "Receive email alerts", + allow_multiple=True, + condition=( lambda item: not item.deleted ), + async_compatible=False ) ] + global_actions = [ + grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository', webapp='community' ) ) + ] + +class ValidRepositoryListGrid( RepositoryListGrid ): class RevisionColumn( grids.GridColumn ): 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. + strings of all download-able revisions of this repository. """ select_field = build_changeset_revision_select_field( trans, repository ) if len( select_field.options ) > 1: return select_field.get_html() return repository.revision - title = "Downloadable repositories" + title = "Valid repositories" columns = [ RepositoryListGrid.NameColumn( "Name", key="name", @@ -209,21 +240,88 @@ class DownloadableRepositoryListGrid( RepositoryListGrid ): attach_popup=False, key="User.username" ) ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) operations = [] def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( self.model_class ) \ .join( model.RepositoryMetadata.table ) \ .join( model.User.table ) +class MatchedRepositoryListGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository.description + class RevisionColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.changeset_revision + class UserColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.repository.user: + return repository_metadata.repository.user.username + return 'no user' + # Grid definition + title = "Matching repositories" + model_class = model.RepositoryMetadata + template='/webapps/community/repository/grid.mako' + default_sort_key = "Repository.name" + columns = [ + NameColumn( "Repository name", + link=( lambda item: dict( operation="view_or_manage_repository", + id=item.id, + webapp="community" ) ), + attach_popup=True ), + DescriptionColumn( "Synopsis", + attach_popup=False ), + RevisionColumn( "Revision" ), + UserColumn( "Owner", + model_class=model.User, + attach_popup=False ) + ] + operations = [] + standard_filters = [] + default_filter = {} + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, trans, **kwd ): + match_tuples = kwd.get( 'match_tuples', [] ) + clause_list = [] + if match_tuples: + for match_tuple in match_tuples: + repository_id, changeset_revision = match_tuple + clause_list.append( "%s=%d and %s='%s'" % ( self.model_class.table.c.repository_id, + int( repository_id ), + self.model_class.table.c.changeset_revision, + changeset_revision ) ) + return trans.sa_session.query( self.model_class ) \ + .join( model.Repository ) \ + .join( model.User.table ) \ + .filter( or_( *clause_list ) ) \ + .order_by( model.Repository.name ) + # Return an empty query + return trans.sa_session.query( self.model_class ) \ + .join( model.Repository ) \ + .join( model.User.table ) \ + .filter( self.model_class.table.c.repository_id == 0 ) + +class InstallMatchedRepositoryListGrid( MatchedRepositoryListGrid ): + columns = [ col for col in MatchedRepositoryListGrid.columns ] + # Override the NameColumn + columns[ 0 ] = MatchedRepositoryListGrid.NameColumn( "Name", + link=( lambda item: dict( operation="view_or_manage_repository", + id=item.id, + webapp="galaxy" ) ), + attach_popup=False ) + class RepositoryController( BaseUIController, ItemRatings ): - downloadable_repository_list_grid = DownloadableRepositoryListGrid() + install_matched_repository_list_grid = InstallMatchedRepositoryListGrid() + matched_repository_list_grid = MatchedRepositoryListGrid() + valid_repository_list_grid = ValidRepositoryListGrid() repository_list_grid = RepositoryListGrid() + email_alerts_repository_list_grid = EmailAlertsRepositoryListGrid() category_list_grid = CategoryListGrid() @web.expose @@ -231,7 +329,12 @@ class RepositoryController( BaseUIController, ItemRatings ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - return trans.fill_template( '/webapps/community/index.mako', message=message, status=status ) + # See if there are any RepositoryMetadata records since menu items require them. + repository_metadata = trans.sa_session.query( model.RepositoryMetadata ).first() + return trans.fill_template( '/webapps/community/index.mako', + repository_metadata=repository_metadata, + message=message, + status=status ) @web.expose def browse_categories( self, trans, **kwd ): if 'f-free-text-search' in kwd: @@ -261,9 +364,8 @@ class RepositoryController( BaseUIController, ItemRatings ): # Render the list view return self.category_list_grid( trans, **kwd ) @web.expose - def browse_downloadable_repositories( self, trans, **kwd ): - # Set the toolshedgalaxyurl cookie so we can get back - # to the calling local Galaxy instance. + def browse_valid_repositories( self, trans, **kwd ): + webapp = kwd.get( 'webapp', 'community' ) galaxy_url = kwd.get( 'galaxy_url', None ) if galaxy_url: trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) @@ -274,9 +376,9 @@ class RepositoryController( BaseUIController, ItemRatings ): repository = get_repository( trans, repository_id ) return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', + webapp=webapp, repository_id=repository_id, changeset_revision=repository.tip ) ) - # The changeset_revision_select_field in the RepositoryListGrid performs a refresh_on_change # which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One # of the many select fields on the grid performed the refresh_on_change, so we loop through @@ -291,29 +393,345 @@ class RepositoryController( BaseUIController, ItemRatings ): if repository.tip != v: return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', + webapp=webapp, repository_id=trans.security.encode_id( repository.id ), changeset_revision=v ) ) - url_args = dict( action='browse_downloadable_repositories', + url_args = dict( action='browse_valid_repositories', operation='preview_tools_in_changeset', + webapp=webapp, repository_id=repository_id ) - self.downloadable_repository_list_grid.operations = [ grids.GridOperation( "Preview and install tools", - url_args=url_args, - allow_multiple=False, - async_compatible=False ) ] - + self.valid_repository_list_grid.operations = [ grids.GridOperation( "Preview and install", + url_args=url_args, + allow_multiple=False, + async_compatible=False ) ] # Render the list view - return self.downloadable_repository_list_grid( trans, **kwd ) + return self.valid_repository_list_grid( trans, **kwd ) + @web.expose + def find_workflows( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + if 'operation' in kwd: + item_id = kwd.get( 'id', '' ) + if item_id: + operation = kwd[ 'operation' ].lower() + is_admin = trans.user_is_admin() + if operation == "view_or_manage_repository": + # The received id is a RepositoryMetadata id, so we have to get the repository id. + repository_metadata = get_repository_metadata_by_id( trans, item_id ) + repository_id = trans.security.encode_id( repository_metadata.repository.id ) + repository = get_repository( trans, repository_id ) + kwd[ 'id' ] = repository_id + kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision + if webapp == 'community' and ( is_admin or repository.user == trans.user ): + a = 'manage_repository' + else: + a = 'view_repository' + return trans.response.send_redirect( web.url_for( controller='repository', + 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 = '%s/admin_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 ) + 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. + return trans.show_error_message( "No items were selected." ) + workflow_names = [ item.lower() for item in util.listify( kwd.get( 'workflow_name', '' ) ) ] + exact_matches = params.get( 'exact_matches', '' ) + exact_matches_checked = CheckboxField.is_checked( exact_matches ) + match_tuples = [] + ok = True + if workflow_names: + ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names ) + if ok: + kwd[ 'match_tuples' ] = match_tuples + # Render the list view + if webapp == 'galaxy': + # Our initial request originated from a Galaxy instance. + global_actions = [ grids.GridAction( "Browse valid repositories", + dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), + grids.GridAction( "Search for valid tools", + dict( controller='repository', action='find_tools', webapp=webapp ) ), + grids.GridAction( "Search for workflows", + dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] + self.install_matched_repository_list_grid.global_actions = global_actions + install_url_args = dict( controller='repository', action='find_workflows', webapp=webapp ) + operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] + self.install_matched_repository_list_grid.operations = operations + return self.install_matched_repository_list_grid( trans, **kwd ) + else: + kwd[ 'message' ] = "workflow name: %s
exact matches only: %s" % \ + ( self.__stringify( workflow_names ), str( exact_matches_checked ) ) + self.matched_repository_list_grid.title = "Repositories with matching workflows" + return self.matched_repository_list_grid( trans, **kwd ) + else: + message = "No search performed - each field must contain the same number of comma-separated items." + status = "error" + exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) + return trans.fill_template( '/webapps/community/repository/find_workflows.mako', + webapp=webapp, + workflow_name=self.__stringify( workflow_names ), + exact_matches_check_box=exact_matches_check_box, + message=message, + status=status ) + @web.expose + def find_tools( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) + galaxy_url = kwd.get( 'galaxy_url', None ) + if galaxy_url: + trans.set_cookie( galaxy_url, name='toolshedgalaxyurl' ) + if 'operation' in kwd: + item_id = kwd.get( 'id', '' ) + if item_id: + operation = kwd[ 'operation' ].lower() + is_admin = trans.user_is_admin() + if operation == "view_or_manage_repository": + # The received id is a RepositoryMetadata id, so we have to get the repository id. + repository_metadata = get_repository_metadata_by_id( trans, item_id ) + repository_id = trans.security.encode_id( repository_metadata.repository.id ) + repository = get_repository( trans, repository_id ) + kwd[ 'id' ] = repository_id + kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision + if webapp == 'community' and ( is_admin or repository.user == trans.user ): + a = 'manage_repository' + else: + a = 'view_repository' + return trans.response.send_redirect( web.url_for( controller='repository', + 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 = '%s/admin_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 ) + 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. + return trans.show_error_message( "No items were selected." ) + tool_ids = [ item.lower() for item in util.listify( kwd.get( 'tool_id', '' ) ) ] + tool_names = [ item.lower() for item in util.listify( kwd.get( 'tool_name', '' ) ) ] + tool_versions = [ item.lower() for item in util.listify( kwd.get( 'tool_version', '' ) ) ] + exact_matches = params.get( 'exact_matches', '' ) + exact_matches_checked = CheckboxField.is_checked( exact_matches ) + match_tuples = [] + ok = True + if tool_ids or tool_names or tool_versions: + ok, match_tuples = self.__search_repository_metadata( trans, exact_matches_checked, tool_ids=tool_ids, tool_names=tool_names, tool_versions=tool_versions ) + if ok: + kwd[ 'match_tuples' ] = match_tuples + # Render the list view + if webapp == 'galaxy': + # Our initial request originated from a Galaxy instance. + global_actions = [ grids.GridAction( "Browse valid repositories", + dict( controller='repository', action='browse_valid_repositories', webapp=webapp ) ), + grids.GridAction( "Search for valid tools", + dict( controller='repository', action='find_tools', webapp=webapp ) ), + grids.GridAction( "Search for workflows", + dict( controller='repository', action='find_workflows', webapp=webapp ) ) ] + self.install_matched_repository_list_grid.global_actions = global_actions + install_url_args = dict( controller='repository', action='find_tools', webapp=webapp ) + operations = [ grids.GridOperation( "Install", url_args=install_url_args, allow_multiple=True, async_compatible=False ) ] + self.install_matched_repository_list_grid.operations = operations + return self.install_matched_repository_list_grid( trans, **kwd ) + else: + kwd[ 'message' ] = "tool id: %s
tool name: %s
tool version: %s
exact matches only: %s" % \ + ( self.__stringify( tool_ids ), self.__stringify( tool_names ), self.__stringify( tool_versions ), str( exact_matches_checked ) ) + self.matched_repository_list_grid.title = "Repositories with matching tools" + return self.matched_repository_list_grid( trans, **kwd ) + else: + message = "No search performed - each field must contain the same number of comma-separated items." + status = "error" + exact_matches_check_box = CheckboxField( 'exact_matches', checked=exact_matches_checked ) + return trans.fill_template( '/webapps/community/repository/find_tools.mako', + webapp=webapp, + tool_id=self.__stringify( tool_ids ), + tool_name=self.__stringify( tool_names ), + tool_version=self.__stringify( tool_versions ), + exact_matches_check_box=exact_matches_check_box, + message=message, + status=status ) + def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='' ): + match_tuples = [] + ok = True + for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): + metadata = repository_metadata.metadata + if tool_ids or tool_names or tool_versions: + if 'tools' in metadata: + tools = metadata[ 'tools' ] + else: + tools = [] + for tool_dict in tools: + if tool_ids and not tool_names and not tool_versions: + for tool_id in tool_ids: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_names and not tool_ids and not tool_versions: + for tool_name in tool_names: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_versions and not tool_ids and not tool_names: + for tool_version in tool_versions: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_ids and tool_names and not tool_versions: + if len( tool_ids ) == len( tool_names ): + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + elif len( tool_ids ) == 1 or len( tool_names ) == 1: + tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + else: + ok = False + elif tool_ids and tool_versions and not tool_names: + if len( tool_ids ) == len( tool_versions ): + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + elif len( tool_ids ) == 1 or len( tool_versions ) == 1: + tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and not tool_ids: + if len( tool_versions ) == len( tool_names ): + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + elif len( tool_versions ) == 1 or len( tool_names ) == 1: + tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and tool_ids: + if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): + for i, tool_version in enumerate( tool_versions ): + tool_name = tool_names[ i ] + tool_id = tool_ids[ i ] + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + ok = False + elif workflow_names: + if 'workflows' in metadata: + workflows = metadata[ 'workflows' ] + else: + workflows = [] + for workflow_dict in workflows: + for workflow_name in workflow_names: + if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return ok, match_tuples + def __in_workflow_dict( self, workflow_dict, exact_matches_checked, workflow_name ): + workflow_dict_workflow_name = workflow_dict[ 'name' ].lower() + return ( workflow_name == workflow_dict_workflow_name ) or \ + ( not exact_matches_checked and workflow_dict_workflow_name.find( workflow_name ) >= 0 ) + def __in_tool_dict( self, tool_dict, exact_matches_checked, tool_id=None, tool_name=None, tool_version=None ): + found = False + if tool_id and not tool_name and not tool_version: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + found = ( tool_id == tool_dict_tool_id ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 ) + elif tool_name and not tool_id and not tool_version: + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_version and not tool_id and not tool_name: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + found = ( tool_version == tool_dict_tool_version ) or \ + ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 ) + elif tool_id and tool_name and not tool_version: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_id == tool_dict_tool_id and tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_id and tool_version and not tool_name: + tool_dict_tool_id = tool_dict[ 'id' ].lower() + tool_dict_tool_version = tool_dict[ 'version' ].lower() + found = ( tool_id == tool_dict_tool_id and tool_version == tool_dict_tool_version ) or \ + ( not exact_matches_checked and tool_dict_tool_id.find( tool_id ) >= 0 and tool_dict_tool_version.find( tool_version ) >= 0 ) + elif tool_version and tool_name and not tool_id: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + found = ( tool_version == tool_dict_tool_version and tool_name == tool_dict_tool_name ) or \ + ( not exact_matches_checked and tool_dict_tool_version.find( tool_version ) >= 0 and tool_dict_tool_name.find( tool_name ) >= 0 ) + elif tool_version and tool_name and tool_id: + tool_dict_tool_version = tool_dict[ 'version' ].lower() + tool_dict_tool_name = tool_dict[ 'name' ].lower() + tool_dict_tool_id = tool_dict[ 'id' ].lower() + found = ( tool_version == tool_dict_tool_version and \ + tool_name == tool_dict_tool_name and \ + tool_id == tool_dict_tool_id ) or \ + ( not exact_matches_checked and \ + tool_dict_tool_version.find( tool_version ) >= 0 and \ + tool_dict_tool_name.find( tool_name ) >= 0 and \ + tool_dict_tool_id.find( tool_id ) >= 0 ) + return found + def __stringify( self, list ): + if list: + return ','.join( list ) + return '' + def __make_same_length( self, list1, list2 ): + # If either list is 1 item, we'll append to it until its + # length is the same as the other. + if len( list1 ) == 1: + for i in range( 1, len( list2 ) ): + list1.append( list1[ 0 ] ) + elif len( list2 ) == 1: + for i in range( 1, len( list1 ) ): + list2.append( list2[ 0 ] ) + return list1, list2 + def __search_ids_names( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ): + for i, tool_id in enumerate( tool_ids ): + tool_name = tool_names[ i ] + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return match_tuples + def __search_ids_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ): + for i, tool_id in enumerate( tool_ids ): + tool_version = tool_versions[ i ] + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return match_tuples + def __search_names_versions( self, tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ): + for i, tool_name in enumerate( tool_names ): + tool_version = tool_versions[ i ] + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + return match_tuples + def __encode_repo_info_dict( self, trans, webapp, repository_metadata_ids ): + repo_info_dict = {} + includes_tools = False + for repository_metadata_id in 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 + repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) + repository_id = trans.security.encode_id( repository.id ) + changeset_revision = repository_metadata.changeset_revision + repository_clone_url = generate_clone_url( trans, repository_id ) + repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) + return encode( repo_info_dict ), includes_tools @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) 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 ) if repository_metadata: + repository_metadata_id = trans.security.encode_id( repository_metadata.id ), metadata = repository_metadata.metadata else: + repository_metadata_id = None metadata = None revision_label = get_revision_label( trans, repository, changeset_revision ) changeset_revision_select_field = build_changeset_revision_select_field( trans, @@ -322,11 +740,12 @@ class RepositoryController( BaseUIController, ItemRatings ): add_id_to_name=False ) return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako', repository=repository, + repository_metadata_id=repository_metadata_id, changeset_revision=changeset_revision, revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, metadata=metadata, - display_for_install=True, + webapp=webapp, message=message, status=status ) @web.expose @@ -334,41 +753,50 @@ class RepositoryController( BaseUIController, ItemRatings ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) 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 ) + # 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 repository_metadata.metadata + repo_info_dict = {} + repo_info_dict[ repository.name ] = ( repository.description, repository_clone_url, changeset_revision ) + encoded_repo_info_dict = encode( repo_info_dict ) # Redirect back to local Galaxy to perform install. - tool_shed_url = trans.request.host - repository_clone_url = generate_clone_url( trans, repository_id ) - # TODO: support https in the following url. - url = 'http://%s/admin/install_tool_shed_repository?tool_shed_url=%s&name=%s&description=%s&repository_clone_url=%s&changeset_revision=%s' % \ - ( galaxy_url, tool_shed_url, repository.name, repository.description, repository_clone_url, changeset_revision ) + url = '%s/admin_toolshed/install_repository?tool_shed_url=%s&repo_info_dict=%s&includes_tools=%s' % \ + ( galaxy_url, url_for( '', qualified=True ), encoded_repo_info_dict, str( includes_tools ) ) return trans.response.send_redirect( url ) @web.expose def check_for_updates( self, trans, **kwd ): + # Handle a request from a local Galaxy instance. If the request originated with the + # Galaxy instances' UpdateManager, the value of 'webapp' will be 'update_manager'. params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - # The sender didn't store galaxy_url in a cookie since - # this method immediately redirects back to the caller. - galaxy_url = kwd[ 'galaxy_url' ] + # If the request originated with the UpdateManager, it will not include a galaxy_url. + galaxy_url = kwd.get( 'galaxy_url', '' ) name = params.get( 'name', None ) owner = params.get( 'owner', None ) changeset_revision = params.get( 'changeset_revision', None ) - webapp = params.get( 'webapp', None ) - tool_shed_url = trans.request.host - # Start building up the url to redirect back to the calling Galaxy instance. - # TODO: support https in the following url. - url = 'http://%s/admin/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, tool_shed_url ) + webapp = params.get( 'webapp', 'community' ) repository = get_repository_by_name_and_owner( trans, name, owner ) - #if error: - # url += '&message=%s&status=error' % message - #else: - url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ - ( repository.name, repository.user.username, changeset_revision ) + from_update_manager = webapp == 'update_manager' + if from_update_manager: + update = 'true' + no_update = 'false' + else: + # Start building up the url to redirect back to the calling Galaxy instance. + url = '%s/admin_toolshed/update_to_changeset_revision?tool_shed_url=%s' % ( galaxy_url, url_for( '', qualified=True ) ) + url += '&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ + ( repository.name, repository.user.username, changeset_revision ) if changeset_revision == repository.tip: # If changeset_revision is the repository tip, then # we know there are no additional updates for the tools. + if from_update_manager: + return no_update url += repository.tip else: repository_metadata = get_repository_metadata_by_changeset_revision( trans, @@ -377,6 +805,8 @@ class RepositoryController( BaseUIController, ItemRatings ): if repository_metadata: # If changeset_revision is in the repository_metadata table for this # repository, then we know there are no additional updates for the tools. + if from_update_manager: + return no_update url += changeset_revision else: # The changeset_revision column in the repository_metadata table has been @@ -390,7 +820,7 @@ class RepositoryController( BaseUIController, ItemRatings ): tool_guids = [] for filename in ctx: # Find all tool configs in this repository changeset_revision. - if filename.endswith( '.xml' ): + if filename != 'datatypes_conf.xml' and filename.endswith( '.xml' ): fctx = ctx[ filename ] # Write the contents of the old tool config to a temporary file. fh = tempfile.NamedTemporaryFile( 'w' ) @@ -401,11 +831,11 @@ class RepositoryController( BaseUIController, ItemRatings ): fh.close() try: tool = load_tool( trans, tmp_filename ) - if tool is not None: - tool_guids.append( generate_tool_guid( trans, repository, tool ) ) + valid = True except: - # File must not be a valid tool config even though it has a .xml extension. - pass + valid = False + if valid and tool is not None: + tool_guids.append( generate_tool_guid( trans, repository, tool ) ) try: os.unlink( tmp_filename ) except: @@ -425,15 +855,21 @@ class RepositoryController( BaseUIController, ItemRatings ): if tool_guids == metadata_tool_guids: # We've found the repository_metadata record whose changeset_revision # value has been updated. + if from_update_manager: + return update url += repository_metadata.changeset_revision found = True break if not found: # There must be a problem in the data, so we'll just send back the received changeset_revision. log.debug( "Possible data corruption - updated repository_metadata cannot be found for repository id %d." % repository.id ) + if from_update_manager: + return no_update url += changeset_revision else: # There are not tools in the changeset_revision, so no tool updates are possible. + if from_update_manager: + return no_update url += changeset_revision return trans.response.send_redirect( url ) @web.expose @@ -441,6 +877,8 @@ class RepositoryController( BaseUIController, ItemRatings ): # We add params to the keyword dict in this method in order to rename the param # with an "f-" prefix, simulating filtering by clicking a search link. We have # to take this approach because the "-" character is illegal in HTTP requests. + if 'webapp' not in kwd: + kwd[ 'webapp' ] = 'community' if 'operation' in kwd: operation = kwd['operation'].lower() if operation == "view_or_manage_repository": @@ -491,6 +929,7 @@ class RepositoryController( BaseUIController, ItemRatings ): elif operation == "receive email alerts": if trans.user: if kwd[ 'id' ]: + kwd[ 'caller' ] = 'browse_repositories' return trans.response.send_redirect( web.url_for( controller='repository', action='set_email_alerts', **kwd ) ) @@ -583,6 +1022,7 @@ class RepositoryController( BaseUIController, ItemRatings ): message = "Repository '%s' has been created." % repository.name trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', + webapp='community', message=message, id=trans.security.encode_id( repository.id ) ) ) return trans.fill_template( '/webapps/community/repository/create_repository.mako', @@ -615,20 +1055,25 @@ class RepositoryController( BaseUIController, ItemRatings ): hgweb_config_copy = '%s/hgweb.config_%s_backup' % ( trans.app.config.root, backup_date ) shutil.copy( os.path.abspath( hgweb_config ), os.path.abspath( hgweb_config_copy ) ) def __add_hgweb_config_entry( self, trans, repository, repository_path ): - # Add an entry in the hgweb.config file for a new repository. - # An entry looks something like: + # Add an entry in the hgweb.config file for a new repository. An entry looks something like: # repos/test/mira_assembler = database/community_files/000/repo_123. hgweb_config = "%s/hgweb.config" % trans.app.config.root - # Make a backup of the hgweb.config file since we're going to be changing it. - self.__make_hgweb_config_copy( trans, hgweb_config ) - entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path.lstrip( './' ) ) + if repository_path.startswith( './' ): + repository_path = repository_path.replace( './', '', 1 ) + entry = "repos/%s/%s = %s" % ( repository.user.username, repository.name, repository_path ) + tmp_fd, tmp_fname = tempfile.mkstemp() if os.path.exists( hgweb_config ): - output = open( hgweb_config, 'a' ) + # Make a backup of the hgweb.config file since we're going to be changing it. + self.__make_hgweb_config_copy( trans, hgweb_config ) + new_hgweb_config = open( tmp_fname, 'wb' ) + for i, line in enumerate( open( hgweb_config ) ): + new_hgweb_config.write( line ) else: - output = open( hgweb_config, 'w' ) - output.write( '[paths]\n' ) - output.write( "%s\n" % entry ) - output.close() + new_hgweb_config = open( tmp_fname, 'wb' ) + new_hgweb_config.write( '[paths]\n' ) + new_hgweb_config.write( "%s\n" % entry ) + new_hgweb_config.flush() + shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) def __change_hgweb_config_entry( self, trans, repository, old_repository_name, new_repository_name ): # Change an entry in the hgweb.config file for a repository. This only happens when # the owner changes the name of the repository. An entry looks something like: @@ -638,7 +1083,6 @@ class RepositoryController( BaseUIController, ItemRatings ): self.__make_hgweb_config_copy( trans, hgweb_config ) repo_dir = repository.repo_path old_lhs = "repos/%s/%s" % ( repository.user.username, old_repository_name ) - old_entry = "%s = %s" % ( old_lhs, repo_dir ) new_entry = "repos/%s/%s = %s\n" % ( repository.user.username, new_repository_name, repo_dir ) tmp_fd, tmp_fname = tempfile.mkstemp() new_hgweb_config = open( tmp_fname, 'wb' ) @@ -647,17 +1091,16 @@ class RepositoryController( BaseUIController, ItemRatings ): new_hgweb_config.write( new_entry ) else: new_hgweb_config.write( line ) + new_hgweb_config.flush() shutil.move( tmp_fname, os.path.abspath( hgweb_config ) ) def __create_hgrc_file( self, repository ): # At this point, an entry for the repository is required to be in the hgweb.config # file so we can call repository.repo_path. - # Create a .hg/hgrc file that looks something like this: - # [web] - # allow_push = test - # name = convert_characters1 - # push_ssl = False # Since we support both http and https, we set push_ssl to False to override # the default (which is True) in the mercurial api. + # The hg purge extension purges all files and directories not being tracked by + # mercurial in the current repository. It'll remove unknown files and empty + # directories. This is used in the update_for_browsing() method. repo = hg.repository( get_configured_ui(), path=repository.repo_path ) fp = repo.opener( 'hgrc', 'wb' ) fp.write( '[paths]\n' ) @@ -667,12 +1110,15 @@ class RepositoryController( BaseUIController, ItemRatings ): fp.write( 'allow_push = %s\n' % repository.user.username ) fp.write( 'name = %s\n' % repository.name ) fp.write( 'push_ssl = false\n' ) + fp.write( '[extensions]\n' ) + fp.write( 'hgext.purge=' ) fp.close() @web.expose def browse_repository( self, trans, id, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) + webapp = params.get( 'webapp', 'community' ) 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 ) @@ -685,6 +1131,7 @@ class RepositoryController( BaseUIController, ItemRatings ): repository=repository, commit_message=commit_message, is_malicious=is_malicious, + webapp=webapp, message=message, status=status ) @web.expose @@ -757,7 +1204,7 @@ class RepositoryController( BaseUIController, ItemRatings ): tip = repository.tip for selected_file in selected_files_to_delete: try: - commands.remove( repo.ui, repo, repo_file, force=True ) + commands.remove( repo.ui, repo, selected_file, force=True ) except Exception, e: # I never have a problem with commands.remove on a Mac, but in the test/production # tool shed environment, it throws an exception whenever I delete all files from a @@ -826,6 +1273,7 @@ class RepositoryController( BaseUIController, ItemRatings ): message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) + webapp = params.get( 'webapp', 'community' ) 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 ) ) @@ -861,8 +1309,10 @@ class RepositoryController( BaseUIController, ItemRatings ): revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: + repository_metadata_id = trans.security.encode_id( repository_metadata.id ), metadata = repository_metadata.metadata else: + repository_metadata_id = None metadata = None is_malicious = change_set_is_malicious( trans, id, repository.tip ) if is_malicious: @@ -874,6 +1324,7 @@ class RepositoryController( BaseUIController, ItemRatings ): return trans.fill_template( '/webapps/community/repository/view_repository.mako', repo=repo, repository=repository, + repository_metadata_id=repository_metadata_id, metadata=metadata, avg_rating=avg_rating, display_reviews=display_reviews, @@ -883,6 +1334,7 @@ class RepositoryController( BaseUIController, ItemRatings ): changeset_revision_select_field=changeset_revision_select_field, revision_label=revision_label, is_malicious=is_malicious, + webapp=webapp, message=message, status=status ) @web.expose @@ -913,14 +1365,20 @@ class RepositoryController( BaseUIController, ItemRatings ): if params.get( 'edit_repository_button', False ): flush_needed = False # TODO: add a can_manage in the security agent. - if user != repository.user: + if not ( user.email == repository.user.email or trans.user_is_admin() ): message = "You are not the owner of this repository, so you cannot manage it." - status = error return trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', id=id, + webapp='community', message=message, - status=status ) ) + status='error' ) ) + if description != repository.description: + repository.description = description + flush_needed = True + if long_description != repository.long_description: + repository.long_description = long_description + flush_needed = True if repo_name != repository.name: message = self.__validate_repository_name( repo_name, user ) if message: @@ -929,12 +1387,6 @@ class RepositoryController( BaseUIController, ItemRatings ): self.__change_hgweb_config_entry( trans, repository, repository.name, repo_name ) repository.name = repo_name flush_needed = True - if description != repository.description: - repository.description = description - flush_needed = True - if long_description != repository.long_description: - repository.long_description = long_description - flush_needed = True if flush_needed: trans.sa_session.add( repository ) trans.sa_session.flush() @@ -999,9 +1451,11 @@ class RepositoryController( BaseUIController, ItemRatings ): revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: + repository_metadata_id = trans.security.encode_id( repository_metadata.id ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious else: + repository_metadata_id = None metadata = None is_malicious = False if is_malicious: @@ -1021,6 +1475,7 @@ class RepositoryController( BaseUIController, ItemRatings ): allow_push_select_field=allow_push_select_field, repo=repo, repository=repository, + repository_metadata_id=repository_metadata_id, changeset_revision=changeset_revision, changeset_revision_select_field=changeset_revision_select_field, revision_label=revision_label, @@ -1045,6 +1500,10 @@ class RepositoryController( BaseUIController, ItemRatings ): changesets = [] for changeset in repo.changelog: ctx = repo.changectx( changeset ) + if get_repository_metadata_by_changeset_revision( trans, id, str( ctx ) ): + has_metadata = True + else: + has_metadata = False t, tz = ctx.date() date = datetime( *time.gmtime( float( t ) - tz )[:6] ) display_date = date.strftime( "%Y-%m-%d" ) @@ -1055,7 +1514,8 @@ class RepositoryController( BaseUIController, ItemRatings ): 'description' : ctx.description(), 'files' : ctx.files(), 'user' : ctx.user(), - 'parent' : ctx.parents()[0] } + 'parent' : ctx.parents()[0], + 'has_metadata' : has_metadata } # Make sure we'll view latest changeset first. changesets.insert( 0, change_dict ) is_malicious = change_set_is_malicious( trans, id, repository.tip ) @@ -1144,7 +1604,9 @@ class RepositoryController( BaseUIController, ItemRatings ): @web.require_login( "set email alerts" ) def set_email_alerts( self, trans, **kwd ): # Set email alerts for selected repositories - params = util.Params( kwd ) + # This method is called from multiple grids, so + # the caller must be passed. + caller = kwd[ 'caller' ] user = trans.user if user: repository_ids = util.listify( kwd.get( 'id', '' ) ) @@ -1176,9 +1638,63 @@ class RepositoryController( BaseUIController, ItemRatings ): kwd[ 'status' ] = 'done' del kwd[ 'operation' ] return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repositories', + action=caller, **kwd ) ) @web.expose + @web.require_login( "manage email alerts" ) + def manage_email_alerts( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + new_repo_alert = params.get( 'new_repo_alert', '' ) + new_repo_alert_checked = CheckboxField.is_checked( new_repo_alert ) + user = trans.user + if params.get( 'new_repo_alert_button', False ): + user.new_repo_alert = new_repo_alert_checked + trans.sa_session.add( user ) + trans.sa_session.flush() + if new_repo_alert_checked: + message = 'You will receive email alerts for all new valid tool shed repositories.' + else: + message = 'You will not receive any email alerts for new valid tool shed repositories.' + checked = new_repo_alert_checked or ( user and user.new_repo_alert ) + new_repo_alert_check_box = CheckboxField( 'new_repo_alert', checked=checked ) + email_alert_repositories = [] + for repository in trans.sa_session.query( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.email_alerts != None ) ) \ + .order_by( trans.model.Repository.table.c.name ): + if user.email in repository.email_alerts: + email_alert_repositories.append( repository ) + return trans.fill_template( "/webapps/community/user/manage_email_alerts.mako", + webapp='community', + new_repo_alert_check_box=new_repo_alert_check_box, + email_alert_repositories=email_alert_repositories, + message=message, + status=status ) + @web.expose + @web.require_login( "manage email alerts" ) + def multi_select_email_alerts( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + if 'webapp' not in kwd: + kwd[ 'webapp' ] = 'community' + if 'operation' in kwd: + operation = kwd['operation'].lower() + if operation == "receive email alerts": + if trans.user: + if kwd[ 'id' ]: + kwd[ 'caller' ] = 'multi_select_email_alerts' + return trans.response.send_redirect( web.url_for( controller='repository', + action='set_email_alerts', + **kwd ) ) + else: + kwd[ 'message' ] = 'You must be logged in to set email alerts.' + kwd[ 'status' ] = 'error' + del kwd[ 'operation' ] + return self.email_alerts_repository_list_grid( trans, **kwd ) + @web.expose @web.require_login( "set repository metadata" ) def set_metadata( self, trans, id, ctx_str, **kwd ): malicious = kwd.get( 'malicious', '' ) @@ -1206,57 +1722,230 @@ class RepositoryController( BaseUIController, ItemRatings ): message=message, status=status ) ) @web.expose + def reset_all_metadata( self, trans, id, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository = get_repository( trans, id ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + if len( repo ) == 1: + message, status = set_repository_metadata( trans, id, repository.tip, **kwd ) + else: + # The list of changeset_revisions refers to repository_metadata records that have been + # created or updated. When the following loop completes, we'll delete all repository_metadata + # records for this repository that do not have a changeset_revision value in this list. + changeset_revisions = [] + ancestor_changeset_revision = None + ancestor_metadata_dict = None + for changeset in repo.changelog: + current_changeset_revision = str( repo.changectx( changeset ) ) + ctx = get_changectx_for_changeset( trans, repo, current_changeset_revision ) + if current_changeset_revision == repository.tip: + current_metadata_dict, invalid_files = generate_metadata_for_repository_tip( trans, id, ctx, current_changeset_revision, repo_dir ) + else: + current_metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, id, ctx, current_changeset_revision, repo_dir ) + if current_metadata_dict: + if ancestor_changeset_revision: + # Compare metadata from ancestor and current. The value of comparsion will be one of: + # 'no metadata' - no metadata for either ancestor or current, so continue from current + # 'equal' - ancestor metadata is equivalent to current metadata, so continue from current + # 'subset' - ancestor metadata is a subset of current metadata, so continue from current + # 'not equal and not subset' - ancestor metadata is neither equal to nor a subset of current + # metadata, so persist ancestor metadata. + comparison = self.__compare_changeset_revisions( ancestor_changeset_revision, + ancestor_metadata_dict, + current_changeset_revision, + current_metadata_dict ) + if comparison in [ 'no metadata', 'equal', 'subset' ]: + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict + elif comparison == 'not equal and not subset': + self.__create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict ) + # Keep track of the changeset_revisions that we've persisted. + changeset_revisions.append( ancestor_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None + else: + # We're either at the first change set in the change log or we have just created or updated + # a repository_metadata record. At this point we set the ancestor changeset to the current + # changeset for comparison in the next iteration. + ancestor_changeset_revision = current_changeset_revision + ancestor_metadata_dict = current_metadata_dict + if not ctx.children(): + # We're at the end of the change log. + self.__create_or_update_repository_metadata( trans, id, repository, current_changeset_revision, current_metadata_dict ) + changeset_revisions.append( current_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None + elif ancestor_metadata_dict: + # Our current change set has no metadata, but our ancestor change set has metadata, so save it. + self.__create_or_update_repository_metadata( trans, id, repository, ancestor_changeset_revision, ancestor_metadata_dict ) + # Keep track of the changeset_revisions that we've persisted. + changeset_revisions.append( ancestor_changeset_revision ) + ancestor_changeset_revision = None + ancestor_metadata_dict = None + self.__clean_repository_metadata( trans, id, changeset_revisions ) + if not message: + message = "Repository metadata has been reset." + status = 'done' + return trans.response.send_redirect( web.url_for( controller='repository', + action='manage_repository', + id=id, + message=message, + status=status ) ) + def __clean_repository_metadata( self, trans, id, changeset_revisions ): + # Delete all repository_metadata reecords associated with the repository + # that have a changeset_revision that is not in changeset_revisions. + for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ): + if repository_metadata.changeset_revision not in changeset_revisions: + trans.sa_session.delete( repository_metadata ) + trans.sa_session.flush() + def __create_or_update_repository_metadata( self, 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() + def __compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): + # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. This changeset_revision + # is an ancestor of current_changeset_revision which is associated with current_metadata_dict. + # + # TODO: a new repository_metadata record will be created only when this method returns the string + # 'not equal and not subset'. However, we're currently also returning the strings 'no metadata', + # 'equal' and 'subset', depending upon how the 2 change sets compare. We'll leave things this way + # for the current time in case we discover a use for these additional result strings. + # + # Get information about tools. + if 'tools' in ancestor_metadata_dict: + ancestor_tools = ancestor_metadata_dict[ 'tools' ] + else: + ancestor_tools = [] + if 'tools' in current_metadata_dict: + current_tools = current_metadata_dict[ 'tools' ] + else: + current_tools = [] + ancestor_guids = [] + for tool_dict in ancestor_tools: + ancestor_guids.append( tool_dict[ 'guid' ] ) + ancestor_guids.sort() + current_guids = [] + for tool_dict in current_tools: + current_guids.append( tool_dict[ 'guid' ] ) + current_guids.sort() + # Get information about workflows. + if 'workflows' in ancestor_metadata_dict: + ancestor_workflows = ancestor_metadata_dict[ 'workflows' ] + else: + ancestor_workflows = [] + if 'workflows' in current_metadata_dict: + current_workflows = current_metadata_dict[ 'workflows' ] + else: + current_workflows = [] + # Get information about datatypes. + if 'datatypes' in ancestor_metadata_dict: + ancestor_datatypes = ancestor_metadata_dict[ 'datatypes' ] + else: + ancestor_datatypes = [] + if 'datatypes' in current_metadata_dict: + current_datatypes = current_metadata_dict[ 'datatypes' ] + else: + current_datatypes = [] + # Handle case where no metadata exists for either changeset. + if not ancestor_guids and not current_guids and not ancestor_workflows and not current_workflows and not ancestor_datatypes and not current_datatypes: + return 'no metadata' + workflow_comparison = self.__compare_workflows( ancestor_workflows, current_workflows ) + datatype_comparison = self.__compare_datatypes( ancestor_datatypes, current_datatypes ) + # Handle case where all metadata is the same. + if ancestor_guids == current_guids and workflow_comparison == 'equal' and datatype_comparison == 'equal': + return 'equal' + if workflow_comparison == 'subset' and datatype_comparison == 'subset': + is_subset = True + for guid in ancestor_guids: + if guid not in current_guids: + is_subset = False + break + if is_subset: + return 'subset' + return 'not equal and not subset' + def __compare_workflows( self, ancestor_workflows, current_workflows ): + # Determine if ancestor_workflows is the same as current_workflows + # or if ancestor_workflows is a subset of current_workflows. + if len( ancestor_workflows ) <= len( current_workflows ): + for ancestor_workflow in ancestor_workflows: + # Currently the only way to differentiate workflows is by name. + ancestor_workflow_name = ancestor_workflow[ 'name' ] + num_ancestor_workflow_steps = len( ancestor_workflow[ 'steps' ] ) + found_in_current = False + for current_workflow in current_workflows: + # Assume that if the name and number of steps are euqal, + # then the workflows are the same. Of course, this may + # not be true... + if current_workflow[ 'name' ] == ancestor_workflow_name and len( current_workflow[ 'steps' ] ) == num_ancestor_workflow_steps: + found_in_current = True + break + if not found_in_current: + return 'not equal and not subset' + if len( ancestor_workflows ) == len( current_workflows ): + return 'equal' + else: + return 'subset' + return 'not equal and not subset' + def __compare_datatypes( self, ancestor_datatypes, current_datatypes ): + # Determine if ancestor_datatypes is the same as current_datatypes + # or if ancestor_datatypes is a subset of current_datatypes. Each + # datatype dict looks something like: + # {"dtype": "galaxy.datatypes.images:Image", "extension": "pdf", "mimetype": "application/pdf"} + if len( ancestor_datatypes ) <= len( current_datatypes ): + for ancestor_datatype in ancestor_datatypes: + # Currently the only way to differentiate datatypes is by name. + ancestor_datatype_dtype = ancestor_datatype[ 'dtype' ] + ancestor_datatype_extension = ancestor_datatype[ 'extension' ] + ancestor_datatype_mimetype = ancestor_datatype[ 'mimetype' ] + found_in_current = False + for current_datatype in current_datatypes: + if current_datatype[ 'dtype' ] == ancestor_datatype_dtype and \ + current_datatype[ 'extension' ] == ancestor_datatype_extension and \ + current_datatype[ 'mimetype' ] == ancestor_datatype_mimetype: + found_in_current = True + break + if not found_in_current: + return 'not equal and not subset' + if len( ancestor_datatypes ) == len( current_datatypes ): + return 'equal' + else: + return 'subset' + return 'not equal and not subset' + @web.expose def display_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - display_for_install = util.string_as_bool( params.get( 'display_for_install', False ) ) + webapp = params.get( 'webapp', 'community' ) repository = get_repository( trans, repository_id ) - repo = hg.repository( get_configured_ui(), repository.repo_path ) + tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) + tool_state = self.__new_state( trans ) + is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) try: - if changeset_revision == repository.tip: - # Get the tool config from the file system we use for browsing. - tool = load_tool( trans, os.path.abspath( tool_config ) ) - else: - # Get the tool config file name from the hgweb url, something like: - # /repos/test/convert_chars1/file/e58dcf0026c7/convert_characters.xml - old_tool_config_file_name = tool_config.split( '/' )[ -1 ] - ctx = get_changectx_for_changeset( trans, repo, changeset_revision ) - fctx = None - for filename in ctx: - filename_head, filename_tail = os.path.split( filename ) - if filename_tail == old_tool_config_file_name: - fctx = ctx[ filename ] - break - if fctx: - # Write the contents of the old tool config to a temporary file. - fh = tempfile.NamedTemporaryFile( 'w' ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'w' ) - fh.write( fctx.data() ) - fh.close() - tool = load_tool( trans, tmp_filename ) - try: - os.unlink( tmp_filename ) - except: - pass - else: - tool = None - tool_state = self.__new_state( trans ) - is_malicious = change_set_is_malicious( trans, repository_id, repository.tip ) return trans.fill_template( "/webapps/community/repository/tool_form.mako", repository=repository, changeset_revision=changeset_revision, tool=tool, tool_state=tool_state, is_malicious=is_malicious, - display_for_install=display_for_install, + webapp=webapp, message=message, status=status ) except Exception, e: - message = "Error loading tool: %s. Click Reset metadata to correct this error." % str( e ) - if display_for_install: + message = "Error displaying tool, probably due to a problem in the tool config. The exception is: %s." % str( e ) + if webapp == 'galaxy': return trans.response.send_redirect( web.url_for( controller='repository', action='preview_tools_in_changeset', repository_id=repository_id, @@ -1286,7 +1975,7 @@ class RepositoryController( BaseUIController, ItemRatings ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - display_for_install = util.string_as_bool( params.get( 'display_for_install', False ) ) + webapp = params.get( 'webapp', 'community' ) repository = get_repository( trans, repository_id ) metadata = {} tool = None @@ -1315,7 +2004,7 @@ class RepositoryController( BaseUIController, ItemRatings ): revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field, is_malicious=is_malicious, - display_for_install=display_for_install, + webapp=webapp, message=message, status=status ) @web.expose diff --git a/lib/galaxy/webapps/community/controllers/upload.py b/lib/galaxy/webapps/community/controllers/upload.py index bc206ac6693..e297e9ee2ed 100644 --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -1,4 +1,4 @@ -import sys, os, shutil, logging, tarfile, tempfile +import sys, os, shutil, logging, tarfile, tempfile, urllib from galaxy.web.base.controller import * from galaxy.model.orm import * from galaxy.datatypes.checkers import * @@ -11,9 +11,6 @@ log = logging.getLogger( __name__ ) SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error" CHUNK_SIZE = 2**20 # 1Mb -class UploadError( Exception ): - pass - class UploadController( BaseUIController ): @web.expose @web.require_login( 'upload', use_panels=True, webapp='community' ) @@ -32,20 +29,44 @@ class UploadController( BaseUIController ): remove_repo_files_not_in_tar = util.string_as_bool( params.get( 'remove_repo_files_not_in_tar', 'true' ) ) uploaded_file = None upload_point = self.__get_upload_point( repository, **kwd ) - # Get the current repository tip. tip = repository.tip + file_data = params.get( 'file_data', '' ) + url = params.get( 'url', '' ) + # Part of the upload process is sending email notification to those that have registered to + # receive them. One scenario occurs when the first change set is produced for the repository. + # See the handle_email_alerts() method for the definition of the scenarios. + new_repo_alert = repository.is_new if params.get( 'upload_button', False ): current_working_dir = os.getcwd() - file_data = params.get( 'file_data', '' ) - if file_data == '': + if file_data == '' and url == '': message = 'No files were entered on the upload form.' status = 'error' uploaded_file = None + elif url: + valid_url = True + try: + stream = urllib.urlopen( url ) + except Exception, e: + valid_url = False + message = 'Error uploading file via http: %s' % str( e ) + status = 'error' + uploaded_file = None + if valid_url: + fd, uploaded_file_name = tempfile.mkstemp() + uploaded_file = open( uploaded_file_name, 'wb' ) + while 1: + chunk = stream.read( CHUNK_SIZE ) + if not chunk: + break + uploaded_file.write( chunk ) + uploaded_file.flush() + uploaded_file_filename = url.split( '/' )[ -1 ] + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 elif file_data not in ( '', None ): uploaded_file = file_data.file uploaded_file_name = uploaded_file.name uploaded_file_filename = file_data.filename - isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 + isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 if uploaded_file: isgzip = False isbz2 = False @@ -70,13 +91,14 @@ class UploadController( BaseUIController ): tar = None istar = False if istar: - ok, message, files_to_remove = self.upload_tar( trans, - repository, - tar, - uploaded_file, - upload_point, - remove_repo_files_not_in_tar, - commit_message ) + ok, message, files_to_remove, content_alert_str = self.upload_tar( trans, + repository, + tar, + uploaded_file, + upload_point, + remove_repo_files_not_in_tar, + commit_message, + new_repo_alert ) else: if ( isgzip or isbz2 ) and uncompress_file: uploaded_file_filename = self.uncompress( repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ) @@ -86,6 +108,13 @@ class UploadController( BaseUIController ): full_path = os.path.abspath( os.path.join( repo_dir, uploaded_file_filename ) ) # Move the uploaded file to the load_point within the repository hierarchy. shutil.move( uploaded_file_name, full_path ) + # See if any admin users have chosen to receive email alerts when a repository is + # updated. If so, check every uploaded file to ensure content is appropriate. + check_contents = check_file_contents( trans ) + if check_contents and os.path.isfile( full_path ): + content_alert_str = self.__check_file_content( full_path ) + else: + content_alert_str = '' commands.add( repo.ui, repo, full_path ) try: commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) @@ -100,14 +129,16 @@ class UploadController( BaseUIController ): # file is being uploaded by parsing the file and adding new entries # to the in-memory trans.app.tool_data_tables dictionary as well as # appending them to the shed's tool_data_table_conf.xml file on disk. - error, error_message = handle_sample_tool_data_table_conf_file( trans, full_path ) + error, error_message = handle_sample_tool_data_table_conf_file( trans.app, full_path ) if error: message = '%s
%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_loc_file( trans, full_path ) - handle_email_alerts( trans, repository ) + copy_sample_loc_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 ) if ok: # Update the repository files for browsing. update_for_browsing( trans, repository, current_working_dir, commit_message=commit_message ) @@ -126,7 +157,7 @@ class UploadController( BaseUIController ): else: message = 'No changes to repository.' # Set metadata on the repository tip - error_message, status = set_repository_metadata( trans, repository_id, repository.tip, **kwd ) + error_message, status = set_repository_metadata( trans, repository_id, repository.tip, content_alert_str=content_alert_str, **kwd ) if error_message: message = '%s
%s' % ( message, error_message ) return trans.response.send_redirect( web.url_for( controller='repository', @@ -138,6 +169,7 @@ class UploadController( BaseUIController ): action='browse_repository', id=repository_id, commit_message='Deleted selected files', + webapp='community', message=message, status=status ) ) else: @@ -145,21 +177,23 @@ class UploadController( BaseUIController ): selected_categories = [ trans.security.decode_id( id ) for id in category_ids ] return trans.fill_template( '/webapps/community/repository/upload.mako', repository=repository, + url=url, commit_message=commit_message, uncompress_file=uncompress_file, remove_repo_files_not_in_tar=remove_repo_files_not_in_tar, message=message, status=status ) - def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message ): + def upload_tar( self, trans, repository, tar, uploaded_file, upload_point, remove_repo_files_not_in_tar, commit_message, new_repo_alert ): # Upload a tar archive of files. repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) files_to_remove = [] + content_alert_str = '' ok, message = self.__check_archive( tar ) if not ok: tar.close() uploaded_file.close() - return ok, message, files_to_remove + return ok, message, files_to_remove, content_alert_str else: if upload_point is not None: full_path = os.path.abspath( os.path.join( repo_dir, upload_point ) ) @@ -214,7 +248,13 @@ class UploadController( BaseUIController ): except OSError, e: # The directory is not empty pass + # See if any admin users have chosen to receive email alerts when a repository is + # updated. If so, check every uploaded file to ensure content is appropriate. + check_contents = check_file_contents( trans ) for filename_in_archive in filenames_in_archive: + # Check file content to ensure it is appropriate. + if check_contents and os.path.isfile( filename_in_archive ): + content_alert_str += self.__check_file_content( filename_in_archive ) commands.add( repo.ui, repo, filename_in_archive ) if filename_in_archive.endswith( 'tool_data_table_conf.xml.sample' ): # Handle the special case where a tool_data_table_conf.xml.sample @@ -223,11 +263,11 @@ class UploadController( BaseUIController ): # appending them to the shed's tool_data_table_conf.xml file on disk. error, message = handle_sample_tool_data_table_conf_file( trans, filename_in_archive ) if error: - return False, message, files_to_remove + return False, message, files_to_remove, content_alert_str if filename_in_archive.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_loc_file( trans, filename_in_archive ) + copy_sample_loc_file( trans.app, filename_in_archive ) try: commands.commit( repo.ui, repo, full_path, user=trans.user.username, message=commit_message ) except Exception, e: @@ -236,8 +276,10 @@ class UploadController( BaseUIController ): # exception. If this happens, we'll try the following. repo.dirstate.write() repo.commit( user=trans.user.username, text=commit_message ) - handle_email_alerts( trans, repository ) - return True, '', files_to_remove + # 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 def uncompress( self, repository, uploaded_file_name, uploaded_file_filename, isgzip, isbz2 ): if isgzip: self.__handle_gzip( repository, uploaded_file_name ) @@ -313,4 +355,10 @@ class UploadController( BaseUIController ): message = "Uploaded archives cannot contain hgrc files." return False, message return True, '' - + def __check_file_content( self, file_path ): + message = '' + if check_html( file_path ): + message = 'The file "%s" contains HTML content.\n' % str( file_path ) + elif check_image( file_path ): + message = 'The file "%s" contains image content.\n' % str( file_path ) + return message diff --git a/lib/galaxy/webapps/community/controllers/workflow.py b/lib/galaxy/webapps/community/controllers/workflow.py new file mode 100644 index 00000000000..ed7d8af418e --- /dev/null +++ b/lib/galaxy/webapps/community/controllers/workflow.py @@ -0,0 +1,393 @@ +import pkg_resources +pkg_resources.require( "simplejson" ) +pkg_resources.require( "SVGFig" ) +import os, logging, ConfigParser, tempfile, shutil, svgfig +from galaxy.webapps.community import model +from galaxy.web.framework.helpers import time_ago, iff, grids +from galaxy.util.json import from_json_string, to_json_string +from galaxy.workflow.modules import InputDataModule, ToolModule, WorkflowModuleFactory +from galaxy.tools import DefaultToolState +from galaxy.web.controllers.workflow import attach_ordered_steps +from galaxy.model.orm import * +from common import * + +class RepoInputDataModule( InputDataModule ): + + type = "data_input" + name = "Input dataset" + + @classmethod + def new( Class, trans, tools_metadata=None, tool_id=None ): + module = Class( trans ) + module.state = dict( name="Input Dataset" ) + return module + @classmethod + def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata=None, secure=True ): + module = Class( trans ) + state = from_json_string( step_dict[ "tool_state" ] ) + module.state = dict( name=state.get( "name", "Input Dataset" ) ) + return module + @classmethod + def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): + module = Class( trans ) + module.state = dict( name="Input Dataset" ) + if step.tool_inputs and "name" in step.tool_inputs: + module.state[ 'name' ] = step.tool_inputs[ 'name' ] + return module + +class RepoToolModule( ToolModule ): + + type = "tool" + + def __init__( self, trans, repository_id, changeset_revision, tools_metadata, tool_id ): + self.trans = trans + self.tools_metadata = tools_metadata + self.tool_id = tool_id + self.tool = None + self.errors = None + for tool_dict in tools_metadata: + if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]: + self.tool, message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_dict[ 'tool_config' ] ) + if message and self.tool is None: + self.errors = 'unavailable' + break + self.post_job_actions = {} + self.workflow_outputs = [] + self.state = None + @classmethod + def new( Class, trans, repository_id, changeset_revision, tools_metadata, tool_id=None ): + module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) + module.state = module.tool.new_state( trans, all_pages=True ) + return module + @classmethod + def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata, secure=True ): + tool_id = step_dict[ 'tool_id' ] + module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) + module.state = DefaultToolState() + if module.tool is not None: + module.state.decode( step_dict[ "tool_state" ], module.tool, module.trans.app, secure=secure ) + module.errors = step_dict.get( "tool_errors", None ) + return module + @classmethod + def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): + module = Class( trans, repository_id, changeset_revision, tools_metadata, step.tool_id ) + module.state = DefaultToolState() + if module.tool: + module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) + else: + module.state.inputs = {} + module.errors = step.tool_errors + return module + def get_data_inputs( self ): + data_inputs = [] + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, DataToolParameter ): + data_inputs.append( dict( name=prefixed_name, + label=prefixed_label, + extensions=input.extensions ) ) + if self.tool: + visit_input_values( self.tool.inputs, self.state.inputs, callback ) + return data_inputs + def get_data_outputs( self ): + data_outputs = [] + if self.tool: + data_inputs = None + for name, tool_output in self.tool.outputs.iteritems(): + if tool_output.format_source != None: + # Default to special name "input" which remove restrictions on connections + formats = [ 'input' ] + if data_inputs == None: + data_inputs = self.get_data_inputs() + # Find the input parameter referenced by format_source + for di in data_inputs: + # Input names come prefixed with conditional and repeat names separated by '|', + # so remove prefixes when comparing with format_source. + if di[ 'name' ] != None and di[ 'name' ].split( '|' )[ -1 ] == tool_output.format_source: + formats = di[ 'extensions' ] + else: + formats = [ tool_output.format ] + for change_elem in tool_output.change_format: + for when_elem in change_elem.findall( 'when' ): + format = when_elem.get( 'format', None ) + if format and format not in formats: + formats.append( format ) + data_outputs.append( dict( name=name, extensions=formats ) ) + return data_outputs + +class RepoWorkflowModuleFactory( WorkflowModuleFactory ): + def __init__( self, module_types ): + self.module_types = module_types + def new( self, trans, type, tools_metadata=None, tool_id=None ): + """Return module for type and (optional) tool_id initialized with new / default state.""" + assert type in self.module_types + return self.module_types[type].new( trans, tool_id ) + def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ): + """Return module initialized from the data in dictionary `step_dict`.""" + type = step_dict[ 'type' ] + assert type in self.module_types + return self.module_types[ type ].from_dict( trans, repository_id, changeset_revision, step_dict, **kwd ) + def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ): + """Return module initialized from the WorkflowStep object `step`.""" + type = step.type + return self.module_types[ type ].from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) + +module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) ) + +class WorkflowController( BaseUIController ): + @web.expose + def view_workflow( self, trans, **kwd ): + repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) + workflow_name = kwd.get( 'workflow_name', '' ) + if workflow_name: + workflow_name = decode( workflow_name ) + webapp = kwd.get( 'webapp', 'community' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + repository = get_repository( trans, trans.security.encode_id( repository_metadata.repository_id ) ) + return trans.fill_template( "/webapps/community/repository/view_workflow.mako", + repository=repository, + changeset_revision=repository_metadata.changeset_revision, + repository_metadata_id=repository_metadata_id, + workflow_name=workflow_name, + webapp=webapp, + message=message, + status=status ) + @web.expose + def generate_workflow_image( self, trans, repository_metadata_id, workflow_name, webapp='community' ): + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + 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 ) + for workflow_dict in metadata[ 'workflows' ]: + if workflow_dict[ 'name' ] == workflow_name: + break + if 'tools' in metadata: + tools_metadata = metadata[ 'tools' ] + else: + tools_metadata = [] + workflow, missing_tool_tups = self.__workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision ) + data = [] + canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" ) + text = svgfig.SVG( "g" ) + connectors = svgfig.SVG( "g" ) + boxes = svgfig.SVG( "g" ) + svgfig.Text.defaults[ "font-size" ] = "10px" + in_pos = {} + out_pos = {} + margin = 5 + # Spacing between input/outputs. + line_px = 16 + # Store px width for boxes of each step. + widths = {} + max_width, max_x, max_y = 0, 0, 0 + for step in workflow.steps: + step.upgrade_messages = {} + module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) + tool_errors = module.type == 'tool' and not module.tool + module_data_inputs = self.__get_data_inputs( step, module ) + module_data_outputs = self.__get_data_outputs( step, module, workflow.steps ) + step_dict = { + 'id' : step.order_index, + 'data_inputs' : module_data_inputs, + 'data_outputs' : module_data_outputs, + 'position' : step.position, + 'tool_errors' : tool_errors + } + input_conn_dict = {} + for conn in step.input_connections: + input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name ) + step_dict[ 'input_connections' ] = input_conn_dict + data.append( step_dict ) + x, y = step.position[ 'left' ], step.position[ 'top' ] + count = 0 + module_name = self.__get_name( module, missing_tool_tups ) + max_len = len( module_name ) * 1.5 + text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() ) + y += 45 + for di in module_data_inputs: + cur_y = y + count * line_px + if step.order_index not in in_pos: + in_pos[ step.order_index ] = {} + in_pos[ step.order_index ][ di[ 'name' ] ] = ( x, cur_y ) + text.append( svgfig.Text( x, cur_y, di[ 'label' ] ).SVG() ) + count += 1 + max_len = max( max_len, len( di[ 'label' ] ) ) + if len( module.get_data_inputs() ) > 0: + y += 15 + for do in module_data_outputs: + cur_y = y + count * line_px + if step.order_index not in out_pos: + out_pos[ step.order_index ] = {} + out_pos[ step.order_index ][ do[ 'name' ] ] = ( x, cur_y ) + text.append( svgfig.Text( x, cur_y, do[ 'name' ] ).SVG() ) + count += 1 + max_len = max( max_len, len( do['name' ] ) ) + widths[ step.order_index ] = max_len * 5.5 + max_x = max( max_x, step.position[ 'left' ] ) + max_y = max( max_y, step.position[ 'top' ] ) + max_width = max( max_width, widths[ step.order_index ] ) + for step_dict in data: + tool_unavailable = step_dict[ 'tool_errors' ] + width = widths[ step_dict[ 'id' ] ] + x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ] + if tool_unavailable: + fill = "#EBBCB2" + else: + fill = "#EBD9B2" + boxes.append( svgfig.Rect( x - margin, y, x + width - margin, y + 30, fill=fill ).SVG() ) + box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * line_px + margin + # Draw separator line. + if len( step_dict[ 'data_inputs' ] ) > 0: + box_height += 15 + sep_y = y + len( step_dict[ 'data_inputs' ] ) * line_px + 40 + text.append( svgfig.Line( x - margin, sep_y, x + width - margin, sep_y ).SVG() ) + # Define an input/output box. + boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() ) + for conn, output_dict in step_dict[ 'input_connections' ].iteritems(): + in_coords = in_pos[ step_dict[ 'id' ] ][ conn ] + out_conn_pos = out_pos[ output_dict[ 'id' ] ][ output_dict[ 'output_name' ] ] + adjusted = ( out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] ) + text.append( svgfig.SVG( "circle", + cx=out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ] - margin, + cy=out_conn_pos[ 1 ] - margin, + r = 5, + fill="#ffffff" ) ) + connectors.append( svgfig.Line( adjusted[ 0 ], + adjusted[ 1 ] - margin, + in_coords[ 0 ] - 10, + in_coords[ 1 ], + arrow_end = "true" ).SVG() ) + canvas.append( connectors ) + canvas.append( boxes ) + canvas.append( text ) + width, height = ( max_x + max_width + 50 ), max_y + 300 + canvas[ 'width' ] = "%s px" % width + canvas[ 'height' ] = "%s px" % height + canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height ) + trans.response.set_content_type( "image/svg+xml" ) + return canvas.standalone_xml() + def __get_name( self, module, missing_tool_tups ): + module_name = module.get_name() + if module.type == 'tool' and module_name == 'unavailable': + for missing_tool_tup in missing_tool_tups: + missing_tool_id, missing_tool_name, missing_tool_version = missing_tool_tup + if missing_tool_id == module.tool_id: + module_name = '%s' % missing_tool_name + return module_name + def __get_data_inputs( self, step, module ): + if module.type == 'tool': + if module.tool: + return module.get_data_inputs() + else: + data_inputs = [] + for wfsc in step.input_connections: + data_inputs_dict = {} + data_inputs_dict[ 'extensions' ] = [ '' ] + data_inputs_dict[ 'name' ] = wfsc.input_name + data_inputs_dict[ 'label' ] = 'Unknown' + data_inputs.append( data_inputs_dict ) + return data_inputs + return module.get_data_inputs() + def __get_data_outputs( self, step, module, steps ): + if module.type == 'tool': + if module.tool: + return module.get_data_outputs() + else: + data_outputs = [] + data_outputs_dict = {} + data_outputs_dict[ 'extensions' ] = [ 'input' ] + found = False + for workflow_step in steps: + for wfsc in workflow_step.input_connections: + if step.name == wfsc.output_step.name: + data_outputs_dict[ 'name' ] = wfsc.output_name + found = True + break + if found: + break + if not found: + # We're at the last step of the workflow. + data_outputs_dict[ 'name' ] = 'output' + data_outputs.append( data_outputs_dict ) + return data_outputs + return module.get_data_outputs() + def __workflow_from_dict( self, trans, workflow_dict, tools_metadata, repository_id, changeset_revision ): + """Creates and returns workflow object from a dictionary.""" + trans.workflow_building_mode = True + workflow = model.Workflow() + workflow.name = workflow_dict[ 'name' ] + workflow.has_errors = False + steps = [] + # Keep ids for each step that we need to use to make connections. + steps_by_external_id = {} + # Keep track of tools required by the workflow that are not available in + # the tool shed repository. Each tuple in the list of missing_tool_tups + # will be ( tool_id, tool_name, tool_version ). + missing_tool_tups = [] + # First pass to build step objects and populate basic values + for key, step_dict in workflow_dict[ 'steps' ].iteritems(): + # Create the model class for the step + step = model.WorkflowStep() + step.name = step_dict[ 'name' ] + step.position = step_dict[ 'position' ] + module = module_factory.from_dict( trans, repository_id, changeset_revision, step_dict, tools_metadata=tools_metadata, secure=False ) + if module.type == 'tool' and module.tool is None: + # A required tool is not available in the current repository. + step.tool_errors = 'unavailable' + missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) + if missing_tool_tup not in missing_tool_tups: + missing_tool_tups.append( missing_tool_tup ) + module.save_to_step( step ) + if step.tool_errors: + workflow.has_errors = True + # Stick this in the step temporarily. + step.temp_input_connections = step_dict[ 'input_connections' ] + steps.append( step ) + steps_by_external_id[ step_dict[ 'id' ] ] = step + # Second pass to deal with connections between steps. + for step in steps: + # Input connections. + for input_name, conn_dict in step.temp_input_connections.iteritems(): + if conn_dict: + output_step = steps_by_external_id[ conn_dict[ 'id' ] ] + conn = model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_step = output_step + conn.output_name = conn_dict[ 'output_name' ] + step.input_connections.append( conn ) + del step.temp_input_connections + # Order the steps if possible. + attach_ordered_steps( workflow, steps ) + return workflow, missing_tool_tups + @web.expose + def import_workflow( self, trans, **kwd ): + repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) + workflow_name = kwd.get( 'workflow_name', '' ) + if workflow_name: + workflow_name = decode( workflow_name ) + webapp = kwd.get( 'webapp', 'community' ) + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) + workflows = repository_metadata.metadata[ 'workflows' ] + workflow_data = None + for workflow_data in workflows: + if workflow_data[ 'name' ] == workflow_name: + break + if workflow_data: + if kwd.get( 'open_for_url', False ): + tmp_fd, tmp_fname = tempfile.mkstemp() + to_file = open( tmp_fname, 'wb' ) + to_file.write( to_json_string( workflow_data ) ) + return open( tmp_fname ) + galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) + url = '%s/workflow/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 ) + return trans.response.send_redirect( url ) + return trans.response.send_redirect( web.url_for( controller='workflow', + action='view_workflow', + message=message, + status=status ) ) diff --git a/lib/galaxy/webapps/community/model/__init__.py b/lib/galaxy/webapps/community/model/__init__.py index 31d6d24cc00..0f6b7d37206 100644 --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -20,12 +20,21 @@ class User( object ): self.deleted = False self.purged = False self.username = None + self.new_repo_alert = False def set_password_cleartext( self, cleartext ): """Set 'self.password' to the digest of 'cleartext'.""" self.password = new_secure_hash( text_type=cleartext ) def check_password( self, cleartext ): """Check if 'cleartext' matches 'self.password' when hashed.""" return self.password == new_secure_hash( text_type=cleartext ) + def get_disk_usage( self, nice_size=False ): + return 0 + def set_disk_usage( self, bytes ): + pass + total_disk_usage = property( get_disk_usage, set_disk_usage ) + @property + def nice_total_disk_usage( self ): + return 0 class Group( object ): def __init__( self, name = None ): @@ -204,6 +213,34 @@ class ItemTagAssociation ( object ): self.value = None self.user_value = None +class Workflow( object ): + def __init__( self ): + self.user = None + self.name = None + self.has_cycles = None + self.has_errors = None + self.steps = [] + +class WorkflowStep( object ): + def __init__( self ): + self.id = None + self.type = None + self.name = None + self.tool_id = None + self.tool_inputs = None + self.tool_errors = None + self.position = None + self.input_connections = [] + #self.output_connections = [] + self.config = None + +class WorkflowStepConnection( object ): + def __init__( self ): + self.output_step = None + self.output_name = None + self.input_step = None + self.input_name = None + ## ---- Utility methods ------------------------------------------------------- def sort_by_attr( seq, attr ): """ diff --git a/lib/galaxy/webapps/community/model/mapping.py b/lib/galaxy/webapps/community/model/mapping.py index 8f2e6c36e9e..51073c83815 100644 --- a/lib/galaxy/webapps/community/model/mapping.py +++ b/lib/galaxy/webapps/community/model/mapping.py @@ -45,6 +45,7 @@ User.table = Table( "galaxy_user", metadata, Column( "username", String( 255 ), index=True ), Column( "password", TrimmedString( 40 ), nullable=False ), Column( "external", Boolean, default=False ), + Column( "new_repo_alert", Boolean, default=False ), Column( "deleted", Boolean, index=True, default=False ), Column( "purged", Boolean, index=True, default=False ) ) @@ -194,7 +195,7 @@ assign_mapper( context, Repository, Repository.table, 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.id ) ) ) ) + downloadable_revisions=relation( RepositoryMetadata, order_by=desc( RepositoryMetadata.table.c.update_time ) ) ) ) assign_mapper( context, RepositoryMetadata, RepositoryMetadata.table, properties=dict( repository=relation( Repository ) ) ) diff --git a/lib/galaxy/webapps/community/model/migrate/versions/0010_add_new_repo_alert_column.py b/lib/galaxy/webapps/community/model/migrate/versions/0010_add_new_repo_alert_column.py new file mode 100644 index 00000000000..2238e267821 --- /dev/null +++ b/lib/galaxy/webapps/community/model/migrate/versions/0010_add_new_repo_alert_column.py @@ -0,0 +1,50 @@ +""" +Migration script to add the new_repo_alert column to the galaxy_user 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. + User_table = Table( "galaxy_user", metadata, autoload=True ) + c = Column( "new_repo_alert", Boolean, default=False, index=True ) + try: + # Create + c.create( User_table ) + assert c is User_table.c.new_repo_alert + # Initialize. + if migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + default_false = "0" + elif migrate_engine.name == 'postgres': + default_false = "false" + db_session.execute( "UPDATE galaxy_user SET new_repo_alert=%s" % default_false ) + except Exception, e: + print "Adding new_repo_alert column to the galaxy_user table failed: %s" % str( e ) + log.debug( "Adding new_repo_alert column to the galaxy_user table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + # Drop new_repo_alert column from galaxy_user table. + User_table = Table( "galaxy_user", metadata, autoload=True ) + try: + User_table.c.new_repo_alert.drop() + except Exception, e: + print "Dropping column new_repo_alert from the galaxy_user table failed: %s" % str( e ) + log.debug( "Dropping column new_repo_alert from the galaxy_user table failed: %s" % str( e ) ) diff --git a/lib/galaxy/webapps/demo_sequencer/config.py b/lib/galaxy/webapps/demo_sequencer/config.py index e5d80248d76..20729c7a1bb 100644 --- a/lib/galaxy/webapps/demo_sequencer/config.py +++ b/lib/galaxy/webapps/demo_sequencer/config.py @@ -40,6 +40,7 @@ class Configuration( object ): self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) + self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/demo_sequencer" ), self.root ) self.admin_users = kwargs.get( "admin_users", "" ) diff --git a/lib/galaxy/webapps/reports/config.py b/lib/galaxy/webapps/reports/config.py index 1a7508d2c6d..3e5aad27454 100644 --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -31,6 +31,8 @@ class Configuration( object ): self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/reports" ), self.root ) self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") + self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) + self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.brand = kwargs.get( 'brand', None ) self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' ) diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py index e57fd0b864b..8c07d6a34e5 100644 --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -8,6 +8,9 @@ from galaxy.util.bunch import Bunch from galaxy.util.json import from_json_string, to_json_string from galaxy.jobs.actions.post import ActionBox from galaxy.model import PostJobAction +import logging + +log = logging.getLogger( __name__ ) class WorkflowModule( object ): @@ -163,35 +166,53 @@ class ToolModule( WorkflowModule ): def __init__( self, trans, tool_id ): self.trans = trans self.tool_id = tool_id - self.tool = trans.app.toolbox.tools_by_id[ tool_id ] + try: + self.tool = trans.app.toolbox.tools_by_id[ tool_id ] + except KeyError, e: + # Handle the case where the workflow requires a tool not available in the local Galaxy instance. + self.tool = None + # The id value of tools installed from a Galaxy tool shed is a guid, but + # these tool's old_id attribute should contain what we're looking for. + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if tool_id == available_tool.old_id: + self.tool = available_tool + break self.post_job_actions = {} self.workflow_outputs = [] self.state = None - self.errors = None - + if self.tool: + self.errors = None + else: + self.errors = {} + self.errors[ tool_id ] = 'Tool unavailable' @classmethod def new( Class, trans, tool_id=None ): module = Class( trans, tool_id ) module.state = module.tool.new_state( trans, all_pages=True ) return module - @classmethod def from_dict( Class, trans, d, secure=True ): - tool_id = d['tool_id'] + tool_id = d[ 'tool_id' ] module = Class( trans, tool_id ) module.state = DefaultToolState() - module.state.decode( d["tool_state"], module.tool, module.trans.app, secure=secure ) + if module.tool is not None: + module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure ) module.errors = d.get( "tool_errors", None ) - module.post_job_actions = d.get("post_job_actions", {}) - module.workflow_outputs = d.get("workflow_outputs", []) + module.post_job_actions = d.get( "post_job_actions", {} ) + module.workflow_outputs = d.get( "workflow_outputs", [] ) return module - @classmethod def from_workflow_step( Class, trans, step ): tool_id = step.tool_id - if tool_id not in trans.app.toolbox.tools_by_id: - return None - else: + install_tool_id = None + if trans.app.toolbox and tool_id not in trans.app.toolbox.tools_by_id: + # The id value of tools installed from a Galaxy tool shed is a guid, but + # these tool's old_id attribute should contain what we're looking for. + for available_tool_id, available_tool in trans.app.toolbox.tools_by_id.items(): + if tool_id == available_tool.old_id: + install_tool_id = available_tool_id + break + if ( trans.app.toolbox and tool_id in trans.app.toolbox.tools_by_id ) or install_tool_id: module = Class( trans, tool_id ) module.state = DefaultToolState() module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) @@ -203,12 +224,16 @@ class ToolModule( WorkflowModule ): pjadict[pja.action_type] = pja module.post_job_actions = pjadict return module - + return None def save_to_step( self, step ): step.type = self.type step.tool_id = self.tool_id - step.tool_version = self.get_tool_version() - step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app ) + if self.tool: + step.tool_version = self.get_tool_version() + step.tool_inputs = self.tool.params_to_strings( self.state.inputs, self.trans.app ) + else: + step.tool_version = None + step.tool_inputs = None step.tool_errors = self.errors for k, v in self.post_job_actions.iteritems(): # Must have action_type, step. output and a_args are optional. @@ -221,9 +246,10 @@ class ToolModule( WorkflowModule ): else: action_arguments = None n_p = PostJobAction(v['action_type'], step, output_name, action_arguments) - def get_name( self ): - return self.tool.name + if self.tool: + return self.tool.name + return 'unavailable' def get_tool_id( self ): return self.tool_id def get_tool_version( self ): @@ -234,7 +260,6 @@ class ToolModule( WorkflowModule ): return self.errors def get_tooltip( self ): return self.tool.help - def get_data_inputs( self ): data_inputs = [] def callback( input, value, prefixed_name, prefixed_label ): @@ -268,15 +293,12 @@ class ToolModule( WorkflowModule ): formats.append( format ) data_outputs.append( dict( name=name, extensions=formats ) ) return data_outputs - def get_post_job_actions( self ): return self.post_job_actions - def get_config_form( self ): self.add_dummy_datasets() return self.trans.fill_template( "workflow/editor_tool_form.mako", tool=self.tool, values=self.state.inputs, errors=( self.errors or {} ) ) - def update_state( self, incoming ): # Build a callback that handles setting an input to be required at # runtime. We still process all other parameters the user might have @@ -306,10 +328,8 @@ class ToolModule( WorkflowModule ): # Update state using incoming values errors = self.tool.update_state( self.trans, self.tool.inputs, self.state.inputs, incoming, item_callback=item_callback ) self.errors = errors or None - def check_and_update_state( self ): return self.tool.check_and_update_param_values( self.state.inputs, self.trans ) - def add_dummy_datasets( self, connections=None): if connections: # Store onnections by input name @@ -324,8 +344,7 @@ class ToolModule( WorkflowModule ): if connections is None or prefixed_name in input_connections_by_name: return DummyDataset() visit_input_values( self.tool.inputs, self.state.inputs, callback ) - - + class WorkflowModuleFactory( object ): def __init__( self, module_types ): self.module_types = module_types diff --git a/locale/zh/LC_MESSAGES/ginga.mo b/locale/zh/LC_MESSAGES/ginga.mo new file mode 100644 index 00000000000..313becab331 Binary files /dev/null and b/locale/zh/LC_MESSAGES/ginga.mo differ diff --git a/locale/zh/LC_MESSAGES/ginga.po b/locale/zh/LC_MESSAGES/ginga.po new file mode 100644 index 00000000000..7f13341e093 --- /dev/null +++ b/locale/zh/LC_MESSAGES/ginga.po @@ -0,0 +1,603 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) YEAR THE PACKAGE'S COPYRIGHT HOLDER +# This file is distributed under the same license as the PACKAGE package. +# FIRST AUTHOR
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ah=$("").addClass("yaxislabel");ah.text(aw.max);ah.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ah.prependTo(this.container_div);var aj=this.view.canvas_manager.new_canvas();aj.width=aC+al;aj.height=an+V;if(aw.dataset_type!="summary_tree"){var at=this.get_summary_tree_data(aw.data,aK,ai,200);if(aw.max){at.max=aw.max}aw=at}var aL=new N.SummaryTreePainter(aw,aK,ai,this.prefs);var aD=aj.getContext("2d");aD.translate(al,V);aL.draw(aD,aC,an);return new l(aI,aE,aj,aw.data,aw.max)}var ax,ap=1;if(az==="no_detail"||az==="Squish"||az==="Pack"){ap=this.incremental_slots(ar,aw.data,az);ax=this.inc_slots[ar].slots}var aq=[];if(aw.data){var au=this.filters_manager.filters;for(var aF=0,aH=aw.data.length;aFB[0]&&G=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(k,x){var u=k("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;OD){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var o=function(B,D,y,A,C,z){n.call(this,B,D,y,A,C);this.alpha_generator=(z?z:new g())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(z){var y=y_scale=this.get_row_height(),A=this.mode;if(A==="no_detail"||A==="Squish"||A==="Pack"){y=z*y_scale}return y+Math.max(Math.round(y_scale/2),5)},draw:function(K,B,J,G){var E=this.data,H=this.view_start,L=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var O=this.view_end-this.view_start,N=B/O,A=this.get_row_height();for(var D=0,F=E.length;DH)&&(this.mode=="Dense"||I!==null)){this.draw_element(K,this.mode,M,I,H,L,N,A,B)}}K.restore()},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.")}});var d=10,j=3,m=5,w=10,f=1,s=3,e=3,a=9,l=2,h="#ccc";var r=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=d}else{if(z==="no_detail"){y=j}else{if(z==="Squish"){y=m}else{y=w}}}return y},draw_element:function(K,D,S,F,M,ac,ag,ah,y){var P=S[0],ae=S[1],W=S[2],N=S[3],X=Math.floor(Math.max(0,(ae-M)*ag)),L=Math.ceil(Math.min(y,Math.max(0,(W-M)*ag))),V=(D==="Dense"?0:(0+F))*ah,J,aa,O=null,ai=null,B=this.prefs.block_color,Z=this.prefs.label_color;K.globalAlpha=this.alpha_generator.gen_alpha(S);if(D=="Dense"){F=1}if(D==="no_detail"){K.fillStyle=B;K.fillRect(X,V+5,L-X,f)}else{var I=S[4],U=S[5],Y=S[6],C=S[7];if(U&&Y){O=Math.floor(Math.max(0,(U-M)*ag));ai=Math.ceil(Math.min(y,Math.max(0,(Y-M)*ag)))}var af,Q;if(D==="Squish"||D==="Dense"){af=1;Q=e}else{af=5;Q=a}if(!C){if(S.strand){if(S.strand==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand_inv")}else{if(S.strand==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand_inv")}}}else{K.fillStyle=B}K.fillRect(X,V,L-X,Q)}else{var H,R;if(D==="Squish"||D==="Dense"){K.fillStyle=h;H=V+Math.floor(e/2)+1;R=1}else{if(I){var H=V;var R=Q;if(I==="+"){K.fillStyle=K.canvas.manager.get_pattern("right_strand")}else{if(I==="-"){K.fillStyle=K.canvas.manager.get_pattern("left_strand")}}}else{K.fillStyle=h;H+=(e/2)+1;R=1}}K.fillRect(X,H,L-X,R);for(var ad=0,A=C.length;adT){continue}K.fillStyle=B;K.fillRect(z,V+(Q-af)/2+1,T-z,af);if(O!==undefined&&Y>U&&!(z>ai||TM){K.fillStyle=Z;if(M===0&&X-K.measureText(N).width<0){K.textAlign="left";K.fillText(N,L+l,V+8)}else{K.textAlign="right";K.fillText(N,X-l,V+8)}}}K.globalAlpha=1}});var b=function(B,D,y,A,C,z){o.call(this,B,D,y,A,C,z)};u(b.prototype,o.prototype,{draw_element:function(R,M,G,C,U,A,J,S,P){var G=data[i],I=G[0],Q=G[1],B=G[2],L=G[3],E=Math.floor(Math.max(0,(Q-U)*J)),H=Math.ceil(Math.min(P,Math.max(0,(B-U)*J))),D=(M==="Dense"?0:(0+C))*S,y,V,z=null,K=null;if(no_label){R.fillStyle=block_color;R.fillRect(E+left_offset,D+5,H-E,1)}else{var T=G[4],O=G[5],F=G[6];y=9;V=1;R.fillRect(E+left_offset,D,H-E,y);if(M!=="Dense"&&L!==undefined&&Q>U){R.fillStyle=label_color;if(U===0&&E-R.measureText(L).width<0){R.textAlign="left";R.fillText(L,H+2+left_offset,D+8)}else{R.textAlign="right";R.fillText(L,E-2+left_offset,D+8)}R.fillStyle=block_color}var N=T+" / "+O;if(Q>U&&R.measureText(N).width<(H-E)){R.fillStyle="white";R.textAlign="center";R.fillText(N,left_offset+E+(H-E)/2,D+8);R.fillStyle=block_color}}}});var t=function(C,E,y,B,D,z,A){o.call(this,C,E,y,B,D,z);this.ref_seq=A};t.prototype.default_prefs=u({},o.prototype.default_prefs,{show_insertions:false});u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=d}else{if(z==="Squish"){y=m}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(U,P,L,Z,A,T,I,F,E){U.textAlign="center";var S=this,z=[Z,A],O=0,V=0,R=0;ref_seq=this.ref_seq,char_width_px=U.canvas.manager.char_width_px;var ae=[];if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){R=Math.round(L/2)}if(!I){I=[[0,F.length]]}for(var M=0,X=I.length;M0){U.fillStyle=this.prefs.block_color;U.fillRect(ad-R,E+1,H-ad,9);U.fillStyle=h;for(var ab=0,y=Q.length;ab=Z&&G+ab<=A){var ac=Math.floor(Math.max(0,(G+ab-Z)*L));U.fillText(Q[ab],ac,E+9)}}}else{U.fillStyle=this.prefs.block_color;U.fillRect(ad,E+4,H-ad,e)}}V+=N;O+=N;break;case"N":U.fillStyle=h;U.fillRect(ad-R,E+5,H-ad,1);O+=N;break;case"D":U.fillStyle="red";U.fillRect(ad-R,E+4,H-ad,3);O+=N;break;case"P":break;case"I":var Y=ad-R;if(is_overlap([G,G+N],z)){var Q=F.slice(V,V+N);if(this.prefs.show_insertions){var D=ad-(H-ad)/2;if((P==="Pack"||this.mode==="Auto")&&F!==undefined&&L>char_width_px){U.fillStyle="yellow";U.fillRect(D-R,E-9,H-ad,9);ae[ae.length]={type:"triangle",data:[Y,E+4,5]};U.fillStyle=h;switch(seq_tile_overlap){case (OVERLAP_START):Q=Q.slice(Z-G);break;case (OVERLAP_END):Q=Q.slice(0,G-A);break;case (CONTAINED_BY):break;case (CONTAINS):Q=Q.slice(Z-G,G-A);break}for(var ab=0,y=Q.length;abchar_width_px){ae[ae.length]={type:"text",data:[Q.length,Y,E+9]}}else{}}}V+=N;break;case"X":V+=N;break}}U.fillStyle="yellow";var aa,C,af;for(var W=0;WR.canvas.manager.char_width_px){var O=Math.round(I/2)}R.fillStyle=V;if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,U,z,E[4][0],E[4][2],E[4][3],C)}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,U,z,E[5][0],E[5][2],E[5][3],C)}if(K>L){R.fillStyle=h;p(R,L-O,C+5,K-O,C+5)}}else{R.fillStyle=V;this.draw_read(R,M,I,U,z,Q,E[4],E[5],C)}if(M==="Pack"&&Q>U){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+l-O,C+8)}else{R.textAlign="right";R.fillText(J,D-l-O,C+8)}R.fillStyle=V}}});x.AlphaGenerator=g;x.SummaryTreePainter=v;x.LinePainter=c;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.VariantPainter=b};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
+var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;ec){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;jak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao=au&&at.offsetY<=ak){if(at.offsetY-au0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,F=9,C=20,T=F+2,y=100,I=12000,Q=200,A=5,u=10,K=5000,v=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",D="No data for this chrom/contig.",t="Currently indexing... please wait",w="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",R=10,H=20;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,ak){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($(""));this.header_div.dblclick(function(al){al.stopPropagation()});var aj=this;this.container_div.hover(function(){aj.icons_div.show()},function(){aj.icons_div.hide()});$("").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(af){if(af.content_visible){af.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");af.hide_contents();af.content_visible=false}else{af.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");af.content_visible=true;af.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ag){var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ah);show_modal("Configure",ag.config.build_form(),{Cancel:ai,OK:af})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(af){$(".tipsy").remove();af.remove()}}];p(q.prototype,{init:function(){},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},from_dict:function(af){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ag,ak,aj,ai,af){var ah=this;this.action_icons[ag]=$("").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tipsy({gravity:"s"}).click(function(){ai(ah)}).appendTo(this.icons_div)},build_action_icons:function(af){var ah;for(var ag=0;ag").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(P.prototype,q.prototype,x.prototype,{action_icons_def:[{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){af.show_composite_track()}}].concat(q.prototype.action_icons_def),build_container_div:function(){return $("").addClass("group").attr("id","group_"+this.id).appendTo(this.container.content_div)},build_header_div:function(){var af=$("").addClass("track-header");af.append($("").addClass(this.drag_handle_class));this.name_div=$("").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var af=true,ah=this.drawables[0].get_type();for(var ag=0;ag").addClass("top-container").appendTo(ah);this.browser_content_div=$("").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("").addClass("nav-container").prependTo(this.top_container);this.nav=$("").addClass("nav").appendTo(this.nav_container);this.overview=$("").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("").attr({name:"chrom"}).css("width","15em").addClass("no-autocomplete").append("").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=v;ah.dbkey=this.dbkey;var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new z(af))}af.chrom_data=aj.chrom_info;var am='';for(var al=0,ai=af.chrom_data.length;al'+ak+""}if(aj.prev_chroms){am+='"}if(aj.next_chroms){am+='"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-v});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+v});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;ajaf.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){x.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;akthis.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("
").appendTo(this.container_div);this.container.content_div.append(this.container_div)};q(j.prototype,r.prototype,{get_type:function(){if(this instanceof ad){return"LabelTrack"}else{if(this instanceof C){return"ReferenceTrack"}else{if(this instanceof k){return"LineTrack"}else{if(this instanceof Z){return"ReadTrack"}else{if(this instanceof X){return"ToolDataFeatureTrack"}else{if(this instanceof W){return"VcfTrack"}else{if(this instanceof e){return"FeatureTrack"}}}}}}}return""},init:function(){var ah=this;ah.enabled=false;ah.tile_cache.clear();ah.data_manager.clear();ah.initial_canvas=undefined;ah.content_div.css("height","auto");ah.container_div.removeClass("nodata error pending");if(!ah.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ah.hda_ldda,dataset_id:ah.dataset_id,chrom:ah.view.chrom},function(ai){if(!ai||ai==="error"||ai.kind==="error"){ah.container_div.addClass("error");ah.content_div.text(p);if(ai.message){var ak=ah.view.tracks.indexOf(ah);var aj=$(" ").text("View error").click(function(){show_modal("Trackster Error","0){var aj=(ai.filters_div.is(":visible")?"Hide filters":"Show filters");ah[aj]=function(){ai.filters_visible=(ai.filters_div.is(":visible"));if(ai.filters_visible){ai.filters_manager.reset_filters()}ai.filters_div.toggle();ai.make_name_popup_menu()}}if(ai.tool){var aj=(ai.dynamic_tool_div.is(":visible")?"Hide tool":"Show tool");ah[aj]=function(){if(!ai.dynamic_tool_div.is(":visible")){ai.set_name(ai.name+ai.tool_region_and_parameters_str())}else{menu_option_text="Show dynamic tool";ai.revert_name()}ai.dynamic_tool_div.toggle();ai.make_name_popup_menu()}}ah.Remove=function(){ai.remove()};make_popupmenu(ai.name_div,ah)},set_is_overview:function(ah){this.is_overview=ah;this.make_name_popup_menu()},get_overview_tile:function(){var ah=this;view=ah.view,resolution=Math.pow(E,Math.ceil(Math.log((view.max_high-view.max_low)/T)/Math.log(E))),view_width=view.container.width(),w_scale=view_width/(view.max_high-view.max_low),overview_tile=$.Deferred();$.when(ah.data_manager.get_data(view.max_low,view.max_high,"Auto",resolution,ah.data_url_extra_params)).then(function(ai){var ak=ah._gen_tile_cache_key(view_width,w_scale,0),am=ah.tile_cache.get(ak);if(!am){am=ah.draw_tile(ai,"Auto",resolution,0,w_scale);ah.tile_cache.set(ak,am)}var ap=$(am.canvas.find("canvas")),al=ap.clone(),ao=ap.get(0).getContext("2d"),aj=al.get(0).getContext("2d"),an=ao.getImageData(0,0,ao.canvas.width,ao.canvas.height);aj.putImageData(an,-ah.left_offset,(am.data.dataset_type==="summary_tree"?V:0));new_tile=new b(-1,resolution,al);overview_tile.resolve(new_tile)});return overview_tile},_gen_tile_cache_key:function(ai,aj,ah){return ai+"_"+aj+"_"+ah},request_draw:function(ai,ah){this.view.request_redraw(false,ai,ah,this)},_draw:function(aj,ar){if(!this.enabled){return}if(!(this instanceof C)&&(!this.dataset_id)){return}var aq=this.view.low,an=this.view.high,ao=an-aq,ak=this.view.container.width(),av=ak/ao,am=this.view.resolution,au=$("");if(!ar){this.content_div.children().remove()}this.content_div.append(au);this.max_height=0;var ai=Math.floor(aq/am/T);var ap=true;var at=[];var ah=0;while((ai*T*am)view.canvas_manager.char_width_px){aw=view.reference_track.data_manager.get_data(ap,ax,al.mode,an,view.reference_track.data_url_extra_params);if(ar(aw)){am=false}}if(am){q(ah,ao);var aq=al.draw_tile(ah,al.mode,an,ak,ay,aw);al.tile_cache.set(at,aq);if(aq!==undefined){al.show_tile(aq,au,ay)}return aq}$.when(ah,aw).then(function(){view.request_redraw()});return null},show_tile:function(ao,aq,ar){var aj=this,ai=ao.canvas,an=ai;if(ao.message){var at=$(""),ap=$("").addClass("tile-message").text(ao.message).css({height:F-1,width:ao.canvas.width}).appendTo(at),al=$("").addClass("icon more-down").appendTo(ap),ah=$("").addClass("icon more-across").appendTo(ap);at.append(ai);an=at;al.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.DEEP_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()});ah.click(function(){ao.stale=true;aj.data_manager.get_more_data(ao.low,ao.high,aj.mode,ao.resolution,{},aj.data_manager.BROAD_DATA_REQ);aj.request_draw()}).dblclick(function(au){au.stopPropagation()})}var am=this.view.high-this.view.low,ak=(ao.low-this.view.low)*ar;if(this.left_offset){ak-=this.left_offset}an.css({position:"absolute",top:0,left:ak,height:""});aq.append(an);aj.max_height=Math.max(aj.max_height,an.height());aj.content_div.css("height",aj.max_height+"px");aq.children().css("height",aj.max_height+"px")},_get_tile_bounds:function(ah,ai){var ak=ah*T*ai,al=T*ai,aj=(ak+al<=this.view.max_high?ak+al:this.view.max_high);return[ak,aj]},tool_region_and_parameters_str:function(aj,ah,ak){var ai=this,al=(aj!==undefined&&ah!==undefined&&ak!==undefined?aj+":"+ah+"-"+ak:"all");return" - region=["+al+"], parameters=["+ai.tool.get_param_values().join(", ")+"]"}});var ad=function(ai,ah){this.hidden=true;j.call(this,"label",ai,ah,{});this.container_div.addClass("label-track")};q(ad.prototype,j.prototype,{_draw:function(){var aj=this.view,ak=aj.high-aj.low,an=Math.floor(Math.pow(10,Math.floor(Math.log(ak)/Math.log(10)))),ah=Math.floor(aj.low/an)*an,al=this.view.container.width(),ai=$("");while(ah"+commatize(ah)+"
").css({position:"absolute",left:am-1}));ah+=an}this.content_div.children(":first").remove();this.content_div.append(ai)}});var C=function(ah){this.hidden=true;j.call(this,"reference",ah,{content_div:ah.top_labeltrack},{});O.call(this);ah.reference_track=this;this.left_offset=200;this.height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url;this.data_url_extra_params={dbkey:ah.dbkey};this.data_manager=new J(D,this,false);this.tile_cache=new c(v)};q(C.prototype,r.prototype,O.prototype,{draw_tile:function(ar,an,am,ai,at){var al=this,aj=T*am;if(at>this.view.canvas_manager.char_width_px){if(ar===null){al.content_div.css("height","0px");return}var ak=this.view.canvas_manager.new_canvas();var aq=ak.getContext("2d");ak.width=Math.ceil(aj*at+al.left_offset);ak.height=al.height_px;aq.font=aq.canvas.manager.default_font;aq.textAlign="center";ar=ar.data;for(var ao=0,ap=ar.length;ao"+ai.message+"",{Close:hide_modal})});ah.content_div.append(aj)}}else{if(ai==="no converter"){ah.container_div.addClass("error");ah.content_div.text(L)}else{if(ai==="no data"||(ai.data!==undefined&&(ai.data===null||ai.data.length===0))){ah.container_div.addClass("nodata");ah.content_div.text(G)}else{if(ai==="pending"){ah.container_div.addClass("pending");ah.content_div.text(u);setTimeout(function(){ah.init()},ah.data_query_wait)}else{if(ai.status==="data"){if(ai.valid_chroms){ah.valid_chroms=ai.valid_chroms;ah.make_name_popup_menu()}ah.content_div.text(ab);if(ah.view.chrom){ah.content_div.text("");ah.content_div.css("height",ah.height_px+"px");ah.enabled=true;$.when(ah.predraw_init()).done(function(){ah.container_div.removeClass("nodata error pending");ah.request_draw()})}}}}}}})},predraw_init:function(){},});var O=function(ao,am){var ai=this,ap=ai.view;n(ai.container_div,ai.drag_handle_class,".group",ai);this.filters_manager=new ac(this,(ao!==undefined?ao:{}));this.filters_available=false;this.filters_visible=false;this.tool=(am!==undefined&&obj_length(am)>0?new s(this,am):undefined);this.is_overview=false;if(ai.hidden){return}if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}if(ai.display_modes!==undefined){if(ai.mode_div===undefined){ai.mode_div=$("").appendTo(ai.header_div);var aj=(ai.config&&ai.config.values.mode?ai.config.values.mode:ai.display_modes[0]);ai.mode=aj;ai.mode_div.text(aj);var ah={};for(var ak=0,an=ai.display_modes.length;ak
").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("
").addClass("param-row").appendTo(am.parent_div);var aw=$("
").addClass("param-label").text(aA.label).appendTo(az);var ay=$("").addClass("slider").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("
").addClass("param-row").appendTo(this.parent_div);var ak=$("").attr("value","Run on complete dataset").appendTo(av);var af=$("").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ah=ag.tool_id+aj.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(aj.container===view){var ai=new P(this.name,this.track.view,this.track.container);aj.container.add_drawable(ai);aj.container.remove_drawable(aj);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);af=ai}else{af=aj.container}var ak=new aj.constructor(ah,view,af,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);af.add_drawable(ak);ak.content_div.text("Starting job.");this.run(ag,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(J)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(w+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var N=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var f=function(ah,ag,aj,ak,ai,af){N.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var g=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){g.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.minaf){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(aq,ay){this.track=aq;this.filters=[];for(var at=0;at").addClass("filters").hide();this.parent_div.bind("drag",function(aA){aA.stopPropagation()}).click(function(aA){aA.stopPropagation()}).bind("dblclick",function(aA){aA.stopPropagation()}).bind("keydown",function(aA){aA.stopPropagation()});var av=$("").addClass("sliders").appendTo(this.parent_div);var an=this;$.each(this.filters,function(aD,aF){aF.container=$("").addClass("filter-row slider-row").appendTo(av);var aE=$("").addClass("elt-label").appendTo(aF.container);var aC=$("").addClass("slider-name").text(aF.name+" ").appendTo(aE);var aB=$("");var aH=$("").addClass("slider-value").appendTo(aE).append("[").append(aB).append("]");var aA=$("").addClass("slider").appendTo(aF.container);aF.control_element=$("").attr("id",aF.name+"-filter-control").appendTo(aA);var aG=[0,0];aF.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aJ,aK){var aI=aK.values;aB.text(aI[0]+"-"+aI[1]);aF.low=aI[0];aF.high=aI[1];an.track.request_draw(true,true)},change:function(aI,aJ){aF.control_element.slider("option","slide").call(aF.control_element,aI,aJ)}});aF.slider=aF.control_element;aF.slider_label=aB;ai(aH,aB,aF.control_element);$("").appendTo(aF.container)});if(this.filters.length!==0){var ak=$("").addClass("param-row").appendTo(av);var am=$("").attr("value","Run on complete dataset").appendTo(ak);var ag=this;am.click(function(){ag.run_on_dataset()})}var ap=$("").addClass("display-controls").appendTo(this.parent_div),ar,al,ao,aj={Transparency:function(aA){an.alpha_filter=aA},Height:function(aA){an.height_filter=aA}};$.each(aj,function(aC,aB){ar=$("").addClass("filter-row").appendTo(ap),al=$("").addClass("elt-label").text(aC+":").appendTo(ar),ao=$("").attr("name",aC+"_dropdown").css("float","right").appendTo(ar);$("").attr("value",-1).text("== None ==").appendTo(ao);for(var aA=0;aA= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var B=function(af,ag){L.Scaler.call(this,ag);this.filter=af};B.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var E=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(E.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("");var ah;function ag(am,aj){for(var ao=0;ao").attr("id",an).addClass("feature-popup"),ax=$("
"),av,au,ay;for(av in at){au=at[av];ay=$("
").append(ax));af[an]=ai}ai.appendTo($(ag.html_elt).parent());var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,ak,aj,al){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(al?al:K);this.dataset_check_url=converted_datasets_state_url;this.data_manager=(ak?ak:new S(H,this));this.content_div=$(""),al,aA=[],at=[],ai=true;for(var ax=0;axthis.view.canvas_manager.char_width_px){if(ap.data===null){aj.content_div.css("height","0px");return}var ai=this.view.canvas_manager.new_canvas();var ao=ai.getContext("2d");ai.width=Math.ceil(ah*aq+aj.left_offset);ai.height=aj.height_px;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";ap=ap.data;for(var am=0,an=ap.length;am");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ar,ak,aj,ah,aq){if(this.vertical_range===undefined){return}var af=this._get_tile_bounds(ah,aj),al=af[0],ap=af[1],ag=Math.ceil((ap-al)*aq),an=this.height_px;var ai=this.view.canvas_manager.new_canvas();ai.width=ag,ai.height=an;var ao=ai.getContext("2d");var am=new L.LinePainter(ar.data,al,ap,this.prefs,ak);am.draw(ao,ag,an);return new b(this.track,ah,aj,ai,ar.data)}});var d=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];M.call(this,af,am,ag,an,aj,ak,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.set_painter_from_config();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.inc_slots={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};p(d.prototype,q.prototype,M.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style=="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(at,an,aj,ah){M.prototype.postdraw_actions.call(this,at,ah);var am=this;if(ah){var ax=am.content_div.children();var aw=false;for(var ap=ax.length-1,aq=0;ap>=aq;ap--){var ai=$(ax[ap]);if(aw){ai.remove()}else{if(ai.children().length!==0){aw=true}}}}if(am.mode=="Histogram"){var ag=-1;for(var ap=0;apag){ag=ao}}for(var ap=0;apah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(atai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},draw_tile:function(au,ax,aB,aF,ap,ai){var ay=this,ak=ay._get_tile_bounds(aF,aB),aI=ak[0],ag=ak[1],aw=ag-aI,az=Math.ceil(aw*ap),aO=25,aj=this.left_offset,av,al;if(ax==="Auto"){if(au.dataset_type==="summary_tree"){ax=au.dataset_type}else{if(au.extra_info==="no_detail"||ay.is_overview){ax="no_detail"}else{var aN=au.data;if(this.view.high-this.view.low>I){ax="Squish"}else{ax="Pack"}}}this.update_auto_mode(ax)}if(ax==="summary_tree"||ax==="Histogram"){al=this.summary_draw_height;this.container_div.find(".yaxislabel").remove();var af=$("").addClass("yaxislabel");af.text(au.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);var ah=this.view.canvas_manager.new_canvas();ah.width=az+aj;ah.height=al+T;if(au.dataset_type!="summary_tree"){var aq=this.get_summary_tree_data(au.data,aI,ag,200);if(au.max){aq.max=au.max}au=aq}var aK=new L.SummaryTreePainter(au,aI,ag,this.prefs);var aA=ah.getContext("2d");aA.translate(aj,T);aK.draw(aA,az,al);return new k(ay,aF,aB,ah,au.data,au.max)}var av,an=1;if(ax==="no_detail"||ax==="Squish"||ax==="Pack"){an=this.incremental_slots(ap,au.data,ax);av=this.inc_slots[ap].slots}var ao=[];if(au.data){var ar=this.filters_manager.filters;for(var aC=0,aE=au.data.length;aCi[0]&&F=0){g-=v;j="left"}else{k+=v;j="right"}}var t=q(g,k);if(t>=0){if(h[t]===undefined){h[t]=[]}h[t].push([g,k]);s[o]=t;n=Math.max(n,t)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y1){C=Math.ceil((T[1][0]-T[0][0])*B)}else{C=10}for(var O=0,P=T.length;OD){Q=true;E=D}}if(I==="Histogram"){E=Math.round(E/J*z);N.fillRect(R,U,C,-E)}else{if(I==="Intensity"){E=255-Math.floor((E-H)/J*255);N.fillStyle="rgb("+E+","+E+","+E+")";N.fillRect(R,0,C,z)}else{E=Math.round(z-(E-H)/J*z);if(F){N.lineTo(R,E)}else{F=true;if(I==="Filled"){N.moveTo(R,z);N.lineTo(R,E)}else{N.moveTo(R,E)}}}}N.fillStyle=this.prefs.overflow_color;if(Q||G){var S;if(I==="Histogram"||I==="Intensity"){S=C}else{R-=2;S=4}if(Q){N.fillRect(R,0,S,3)}if(G){N.fillRect(R,z-3,S,3)}}N.fillStyle=this.prefs.color}if(I==="Filled"){if(F){N.lineTo(R,U);N.lineTo(0,U)}N.fill()}else{N.stroke()}N.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,E=I/H,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;ND)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;akY){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||YO){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;afF){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;acR.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window);
\ No newline at end of file
diff --git a/static/scripts/packed/trackster_ui.js b/static/scripts/packed/trackster_ui.js
index 0dd3b73f91e..483ca3f230d 100644
--- a/static/scripts/packed/trackster_ui.js
+++ b/static/scripts/packed/trackster_ui.js
@@ -1 +1 @@
-var add_bookmark=function(b,a){var g=$("#bookmarks-container"),d=$("").addClass("bookmark").appendTo(g),c=$("").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("").addClass("icon-button delete").appendTo(c),f=$("").addClass("position").appendTo(d),h=$("").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,ReadTrack:ReadTrack,DrawableGroup:DrawableGroup};var track_from_dict=function(c,b){var a=new addable_objects[c.track_type](c.name,view,b,c.hda_ldda,c.dataset_id,c.prefs,c.filters,c.tool);if(c.mode){a.change_mode(c.mode)}return a};var drawable_collection_from_dict=function(f,a){var e=new addable_objects[f.obj_type](f.name,view,a,f.prefs,view.viewport_container,view);for(var d=0;d").addClass("bookmark").appendTo(g),c=$("").addClass("delete-icon-container").appendTo(d).click(function(){d.slideUp("fast");d.remove();view.has_changes=true;return false}),e=$("").addClass("icon-button delete").appendTo(c),f=$("").addClass("position").appendTo(d),h=$("").text(b).appendTo(f).click(function(){view.go_to(b);return false});annotation_div=get_editable_text_elt(a,true).addClass("annotation").appendTo(d);view.has_changes=true;return d};var addable_objects={LineTrack:LineTrack,FeatureTrack:FeatureTrack,VcfTrack:VcfTrack,ReadTrack:ReadTrack,CompositeTrack:CompositeTrack,DrawableGroup:DrawableGroup};var create_visualization=function(b,e,g,c,a,d,f){view=new View(b,e,g,c);view.editor=true;$.when(view.load_chroms_deferred).then(function(){if(a){var q=a.chrom,h=a.start,n=a.end,k=a.overview;if(q&&(h!==undefined)&&n){view.change_chrom(q,h,n)}}if(d){var l,j,m;for(var o=0;o> 16;
+ ng = ( new_color & 0x00ff00 ) >> 8;
+ nb = new_color & 0x0000ff;
+ n_brightness = brightness(nr, ng, nb);
+ ok = true;
+ for (var i = 0; i < colors.length; i++) {
+ other_color = colors[i];
+ or = ( other_color & 0xff0000 ) >> 16;
+ og = ( other_color & 0x00ff00 ) >> 8;
+ ob = other_color & 0x0000ff;
+ o_brightness = brightness(or, og, ob);
+ diff = difference(nr, ng, nb, or, og, ob);
+ // These thresholds may need to be adjusted. Brightness difference range is 125;
+ // color difference range is 500.
+ if ( ( Math.abs(n_brightness - o_brightness) < 40 ) ||
+ ( diff < 200 ) ) {
+ ok = false;
+ break;
+ }
+ }
+
+ num_tries++
+ } while (!ok && num_tries <= 10 );
+
+ // Add 0x1000000 to left pad number with 0s.
+ return '#' + ( 0x1000000 + new_color ).toString(16).substr(1,6);
+};
+
// Encapsulate -- anything to be availabe outside this block is added to exports
var trackster_module = function(require, exports) {
@@ -306,13 +377,21 @@ var
DATA_CANNOT_RUN_TOOL = "Tool cannot be rerun: ",
DATA_LOADING = "Loading data...",
DATA_OK = "Ready for display",
- CACHED_TILES_FEATURE = 10,
- CACHED_TILES_LINE = 5,
- CACHED_DATA = 5;
-
-function round_1000(num) {
- return Math.round(num * 1000) / 1000;
-};
+ TILE_CACHE_SIZE = 10,
+ DATA_CACHE_SIZE = 20;
+
+/**
+ * Round a number to a given number of decimal places.
+ */
+function round(num, places) {
+ // Default rounding is to integer.
+ if (!places) {
+ places = 0;
+ }
+
+ var val = Math.pow(10, places);
+ return Math.round(num * val) / val;
+}
/**
* Generic cache that handles key/value pairs.
@@ -454,7 +533,7 @@ extend(DataManager.prototype, Cache.prototype, {
// data is ready, it then replaces itself with the actual data
entry = this.load_data(low, high, mode, resolution, extra_params);
this.set_data(low, high, mode, entry);
- return entry
+ return entry;
},
/** "Deep" data request; used as a parameter for DataManager.get_more_data() */
DEEP_DATA_REQ: "deep",
@@ -552,13 +631,13 @@ var ReferenceTrackDataManager = function(num_elements, track, subset) {
DataManager.call(this, num_elements, track, subset);
};
extend(ReferenceTrackDataManager.prototype, DataManager.prototype, Cache.prototype, {
- load_data: function(chrom, low, high, mode, resolution, extra_params) {
+ load_data: function(low, high, mode, resolution, extra_params) {
if (resolution > 1) {
// Now that data is pre-fetched before draw, we don't load reference tracks
- // unless it's at the bottom level
- return;
+ // unless it's at the bottom level.
+ return { data: null };
}
- return DataManager.prototype.load_data.call(this, chrom, low, high, mode, resolution, extra_params);
+ return DataManager.prototype.load_data.call(this, low, high, mode, resolution, extra_params);
}
});
@@ -573,14 +652,20 @@ extend(ReferenceTrackDataManager.prototype, DataManager.prototype, Cache.prototy
*/
/**
- * Base interface for all drawable objects. Drawable objects have a name and are
- * associated with a view and container. They optionally have a drag handle class.
+ * Base class for all drawable objects. Drawable objects are associated with a view and live in a
+ * container. They have the following HTML elements and structure:
+ *
+ *
+ *
+ *
+ * They optionally have a drag handle class.
*/
var Drawable = function(name, view, container, prefs, drag_handle_class) {
+ if (!Drawable.id_counter) { Drawable.id_counter = 0; }
+ this.id = Drawable.id_counter++;
this.name = name;
this.view = view;
this.container = container;
- this.drag_handle_class = drag_handle_class;
this.config = new DrawableConfig({
track: this,
params: [
@@ -592,14 +677,119 @@ var Drawable = function(name, view, container, prefs, drag_handle_class) {
}
});
this.prefs = this.config.values;
+ this.drag_handle_class = drag_handle_class;
+ this.is_overview = false;
+ this.action_icons = {};
+
+ // FIXME: this should be a saved setting
+ this.content_visible = true;
+
+ // Build Drawable HTML and behaviors.
+ this.container_div = this.build_container_div();
+ this.header_div = this.build_header_div();
+
+ if (this.header_div) {
+ this.container_div.append(this.header_div);
+
+ this.icons_div = $("").css("float", "left").hide().appendTo(this.header_div);
+ this.build_action_icons(this.action_icons_def);
+ this.header_div.append( $("") );
+
+
+ // Suppress double clicks in header so that they do not impact viz.
+ this.header_div.dblclick( function(e) { e.stopPropagation(); } );
+
+ // Show icons when users is hovering over track.
+ var drawable = this;
+ this.container_div.hover(
+ function() { drawable.icons_div.show(); },
+ function() { drawable.icons_div.hide(); }
+ );
+
+ // Needed for floating elts in header.
+ $("").appendTo(this.container_div);
+ }
};
+Drawable.prototype.action_icons_def = [
+ // Hide/show drawable content.
+ {
+ name: "toggle_icon",
+ title: "Hide/show content",
+ css_class: "toggle",
+ on_click_fn: function(drawable) {
+ if ( drawable.content_visible ) {
+ drawable.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");
+ drawable.hide_contents();
+ drawable.content_visible = false;
+ } else {
+ drawable.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");
+ drawable.content_visible = true;
+ drawable.show_contents();
+ }
+ }
+ },
+ // Edit settings.
+ {
+ name: "settings_icon",
+ title: "Edit settings",
+ css_class: "settings-icon",
+ on_click_fn: function(drawable) {
+ var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); },
+ ok_fn = function() {
+ drawable.config.update_from_form( $(".dialog-box") );
+ hide_modal();
+ $(window).unbind("keypress.check_enter_esc");
+ },
+ check_enter_esc = function(e) {
+ if ((e.keyCode || e.which) === 27) { // Escape key
+ cancel_fn();
+ } else if ((e.keyCode || e.which) === 13) { // Enter key
+ ok_fn();
+ }
+ };
+
+ $(window).bind("keypress.check_enter_esc", check_enter_esc);
+ show_modal("Configure", drawable.config.build_form(), {
+ "Cancel": cancel_fn,
+ "OK": ok_fn
+ });
+ }
+ },
+ // Remove.
+ {
+ name: "remove_icon",
+ title: "Remove",
+ css_class: "remove-icon",
+ on_click_fn: function(drawable) {
+ // Tipsy for remove icon must be deleted when drawable is deleted.
+ $(".tipsy").remove();
+ drawable.remove();
+ }
+ }
+];
+
extend(Drawable.prototype, {
init: function() {},
+ can_draw: function() {
+ if (this.enabled && this.content_visible) {
+ return true;
+ }
+
+ return false;
+ },
request_draw: function() {},
_draw: function() {},
- to_json: function() {},
- make_name_popup_menu: function() {},
+ /**
+ * Returns representation of object in a dictionary for easy saving.
+ * Use from_dict to recreate object.
+ */
+ to_dict: function() {},
+ /**
+ * Restore object from a dictionary created by to_dict()
+ */
+ from_dict: function(object_dict) {},
+ update_icons: function() {},
/**
* Set drawable name.
*/
@@ -621,13 +811,55 @@ extend(Drawable.prototype, {
remove: function() {
this.container.remove_drawable(this);
- this.container_div.fadeOut('slow', function() {
+ this.container_div.hide(0, function() {
$(this).remove();
// HACK: is there a better way to update the view?
view.update_intro_div();
view.has_changes = true;
});
- }
+ },
+ /**
+ * Build drawable's container div; this is the parent div for all drawable's elements.
+ */
+ build_container_div: function() {},
+ /**
+ * Build drawable's header div.
+ */
+ build_header_div: function() {},
+ /**
+ * Add an action icon to this object. Appends icon unless prepend flag is specified.
+ */
+ add_action_icon: function(name, title, css_class, on_click_fn, prepend) {
+ var drawable = this;
+ this.action_icons[name] = $("").attr("href", "javascript:void(0);").attr("title", title)
+ .addClass("icon-button").addClass(css_class).tipsy( {gravity: 's'} )
+ .click( function() { on_click_fn(drawable); } )
+ .appendTo(this.icons_div);
+ },
+ /**
+ * Build drawable's icons div from object's icons_dict.
+ */
+ build_action_icons: function(action_icons_def) {
+ // Create icons.
+ var icon_dict;
+ for (var i = 0; i < action_icons_def.length; i++) {
+ icon_dict = action_icons_def[i];
+ this.add_action_icon(icon_dict.name, icon_dict.title, icon_dict.css_class,
+ icon_dict.on_click_fn, icon_dict.prepend);
+ }
+ },
+ /**
+ * Update icons.
+ */
+ update_icons: function() {},
+ /**
+ * Hide drawable's contents.
+ */
+ hide_contents: function () {},
+ /**
+ * Show drawable's contents.
+ */
+ show_contents: function() {}
});
/**
@@ -657,21 +889,44 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
this.drawables[i]._draw();
}
},
- /**
- * Returns jsonified representation of collection.
+ /**
+ * Returns representation of object in a dictionary for easy saving.
+ * Use from_dict to recreate object.
*/
- to_json: function() {
- var jsonified_drawables = [];
+ to_dict: function() {
+ var dictified_drawables = [];
for (var i = 0; i < this.drawables.length; i++) {
- jsonified_drawables.push(this.drawables[i].to_json());
+ dictified_drawables.push(this.drawables[i].to_dict());
}
return {
name: this.name,
prefs: this.prefs,
obj_type: this.obj_type,
- drawables: jsonified_drawables
+ drawables: dictified_drawables
};
},
+ /**
+ * Restore object from a dictionary created by to_dict()
+ */
+ from_dict: function(collection_dict, container) {
+ var collection = new this.constructor( collection_dict.name, view,
+ container, collection_dict.prefs,
+ view.viewport_container, view);
+ var drawable_dict,
+ drawable_type,
+ drawable;
+ for (var i = 0; i < collection_dict.drawables.length; i++) {
+ drawable_dict = collection_dict.drawables[i];
+ drawable_type = drawable_dict['obj_type'];
+ // For backward compatibility:
+ if (!drawable_type) {
+ drawable_type = drawable_dict['track_type'];
+ }
+ drawable = addable_objects[ drawable_type ].prototype.from_dict( drawable_dict, collection );
+ collection.add_drawable( drawable );
+ }
+ return collection;
+ },
/**
* Add a drawable to the end of the collection.
*/
@@ -725,67 +980,91 @@ extend(DrawableCollection.prototype, Drawable.prototype, {
var DrawableGroup = function(name, view, container, prefs) {
DrawableCollection.call(this, "DrawableGroup", name, view, container, prefs, "group-handle");
- // HTML elements.
- if (!DrawableGroup.id_counter) { DrawableGroup.id_counter = 0; }
- var group_id = DrawableGroup.id_counter++
- this.container_div = $("").addClass("group").attr("id", "group_" + group_id).appendTo(this.container.content_div);
- this.header_div = $("").addClass("track-header").appendTo(this.container_div);
- this.header_div.append($("").addClass(this.drag_handle_class));
- this.name_div = $("").addClass("group-name menubutton popup").text(this.name).appendTo(this.header_div);
- this.content_div = $("").addClass("content-div").attr("id", "group_" + group_id + "_content_div").appendTo(this.container_div);
-
// Set up containers/moving for group: register both container_div and content div as container
// because both are used as containers (container div to recognize container, content_div to
// store elements). Group can be moved.
+ this.content_div = $("").addClass("content-div").attr("id", "group_" + this.id + "_content_div").appendTo(this.container_div);
is_container(this.container_div, this);
is_container(this.content_div, this);
moveable(this.container_div, this.drag_handle_class, ".group", this);
-
- this.make_name_popup_menu();
};
extend(DrawableGroup.prototype, Drawable.prototype, DrawableCollection.prototype, {
+ action_icons_def: [
+ // Create composite track from group's tracks.
+ {
+ name: "composite_icon",
+ title: "Show composite track",
+ css_class: "layers-stack",
+ on_click_fn: function(group) {
+ group.show_composite_track();
+ }
+ }
+ ].concat(Drawable.prototype.action_icons_def),
+ build_container_div: function() {
+ return $("").addClass("group").attr("id", "group_" + this.id).appendTo(this.container.content_div);
+ },
+ build_header_div: function() {
+ var header_div = $("").addClass("track-header");
+ header_div.append($("").addClass(this.drag_handle_class));
+ this.name_div = $("").addClass("track-name").text(this.name).appendTo(header_div);
+ return header_div;
+ },
+ hide_contents: function () {
+ this.content_div.hide();
+ },
+ show_contents: function() {
+ // Show the contents div and labels (if present)
+ this.content_div.show();
+ // Request a redraw of the content
+ this.request_draw();
+ },
+ update_icons: function() {
+ // Only show composite icon if all tracks are the same type.
+ var can_composite = true,
+ a_type = this.drawables[0].get_type();
+ for (var i = 0; i < this.drawables.length; i++) {
+ if ( this.drawables[i].get_type() !== a_type ) {
+ can_composite = false;
+ break;
+ }
+ }
+
+ if (can_composite) {
+ this.action_icons.composite_icon.show();
+ }
+ else {
+ this.action_icons.composite_icon.hide();
+ $(".tipsy").remove();
+ }
+ },
/**
- * Make popup menu for group.
+ * Add composite track to group that includes all of group's tracks.
*/
- make_name_popup_menu: function() {
- var group = this;
+ show_composite_track: function() {
+ var composite_track = new CompositeTrack("Composite Track", this.view, this, this.drawables);
+ this.add_drawable(composite_track);
+ composite_track.request_draw();
+ },
+ add_drawable: function(drawable) {
+ DrawableCollection.prototype.add_drawable.call(this, drawable);
+ this.update_icons();
+ },
+ remove_drawable: function(drawable) {
+ DrawableCollection.prototype.remove_drawable.call(this, drawable);
+ this.update_icons();
+ },
+ /**
+ * Restore object from a dictionary created by to_dict()
+ */
+ from_dict: function(collection_dict, container) {
+ var group = DrawableCollection.prototype.from_dict.call(this, collection_dict, container);
- var group_dropdown = {};
-
- //
- // Edit config option.
- //
- group_dropdown["Edit configuration"] = function() {
- var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); },
- ok_fn = function() {
- group.config.update_from_form( $(".dialog-box") );
- hide_modal();
- $(window).unbind("keypress.check_enter_esc");
- },
- check_enter_esc = function(e) {
- if ((e.keyCode || e.which) === 27) { // Escape key
- cancel_fn();
- } else if ((e.keyCode || e.which) === 13) { // Enter key
- ok_fn();
- }
- };
-
- $(window).bind("keypress.check_enter_esc", check_enter_esc);
- show_modal("Configure Group", group.config.build_form(), {
- "Cancel": cancel_fn,
- "OK": ok_fn
- });
- };
-
- //
- // Remove option.
- //
- group_dropdown.Remove = function() {
- group.remove();
- };
-
- make_popupmenu(group.name_div, group_dropdown);
+ // Add drawables to group's content div to make them visible.
+ for (var i = 0; i < group.drawables.length; i++) {
+ group.content_div.append(group.drawables[i].container_div);
+ }
+ return group;
}
});
@@ -799,8 +1078,6 @@ var View = function(container, title, vis_id, dbkey) {
this.vis_id = vis_id;
this.dbkey = dbkey;
this.title = title;
- // Alias tracks to point at drawables. TODO: changes tracks to 'drawables' or something similar.
- this.tracks = this.drawables;
this.label_tracks = [];
this.tracks_to_be_redrawn = [];
this.max_low = 0;
@@ -833,7 +1110,7 @@ extend( View.prototype, DrawableCollection.prototype, {
this.content_div = this.viewport_container;
is_container(this.viewport_container, view);
// Introduction div shown when there are no tracks.
- this.intro_div = $("").addClass("intro");
+ this.intro_div = $("").addClass("intro").appendTo(this.viewport_container).hide();
var add_tracks_button = $("").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () {
add_tracks();
});
@@ -845,7 +1122,7 @@ extend( View.prototype, DrawableCollection.prototype, {
// Overview (scrollbar and overview plot) at bottom
this.overview = $("").addClass("overview").appendTo(this.bottom_container);
this.overview_viewport = $("").addClass("overview-viewport").appendTo(this.overview);
- this.overview_close = $("Close Overview").addClass("overview-close").hide().appendTo(this.overview_viewport);
+ this.overview_close = $("").attr("href", "javascript:void(0);").attr("title", "Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);
this.overview_highlight = $("").addClass("overview-highlight").hide().appendTo(this.overview_viewport);
this.overview_box_background = $("").addClass("overview-boxback").appendTo(this.overview_viewport);
this.overview_box = $("").addClass("overview-box").appendTo(this.overview_viewport);
@@ -865,7 +1142,7 @@ extend( View.prototype, DrawableCollection.prototype, {
}
};
this.nav_input = $("").addClass("nav-input").hide().bind("keyup focusout", submit_nav).appendTo(this.nav_controls);
- this.location_span = $("").addClass("location").appendTo(this.nav_controls);
+ this.location_span = $("").addClass("location").attr('original-title', 'Click to change location').tipsy( { gravity: 'n' } ).appendTo(this.nav_controls);
this.location_span.click(function() {
view.location_span.hide();
view.chrom_select.hide();
@@ -877,8 +1154,11 @@ extend( View.prototype, DrawableCollection.prototype, {
if (this.vis_id !== undefined) {
this.hidden_input = $("").attr("type", "hidden").val(this.vis_id).appendTo(this.nav_controls);
}
- this.zo_link = $("").click(function() { view.zoom_out(); view.request_redraw(); }).appendTo(this.nav_controls);
- this.zi_link = $("").click(function() { view.zoom_in(); view.request_redraw(); }).appendTo(this.nav_controls);
+
+ this.zo_link = $("").attr("id", "zoom-out").attr("title", "Zoom out").tipsy( {gravity: 'n'} )
+ .click(function() { view.zoom_out(); view.request_redraw(); }).appendTo(this.nav_controls);
+ this.zi_link = $("").attr("id", "zoom-in").attr("title", "Zoom in").tipsy( {gravity: 'n'} )
+ .click(function() { view.zoom_in(); view.request_redraw(); }).appendTo(this.nav_controls);
// Get initial set of chroms.
this.load_chroms_deferred = this.load_chroms({low: 0});
@@ -948,6 +1228,7 @@ extend( View.prototype, DrawableCollection.prototype, {
// Only act on x axis scrolling if we see if, y will be i
// handled by the browser when the event bubbles up
if ( dx ) {
+ dx *= 50;
var delta_chrom = Math.round( - dx / view.viewport_container.width() * (view.high - view.low) );
view.move_delta( delta_chrom );
}
@@ -993,15 +1274,14 @@ extend( View.prototype, DrawableCollection.prototype, {
this.reset();
$(window).trigger("resize");
- this.update_intro_div();
},
/** Add or remove intro div depending on view state. */
update_intro_div: function() {
- if (this.num_tracks === 0) {
- this.intro_div.appendTo(this.viewport_container);
+ if (this.drawables.length === 0) {
+ this.intro_div.show();
}
else {
- this.intro_div.remove();
+ this.intro_div.hide();
}
},
update_location: function(low, high) {
@@ -1013,7 +1293,8 @@ extend( View.prototype, DrawableCollection.prototype, {
*/
load_chroms: function(url_parms) {
url_parms['num'] = MAX_CHROMS_SELECTABLE;
- $.extend( url_parms, (this.vis_id !== undefined ? { vis_id: this.vis_id } : { dbkey: this.dbkey } ) );
+ url_parms['dbkey'] = this.dbkey;
+
var
view = this,
chrom_data = $.Deferred();
@@ -1097,10 +1378,10 @@ extend( View.prototype, DrawableCollection.prototype, {
view.reset();
view.request_redraw(true);
- for (var track_id = 0, len = view.tracks.length; track_id < len; track_id++) {
- var track = view.tracks[track_id];
- if (track.init) {
- track.init();
+ for (var i = 0, len = view.drawables.length; i < len; i++) {
+ var drawable = view.drawables[i];
+ if (drawable.init) {
+ drawable.init();
}
}
}
@@ -1113,6 +1394,10 @@ extend( View.prototype, DrawableCollection.prototype, {
}
},
go_to: function(str) {
+ // Preprocess str to remove spaces and commas.
+ str = str.replace(/ |,/g, "");
+
+ // Go to new location.
var view = this,
new_low,
new_high,
@@ -1123,8 +1408,8 @@ extend( View.prototype, DrawableCollection.prototype, {
if (pos !== undefined) {
try {
var pos_split = pos.split("-");
- new_low = parseInt(pos_split[0].replace(/,/g, ""), 10);
- new_high = parseInt(pos_split[1].replace(/,/g, ""), 10);
+ new_low = parseInt(pos_split[0], 10);
+ new_high = parseInt(pos_split[1], 10);
} catch (e) {
return false;
}
@@ -1173,7 +1458,7 @@ extend( View.prototype, DrawableCollection.prototype, {
DrawableCollection.prototype.remove_drawable.call(this, drawable);
if (hide) {
var view = this;
- drawable.container_div.fadeOut('slow', function() {
+ drawable.container_div.hide(0, function() {
$(this).remove();
view.update_intro_div();
});
@@ -1188,13 +1473,14 @@ extend( View.prototype, DrawableCollection.prototype, {
/**
* Request that view redraw some or all tracks. If a track is not specificied, redraw all tracks.
*/
+ // FIXME: change method call so that track is first and additional parameters are optional.
request_redraw: function(nodraw, force, clear_after, track) {
var
view = this,
- // Either redrawing a single track or all view's tracks.
- track_list = (track ? [track] : view.tracks),
+ // Either redrawing a single drawable or all view's drawables.
+ track_list = (track ? [track] : view.drawables),
track_index;
-
+
// Add/update tracks in track list to redraw list.
var track;
for (var i = 0; i < track_list.length; i++) {
@@ -1311,42 +1597,44 @@ extend( View.prototype, DrawableCollection.prototype, {
this.nav_container.width( this.container.width() );
this.request_redraw();
},
- /** Show a track in the overview. */
- set_overview: function(track) {
- // Get data and draw tile.
- $.when(track.get_overview_tile()).then(function(tile) {
- // Update UI.
- view.overview_viewport.find(".track-tile").remove();
- view.overview_close.show();
- view.overview_viewport.append(tile.canvas);
- view.overview_highlight.show().height(tile.canvas.height());
- view.overview_viewport.height(tile.canvas.height() + view.overview_box.outerHeight());
- view.resize_window();
-
- // Update view, track states.
- if (view.overview_track) {
- view.overview_track.set_is_overview(false);
+ /** Show a Drawable in the overview. */
+ set_overview: function(drawable) {
+ if (this.overview_drawable) {
+ // If drawable to be set as overview is already in overview, do nothing.
+ // Otherwise, remove overview.
+ if (this.overview_drawable.dataset_id === drawable.dataset_id) {
+ return;
}
- view.overview_track = track;
- track.set_is_overview(true);
- });
+ this.overview_viewport.find(".track").remove();
+ }
+
+ // Set new overview.
+ var
+ overview_drawable = drawable.copy( { content_div: this.overview_viewport } ),
+ view = this;
+ overview_drawable.header_div.hide();
+ overview_drawable.is_overview = true;
+ view.overview_drawable = overview_drawable;
+ this.overview_drawable.postdraw_actions = function() {
+ view.overview_highlight.show().height(view.overview_drawable.content_div.height());
+ view.overview_viewport.height(view.overview_drawable.content_div.height() + view.overview_box.outerHeight());
+ view.overview_close.show();
+ view.resize_window();
+ };
+ view.overview_drawable.request_draw();
view.has_changes = true;
},
/** Close and reset overview. */
reset_overview: function() {
// Update UI.
+ $(".tipsy").remove();
this.overview_viewport.find(".track-tile").remove();
this.overview_viewport.height(this.default_overview_height);
this.overview_box.height(this.default_overview_height);
this.overview_close.hide();
this.overview_highlight.hide();
view.resize_window();
-
- // Update view, track states.
- if (view.overview_track) {
- view.overview_track.set_is_overview(false);
- }
- view.overview_track = null;
+ view.overview_drawable = null;
}
});
@@ -1494,8 +1782,7 @@ extend(Tool.prototype, {
// Set name of track to include tool name, parameters, and region used.
track_name = url_params.tool_id +
current_track.tool_region_and_parameters_str(url_params.chrom, url_params.low, url_params.high),
- container,
- new_track;
+ container;
// If track not in a group, create a group for it and add new track to group. If track
// already in group, add track to group.
@@ -1512,11 +1799,12 @@ extend(Tool.prototype, {
else {
container = current_track.container;
}
- if (current_track instanceof FeatureTrack) {
- new_track = new ToolDataFeatureTrack(track_name, view, container, "hda");
- new_track.change_mode(current_track.mode);
- container.add_drawable(new_track);
- }
+
+ // Create and init new track.
+ var new_track = new current_track.constructor(track_name, view, container, "hda");
+ new_track.init_for_tool_data();
+ new_track.change_mode(current_track.mode);
+ container.add_drawable(new_track);
new_track.content_div.text("Starting job.");
// Run tool.
@@ -1629,7 +1917,7 @@ extend(NumberFilter.prototype, {
// No element to filter on.
return true;
}
- var val = parseFloat(element[this.index]);
+ var val = element[this.index];
return (isNaN(val) || (val >= this.low && val <= this.high));
},
/**
@@ -1797,7 +2085,7 @@ var FiltersManager = function(track, filters_list) {
var sliders_div = $("").addClass("sliders").appendTo(this.parent_div);
var manager = this;
$.each(this.filters, function(index, filter) {
- filter.container = $("").addClass("slider-row").appendTo(sliders_div);
+ filter.container = $("").addClass("filter-row slider-row").appendTo(sliders_div);
// Set up filter label (name, values).
var filter_label = $("").addClass("elt-label").appendTo(filter.container)
@@ -1853,25 +2141,39 @@ var FiltersManager = function(track, filters_list) {
//
var
display_controls_div = $("").addClass("display-controls").appendTo(this.parent_div),
- header_text = $("").addClass("elt-label").text("Transparency:").appendTo(display_controls_div),
- alpha_select = $("").attr("name", "alpha_dropdown").appendTo(display_controls_div);
-
- // Dropdown for selecting attribute to use for alpha channel manipulation.
- this.alpha_filter = null;
- $("").attr("value", -1).text("== None ==").appendTo(alpha_select);
- for (var i = 0; i < this.filters.length; i++) {
- $("").attr("value", i).text(this.filters[i].name).appendTo(alpha_select);
- }
- alpha_select.change(function() {
- $(this).children("option:selected").each(function() {
- var filterIndex = parseInt($(this).val());
- manager.alpha_filter = (filterIndex >= 0 ? manager.filters[filterIndex] : null);
- manager.track.request_draw(true, true);
- })
+ formatting_div,
+ header_text,
+ select,
+ // TODO: find better way to specify and change control filters.
+ filter_controls_dict = {
+ "Transparency": function(new_filter) { manager.alpha_filter = new_filter; },
+ "Height" : function(new_filter) { manager.height_filter = new_filter; }
+ };
+
+ $.each(filter_controls_dict, function(control_name, filter) {
+ // Display name and select option.
+ formatting_div = $("").addClass("filter-row").appendTo(display_controls_div),
+ header_text = $("").addClass("elt-label").text(control_name + ":").appendTo(formatting_div),
+ select = $("").attr("name", control_name + "_dropdown").css("float", "right").appendTo(formatting_div);
+
+ // Dropdown for selecting filter.
+ $("").attr("value", -1).text("== None ==").appendTo(select);
+ for (var i = 0; i < manager.filters.length; i++) {
+ $("").attr("value", i).text(manager.filters[i].name).appendTo(select);
+ }
+ select.change(function() {
+ $(this).children("option:selected").each(function() {
+ var filterIndex = parseInt($(this).val());
+ filter_controls_dict[control_name]( (filterIndex >= 0 ? manager.filters[filterIndex] : null) );
+ manager.track.request_draw(true, true);
+ })
+ });
+
+ // Clear floating.
+ $("").appendTo(formatting_div);
});
// Clear floating.
- // Add to clear floating layout.
$("").appendTo(this.parent_div);
};
@@ -1885,6 +2187,7 @@ extend(FiltersManager.prototype, {
filter.slider.slider("option", "values", [filter.min, filter.max]);
}
this.alpha_filter = null;
+ this.height_filter = null;
},
run_on_dataset: function() {
// Get or create dictionary item.
@@ -1972,20 +2275,20 @@ extend(FiltersManager.prototype, {
});
/**
- * Generates alpha values based on filter and feature's value for filter.
+ * Generates scale values based on filter and feature's value for filter.
*/
-var FilterAlphaGenerator = function(filter, default_alpha) {
- painters.AlphaGenerator.call(this, default_alpha);
+var FilterScaler = function(filter, default_val) {
+ painters.Scaler.call(this, default_val);
this.filter = filter;
};
-FilterAlphaGenerator.prototype.gen_alpha = function(feature_data) {
- // If filter is not initalized yet, return default alpha.
+FilterScaler.prototype.gen_val = function(feature_data) {
+ // If filter is not initalized yet, return default val.
if (this.filter.high === Number.MAX_VALUE || this.filter.low === -Number.MAX_VALUE || this.filter.low === this.filter.high) {
- return this.default_alpha;
+ return this.default_val;
}
- // Alpha value is ratio of (filter's value compared to low) to (complete filter range).
+ // Scaling value is ratio of (filter's value compared to low) to (complete filter range).
return ( ( parseFloat(feature_data[this.filter.index]) - this.filter.low ) / ( this.filter.high - this.filter.low ) );
};
@@ -2014,31 +2317,49 @@ extend(DrawableConfig.prototype, {
build_form: function() {
var track_config = this;
var container = $("");
- $.each( this.params, function( index, param ) {
- if ( ! param.hidden ) {
+ var param;
+ // Function to process parameters recursively
+ function handle_params( params, container ) {
+ for ( var index = 0; index < params.length; index++ ) {
+ param = params[index];
+ // Hidden params have no representation in the form
+ if ( param.hidden ) { continue; }
+ // Build row for param
var id = 'param_' + index;
var value = track_config.values[ param.key ];
var row = $("").appendTo( container );
row.append( $('').attr("for", id ).text( param.label + ":" ) );
+ // Draw parameter as checkbox
if ( param.type === 'bool' ) {
row.append( $('').attr("id", id ).attr("name", id ).attr( 'checked', value ) );
+ // Draw parameter as textbox
} else if ( param.type === 'text' ) {
row.append( $('').attr("id", id ).val(value).click( function() { $(this).select() }));
+ // Draw paramter as select area
+ } else if ( param.type == 'select' ) {
+ var select = $('').attr("id", id);
+ for ( var i = 0; i < param.options.length; i++ ) {
+ $("").text( param.options[i].label ).attr( "value", param.options[i].value ).appendTo( select );
+ }
+ select.val( value );
+ row.append( select );
+ // Draw parameter as color picker
} else if ( param.type === 'color' ) {
var input = $('').attr("id", id ).attr("name", id ).val( value );
// Color picker in tool tip style float
- var tip = $( "" ).hide();
+ var tip = $( "" ).hide();
// Inner div for padding purposes
var tip_inner = $("").appendTo(tip);
var farb_container = $("")
.appendTo(tip_inner)
.farbtastic( { width: 100, height: 100, callback: input, color: value });
-
// Outer div container input and tip for hover to work
$("").append( input ).append( tip ).appendTo( row ).bind( "click", function ( e ) {
tip.css( {
- left: $(this).position().left + ( $(input).width() / 2 ) - 60,
- top: $(this).position().top + $(this.height)
+ // left: $(this).position().left + ( $(input).width() / 2 ) - 60,
+ // top: $(this).position().top + $(this.height)
+ left: $(this).position().left + $(input).width() + 5,
+ top: $(this).position().top - ( $(tip).height() / 2 ) + ( $(input).height() / 2 )
} ).show();
$(document).bind( "click.color-picker", function() {
tip.hide();
@@ -2050,8 +2371,15 @@ extend(DrawableConfig.prototype, {
else {
row.append( $('').attr("id", id ).attr("name", id ).val( value ) );
}
+ // Help text
+ if ( param.help ) {
+ row.append( $("").text( param.help ) );
+ }
}
- });
+ }
+ // Handle top level parameters in order
+ handle_params( this.params, container );
+ // Return element containing constructed form
return container;
},
update_from_form: function( container ) {
@@ -2085,25 +2413,170 @@ extend(DrawableConfig.prototype, {
/**
* Tiles drawn by tracks.
*/
-var Tile = function(index, resolution, canvas, data) {
+var Tile = function(track, index, resolution, canvas, data) {
+ this.track = track;
this.index = index;
this.low = index * DENSITY * resolution;
this.high = (index + 1) * DENSITY * resolution;
this.resolution = resolution;
// Wrap element in div for background.
- this.canvas = $("").append(canvas);
+ this.html_elt = $("").append(canvas);
this.data = data;
this.stale = false;
};
-var SummaryTreeTile = function(index, resolution, canvas, data, max_val) {
- Tile.call(this, index, resolution, canvas, data);
+/**
+ * Perform pre-display actions.
+ */
+Tile.prototype.predisplay_actions = function() {};
+
+var SummaryTreeTile = function(track, index, resolution, canvas, data, max_val) {
+ Tile.call(this, track, index, resolution, canvas, data);
this.max_val = max_val;
};
+extend(SummaryTreeTile.prototype, Tile.prototype);
-var FeatureTrackTile = function(index, resolution, canvas, data, message) {
- Tile.call(this, index, resolution, canvas, data);
+var FeatureTrackTile = function(track, index, resolution, canvas, data, mode, message, feature_mapper) {
+ // Attribute init.
+ Tile.call(this, track, index, resolution, canvas, data);
+ this.mode = mode;
this.message = message;
+ this.feature_mapper = feature_mapper;
+
+ // Add message + action icons to tile's html.
+ if (this.message) {
+ var
+ canvas = this.html_elt.children()[0],
+ message_div = $("").addClass("tile-message").text(this.message).
+ // -1 to account for border.
+ css({'height': ERROR_PADDING-1, 'width': canvas.width}).prependTo(this.html_elt),
+ more_down_icon = $("").addClass("icon more-down").appendTo(message_div),
+ more_across_icon = $("").addClass("icon more-across").appendTo(message_div);
+
+ // Set up actions for icons.
+ var tile = this;
+ more_down_icon.click(function() {
+ // Mark tile as stale, request more data, and redraw track.
+ tile.stale = true;
+ track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.DEEP_DATA_REQ);
+ track.request_draw();
+ }).dblclick(function(e) {
+ // Do not propogate as this would normally zoom in.
+ e.stopPropagation();
+ });
+
+ more_across_icon.click(function() {
+ // Mark tile as stale, request more data, and redraw track.
+ tile.stale = true;
+ track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.BROAD_DATA_REQ);
+ track.request_draw();
+ }).dblclick(function(e) {
+ // Do not propogate as this would normally zoom in.
+ e.stopPropagation();
+ });
+ }
+};
+extend(FeatureTrackTile.prototype, Tile.prototype);
+
+/**
+ * Sets up support for popups.
+ */
+FeatureTrackTile.prototype.predisplay_actions = function() {
+ //
+ // Add support for popups.
+ //
+ var tile = this,
+ popups = {};
+
+ // Only show popups in Pack mode.
+ if (tile.mode !== "Pack") { return; }
+
+ $(this.html_elt).hover( function() {
+ this.hovered = true;
+ $(this).mousemove();
+ }, function() {
+ this.hovered = false;
+ // Clear popup if it is still hanging around (this is probably not needed)
+ $(this).siblings(".feature-popup").remove();
+ } ).mousemove(function (e) {
+ // Use the hover plugin to get a delay before showing popup
+ if ( !this.hovered ) { return; }
+ // Get feature data for position.
+ var
+ this_offset = $(this).offset(),
+ offsetX = e.pageX - this_offset.left,
+ offsetY = e.pageY - this_offset.top,
+ feature_data = tile.feature_mapper.get_feature_data(offsetX, offsetY),
+ feature_uid = (feature_data ? feature_data[0] : null);
+ // Hide visible popup if not over a feature or over a different feature.
+ $(this).siblings(".feature-popup").each(function() {
+ if ( !feature_uid ||
+ $(this).attr("id") !== feature_uid.toString() ) {
+ $(this).remove();
+ }
+ });
+
+ if (feature_data) {
+ // Get or create popup.
+ var popup = popups[feature_uid];
+ if (!popup) {
+ // Create feature's popup element.
+ var
+ feature_uid = feature_data[0],
+ feature_dict = {
+ name: feature_data[3],
+ start: feature_data[1],
+ end: feature_data[2],
+ strand: feature_data[4]
+ },
+ filters = tile.track.filters_manager.filters,
+ filter;
+
+ // Add filter values to feature dict.
+ for (var i = 0; i < filters.length; i++) {
+ filter = filters[i];
+ feature_dict[filter.name] = feature_data[filter.index];
+ }
+
+ // Build popup.
+
+ var popup = $("").attr("id", feature_uid).addClass("feature-popup"),
+ table = $("
"),
+ key, value, row;
+ for (key in feature_dict) {
+ value = feature_dict[key];
+ row = $("
").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){af.filters_div.toggle();af.filters_manager.reset_filters()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("");if(this.view.editor){this.drag_div=$("").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);var ag=this;if(ag.display_modes!==undefined){var ak=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=ak;this.action_icons.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah").text("View error").click(function(){show_modal("Trackster Error","view.canvas_manager.char_width_px){ak=view.reference_track.data_manager.get_data(av,ag,ap.mode,ar,view.reference_track.data_url_extra_params);if(am(ak)){ao=false}}if(ao){p(at,an);var aw=ap.draw_tile(at,ap.mode,ar,au,aj,ak);if(aw!==undefined){ap.tile_cache.set(ax,aw);ap.show_tile(aw,ai,aj)}return aw}var ah=$.Deferred();$.when(at,ak).then(function(){view.request_redraw(false,false,false,ap);ah.resolve()});return ah},draw_tile:function(af,aj,ai,ag,ak,ah){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai,height:""});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.max_height=Math.max(ag.max_height,af.height());ag.content_div.css("height",ag.max_height+"px");aj.children().css("height",ag.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*Q*ag,aj=Q*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=K;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("");while(af"+commatize(af)+"
").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var h=function(ai,ah,ag,af){this.display_modes=["Histogram","Line","Filled","Intensity"];M.call(this,ai,ah,ag);this.drawables=[];if(af){var al=[],ak;for(var aj=0;aj"+ag.message+"",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(D)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var M=function(aj,ah,ag,ai,am,al,ak){i.call(this,aj,ah,ag,ai,ak);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(am!==undefined?am:{}));this.filters_available=false;this.filters_visible=false;this.tool=(al!==undefined&&obj_length(al)>0?new r(this,al):undefined);this.tile_cache=new c(R);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(M.prototype,q.prototype,i.prototype,{copy:function(af){var ag=new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool,this.data_manager);ag.enabled=this.enabled;return ag},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},from_dict:function(ah,ag){var af=new this.constructor(ah.name,view,ag,ah.hda_ldda,ah.dataset_id,ah.prefs,ah.filters,ah.tool);if(ah.mode){af.change_mode(ah.mode)}return af},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show()}else{af.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ar){if(!this.can_draw()){return}var ap=this.view.low,al=this.view.high,an=al-ap,ai=this.view.container.width(),av=ai/an,ak=this.view.resolution,au=this.content_div;if(this.is_overview){ap=this.view.max_low;al=this.view.max_high;ak=Math.pow(A,Math.ceil(Math.log((view.max_high-view.max_low)/Q)/Math.log(A)));av=ai/(view.max_high-view.max_low)}if(!ar){this.content_div.children().addClass("remove")}this.max_height=0;var ag=Math.floor(ap/ak/Q);var ao=true;var at=[];var af=0;var am=function(aw){return("track" in aw)};while((ag*Q*ak)
").append( table ) );
+ popups[feature_uid] = popup;
+ }
+
+ // Attach popup to canvas's parent.
+ popup.appendTo($(tile.html_elt).parent());
+
+ // Offsets are within canvas, but popup must be positioned relative to parent element.
+ // parseInt strips "px" from left, top measurements. +7 so that mouse pointer does not
+ // overlap popup.
+ var
+ popupX = offsetX + parseInt( tile.html_elt.css("left") ) - popup.width() / 2,
+ popupY = offsetY + parseInt( tile.html_elt.css("top") ) + 7;
+ popup.css("left", popupX + "px").css("top", popupY + "px")
+ }
+ else if (!e.isPropagationStopped()) {
+ // Propogate event to other tiles because overlapping tiles prevent mousemove from being
+ // called on tiles under this tile.
+ e.stopPropagation();
+ $(this).siblings().each(function() {
+ $(this).trigger(e);
+ });
+ }
+ })
+ .mouseleave(function() {
+ $(this).siblings(".feature-popup").remove();
+ });
};
/**
@@ -2117,10 +2590,9 @@ var FeatureTrackTile = function(index, resolution, canvas, data, message) {
* ----> ReferenceTrack
* ----> FeatureTrack
* -------> ReadTrack
- * -------> ToolDataFeatureTrack
* -------> VcfTrack
*/
-var Track = function(name, view, container, prefs, data_url, data_query_wait) {
+var Track = function(name, view, container, prefs, data_manager, data_url, data_query_wait) {
// For now, track's container is always view.
Drawable.call(this, name, view, container, {}, "draghandle");
@@ -2131,28 +2603,139 @@ var Track = function(name, view, container, prefs, data_url, data_query_wait) {
this.data_url_extra_params = {}
this.data_query_wait = (data_query_wait ? data_query_wait : DEFAULT_DATA_QUERY_WAIT);
this.dataset_check_url = converted_datasets_state_url;
-
+ this.data_manager = (data_manager ? data_manager : new DataManager(DATA_CACHE_SIZE, this));
+
//
- // Create HTML element structure for track.
- //
- if (!Track.id_counter) { Track.id_counter = 0; }
- this.container_div = $("").addClass('track').attr("id", "track_" + Track.id_counter++).css("position", "relative");
- if (!this.hidden) {
- this.header_div = $("").appendTo(this.container_div);
- if (this.view.editor) { this.drag_div = $("").addClass(this.drag_handle_class).appendTo(this.header_div); }
- this.name_div = $("").appendTo(this.header_div);
- this.name_div.text(this.name);
- this.name_div.attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() );
- }
-
- //
- // Create content div, which is where track is displayed.
+ // Create content div, which is where track is displayed, and add to container if available.
//
this.content_div = $("
").appendTo(this.container_div);
- this.container.content_div.append(this.container_div);
+ if (this.container) { this.container.content_div.append(this.container_div); }
};
+
extend(Track.prototype, Drawable.prototype, {
- /** Returns track type. */
+ action_icons_def: [
+ // Change track mode.
+ {
+ name: "mode_icon",
+ title: "Set display mode",
+ css_class: "chevron-expand",
+ on_click_fn: function() {}
+ },
+ // Hide/show content.
+ Drawable.prototype.action_icons_def[0],
+ // Set track as overview.
+ {
+ name: "overview_icon",
+ title: "Set as overview",
+ css_class: "overview-icon",
+ on_click_fn: function(track) {
+ track.view.set_overview(track);
+ }
+ },
+ // Edit config.
+ Drawable.prototype.action_icons_def[1],
+ // Toggle track filters.
+ {
+ name: "filters_icon",
+ title: "Filters",
+ css_class: "filters-icon",
+ on_click_fn: function(track) {
+ // TODO: update tipsy text.
+ track.filters_div.toggle();
+ track.filters_manager.reset_filters();
+ }
+ },
+ // Toggle track tool.
+ {
+ name: "tools_icon",
+ title: "Tools",
+ css_class: "tools-icon",
+ on_click_fn: function(track) {
+ // TODO: update tipsy text.
+
+ track.dynamic_tool_div.toggle();
+
+ // Update track name.
+ if (track.dynamic_tool_div.is(":visible")) {
+ track.set_name(track.name + track.tool_region_and_parameters_str());
+ }
+ else {
+ track.revert_name();
+ }
+ // HACK: name change modifies icon placement, which leaves tooltip incorrectly placed.
+ $(".tipsy").remove();
+ }
+ },
+ // Remove track.
+ Drawable.prototype.action_icons_def[2]
+ ],
+ can_draw: function() {
+ if ( this.dataset_id && Drawable.prototype.can_draw.call(this) ) {
+ return true;
+ }
+ return false;
+ },
+ build_container_div: function () {
+ return $("").addClass('track').attr("id", "track_" + this.id).css("position", "relative");
+ },
+ build_header_div: function() {
+ var header_div = $("");
+ if (this.view.editor) { this.drag_div = $("").addClass(this.drag_handle_class).appendTo(header_div); }
+ this.name_div = $("").addClass("track-name").appendTo(header_div).text(this.name)
+ .attr( "id", this.name.replace(/\s+/g,'-').replace(/[^a-zA-Z0-9\-]/g,'').toLowerCase() );
+ return header_div;
+ },
+ build_action_icons: function() {
+ Drawable.prototype.build_action_icons.call(this, this.action_icons_def);
+
+ // Set up behavior for modes popup.
+ var track = this;
+ if (track.display_modes !== undefined) {
+ var init_mode = (track.config && track.config.values['mode'] ?
+ track.config.values['mode'] : track.display_modes[0]);
+ track.mode = init_mode;
+
+ this.action_icons.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")");
+
+ var mode_mapping = {};
+ for (var i = 0, len = track.display_modes.length; i < len; i++) {
+ var mode = track.display_modes[i];
+ mode_mapping[mode] = function(mode) {
+ return function() {
+ track.change_mode(mode);
+ // HACK: the popup menu messes with the track's hover event, so manually show/hide
+ // icons div for now.
+ track.icons_div.show();
+ track.container_div.mouseleave(function() { track.icons_div.hide(); } ); };
+ }(mode);
+ }
+
+ make_popupmenu(this.action_icons.mode_icon, mode_mapping);
+ }
+ },
+ /**
+ * Hide any elements that are part of the tracks contents area. Should
+ * remove as approprite, the track will be redrawn by show_contents.
+ */
+ hide_contents : function () {
+ // Clear contents by removing any elements that are contained in
+ // the tracks content_div
+ this.content_div.children().remove();
+ // Hide the content div
+ this.content_div.hide();
+ // And any y axis labels (common to several track types)
+ this.container_div.find(".yaxislabel, .track-resize").hide()
+ },
+ show_contents : function() {
+ // Show the contents div and labels (if present)
+ this.content_div.show();
+ this.container_div.find(".yaxislabel, .track-resize").show()
+ // Request a redraw of the content
+ this.request_draw();
+ },
+ /**
+ * Returns track type.
+ */
get_type: function() {
// Order is important: start with most-specific classes and go up the track hierarchy.
if (this instanceof LabelTrack) {
@@ -2167,12 +2750,12 @@ extend(Track.prototype, Drawable.prototype, {
else if (this instanceof ReadTrack) {
return "ReadTrack";
}
- else if (this instanceof ToolDataFeatureTrack) {
- return "ToolDataFeatureTrack";
- }
else if (this instanceof VcfTrack) {
return "VcfTrack";
}
+ else if (this instanceof CompositeTrack) {
+ return "CompositeTrack";
+ }
else if (this instanceof FeatureTrack) {
return "FeatureTrack";
}
@@ -2186,7 +2769,6 @@ extend(Track.prototype, Drawable.prototype, {
track.enabled = false;
track.tile_cache.clear();
track.data_manager.clear();
- track.initial_canvas = undefined;
track.content_div.css("height", "auto");
/*
if (!track.content_div.text()) {
@@ -2211,7 +2793,6 @@ extend(Track.prototype, Drawable.prototype, {
track.container_div.addClass("error");
track.content_div.text(DATA_ERROR);
if (result.message) {
- var track_id = track.view.tracks.indexOf(track);
var error_link = $(" ").text("View error").click(function() {
show_modal( "Trackster Error", "
" + result.message + "", { "Close" : hide_modal } ); }); @@ -2230,7 +2811,7 @@ extend(Track.prototype, Drawable.prototype, { } else if (result['status'] === "data") { if (result['valid_chroms']) { track.valid_chroms = result['valid_chroms']; - track.make_name_popup_menu(); + track.update_icons(); } track.content_div.text(DATA_OK); if (track.view.chrom) { @@ -2245,14 +2826,18 @@ extend(Track.prototype, Drawable.prototype, { } } }); + + this.update_icons(); }, /** * Additional initialization required before drawing track for the first time. */ - predraw_init: function() {}, + predraw_init: function() {} }); -var TiledTrack = function(filters_list, tool_dict) { +var TiledTrack = function(name, view, container, prefs, filters_list, tool_dict, data_manager) { + Track.call(this, name, view, container, prefs, data_manager); + var track = this, view = track.view; @@ -2265,57 +2850,43 @@ var TiledTrack = function(filters_list, tool_dict) { this.filters_available = false; this.filters_visible = false; this.tool = (tool_dict !== undefined && obj_length(tool_dict) > 0 ? new Tool(this, tool_dict) : undefined); - this.is_overview = false; + this.tile_cache = new Cache(TILE_CACHE_SIZE); - if (track.hidden) { return; } + if (this.header_div) { + // + // Create filters div. + // + if (this.filters_manager) { + this.filters_div = this.filters_manager.parent_div + this.header_div.after(this.filters_div); + } - // - // Create filters div. - // - if (this.filters_manager) { - this.filters_div = this.filters_manager.parent_div - this.header_div.after(this.filters_div); - } - - // - // Create dynamic tool div. - // - if (this.tool) { - this.dynamic_tool_div = this.tool.parent_div; - this.header_div.after(this.dynamic_tool_div); - } - - // - // Create modes control. - // - if (track.display_modes !== undefined) { - if (track.mode_div === undefined) { - track.mode_div = $("").appendTo(track.header_div); - var init_mode = (track.config && track.config.values['mode'] ? - track.config.values['mode'] : track.display_modes[0]); - track.mode = init_mode; - track.mode_div.text(init_mode); - - var mode_mapping = {}; - for (var i = 0, len = track.display_modes.length; i < len; i++) { - var mode = track.display_modes[i]; - mode_mapping[mode] = function(mode) { - return function() { track.change_mode(mode); }; - }(mode); - } - make_popupmenu(track.mode_div, mode_mapping); - } else { - track.mode_div.hide(); + // + // Create dynamic tool div. + // + if (this.tool) { + this.dynamic_tool_div = this.tool.parent_div; + this.header_div.after(this.dynamic_tool_div); } } - - this.make_name_popup_menu(); }; extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { /** - * Convert track to JSON object. + * Returns a copy of the track. The copy uses the same data manager so that the tracks can share data. */ - to_json: function() { + copy: function(container) { + // Create copy. + var new_track = new this.constructor(this.name, this.view, container, this.hda_ldda, this.dataset_id, this.prefs, + this.filters, this.tool, this.data_manager); + // Misc. init and return. + new_track.enabled = this.enabled; + return new_track; + }, + /** + * Returns representation of object in a dictionary for easy saving. + * Use from_dict to recreate object. + */ + to_dict: function() { return { "track_type": this.get_type(), "name": this.name, @@ -2325,101 +2896,57 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { "mode": this.mode, }; }, + /** + * Restore object from a dictionary created by to_dict() + */ + from_dict: function(track_dict, container) { + var track = new this.constructor( + track_dict.name, view, container, track_dict.hda_ldda, track_dict.dataset_id, + track_dict.prefs, track_dict.filters, track_dict.tool); + if (track_dict.mode) { + track.change_mode(track_dict.mode); + } + return track; + }, /** * Change track's mode. */ - change_mode: function(name) { + change_mode: function(new_mode) { var track = this; - track.mode_div.text(name); // TODO: is it necessary to store the mode in two places (.mode and track_config)? - track.mode = name; - track.config.values['mode'] = name; + track.mode = new_mode; + track.config.values['mode'] = new_mode; track.tile_cache.clear(); track.request_draw(); + this.action_icons.mode_icon.attr("title", "Set display mode (now: " + track.mode + ")"); return track; }, /** - * Make popup menu for track name. + * Update track's buttons. */ - make_name_popup_menu: function() { + update_icons: function() { var track = this; - var track_dropdown = {}; - // - // Make track overview option. + // Show/hide filter icon. // - track_dropdown[(this.is_overview ? "Hide overview" : "Set as overview")] = function() { - if (track.is_overview) { - track.view.reset_overview(); - } - else { - track.view.set_overview(track); - } - }; - - // - // Edit config option. - // - track_dropdown["Edit configuration"] = function() { - var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, - ok_fn = function() { - track.config.update_from_form( $(".dialog-box") ); - hide_modal(); - $(window).unbind("keypress.check_enter_esc"); - }, - check_enter_esc = function(e) { - if ((e.keyCode || e.which) === 27) { // Escape key - cancel_fn(); - } else if ((e.keyCode || e.which) === 13) { // Enter key - ok_fn(); - } - }; - - $(window).bind("keypress.check_enter_esc", check_enter_esc); - show_modal("Configure Track", track.config.build_form(), { - "Cancel": cancel_fn, - "OK": ok_fn - }); - }; - - // - // Show/hide filters option. - // - if (track.filters_available > 0) { - // Show/hide filters menu item. - var text = (track.filters_div.is(":visible") ? "Hide filters" : "Show filters"); - track_dropdown[text] = function() { - // Toggle filtering div, reset filters, and remake menu. - track.filters_visible = (track.filters_div.is(":visible")); - if (track.filters_visible) { - track.filters_manager.reset_filters(); - } - track.filters_div.toggle(); - track.make_name_popup_menu(); - }; + if (track.filters_available) { + track.action_icons.filters_icon.show(); + } + else { + track.action_icons.filters_icon.hide(); } // - // Show/hide tool option. + // Show/hide tool icon. // if (track.tool) { - // Show/hide dynamic tool menu item. - var text = (track.dynamic_tool_div.is(":visible") ? "Hide tool" : "Show tool"); - track_dropdown[text] = function() { - // Set track name, toggle tool div, and remake menu. - if (!track.dynamic_tool_div.is(":visible")) { - track.set_name(track.name + track.tool_region_and_parameters_str()); - } - else { - menu_option_text = "Show dynamic tool"; - track.revert_name(); - } - track.dynamic_tool_div.toggle(); - track.make_name_popup_menu(); - }; + track.action_icons.tools_icon.show(); } - + else { + track.action_icons.tools_icon.hide(); + } + // // List chrom/contigs with data option. // @@ -2430,61 +2957,6 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { }; } */ - - // - // Remove option. - // - track_dropdown.Remove = function() { - track.remove(); - }; - - make_popupmenu(track.name_div, track_dropdown); - }, - /** - * Set track's overview status. - */ - set_is_overview: function(is_overview) { - this.is_overview = is_overview; - this.make_name_popup_menu(); - }, - /** - * Returns a jQuery Deferred object that resolves to a Tile with track's overview. - * TODO: this should be the approach used when drawing any tile so that tile drawing is not blocking. - */ - get_overview_tile: function() { - var - track = this; - view = track.view, - resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / DENSITY ) / Math.log(RESOLUTION) )), - view_width = view.container.width(), - // w_scale units are pixels per base. - w_scale = view_width / (view.max_high - view.max_low), - overview_tile = $.Deferred(); - $.when(track.data_manager.get_data(view.max_low, view.max_high, "Auto", resolution, track.data_url_extra_params)).then(function(overview_data) { - var - key = track._gen_tile_cache_key(view_width, w_scale, 0), - tile = track.tile_cache.get(key); - - // Draw tile if necessary. - if (!tile) { - tile = track.draw_tile(overview_data, "Auto", resolution, 0, w_scale); - track.tile_cache.set(key, tile); - } - - // Always copy tile because it may need to be used in viz. - var - src_canvas = $(tile.canvas.find("canvas")), - new_canvas = src_canvas.clone(), - src_ctx = src_canvas.get(0).getContext("2d"), - tgt_ctx = new_canvas.get(0).getContext("2d"), - data = src_ctx.getImageData(0, 0, src_ctx.canvas.width, src_ctx.canvas.height); - // Need to undo offsets when placing image data. - tgt_ctx.putImageData(data, -track.left_offset, (tile.data.dataset_type === "summary_tree" ? SUMMARY_TREE_TOP_PADDING : 0)); - new_tile = new Tile(-1, resolution, new_canvas); - overview_tile.resolve(new_tile); - }); - - return overview_tile; }, /** * Generate a key for the tile cache. @@ -2506,10 +2978,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { * can manage drawing. */ _draw: function(force, clear_after) { - if (!this.enabled) { return; } - - // HACK: ReferenceTrack can draw without dataset ID, but other tracks cannot. - if ( !(this instanceof ReferenceTrack) && (!this.dataset_id) ) { return; } + if ( !this.can_draw() ) { return; } var low = this.view.low, high = this.view.high, @@ -2518,10 +2987,29 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { // w_scale units are pixels per base. w_scale = width / range, resolution = this.view.resolution, - parent_element = $(""); + // FIXME: parent element is not currently needed, but it may be useful for multitrack drawing. + parent_element = this.content_div; + + // For overview, adjust high, low, resolution, and w_scale. + if (this.is_overview) { + low = this.view.max_low; + high = this.view.max_high; + resolution = Math.pow(RESOLUTION, Math.ceil( Math.log( (view.max_high - view.max_low) / DENSITY ) / Math.log(RESOLUTION) )); + w_scale = width / (view.max_high - view.max_low); + } + + // + // Method for moving and/or removing tiles: + // (a) mark all elements for removal using class 'remove' + // (b) during tile drawing/placement, remove class for elements that are moved; + // this occurs in show_tile() + // (c) after drawing all tiles, remove elements still marked for removal + // (i.e. that still have class 'remove'). + // - if (!clear_after) { this.content_div.children().remove(); } - this.content_div.append( parent_element ); + // Step (a) for (re)moving tiles. + if (!clear_after) { this.content_div.children().addClass("remove"); } + this.max_height = 0; // Index of first tile that overlaps visible region var tile_index = Math.floor( low / resolution / DENSITY ); @@ -2529,17 +3017,21 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { var all_tiles_drawn = true; var drawn_tiles = []; var tile_count = 0; + var is_tile = function(o) { return (o && 'track' in o) }; // Draw or fetch and show tiles. while ( ( tile_index * DENSITY * resolution ) < high ) { - tile = this.draw_helper( force, width, tile_index, resolution, parent_element, w_scale ); - if ( tile ) { - drawn_tiles.push( tile ); + var draw_result = this.draw_helper( force, width, tile_index, resolution, parent_element, w_scale ); + if ( is_tile(draw_result) ) { + drawn_tiles.push( draw_result ); } else { all_tiles_drawn = false; } tile_index += 1; tile_count++; } + + // Step (c) for (re)moving tiles. + if (!clear_after) { this.content_div.children(".remove").remove(); } // Use interval to check if tiles have been drawn. When all tiles are drawn, call post-draw actions. var track = this; @@ -2570,16 +3062,16 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { tile = tiles[tile_index]; if (!tile.message) { // Need to align with other tile(s) that have message(s). - tile.canvas.css("padding-top", ERROR_PADDING); + tile.html_elt.css("padding-top", ERROR_PADDING); } } } }, /** - * Handle a single tile, either from cache or by setting up a deferred - * operation and then requesting another redraw + * Retrieves from cache, draws, or sets up drawing for a single tile. Returns either a Tile object or a + * jQuery.Deferred object that is fulfilled when tile can be drawn again. */ - draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, drawn_tiles, more_tile_data) { + draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, more_tile_data) { var track = this, key = this._gen_tile_cache_key(width, w_scale, tile_index), tile_low = tile_index * DENSITY * resolution, @@ -2595,7 +3087,7 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { // Helper to determine if object is jQuery deferred var is_deferred = function ( d ) { return ( 'isResolved' in d ); - } + }; // Flag to track whether we can draw everything now var can_draw_now = true @@ -2615,85 +3107,101 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { } } - // If we can draw now, do so + // If we can draw now, do so. if ( can_draw_now ) { - extend( tile_data, more_tile_data ); - var tile = track.draw_tile(tile_data, track.mode, resolution, tile_index, w_scale, seq_data); - track.tile_cache.set(key, tile); - // Don't show if no tile + // Set up and draw tile. + extend(tile_data, more_tile_data); + + // HACK: this is FeatureTrack-specific. + // If track mode is Auto, determine mode and update. + var mode = track.mode; + if (mode === "Auto") { + mode = track.get_mode(tile_data); + track.update_auto_mode(mode); + } + + // Draw canvas. + var + canvas = track.view.canvas_manager.new_canvas(), + tile_bounds = track._get_tile_bounds(tile_index, resolution), + tile_low = tile_bounds[0], + tile_high = tile_bounds[1], + width = Math.ceil( (tile_high - tile_low) * w_scale ) + track.left_offset, + height = track.get_canvas_height(tile_data, mode, w_scale, width); + + canvas.width = width; + canvas.height = height; + var tile = track.draw_tile(tile_data, canvas, mode, resolution, tile_index, w_scale, seq_data); + + // Don't cache, show if no tile. if (tile !== undefined) { + track.tile_cache.set(key, tile); track.show_tile(tile, parent_element, w_scale); } - return tile + return tile; } // Can't draw now, so trigger another redraw when the data is ready + var can_draw = $.Deferred(); $.when( tile_data, seq_data ).then( function() { - view.request_redraw(); + view.request_redraw(false, false, false, track); + can_draw.resolve(); }); - // Indicate to caller that this tile could not be drawn - return null; - }, + // Returned Deferred is resolved when tile can be drawn. + return can_draw; + }, /** - * Show track tile and perform associated actions. + * Returns canvas height needed to display data; return value is an integer that denotes the + * number of pixels required. + */ + get_canvas_height: function(result, mode, w_scale, canvas_width) { + return this.height_px; + }, + /** + * Draw a track tile. + * @param result result from server + * @param canvas canvas to draw on + * @param mode mode to draw in + * @param resolution view resolution + * @param tile_index index of tile to be drawn + * @param w_scale pixels per base + * @param ref_seq reference sequence data + */ + draw_tile: function(result, canvas, mode, resolution, tile_index, w_scale, ref_seq) { + console.log("Warning: TiledTrack.draw_tile() not implemented."); + }, + /** + * Show track tile and perform associated actions. Showing tile may actually move + * an existing tile rather than reshowing it. */ show_tile: function(tile, parent_element, w_scale) { - // Readability. var track = this, - canvas = tile.canvas, - tile_element = canvas; + tile_element = tile.html_elt; // - // If tile has message, display message and button to show more data. - // TODO: need to handle other messages, not assume message === show more data. + // Show/move tile element. // - if (tile.message) { - var - container_div = $(""), - message_div = $("").addClass("tile-message").text(tile.message). - // -1 to account for border. - css({'height': ERROR_PADDING-1, 'width': tile.canvas.width}).appendTo(container_div), - more_down_icon = $("").addClass("icon more-down").appendTo(message_div), - more_across_icon = $("").addClass("icon more-across").appendTo(message_div); - container_div.append(canvas); - tile_element = container_div; - - // Set up actions for icons. - more_down_icon.click(function() { - // Mark tile as stale, request more data, and redraw track. - tile.stale = true; - track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.DEEP_DATA_REQ); - track.request_draw(); - }).dblclick(function(e) { - // Do not propogate as this would normally zoom in. - e.stopPropagation(); - }); - - more_across_icon.click(function() { - // Mark tile as stale, request more data, and redraw track. - tile.stale = true; - track.data_manager.get_more_data(tile.low, tile.high, track.mode, tile.resolution, {}, track.data_manager.BROAD_DATA_REQ); - track.request_draw(); - }).dblclick(function(e) { - // Do not propogate as this would normally zoom in. - e.stopPropagation(); - }); - } - // - // Show tile element. - // + tile.predisplay_actions(); - // Position tile element, recalculate left position at display time - var range = this.view.high - this.view.low, - left = (tile.low - this.view.low) * w_scale; + // Position tile element based on current viewport. + var left = ( tile.low - (this.is_overview? this.view.max_low : this.view.low) ) * w_scale; if (this.left_offset) { left -= this.left_offset; } tile_element.css({ position: 'absolute', top: 0, left: left, height: '' }); - parent_element.append(tile_element); + + if ( tile_element.hasClass("remove") ) { + // Step (b) for (re)moving tiles. See _draw() function for description of algorithm + // for removing tiles. + tile_element.removeClass("remove"); + } + else { + // Showing new tile. + parent_element.append(tile_element); + } // Set track height. track.max_height = Math.max(track.max_height, tile_element.height()); @@ -2721,15 +3229,48 @@ extend(TiledTrack.prototype, Drawable.prototype, Track.prototype, { region = (chrom !== undefined && low !== undefined && high !== undefined ? chrom + ":" + low + "-" + high : "all"); return " - region=[" + region + "], parameters=[" + track.tool.get_param_values().join(", ") + "]"; + }, + /** + * Set up track to receive tool data. + */ + init_for_tool_data: function() { + // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets-- + // is ready. + this.data_url = raw_data_url; + this.data_query_wait = 1000; + this.dataset_check_url = dataset_state_url; + + /** + * Predraw init sets up postdraw init. + */ + this.predraw_init = function() { + // Postdraw init: once data has been fetched, reset data url, wait time and start indexing. + var track = this; + var post_init = function() { + if (track.data_manager.size() === 0) { + // Track still drawing initial data, so do nothing. + setTimeout(post_init, 300); + } + else { + // Track drawing done: reset dataset check, data URL, wait time and get dataset state to start + // indexing. + track.data_url = default_data_url; + track.data_query_wait = DEFAULT_DATA_QUERY_WAIT; + track.dataset_state_url = converted_datasets_state_url; + $.getJSON(track.dataset_state_url, {dataset_id : track.dataset_id, hda_ldda: track.hda_ldda}, function(track_data) {}); + } + }; + post_init(); + } } }); var LabelTrack = function (view, container) { - this.hidden = true; - Track.call(this, "label", view, container, {} ); + Track.call(this, "label", view, container, false, {} ); this.container_div.addClass( "label-track" ); }; extend(LabelTrack.prototype, Track.prototype, { + build_header_div: function() {}, init: function() { // Enable by default because there should always be data when drawing track. this.enabled = true; @@ -2755,10 +3296,181 @@ extend(LabelTrack.prototype, Track.prototype, { } }); +/** + * A tiled track composed of multiple other tracks. + */ +var CompositeTrack = function(name, view, container, drawables) { + // HACK: modes should be static class vars for most tracks and should update as + // needed for CompositeTracks + this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; + TiledTrack.call(this, name, view, container); + + // Init drawables; each drawable is a copy so that config/preferences + // are independent of each other. + this.drawables = []; + if (drawables) { + var + ids = [], + drawable; + for (var i = 0; i < drawables.length; i++) { + drawable = drawables[i]; + ids.push(drawable.dataset_id); + this.drawables[i] = drawable.copy(); + } + this.enabled = true; + } + + this.update_icons(); + + // HACK: needed for saving object for now. Need to generalize get_type() to all Drawables and use + // that for object type. + this.obj_type = "CompositeTrack"; +}; + +extend(CompositeTrack.prototype, TiledTrack.prototype, { + // HACK: CompositeTrack should inherit from DrawableCollection as well. + /** + * Returns representation of object in a dictionary for easy saving. + * Use from_dict to recreate object. + */ + to_dict: DrawableCollection.prototype.to_dict, + add_drawable: DrawableCollection.prototype.add_drawable, + /** + * Restore object from a dictionary created by to_dict() + */ + // TODO: unify with DrawableCollection.prototype.from_dict? + from_dict: function(collection_dict, container) { + var collection = new this.constructor( collection_dict.name, view, + container, collection_dict.prefs, + view.viewport_container, view); + var drawable_dict, + drawable_type, + drawable; + for (var i = 0; i < collection_dict.drawables.length; i++) { + drawable_dict = collection_dict.drawables[i]; + drawable_type = drawable_dict['obj_type']; + // For backward compatibility: + if (!drawable_type) { + drawable_type = drawable_dict['track_type']; + } + // No container for tracks so that it is not made visible. + drawable = addable_objects[ drawable_type ].prototype.from_dict( drawable_dict ); + collection.add_drawable( drawable ); + } + return collection; + }, + change_mode: function(new_mode) { + TiledTrack.prototype.change_mode.call(this, new_mode); + for (var i = 0; i < this.drawables.length; i++) { + this.drawables[i].change_mode(new_mode); + } + }, + init: function() { + // FIXME: probably should enable based on whether/how many drawaables are enabled. + this.enabled = true; + this.request_draw(); + }, + update_icons: function() { + // For now, hide filters and tool. + this.action_icons.filters_icon.hide(); + this.action_icons.tools_icon.hide(); + }, + can_draw: Drawable.prototype.can_draw, + draw_helper: function(force, width, tile_index, resolution, parent_element, w_scale, more_tile_data) { + // FIXME: this function is similar to TiledTrack.draw_helper -- can the two be merged/refactored? + var track = this, + key = this._gen_tile_cache_key(width, w_scale, tile_index), + tile_low = tile_index * DENSITY * resolution, + tile_high = tile_low + DENSITY * resolution; + + // Check tile cache, if found show existing tile in correct position + var tile = (force ? undefined : track.tile_cache.get(key)); + if (tile) { + track.show_tile(tile, parent_element, w_scale); + return tile; + } + + // Helper to determine if object is jQuery deferred + var is_deferred = function ( d ) { + return ( 'isResolved' in d ); + }; + + // Try to get drawables' data. + var all_data = [], + track, + // Flag to track whether we can draw everything now + can_draw_now = true, + tile_data, + seq_data; + for (var i = 0; i < this.drawables.length; i++) { + track = this.drawables[i]; + // Get the track data, maybe a deferred. + tile_data = track.data_manager.get_data( tile_low, tile_high, track.mode, resolution, track.data_url_extra_params ); + if ( is_deferred( tile_data ) ) { + can_draw_now = false; + } + all_data.push(tile_data); + + // Get seq data if needed, maybe a deferred. + seq_data = null; + if ( view.reference_track && w_scale > view.canvas_manager.char_width_px ) { + seq_data = view.reference_track.data_manager.get_data(tile_low, tile_high, track.mode, resolution, view.reference_track.data_url_extra_params) + if ( is_deferred( seq_data ) ) { + can_draw_now = false; + } + } + all_data.push(seq_data); + } + + // If we can draw now, do so. + if ( can_draw_now ) { + // Set up and draw tile. + extend(tile_data, more_tile_data); + + var + canvas = track.view.canvas_manager.new_canvas(), + tile_bounds = track._get_tile_bounds(tile_index, resolution), + tile_low = tile_bounds[0], + tile_high = tile_bounds[1], + width = Math.ceil( (tile_high - tile_low) * w_scale ), + height = track.get_canvas_height(tile_data, mode, w_scale, width); + + // FIXME: + // (a) right now, only LineTracks respect width/height setting and do not set it in draw_tile; + // however, other track types be modified to work this way. This is necessary b/c setting the width/height + // clears the canvas and hence prevents non-compliant tracks from being used in CompositeTracks. + // (b) need to normalize across tracks before displaying, e.g. set LineTracks' min/max appropriately. + canvas.width = width; + canvas.height = height; + var all_data_index = 0 + for (var i = 0; i < this.drawables.length; i++, all_data_index += 2) { + track = this.drawables[i]; + tile_data = all_data[ all_data_index ]; + seq_data = all_data[ all_data_index + 1 ]; + tile = track.draw_tile(tile_data, canvas, track.mode, resolution, tile_index, w_scale, seq_data); + } + + // Don't cache, show if no tile. + track.tile_cache.set(key, tile); + track.show_tile(tile, parent_element, w_scale); + return tile; + } + + // Can't draw now, so trigger another redraw when the data is ready + var can_draw = $.Deferred(), + track = this; + $.when.apply($, all_data).then(function() { + view.request_redraw(false, false, false, track); + can_draw.resolve(); + }); + + // Returned Deferred that is resolved when tile can be drawn. + return can_draw; + } +}); + var ReferenceTrack = function (view) { - this.hidden = true; - Track.call(this, "reference", view, { content_div: view.top_labeltrack }, {}); - TiledTrack.call(this); + TiledTrack.call(this, "reference", view, { content_div: view.top_labeltrack }, {}); view.reference_track = this; this.left_offset = 200; @@ -2769,30 +3481,27 @@ var ReferenceTrack = function (view) { this.content_div.css("border", "none"); this.data_url = reference_url; this.data_url_extra_params = {dbkey: view.dbkey}; - this.data_manager = new ReferenceTrackDataManager(CACHED_DATA, this, false); - this.tile_cache = new Cache(CACHED_TILES_LINE); + this.data_manager = new ReferenceTrackDataManager(DATA_CACHE_SIZE, this, false); }; extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { + build_header_div: function() {}, init: function() { // Enable by default because there should always be data when drawing track. this.enabled = true; }, + can_draw: Drawable.prototype.can_draw, /** * Draw ReferenceTrack tile. */ - draw_tile: function(seq, mode, resolution, tile_index, w_scale) { - var track = this, - tile_length = DENSITY * resolution; + draw_tile: function(seq, canvas, mode, resolution, tile_index, w_scale) { + var track = this; if (w_scale > this.view.canvas_manager.char_width_px) { - if (seq === null) { + if (seq.data === null) { track.content_div.css("height", "0px"); return; } - var canvas = this.view.canvas_manager.new_canvas(); - var ctx = canvas.getContext("2d"); - canvas.width = Math.ceil(tile_length * w_scale + track.left_offset); - canvas.height = track.height_px; + var ctx = canvas.getContext("2d"); ctx.font = ctx.canvas.manager.default_font; ctx.textAlign = "center"; seq = seq.data; @@ -2800,27 +3509,25 @@ extend(ReferenceTrack.prototype, Drawable.prototype, TiledTrack.prototype, { var c_start = Math.round(c * w_scale); ctx.fillText(seq[c], c_start + track.left_offset, 10); } - return new Tile(tile_index, resolution, canvas, seq); + return new Tile(track, tile_index, resolution, canvas, seq); } this.content_div.css("height", "0px"); } }); -var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) { +var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) { var track = this; this.display_modes = ["Histogram", "Line", "Filled", "Intensity"]; this.mode = "Histogram"; - Track.call( this, name, view, container, prefs ); - TiledTrack.call( this ); + TiledTrack.call(this, name, view, container, prefs, filters, tool, data_manager); this.min_height_px = 16; this.max_height_px = 400; - this.height_px = 80; + // Default height for new tracks, should be a defined constant? + this.height_px = 32; this.hda_ldda = hda_ldda; this.dataset_id = dataset_id; this.original_dataset_id = dataset_id; - this.data_manager = new DataManager(CACHED_DATA, this); - this.tile_cache = new Cache(CACHED_TILES_LINE); this.left_offset = 0; // Define track configuration @@ -2828,7 +3535,7 @@ var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) { track: this, params: [ { key: 'name', label: 'Name', type: 'text', default_value: name }, - { key: 'color', label: 'Color', type: 'color', default_value: 'black' }, + { key: 'color', label: 'Color', type: 'color', default_value: get_random_color() }, { key: 'min_value', label: 'Min Value', type: 'float', default_value: undefined }, { key: 'max_value', label: 'Max Value', type: 'float', default_value: undefined }, { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, @@ -2839,8 +3546,8 @@ var LineTrack = function (name, view, container, hda_ldda, dataset_id, prefs) { track.set_name(track.prefs.name); track.vertical_range = track.prefs.max_value - track.prefs.min_value; // Update the y-axis - $('#linetrack_' + track.track_id + '_minval').text(track.prefs.min_value); - $('#linetrack_' + track.track_id + '_maxval').text(track.prefs.max_value); + $('#linetrack_' + track.dataset_id + '_minval').text(track.prefs.min_value); + $('#linetrack_' + track.dataset_id + '_maxval').text(track.prefs.max_value); track.tile_cache.clear(); track.request_draw(); } @@ -2863,8 +3570,10 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, { var drag_control = $( "
" )
// Control shows on hover over track, stays while dragging
$(track.container_div).hover( function() {
- in_handle = true;
- drag_control.show();
+ if ( track.content_visible ) {
+ in_handle = true;
+ drag_control.show();
+ }
}, function() {
in_handle = false;
if ( ! in_drag ) { drag_control.hide(); }
@@ -2887,8 +3596,7 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
}).appendTo(track.container_div);
},
predraw_init: function() {
- var track = this,
- track_id = track.view.tracks.indexOf(track);
+ var track = this;
track.vertical_range = undefined;
return $.getJSON( track.data_url, { stats: true, chrom: track.view.chrom, low: null, high: null,
@@ -2896,11 +3604,22 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
track.container_div.addClass( "line-track" );
var data = result.data;
if ( isNaN(parseFloat(track.prefs.min_value)) || isNaN(parseFloat(track.prefs.max_value)) ) {
- track.prefs.min_value = data.min;
- track.prefs.max_value = data.max;
+ // Compute default minimum and maximum values
+ var min_value = data.min
+ var max_value = data.max
+ // If mean and sd are present, use them to compute a ~95% window
+ // but only if it would shrink the range on one side
+ min_value = Math.floor( Math.min( 0, Math.max( min_value, data.mean - 2 * data.sd ) ) )
+ max_value = Math.ceil( Math.max( 0, Math.min( max_value, data.mean + 2 * data.sd ) ) )
+ // Update the prefs
+ track.prefs.min_value = min_value;
+ track.prefs.max_value = max_value;
// Update the config
- $('#track_' + track_id + '_minval').val(track.prefs.min_value);
- $('#track_' + track_id + '_maxval').val(track.prefs.max_value);
+ // FIXME: we should probably only save this when the user explicately sets it
+ // since we lose the ability to compute it on the fly (when changing
+ // chromosomes for example).
+ $('#track_' + track.dataset_id + '_minval').val(track.prefs.min_value);
+ $('#track_' + track.dataset_id + '_maxval').val(track.prefs.max_value);
}
track.vertical_range = track.prefs.max_value - track.prefs.min_value;
track.total_frequency = data.total_frequency;
@@ -2908,8 +3627,8 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
// Draw y-axis labels if necessary
track.container_div.find(".yaxislabel").remove();
- var min_label = $("").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_minval').text(round_1000(track.prefs.min_value));
- var max_label = $("").addClass('yaxislabel').attr("id", 'linetrack_' + track_id + '_maxval').text(round_1000(track.prefs.max_value));
+ var min_label = $("").addClass('yaxislabel').attr("id", 'linetrack_' + track.dataset_id + '_minval').text(round(track.prefs.min_value, 3));
+ var max_label = $("").addClass('yaxislabel').attr("id", 'linetrack_' + track.dataset_id + '_maxval').text(round(track.prefs.max_value, 3));
max_label.css({ position: "absolute", top: "24px", left: "10px" });
max_label.prependTo(track.container_div);
@@ -2921,33 +3640,29 @@ extend(LineTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
/**
* Draw LineTrack tile.
*/
- draw_tile: function(result, mode, resolution, tile_index, w_scale) {
+ draw_tile: function(result, canvas, mode, resolution, tile_index, w_scale) {
+ // FIXME: is this needed?
if (this.vertical_range === undefined) {
return;
}
-
+
+ // Paint onto canvas.
var
+ ctx = canvas.getContext("2d"),
tile_bounds = this._get_tile_bounds(tile_index, resolution),
tile_low = tile_bounds[0],
tile_high = tile_bounds[1],
- width = Math.ceil( (tile_high - tile_low) * w_scale ),
- height = this.height_px;
+ painter = new painters.LinePainter(result.data, tile_low, tile_high, this.prefs, mode);
+ // HACK: this is needed for compositing tracks. This should be a config setting somewhere; also,
+ // "darker" may not be included in future canvas implementations.
+ ctx.globalCompositeOperation = "darker";
+ painter.draw(ctx, canvas.width, canvas.height);
- // Create canvas
- var canvas = this.view.canvas_manager.new_canvas();
- canvas.width = width,
- canvas.height = height;
-
- // Paint line onto full canvas
- var ctx = canvas.getContext("2d");
- var painter = new painters.LinePainter(result.data, tile_low, tile_high, this.prefs, mode);
- painter.draw(ctx, width, height);
-
- return new Tile(tile_index, resolution, canvas, result.data);
- }
+ return new Tile(this.track, tile_index, resolution, canvas, result.data);
+ }
});
-var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool) {
+var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) {
//
// Preinitialization: do things that need to be done before calling Track and TiledTrack
// initialization code.
@@ -2957,26 +3672,27 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
//
// Initialization.
- //
-
- // FIXME: cleaner init needed; should just be able to call TiledTrack()
- Track.call(this, name, view, container, prefs);
- TiledTrack.call(this, filters, tool);
+ //
+ TiledTrack.call(this, name, view, container, prefs, filters, tool, data_manager);
// Define and restore track configuration.
this.config = new DrawableConfig( {
track: this,
params: [
{ key: 'name', label: 'Name', type: 'text', default_value: name },
- { key: 'block_color', label: 'Block color', type: 'color', default_value: '#444' },
+ { key: 'block_color', label: 'Block color', type: 'color', default_value: get_random_color() },
{ key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
- { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true },
+ { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true,
+ help: 'Show the number of items in each bin when drawing summary histogram' },
+ { key: 'connector_style', label: 'Connector style', type: 'select', default_value: 'fishbones',
+ options: [ { label: 'Line with arrows', value: 'fishbone' }, { label: 'Arcs', value: 'arcs' } ] },
{ key: 'mode', type: 'string', default_value: this.mode, hidden: true },
],
saved_values: prefs,
onchange: function() {
track.set_name(track.prefs.name);
track.tile_cache.clear();
+ track.set_painter_from_config();
track.request_draw();
}
});
@@ -2992,13 +3708,19 @@ var FeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs,
this.summary_draw_height = 30;
this.inc_slots = {};
this.start_end_dct = {};
- this.tile_cache = new Cache(CACHED_TILES_FEATURE);
- this.data_manager = new DataManager(20, this);
this.left_offset = 200;
- this.painter = painters.LinkedFeaturePainter;
+ // this.painter = painters.LinkedFeaturePainter;
+ this.set_painter_from_config();
};
extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
+ set_painter_from_config: function() {
+ if ( this.config.values['connector_style'] == 'arcs' ) {
+ this.painter = painters.ArcLinkedFeaturePainter;
+ } else {
+ this.painter = painters.LinkedFeaturePainter;
+ }
+ },
/**
* Actions to be taken after draw has been completed. Draw is completed when all tiles have been
* drawn/fetched and shown.
@@ -3042,8 +3764,8 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
for (var i = 0; i < tiles.length; i++) {
var tile = tiles[i];
if (tile.max_val !== global_max) {
- tile.canvas.remove();
- track.draw_helper(true, width, tile.index, tile.resolution, tile.canvas.parent(), w_scale, [], { max: global_max });
+ tile.html_elt.remove();
+ track.draw_helper(true, width, tile.index, tile.resolution, tile.html_elt.parent(), w_scale, { max: global_max });
}
}
}
@@ -3060,13 +3782,17 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
}
// Determine if filters are available; this is based on the tiles' data.
+ // Criteria for filter to be available: (a) it is applicable to tile data and (b) filter min != filter max.
var filters_available = false,
- example_feature;
+ example_feature,
+ filter;
for (var i = 0; i < tiles.length; i++) {
if (tiles[i].data.length) {
example_feature = tiles[i].data[0];
for (var f = 0; f < filters.length; f++) {
- if (filters[f].applies_to(example_feature)) {
+ filter = filters[f];
+ if ( filter.applies_to(example_feature) &&
+ filter.min !== filter.max ) {
filters_available = true;
break;
}
@@ -3080,18 +3806,19 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
if (!track.filters_available) {
track.filters_div.hide();
}
- track.make_name_popup_menu();
+ track.update_icons();
}
}
},
update_auto_mode: function( mode ) {
+ var mode;
if ( this.mode == "Auto" ) {
if ( mode == "no_detail" ) {
mode = "feature spans";
} else if ( mode == "summary_tree" ) {
mode = "coverage histogram";
}
- this.mode_div.text( "Auto (" + mode + ")" );
+ this.action_icons.mode_icon.attr("title", "Set display mode (now: Auto/" + mode + ")");
}
},
/**
@@ -3197,58 +3924,76 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
}
return {max: max_count, delta: bin_size, data: bins};
},
+ /**
+ * Returns appropriate display mode based on data.
+ */
+ get_mode: function(data) {
+ if (data.dataset_type === "summary_tree") {
+ mode = "summary_tree";
+ }
+ // HACK: use no_detail mode track is in overview to prevent overview from being too large.
+ else if (data.extra_info === "no_detail" || this.is_overview) {
+ mode = "no_detail";
+ }
+ else {
+ // Choose b/t Squish and Pack.
+ // Proxy measures for using Squish:
+ // (a) error message re: limiting number of features shown;
+ // (b) X number of features shown;
+ // (c) size of view shown.
+ // TODO: cannot use (a) and (b) because it requires coordinating mode across tiles;
+ // fix this so that tiles are redrawn as necessary to use the same mode.
+ //if ( (result.message && result.message.match(/^Only the first [\d]+/)) ||
+ // (result.data && result.data.length > 2000) ||
+ //var data = result.data;
+ // if ( (data.length && data.length < 4) ||
+ // (this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH) ) {
+ if ( this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH ) {
+ mode = "Squish";
+ } else {
+ mode = "Pack";
+ }
+ }
+ return mode;
+ },
+ /**
+ * Returns canvas height needed to display data; return value is an integer that denotes the
+ * number of pixels required.
+ */
+ get_canvas_height: function(result, mode, w_scale, canvas_width) {
+ if (mode === "summary_tree" || mode === "Histogram") {
+ // Extra padding at top of summary tree so label does not overlap data.
+ return this.summary_draw_height + SUMMARY_TREE_TOP_PADDING;
+ }
+ else {
+ // All other modes require slotting.
+ var rows_required = this.incremental_slots(w_scale, result.data, mode);
+ // HACK: use dummy painter to get required height. Painter should be extended so that get_required_height
+ // works as a static function.
+ var dummy_painter = new (this.painter)(null, null, null, this.prefs, mode);
+ return Math.max(MIN_TRACK_HEIGHT, dummy_painter.get_required_height(rows_required, canvas_width) );
+ }
+ },
/**
* Draw FeatureTrack tile.
* @param result result from server
+ * @param canvas canvas to draw on
* @param mode mode to draw in
* @param resolution view resolution
* @param tile_index index of tile to be drawn
* @param w_scale pixels per base
* @param ref_seq reference sequence data
*/
- draw_tile: function(result, mode, resolution, tile_index, w_scale, ref_seq) {
+ draw_tile: function(result, canvas, mode, resolution, tile_index, w_scale, ref_seq) {
var track = this,
- tile_bounds = track._get_tile_bounds(tile_index, resolution),
+ tile_bounds = this._get_tile_bounds(tile_index, resolution),
tile_low = tile_bounds[0],
tile_high = tile_bounds[1],
- tile_span = tile_high - tile_low,
- width = Math.ceil(tile_span * w_scale),
min_height = 25,
- left_offset = this.left_offset,
- slots,
- required_height;
-
- // Set display mode if Auto.
- if (mode === "Auto") {
- if (result.dataset_type === "summary_tree") {
- mode = result.dataset_type;
- } else if (result.extra_info === "no_detail") {
- mode = "no_detail";
- } else {
- // Choose b/t Squish and Pack.
- // Proxy measures for using Squish:
- // (a) error message re: limiting number of features shown;
- // (b) X number of features shown;
- // (c) size of view shown.
- // TODO: cannot use (a) and (b) because it requires coordinating mode across tiles;
- // fix this so that tiles are redrawn as necessary to use the same mode.
- //if ( (result.message && result.message.match(/^Only the first [\d]+/)) ||
- // (result.data && result.data.length > 2000) ||
- var data = result.data;
- // if ( (data.length && data.length < 4) ||
- // (this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH) ) {
- if ( this.view.high - this.view.low > MIN_SQUISH_VIEW_WIDTH ) {
- mode = "Squish";
- } else {
- mode = "Pack";
- }
- }
- this.update_auto_mode( mode );
- }
+ left_offset = this.left_offset;
// Drawing the summary tree (feature coverage histogram)
if (mode === "summary_tree" || mode === "Histogram") {
- required_height = this.summary_draw_height;
// Add label to container div showing maximum count
// TODO: this shouldn't be done at the tile level
this.container_div.find(".yaxislabel").remove();
@@ -3256,11 +4001,6 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
max_label.text(result.max);
max_label.css({ position: "absolute", top: "24px", left: "10px", color: this.prefs.label_color });
max_label.prependTo(this.container_div);
- // Create canvas
- var canvas = this.view.canvas_manager.new_canvas();
- canvas.width = width + left_offset;
- // Extra padding at top of summary tree
- canvas.height = required_height + SUMMARY_TREE_TOP_PADDING;
// Get summary tree data if necessary and set max if there is one.
if (result.dataset_type != "summary_tree") {
@@ -3275,18 +4015,11 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
var ctx = canvas.getContext("2d");
// Deal with left_offset by translating.
ctx.translate(left_offset, SUMMARY_TREE_TOP_PADDING);
- painter.draw(ctx, width, required_height);
- return new SummaryTreeTile(tile_index, resolution, canvas, result.data, result.max);
+ painter.draw(ctx, canvas.width, canvas.height);
+ return new SummaryTreeTile(track, tile_index, resolution, canvas, result.data, result.max);
}
- // Start dealing with row-by-row tracks
-
- // If working with a mode where slotting is necessary, update the incremental slotting
- var slots, slots_required = 1;
- if ( mode === "no_detail" || mode === "Squish" || mode === "Pack" ) {
- slots_required = this.incremental_slots(w_scale, result.data, mode);
- slots = this.inc_slots[w_scale].slots;
- }
+ // Handle row-by-row tracks
// Filter features.
var filtered = [];
@@ -3310,15 +4043,12 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
}
}
- // Create painter, and canvas of sufficient size to contain all features.
- var filter_alpha_generator = (this.filters_manager.alpha_filter ? new FilterAlphaGenerator(this.filters_manager.alpha_filter) : null);
+ // Create painter.
+ var filter_alpha_scaler = (this.filters_manager.alpha_filter ? new FilterScaler(this.filters_manager.alpha_filter) : null);
+ var filter_height_scaler = (this.filters_manager.height_filter ? new FilterScaler(this.filters_manager.height_filter) : null);
// HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument
- var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_generator, ref_seq);
- var required_height = Math.max(MIN_TRACK_HEIGHT, painter.get_required_height(slots_required));
- var canvas = this.view.canvas_manager.new_canvas();
-
- canvas.width = width + left_offset;
- canvas.height = required_height;
+ var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_scaler, filter_height_scaler, ref_seq);
+ var feature_mapper = null;
// console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale);
var ctx = canvas.getContext("2d");
@@ -3329,30 +4059,55 @@ extend(FeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, {
if (result.data) {
// Draw features.
+ slots = this.inc_slots[w_scale].slots;
ctx.translate(left_offset, 0);
- painter.draw(ctx, width, required_height, slots);
+ feature_mapper = painter.draw(ctx, canvas.width, canvas.height, slots);
+ feature_mapper.translation = -left_offset;
}
- return new FeatureTrackTile(tile_index, resolution, canvas, result.data, result.message);
+ return new FeatureTrackTile(track, tile_index, resolution, canvas, result.data, mode, result.message, feature_mapper);
}
});
-var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters) {
- FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters);
- this.painter = painters.VariantPainter;
-};
-
-extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype);
-
-
-var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters) {
- FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters);
+var VcfTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager) {
+ FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, tool, data_manager);
this.config = new DrawableConfig( {
track: this,
params: [
{ key: 'name', label: 'Name', type: 'text', default_value: name },
- { key: 'block_color', label: 'Block color', type: 'color', default_value: '#444' },
+ { key: 'block_color', label: 'Block color', type: 'color', default_value: get_random_color() },
+ { key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
+ { key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false },
+ { key: 'show_counts', label: 'Show summary counts', type: 'bool', default_value: true },
+ { key: 'mode', type: 'string', default_value: this.mode, hidden: true },
+ ],
+ saved_values: prefs,
+ onchange: function() {
+ this.track.set_name(this.track.prefs.name);
+ this.track.tile_cache.clear();
+ this.track.request_draw();
+ }
+ });
+ this.prefs = this.config.values;
+
+ this.painter = painters.ReadPainter;
+};
+
+extend(VcfTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype);
+
+var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, filters, data_manager) {
+ FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, data_manager);
+
+ var
+ block_color = get_random_color(),
+ reverse_strand_color = get_random_color( [ block_color, "#ffffff" ] );
+ this.config = new DrawableConfig( {
+ track: this,
+ params: [
+ { key: 'name', label: 'Name', type: 'text', default_value: name },
+ { key: 'block_color', label: 'Block and sense strand color', type: 'color', default_value: block_color },
+ { key: 'reverse_strand_color', label: 'Antisense strand color', type: 'color', default_value: reverse_strand_color },
{ key: 'label_color', label: 'Label color', type: 'color', default_value: 'black' },
{ key: 'show_insertions', label: 'Show insertions', type: 'bool', default_value: false },
{ key: 'show_differences', label: 'Show differences only', type: 'bool', default_value: true },
@@ -3369,55 +4124,18 @@ var ReadTrack = function (name, view, container, hda_ldda, dataset_id, prefs, fi
this.prefs = this.config.values;
this.painter = painters.ReadPainter;
- this.make_name_popup_menu();
+ this.update_icons();
};
extend(ReadTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype);
-/**
- * Feature track that displays data generated from tool.
- */
-var ToolDataFeatureTrack = function(name, view, container, hda_ldda, dataset_id, prefs, filters) {
- FeatureTrack.call(this, name, view, container, hda_ldda, dataset_id, prefs, filters, {});
-
- // Set up track to fetch initial data from raw data URL when the dataset--not the converted datasets--
- // is ready.
- this.data_url = raw_data_url;
- this.data_query_wait = 1000;
- this.dataset_check_url = dataset_state_url;
-};
-
-extend(ToolDataFeatureTrack.prototype, Drawable.prototype, TiledTrack.prototype, FeatureTrack.prototype, {
- /**
- * For this track type, the predraw init sets up postdraw init.
- */
- predraw_init: function() {
- // Postdraw init: once data has been fetched, reset data url, wait time and start indexing.
- var track = this;
- var post_init = function() {
- if (track.data_manager.size() === 0) {
- // Track still drawing initial data, so do nothing.
- setTimeout(post_init, 300);
- }
- else {
- // Track drawing done: reset dataset check, data URL, wait time and get dataset state to start
- // indexing.
- track.data_url = default_data_url;
- track.data_query_wait = DEFAULT_DATA_QUERY_WAIT;
- track.dataset_state_url = converted_datasets_state_url;
- $.getJSON(track.dataset_state_url, {dataset_id : track.dataset_id, hda_ldda: track.hda_ldda}, function(track_data) {});
- }
- };
- post_init();
- }
-});
-
// Exports
-
exports.View = View;
exports.DrawableGroup = DrawableGroup;
exports.LineTrack = LineTrack;
exports.FeatureTrack = FeatureTrack;
exports.ReadTrack = ReadTrack;
+exports.VcfTrack = VcfTrack;
+exports.CompositeTrack = CompositeTrack;
// End trackster_module encapsulation
};
@@ -3645,17 +4363,17 @@ var drawDownwardEquilateralTriangle = function(ctx, down_vertex_x, down_vertex_y
};
/**
- * Base class for all alpha generators.
+ * Base class for all scalers. Scalers produce values that are used to change (scale) drawing attributes.
*/
-var AlphaGenerator = function(default_alpha) {
- this.default_alpha = (default_alpha ? default_alpha : 1);
+var Scaler = function(default_val) {
+ this.default_val = (default_val ? default_val : 1);
};
/**
- * Base method for generating an alpha channel value; returns default alpha if not implemented.
+ * Produce a scaling value.
*/
-AlphaGenerator.prototype.gen_alpha = function(data) {
- return this.default_alpha;
+Scaler.prototype.gen_val = function(input) {
+ return this.default_val;
};
/**
@@ -3773,8 +4491,17 @@ LinePainter.prototype.draw = function(ctx, width, height) {
} else {
delta_x_px = 10;
}
+
+ // Extract RGB from preference color.
+ var
+ pref_color = parseInt( this.prefs.color.slice(1), 16 ),
+ pref_r = (pref_color & 0xff0000) >> 16,
+ pref_g = (pref_color & 0x00ff00) >> 8,
+ pref_b = pref_color & 0x0000ff;
+
+ // Paint track.
for (var i = 0, len = data.length; i < len; i++) {
- ctx.fillStyle = this.prefs.color;
+ ctx.fillStyle = ctx.strokeStyle = this.prefs.color;
x_scaled = Math.round((data[i][0] - view_start) * w_scale);
y = data[i][1];
var top_overflow = false, bot_overflow = false;
@@ -3797,9 +4524,14 @@ LinePainter.prototype.draw = function(ctx, width, height) {
// y becomes the bar height in pixels, which is the negated for canvas coords
y = Math.round( y / vertical_range * height_px );
ctx.fillRect(x_scaled, y_zero, delta_x_px, - y );
- } else if (mode === "Intensity" ) {
- y = 255 - Math.floor( (y - min_value) / vertical_range * 255 );
- ctx.fillStyle = "rgb(" +y+ "," +y+ "," +y+ ")";
+ } else if (mode === "Intensity") {
+ var
+ saturation = (y - min_value) / vertical_range,
+ // Range is [pref_color, 255] where saturation = 0 --> 255 and saturation = 1 --> pref color
+ new_r = Math.round( pref_r + (255 - pref_r) * (1 - saturation) ),
+ new_g = Math.round( pref_g + (255 - pref_g) * (1 - saturation) ),
+ new_b = Math.round( pref_b + (255 - pref_b) * (1 - saturation) );
+ ctx.fillStyle = "rgb(" + new_r + "," + new_g + "," + new_b + ")";
ctx.fillRect(x_scaled, 0, delta_x_px, height_px);
} else {
// console.log(y, track.min_value, track.vertical_range, (y - track.min_value) / track.vertical_range * track.height_px);
@@ -3847,32 +4579,90 @@ LinePainter.prototype.draw = function(ctx, width, height) {
}
ctx.restore();
-}
+};
+
+/**
+ * Mapper that contains information about feature locations and data.
+ */
+var FeaturePositionMapper = function(slot_height) {
+ this.feature_positions = {};
+ this.slot_height = slot_height;
+ this.translation = 0;
+ this.y_translation = 0;
+};
+
+/**
+ * Map feature data to a position defined by .
+ */
+FeaturePositionMapper.prototype.map_feature_data = function(feature_data, slot, x_start, x_end) {
+ if (!this.feature_positions[slot]) {
+ this.feature_positions[slot] = [];
+ }
+ this.feature_positions[slot].push({
+ data: feature_data,
+ x_start: x_start,
+ x_end: x_end
+ });
+};
+
+/**
+ * Get feature data for position
+ */
+FeaturePositionMapper.prototype.get_feature_data = function(x, y) {
+ // Find slot using Y.
+ var slot = Math.floor( (y-this.y_translation)/this.slot_height ),
+ feature_dict;
+
+ // May not be over a slot due to padding, margin, etc.
+ if (!this.feature_positions[slot]) {
+ return null;
+ }
+
+ // Find feature using X.
+ x += this.translation;
+ for (var i = 0; i < this.feature_positions[slot].length; i++) {
+ feature_dict = this.feature_positions[slot][i];
+ if (x >= feature_dict.x_start && x <= feature_dict.x_end) {
+ return feature_dict.data;
+ }
+ }
+};
/**
* Abstract object for painting feature tracks. Subclasses must implement draw_element() for painting to work.
+ * Painter uses a 0-based, half-open coordinate system; start coordinate is closed--included--and the end is open.
+ * This coordinate system matches the BED format.
*/
-var FeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_generator) {
+var FeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
Painter.call(this, data, view_start, view_end, prefs, mode);
- this.alpha_generator = (alpha_generator ? alpha_generator : new AlphaGenerator());
-}
+ this.alpha_scaler = (alpha_scaler ? alpha_scaler : new Scaler());
+ this.height_scaler = (height_scaler ? height_scaler : new Scaler());
+};
FeaturePainter.prototype.default_prefs = { block_color: "#FFF", connector_color: "#FFF" };
extend(FeaturePainter.prototype, {
- get_required_height: function(rows_required) {
+ get_required_height: function(rows_required, width) {
// y_scale is the height per row
var required_height = y_scale = this.get_row_height(), mode = this.mode;
// If using a packing mode, need to multiply by the number of slots used
if (mode === "no_detail" || mode === "Squish" || mode === "Pack") {
required_height = rows_required * y_scale;
}
+ return required_height + this.get_top_padding(width) + this.get_bottom_padding(width);
+ },
+ /** Extra padding before first row of features */
+ get_top_padding: function(width) {
+ return 0;
+ },
+ /** Extra padding after last row of features */
+ get_bottom_padding: function(width) {
// Pad bottom by half a row, at least 5 px
- return required_height + Math.max( Math.round( y_scale / 2 ), 5 );
+ return Math.max( Math.round( this.get_row_height() / 2 ), 5 )
},
-
/**
- * Draw data on ctx using slots and within the rectangle defined by width and height.
+ * Draw data on ctx using slots and within the rectangle defined by width and height. Returns
+ * a FeaturePositionMapper object with information about where features were drawn.
*/
draw: function(ctx, width, height, slots) {
var data = this.data, view_start = this.view_start, view_end = this.view_end;
@@ -3884,7 +4674,9 @@ extend(FeaturePainter.prototype, {
var view_range = this.view_end - this.view_start,
w_scale = width / view_range,
- y_scale = this.get_row_height();
+ y_scale = this.get_row_height(),
+ feature_mapper = new FeaturePositionMapper(y_scale),
+ x_draw_coords;
for (var i = 0, len = data.length; i < len; i++) {
var feature = data[i],
@@ -3897,18 +4689,21 @@ extend(FeaturePainter.prototype, {
// Draw feature if there's overlap and mode is dense or feature is slotted (as it must be for all non-dense modes).
if ( ( feature_start < view_end && feature_end > view_start ) && (this.mode == "Dense" || slot !== null) ) {
- this.draw_element(ctx, this.mode, feature, slot, view_start, view_end, w_scale, y_scale, width);
+ x_draw_coords = this.draw_element(ctx, this.mode, feature, slot, view_start, view_end, w_scale, y_scale, width);
+ feature_mapper.map_feature_data(feature, slot, x_draw_coords[0], x_draw_coords[1]);
}
}
ctx.restore();
+ feature_mapper.y_translation = this.get_top_padding(width);
+ return feature_mapper;
},
-
/**
* Abstract function for drawing an individual feature.
*/
draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) {
console.log("WARNING: Unimplemented function.");
+ return [0, 0];
}
});
@@ -3919,14 +4714,18 @@ var DENSE_TRACK_HEIGHT = 10,
SQUISH_TRACK_HEIGHT = 5,
PACK_TRACK_HEIGHT = 10,
NO_DETAIL_FEATURE_HEIGHT = 1,
- DENSE_FEATURE_HEIGHT = 3,
+ DENSE_FEATURE_HEIGHT = 9,
SQUISH_FEATURE_HEIGHT = 3,
PACK_FEATURE_HEIGHT = 9,
LABEL_SPACING = 2,
CONNECTOR_COLOR = "#ccc";
-var LinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_generator) {
- FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_generator);
+var LinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
+ FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
+ // Whether to draw a single connector in the background that spans the entire feature (the intron fishbone)
+ this.draw_background_connector = true;
+ // Whether to call draw_connector for every pair of blocks
+ this.draw_individual_connectors = false;
};
extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
@@ -3935,51 +4734,53 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
* Height of a single row, depends on mode
*/
get_row_height: function() {
- var mode = this.mode, y_scale;
+ var mode = this.mode, height;
if (mode === "Dense") {
- y_scale = DENSE_TRACK_HEIGHT;
+ height = DENSE_TRACK_HEIGHT;
}
else if (mode === "no_detail") {
- y_scale = NO_DETAIL_TRACK_HEIGHT;
+ height = NO_DETAIL_TRACK_HEIGHT;
}
else if (mode === "Squish") {
- y_scale = SQUISH_TRACK_HEIGHT;
+ height = SQUISH_TRACK_HEIGHT;
}
else { // mode === "Pack"
- y_scale = PACK_TRACK_HEIGHT;
+ height = PACK_TRACK_HEIGHT;
}
- return y_scale;
+ return height;
},
/**
- * Draw a feature.
+ * Draw a feature. Returns an array with feature's start and end X coordinates.
*/
draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) {
var
feature_uid = feature[0],
feature_start = feature[1],
- feature_end = feature[2],
+ // -1 because end is not included in feature; see FeaturePainter documentation for details.
+ feature_end = feature[2] - 1,
feature_name = feature[3],
f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
- y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
+ draw_start = f_start,
+ draw_end = f_end,
+ y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale + this.get_top_padding(width),
thickness, y_start, thick_start = null, thick_end = null,
// TODO: is there any reason why block, label color cannot be set at the Painter level?
block_color = this.prefs.block_color,
label_color = this.prefs.label_color;
// Set global alpha.
- ctx.globalAlpha = this.alpha_generator.gen_alpha(feature);
-
+ ctx.globalAlpha = this.alpha_scaler.gen_val(feature);
+
// In dense mode, put all data in top slot.
- if (mode == "Dense") {
+ if (mode === "Dense") {
slot = 1;
}
if (mode === "no_detail") {
// No details for feature, so only one way to display.
ctx.fillStyle = block_color;
- // TODO: what should width be here?
ctx.fillRect(f_start, y_center + 5, f_end - f_start, NO_DETAIL_FEATURE_HEIGHT);
}
else { // Mode is either Squish or Pack:
@@ -3987,7 +4788,9 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
var feature_strand = feature[4],
feature_ts = feature[5],
feature_te = feature[6],
- feature_blocks = feature[7];
+ feature_blocks = feature[7],
+ // Whether we are drawing full height or squished features
+ full_height = true;
if (feature_ts && feature_te) {
thick_start = Math.floor( Math.max(0, (feature_ts - tile_low) * w_scale) );
@@ -3996,9 +4799,13 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
// Set vars that depend on mode.
var thin_height, thick_height;
- if (mode === "Squish" || mode === "Dense" ) {
+ if (mode === "Squish" ) {
thin_height = 1;
thick_height = SQUISH_FEATURE_HEIGHT;
+ full_height = false;
+ } else if ( mode === "Dense" ) {
+ thin_height = 5;
+ thick_height = DENSE_FEATURE_HEIGHT;
} else { // mode === "Pack"
thin_height = 5;
thick_height = PACK_FEATURE_HEIGHT;
@@ -4007,71 +4814,87 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
// Draw feature/feature blocks + connectors.
if (!feature_blocks) {
// If there are no blocks, treat the feature as one big exon.
- if ( feature.strand ) {
- if (feature.strand === "+") {
+ ctx.fillStyle = block_color;
+ ctx.fillRect(f_start, y_center + 1, f_end - f_start, thick_height);
+ // If strand is specified, draw arrows over feature
+ if ( feature_strand && full_height ) {
+ if (feature_strand === "+") {
ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand_inv' );
- } else if (feature.strand === "-") {
+ } else if (feature_strand === "-") {
ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand_inv' );
}
+ ctx.fillRect(f_start, y_center + 1, f_end - f_start, thick_height);
}
- else { // No strand.
- ctx.fillStyle = block_color;
- }
- ctx.fillRect(f_start, y_center, f_end - f_start, thick_height);
} else {
+ //
// There are feature blocks and mode is either Squish or Pack.
//
// Approach: (a) draw whole feature as connector/intron and (b) draw blocks as
// needed. This ensures that whole feature, regardless of whether it starts with
// a block, is visible.
//
-
- // Draw whole feature as connector/intron.
+
+ // Compute y axis center position and height
var cur_y_center, cur_height;
if (mode === "Squish" || mode === "Dense") {
- ctx.fillStyle = CONNECTOR_COLOR;
cur_y_center = y_center + Math.floor(SQUISH_FEATURE_HEIGHT/2) + 1;
cur_height = 1;
}
else { // mode === "Pack"
if (feature_strand) {
- var cur_y_center = y_center;
- var cur_height = thick_height;
- if (feature_strand === "+") {
- ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand' );
- } else if (feature_strand === "-") {
- ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand' );
- }
+ cur_y_center = y_center;
+ cur_height = thick_height;
}
else {
- ctx.fillStyle = CONNECTOR_COLOR;
cur_y_center += (SQUISH_FEATURE_HEIGHT/2) + 1;
cur_height = 1;
}
}
- ctx.fillRect(f_start, cur_y_center, f_end - f_start, cur_height);
+
+ // Draw whole feature as connector/intron.
+ if ( this.draw_background_connector ) {
+ if (mode === "Squish" || mode === "Dense") {
+ ctx.fillStyle = CONNECTOR_COLOR;
+ }
+ else { // mode === "Pack"
+ if (feature_strand) {
+ if (feature_strand === "+") {
+ ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand' );
+ } else if (feature_strand === "-") {
+ ctx.fillStyle = ctx.canvas.manager.get_pattern( 'left_strand' );
+ }
+ }
+ else {
+ ctx.fillStyle = CONNECTOR_COLOR;
+ }
+ }
+ ctx.fillRect(f_start, cur_y_center, f_end - f_start, cur_height);
+ }
+ // Draw blocks.
+ var start_and_height;
for (var k = 0, k_len = feature_blocks.length; k < k_len; k++) {
var block = feature_blocks[k],
block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ),
- block_end = Math.ceil( Math.min(width, Math.max((block[1] - tile_low) * w_scale)) );
+ // -1 because end is not included in feature; see FeaturePainter documentation for details.
+ block_end = Math.ceil( Math.min(width, Math.max((block[1] - 1 - tile_low) * w_scale)) ),
+ last_block_start, last_block_end;
// Skip drawing if block not on tile.
if (block_start > block_end) { continue; }
// Draw thin block.
ctx.fillStyle = block_color;
- ctx.fillRect(block_start, y_center + (thick_height-thin_height)/2 + 1,
- block_end - block_start, thin_height);
+ ctx.fillRect(block_start, y_center + (thick_height-thin_height)/2 + 1, block_end - block_start, thin_height );
// If block intersects with thick region, draw block as thick.
// - No thick is sometimes encoded as thick_start == thick_end, so don't draw in that case
if (thick_start !== undefined && feature_te > feature_ts && !(block_start > thick_end || block_end < thick_start) ) {
var block_thick_start = Math.max(block_start, thick_start),
- block_thick_end = Math.min(block_end, thick_end);
- ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height);
+ block_thick_end = Math.min(block_end, thick_end);
+ ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height );
if ( feature_blocks.length == 1 && mode == "Pack") {
- // Exactly one block means we have no introns, but do have a distinct "thick" region,
+ // Exactly one block means we have no introns, but do have a distinct "thick" region,
// draw arrows over it if in pack mode
if (feature_strand === "+") {
ctx.fillStyle = ctx.canvas.manager.get_pattern( 'right_strand_inv' );
@@ -4083,12 +4906,39 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
block_thick_start += 2;
block_thick_end -= 2;
}
- ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height);
+ ctx.fillRect(block_thick_start, y_center + 1, block_thick_end - block_thick_start, thick_height );
}
}
+ // Draw individual connectors if required
+ if ( this.draw_individual_connectors && last_block_start ) {
+ this.draw_connector( ctx, last_block_start, last_block_end, block_start, block_end, y_center );
+ }
+ last_block_start = block_start;
+ last_block_end = block_end;
}
+
+ // FIXME: Height scaling only works in Pack mode right now.
+ if (mode === "Pack") {
+ // Reset alpha so height scaling is not impacted by alpha scaling.
+ ctx.globalAlpha = 1;
+
+ // Height scaling: draw white lines to reduce height according to height scale factor.
+ ctx.fillStyle = "white"; // TODO: set this to background color.
+ var
+ hscale_factor = this.height_scaler.gen_val(feature),
+ // Ceil ensures that min height is >= 1.
+ new_height = Math.ceil(thick_height * hscale_factor),
+ ws_height = Math.round( (thick_height-new_height)/2 );
+ if (hscale_factor !== 1) {
+ ctx.fillRect(f_start, cur_y_center + 1, f_end - f_start, ws_height);
+ ctx.fillRect(f_start, cur_y_center + thick_height - ws_height + 1, f_end - f_start, ws_height);
+ }
+ }
}
+ // Reset alpha so that label is not transparent.
+ ctx.globalAlpha = 1;
+
// Draw label for Pack mode.
if (mode === "Pack" && feature_start > tile_low) {
ctx.fillStyle = label_color;
@@ -4096,9 +4946,11 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) {
ctx.textAlign = "left";
ctx.fillText(feature_name, f_end + LABEL_SPACING, y_center + 8);
+ draw_end += ctx.measureText(feature_name).width + LABEL_SPACING;
} else {
ctx.textAlign = "right";
ctx.fillText(feature_name, f_start - LABEL_SPACING, y_center + 8);
+ draw_start -= ctx.measureText(feature_name).width + LABEL_SPACING;
}
//ctx.fillStyle = block_color;
}
@@ -4106,105 +4958,49 @@ extend(LinkedFeaturePainter.prototype, FeaturePainter.prototype, {
// Reset global alpha.
ctx.globalAlpha = 1;
+
+ return [draw_start, draw_end];
}
});
-
-var VariantPainter = function(data, view_start, view_end, prefs, mode, alpha_generator) {
- FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_generator);
-}
-
-extend(VariantPainter.prototype, FeaturePainter.prototype, {
- draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width) {
- var feature = data[i],
- feature_uid = feature[0],
- feature_start = feature[1],
- feature_end = feature[2],
- feature_name = feature[3],
- // All features need a start, end, and vertical center.
- f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
- f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
- y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
- thickness, y_start, thick_start = null, thick_end = null;
-
- if (no_label) {
- ctx.fillStyle = block_color;
- ctx.fillRect(f_start + left_offset, y_center + 5, f_end - f_start, 1);
- } else { // Show blocks, labels, etc.
- // Unpack.
- var ref_base = feature[4], alt_base = feature[5], qual = feature[6];
-
- // Draw block for entry.
- thickness = 9;
- y_start = 1;
- ctx.fillRect(f_start + left_offset, y_center, f_end - f_start, thickness);
-
- // Add label for entry.
- if (mode !== "Dense" && feature_name !== undefined && feature_start > tile_low) {
- // Draw label
- ctx.fillStyle = label_color;
- if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) {
- ctx.textAlign = "left";
- ctx.fillText(feature_name, f_end + 2 + left_offset, y_center + 8);
- } else {
- ctx.textAlign = "right";
- ctx.fillText(feature_name, f_start - 2 + left_offset, y_center + 8);
- }
- ctx.fillStyle = block_color;
- }
-
- // Show additional data on block.
- var vcf_label = ref_base + " / " + alt_base;
- if (feature_start > tile_low && ctx.measureText(vcf_label).width < (f_end - f_start)) {
- ctx.fillStyle = "white";
- ctx.textAlign = "center";
- ctx.fillText(vcf_label, left_offset + f_start + (f_end-f_start)/2, y_center + 8);
- ctx.fillStyle = block_color;
- }
- }
- }
-});
-
-var ReadPainter = function(data, view_start, view_end, prefs, mode, alpha_generator, ref_seq) {
- FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_generator);
- this.ref_seq = ref_seq;
+var ReadPainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler, ref_seq) {
+ FeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
+ this.ref_seq = (ref_seq ? ref_seq.data : null);
};
-ReadPainter.prototype.default_prefs = extend({}, FeaturePainter.prototype.default_prefs, { show_insertions: false });
-
extend(ReadPainter.prototype, FeaturePainter.prototype, {
/**
- * Returns y_scale based on mode.
+ * Returns height based on mode.
*/
get_row_height: function() {
- var y_scale, mode = this.mode;
+ var height, mode = this.mode;
if (mode === "Dense") {
- y_scale = DENSE_TRACK_HEIGHT;
+ height = DENSE_TRACK_HEIGHT;
}
else if (mode === "Squish") {
- y_scale = SQUISH_TRACK_HEIGHT;
+ height = SQUISH_TRACK_HEIGHT;
}
else { // mode === "Pack"
- y_scale = PACK_TRACK_HEIGHT;
+ height = PACK_TRACK_HEIGHT;
if (this.prefs.show_insertions) {
- y_scale *= 2;
+ height *= 2;
}
}
- return y_scale;
+ return height;
},
/**
* Draw a single read.
*/
- draw_read: function(ctx, mode, w_scale, tile_low, tile_high, feature_start, cigar, orig_seq, y_center) {
+ draw_read: function(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, cigar, strand, orig_seq) {
ctx.textAlign = "center";
var track = this,
tile_region = [tile_low, tile_high],
base_offset = 0,
seq_offset = 0,
- gap = 0
- ref_seq = this.ref_seq,
- char_width_px = ctx.canvas.manager.char_width_px;
+ gap = 0,
+ char_width_px = ctx.canvas.manager.char_width_px,
+ block_color = (strand === "+" ? this.prefs.block_color : this.prefs.reverse_strand_color);
// Keep list of items that need to be drawn on top of initial drawing layer.
var draw_last = [];
@@ -4251,14 +5047,14 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
// Draw.
var seq = orig_seq.slice(seq_offset, seq_offset + cig_len);
if (gap > 0) {
- ctx.fillStyle = this.prefs.block_color;
+ ctx.fillStyle = block_color;
ctx.fillRect(s_start - gap, y_center + 1, s_end - s_start, 9);
ctx.fillStyle = CONNECTOR_COLOR;
// TODO: this can be made much more efficient by computing the complete sequence
// to draw and then drawing it.
for (var c = 0, str_len = seq.length; c < str_len; c++) {
- if (this.prefs.show_differences && ref_seq) {
- var ref_char = ref_seq[seq_start - tile_low + c];
+ if (this.prefs.show_differences && this.ref_seq) {
+ var ref_char = this.ref_seq[seq_start - tile_low + c];
if (!ref_char || ref_char.toLowerCase() === seq[c].toLowerCase()) {
continue;
}
@@ -4269,7 +5065,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
}
}
} else {
- ctx.fillStyle = this.prefs.block_color;
+ ctx.fillStyle = block_color;
// TODO: This is a pretty hack-ish way to fill rectangle based on mode.
ctx.fillRect(s_start, y_center + 4, s_end - s_start, SQUISH_FEATURE_HEIGHT);
}
@@ -4317,7 +5113,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
draw_last[draw_last.length] = {type: "triangle", data: [insert_x_coord, y_center + 4, 5]};
ctx.fillStyle = CONNECTOR_COLOR;
// Based on overlap b/t sequence and tile, get sequence to be drawn.
- switch(seq_tile_overlap) {
+ switch( compute_overlap( [seq_start, seq_start + cig_len], tile_region ) ) {
case(OVERLAP_START):
seq = seq.slice(tile_low-seq_start);
break;
@@ -4348,7 +5144,7 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
else {
if ( (mode === "Pack" || this.mode === "Auto") && orig_seq !== undefined && w_scale > char_width_px) {
// Show insertions with a single number at the insertion point.
- draw_last[draw_last.length] = {type: "text", data: [seq.length, insert_x_coord, y_center + 9]};
+ draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_center + 9] } );
}
else {
// TODO: probably can merge this case with code above.
@@ -4398,7 +5194,6 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
f_start = Math.floor( Math.max(0, (feature_start - tile_low) * w_scale) ),
f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low) * w_scale)) ),
y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale,
- block_color = this.prefs.block_color,
label_color = this.prefs.label_color,
// Left-gap for label text since we align chrom text to the position tick.
gap = 0;
@@ -4409,7 +5204,6 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
}
// Draw read.
- ctx.fillStyle = block_color;
if (feature[5] instanceof Array) {
// Read is paired.
var b1_start = Math.floor( Math.max(0, (feature[4][0] - tile_low) * w_scale) ),
@@ -4418,12 +5212,12 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
b2_end = Math.ceil( Math.min(width, Math.max(0, (feature[5][1] - tile_low) * w_scale)) );
// Draw left/forward read.
- if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) {
- this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], y_center);
+ if (feature[4][1] >= tile_low && feature[4][0] <= tile_high && feature[4][2]) {
+ this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature[4][0], feature[4][2], feature[4][3], feature[4][4]);
}
// Draw right/reverse read.
if (feature[5][1] >= tile_low && feature[5][0] <= tile_high && feature[5][2]) {
- this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], y_center);
+ this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature[5][0], feature[5][2], feature[5][3], feature[5][4]);
}
// Draw connector.
if (b2_start > b1_end) {
@@ -4432,10 +5226,9 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
}
} else {
// Read is single.
- ctx.fillStyle = block_color;
- this.draw_read(ctx, mode, w_scale, tile_low, tile_high, feature_start, feature[4], feature[5], y_center);
+ this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]);
}
- if (mode === "Pack" && feature_start > tile_low) {
+ if (mode === "Pack" && feature_start > tile_low && feature_name !== ".") {
// Draw label.
ctx.fillStyle = this.prefs.label_color;
// FIXME: eliminate tile_index
@@ -4447,17 +5240,58 @@ extend(ReadPainter.prototype, FeaturePainter.prototype, {
ctx.textAlign = "right";
ctx.fillText(feature_name, f_start - LABEL_SPACING - gap, y_center + 8);
}
- ctx.fillStyle = block_color;
+ }
+
+ // FIXME: provide actual coordinates for drawn read.
+ return [0,0];
+ }
+});
+
+var ArcLinkedFeaturePainter = function(data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler) {
+ LinkedFeaturePainter.call(this, data, view_start, view_end, prefs, mode, alpha_scaler, height_scaler);
+ // Need to know the longest feature length for adding spacing
+ this.longest_feature_length = this.calculate_longest_feature_length();
+ this.draw_background_connector = false;
+ this.draw_individual_connectors = true;
+};
+
+extend(ArcLinkedFeaturePainter.prototype, FeaturePainter.prototype, LinkedFeaturePainter.prototype, {
+
+ calculate_longest_feature_length: function () {
+ var longest_feature_length = 0;
+ for (var i = 0, len = this.data.length; i < len; i++) {
+ var feature = this.data[i], feature_start = feature[1], feature_end = feature[2];
+ longest_feature_length = Math.max( longest_feature_length, feature_end - feature_start );
+ }
+ return longest_feature_length;
+ },
+
+ get_top_padding: function( width ) {
+ var view_range = this.view_end - this.view_start,
+ w_scale = width / view_range;
+ return Math.min( 128, Math.ceil( ( this.longest_feature_length / 2 ) * w_scale ) );
+ },
+
+ draw_connector: function( ctx, block1_start, block1_end, block2_start, block2_end, y_center ) {
+ // Arc drawing -- from closest endpoints
+ var x_center = ( block1_end + block2_start ) / 2,
+ radius = block2_start - x_center;
+ // For full half circles
+ var angle1 = Math.PI, angle2 = 0;
+ if ( radius > 0 ) {
+ ctx.beginPath();
+ ctx.arc( x_center, y_center, block2_start - x_center, Math.PI, 0 );
+ ctx.stroke();
}
}
});
-exports.AlphaGenerator = AlphaGenerator;
+exports.Scaler = Scaler;
exports.SummaryTreePainter = SummaryTreePainter;
exports.LinePainter = LinePainter;
exports.LinkedFeaturePainter = LinkedFeaturePainter;
exports.ReadPainter = ReadPainter;
-exports.VariantPainter = VariantPainter;
+exports.ArcLinkedFeaturePainter = ArcLinkedFeaturePainter;
// End painters_module encapsulation
};
@@ -4488,4 +5322,4 @@ exports.VariantPainter = VariantPainter;
for ( key in modules.trackster ) {
target[key] = modules.trackster[key];
}
-})(window);
\ No newline at end of file
+})(window);
diff --git a/static/scripts/trackster_ui.js b/static/scripts/trackster_ui.js
index 691c2ac385a..d1a169c886b 100644
--- a/static/scripts/trackster_ui.js
+++ b/static/scripts/trackster_ui.js
@@ -28,62 +28,34 @@ var add_bookmark = function(position, annotation) {
return new_bookmark;
};
+/**
+ * Create object from a dictionary.
+ */
+var object_from_dict = function(track_dict, container) {
+ var
+ drawable_type = track_dict['obj_type'];
+ // For backward compatibility:
+ if (!drawable_type) {
+ drawable_type = track_dict['track_type'];
+ }
+ return addable_objects[ drawable_type ].prototype.from_dict(track_dict, container);
+};
+
/**
* Objects that can be added to a view.
*/
-var addable_objects = { "LineTrack": LineTrack, "FeatureTrack": FeatureTrack, "ReadTrack": ReadTrack, "DrawableGroup": DrawableGroup };
-
-/**
- * Decode a track from a dictionary.
- */
-var track_from_dict = function(track_dict, container) {
- var track = new addable_objects[track_dict.track_type](
- track_dict.name, view, container, track_dict.hda_ldda, track_dict.dataset_id,
- track_dict.prefs, track_dict.filters, track_dict.tool);
- if (track_dict.mode) {
- track.change_mode(track_dict.mode);
- }
- return track;
-};
-
-/**
- * Decode a drawable collection from a dictionary.
- */
-var drawable_collection_from_dict = function(collection_dict, container) {
- var collection = new addable_objects[collection_dict.obj_type](collection_dict.name, view, container, collection_dict.prefs, view.viewport_container, view);
- for (var i = 0; i < collection_dict.drawables.length; i++) {
- var
- drawable_dict = collection_dict.drawables[i],
- drawable;
- if (drawable_dict['track_type']) {
- drawable = track_from_dict(drawable_dict, collection);
- }
- else {
- drawable = drawable_collection_from_dict(drawable_dict);
- }
- collection.add_drawable(drawable);
- // HACK: move track from view to collection's content_div.
- // FIX: Tracks should be able to be be added to arbitrary containers;
- // every moveable should have a container_div, and every container should have
- // a content_div (though perhaps name changes are needed).
- collection.content_div.append(drawable.container_div);
- }
- return collection;
-};
-
-/**
- * Decode a drawable from a dict.
- */
-var drawable_from_dict = function(drawable_dict, container) {
- return (drawable_dict['track_type'] ?
- track_from_dict(drawable_dict, container) :
- drawable_collection_from_dict(drawable_dict, container));
-};
+var addable_objects = {
+ "LineTrack": LineTrack,
+ "FeatureTrack": FeatureTrack,
+ "VcfTrack": VcfTrack,
+ "ReadTrack": ReadTrack,
+ "CompositeTrack": CompositeTrack,
+ "DrawableGroup": DrawableGroup };
/**
* Create a complete Trackster visualization. Returns view.
*/
-var create_visualization = function(parent_elt, title, id, dbkey, viewport_config, tracks_config, bookmarks_config) {
+var create_visualization = function(parent_elt, title, id, dbkey, viewport_config, drawables_config, bookmarks_config) {
// Create view.
view = new View(parent_elt, title, id, dbkey);
@@ -95,7 +67,7 @@ var create_visualization = function(parent_elt, title, id, dbkey, viewport_confi
chrom = viewport_config.chrom,
start = viewport_config.start,
end = viewport_config.end,
- overview_track_name = viewport_config.overview;
+ overview_drawable_name = viewport_config.overview;
if (chrom && (start !== undefined) && end) {
view.change_chrom(chrom, start, end);
@@ -103,19 +75,24 @@ var create_visualization = function(parent_elt, title, id, dbkey, viewport_confi
}
// Add drawables to view.
- if (tracks_config) {
- var track_config;
- for (var i = 0; i < tracks_config.length; i++) {
- track_config = tracks_config[i];
- view.add_drawable( drawable_from_dict(track_config, view) );
+ if (drawables_config) {
+ // FIXME: can from_dict() be used to create view and add drawables?
+ var drawable_config,
+ drawable_type,
+ drawable;
+ for (var i = 0; i < drawables_config.length; i++) {
+ view.add_drawable( object_from_dict( drawables_config[i], view ) );
}
}
+ // Need to update intro div after drawables have been added.
+ view.update_intro_div();
+
// Set overview.
- var overview_track;
- for (var i = 0; i < view.tracks.length; i++) {
- if (view.tracks[i].name == overview_track_name) {
- view.set_overview(view.tracks[i]);
+ var overview_drawable;
+ for (var i = 0; i < view.drawables.length; i++) {
+ if (view.drawables[i].name === overview_drawable_name) {
+ view.set_overview(view.drawables[i]);
break;
}
}
@@ -154,14 +131,14 @@ var init_keyboard_nav = function(view) {
break
case 38:
var change = Math.round(view.viewport_container.height()/15.0);
- view.viewport_container.scrollTo('-=' + change + 'px');
+ view.viewport_container.scrollTop( view.viewport_container.scrollTop() - 20);
break;
case 39:
view.move_fraction(-0.25);
break;
case 40:
var change = Math.round(view.viewport_container.height()/15.0);
- view.viewport_container.scrollTo('+=' + change + 'px');
+ view.viewport_container.scrollTop( view.viewport_container.scrollTop() + 20);
break;
}
});
diff --git a/templates/admin/impersonate.mako b/templates/admin/impersonate.mako
new file mode 100644
index 00000000000..a53e2034ab7
--- /dev/null
+++ b/templates/admin/impersonate.mako
@@ -0,0 +1,29 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if message:
+ ${render_msg( message, status )}
+%endif
+
+%if emails:
+
- -
- -
+
+
+ +
+ +
+
+
+%endif
diff --git a/templates/admin/select_tool_panel_section.mako b/templates/admin/select_tool_panel_section.mako
deleted file mode 100644
index 125e32f323d..00000000000
--- a/templates/admin/select_tool_panel_section.mako
+++ /dev/null
@@ -1,54 +0,0 @@
-<%inherit file="/base.mako"/>
-<%namespace file="/message.mako" import="render_msg" />
-
-%if message:
- ${render_msg( message, status )}
-%endif
-
-
-Impersonate another user
+
+
+
+ - -
- -
-
diff --git a/templates/admin/tool_shed_repository/browse_repository.mako b/templates/admin/tool_shed_repository/browse_repository.mako
new file mode 100644
index 00000000000..2b1c7d85658
--- /dev/null
+++ b/templates/admin/tool_shed_repository/browse_repository.mako
@@ -0,0 +1,20 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
+
+<% from galaxy.web.base.controller import tool_shed_encode, tool_shed_decode %>
+
+Install tools from repository '${name}'
-
-
-
-+
-
+
- Repository Actions +
+ Manage repository
+ Get updates
+
+
+
+
diff --git a/templates/admin/tool_shed_repository/manage_repository.mako b/templates/admin/tool_shed_repository/manage_repository.mako
new file mode 100644
index 00000000000..9eaef83d917
--- /dev/null
+++ b/templates/admin/tool_shed_repository/manage_repository.mako
@@ -0,0 +1,61 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/admin/tool_shed_repository/common.mako" import="*" />
+
+Repository contents
+
+ <% metadata = repository.metadata %>
+ %if metadata:
+ %if 'tools' in metadata:
+
+
+
+
+
+ | Tools - click the name to view tool related information | +
+ <% tool_dicts = metadata[ 'tools' ] %>
+
+
+
+
+ %endif
+ %if 'workflows' in metadata:
+ | name | +description | +version | +requirements | +
| + + ${tool_dict[ 'name' ]} + + | +${tool_dict[ 'description' ]} | +${tool_dict[ 'version' ]} | ++ <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: + <% + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + | +
+
+
+
+
+ | Workflows - click the name to import | +
+ <% workflow_tups = metadata[ 'workflows' ] %>
+
+
+
+
+ %endif
+ %if 'datatypes' in metadata:
+ | name | +steps | +format-version | +annotation | +
| + + | ++ %if steps: + ${len( steps )} + %else: + unknown + %endif + | +${format_version} | +${annotation} | +
+
+
+
+
+ | Data types | +
+ <% datatypes_dicts = metadata[ 'datatypes' ] %>
+
+
+
+
+ %endif
+ %endif
+ %if can_reset_metadata:
+
+ %endif
+ | extension | +type | +mimetype | +subclass | +
| ${extension} | +${dtype} | +${mimetype} | +${subclass} | +
+
-
+
- Repository Actions +
+ Browse repository
+ Get updates
+
+
+
+
+${render_metadata( repository, can_reset_metadata=True )}
+
diff --git a/templates/admin/tool_shed_repository/select_tool_panel_section.mako b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
new file mode 100644
index 00000000000..5200e7c7f29
--- /dev/null
+++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
@@ -0,0 +1,64 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+%if message:
+ ${render_msg( message, status )}
+%endif
+
+
+Installed tool shed repository '${repository.name}'
+
+
+
++ +
+ +
+
diff --git a/templates/admin/tool_shed_repository/view_tool_metadata.mako b/templates/admin/tool_shed_repository/view_tool_metadata.mako
new file mode 100644
index 00000000000..525e501ee84
--- /dev/null
+++ b/templates/admin/tool_shed_repository/view_tool_metadata.mako
@@ -0,0 +1,155 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+
+Choose tool panel section to contain installed tools (optional)
+
+
+
++
-
+
- Repository Actions + +
+
+%endif
diff --git a/templates/dataset/display.mako b/templates/dataset/display.mako
index c1b925638b7..4085fadbc2d 100644
--- a/templates/dataset/display.mako
+++ b/templates/dataset/display.mako
@@ -9,11 +9,11 @@
<%def name="init()">
<%
- self.has_left_panel=False
- self.has_right_panel=True
- self.message_box_visible=False
- self.active_view="user"
- self.overlay_visible=False
+ self.has_left_panel=False
+ self.has_right_panel=True
+ self.message_box_visible=False
+ self.active_view="user"
+ self.overlay_visible=False
%>
@@ -44,10 +44,10 @@
<%def name="center_panel()">
${metadata[ 'name' ]} tool metadata
+
+
+
+
+ ${metadata[ 'name' ]}
+
+
+ %if 'description' in metadata:
+
+
+ ${metadata[ 'description' ]}
+
+
+ %endif
+ %if 'id' in metadata:
+
+
+ ${metadata[ 'id' ]}
+
+
+ %endif
+ %if 'guid' in metadata:
+
+
+ ${metadata[ 'guid' ]}
+
+
+ %endif
+ %if 'version' in metadata:
+
+
+ ${metadata[ 'version' ]}
+
+
+ %endif
+ %if 'version_string_cmd' in metadata:
+
+
+ ${metadata[ 'version_string_cmd' ]}
+
+
+ %endif
+ %if tool:
+
+
+
+ ${tool.command}
+
+
+
+ ${tool.interpreter}
+
+
+
+
+ ${tool.is_multi_byte}
+
+
+
+
+ ${tool.force_history_refresh}
+
+
+
+
+ ${tool.parallelism}
+
+
+ %endif
+ <%
+ if 'requirements' in metadata:
+ requirements = metadata[ 'requirements' ]
+ else:
+ requirements = None
+ %>
+ %if requirements:
+ <%
+ requirements_str = ''
+ for requirement_dict in metadata[ 'requirements' ]:
+ requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] )
+ requirements_str = requirements_str.rstrip( ', ' )
+ %>
+
+
+ ${requirements_str}
+
+
+ %endif
+ <%
+ if 'tests' in metadata:
+ tests = metadata[ 'tests' ]
+ else:
+ tests = None
+ %>
+ %if tests:
+
+
+
+
+
+ %endif
+ | name | +inputs | +outputs | +required files | +
| ${test_dict[ 'name' ]} | +
+ %for input in inputs:
+ ${input[0]}: ${input[1]} + %endfor + |
+
+ %for output in outputs:
+ ${output[0]}: ${output[1]} + %endfor + |
+
+ %for required_file in required_files:
+ ${required_file[0]} + %endfor + |
+
-
- ${get_class_display_name( item.__class__ )}
- | ${get_item_name( item ) | h}
-
+
+ ${get_class_display_name( item.__class__ )}
+ | ${get_item_name( item ) | h}
+
diff --git a/templates/dataset/edit_attributes.mako b/templates/dataset/edit_attributes.mako
index 5c5c017bf3f..8a6abebbb27 100644
--- a/templates/dataset/edit_attributes.mako
+++ b/templates/dataset/edit_attributes.mako
@@ -39,7 +39,7 @@
Name:
diff --git a/templates/dataset/errors.mako b/templates/dataset/errors.mako
index 3f4ef586ba1..3d8eaec23bc 100644
--- a/templates/dataset/errors.mako
+++ b/templates/dataset/errors.mako
@@ -24,21 +24,21 @@
<% job = hda.creating_job_associations[0].job %>
%if job.traceback:
The Galaxy framework encountered the following error while attempting to run the tool:
-
-
+
${job.traceback}
+ ${job.traceback | h}
%endif
%if job.stderr or job.info:
Tool execution generated the following error message:
%if job.stderr:
- ${job.stderr}
+ ${job.stderr | h}
%elif job.info:
- ${job.info}
+ ${job.info | h}
%endif
%else:
Tool execution did not generate any error messages.
%endif
%if job.stdout:
The tool produced the following additional output:
- ${job.stdout}
+ ${job.stdout | h}
%endif
%else:
The tool did not create any additional job / error info.
diff --git a/templates/display_common.mako b/templates/display_common.mako
index 937fec95b85..c8aef4f7271 100644
--- a/templates/display_common.mako
+++ b/templates/display_common.mako
@@ -138,7 +138,7 @@
%if history.slug and history.user.username:
<% return h.url_for( controller='/history', action='display_by_username_and_slug', username=history.user.username, slug=history.slug, qualified=qualify ) %>
%else:
- <% return h.url_for( controller='/history', action='view', id=trans.security.encode_id( history.id ), qualified=qualify ) %>
+ <% return h.url_for( controller='/history', action='view', id=trans.security.encode_id( history.id ), qualified=qualify, use_panels=context.get('use_panels', True) ) %>
%endif
diff --git a/templates/embed_base.mako b/templates/embed_base.mako
index b55ebb13b93..f5af1de33b3 100644
--- a/templates/embed_base.mako
+++ b/templates/embed_base.mako
@@ -44,7 +44,7 @@
${self.render_item_links( item )}
diff --git a/templates/grid_base.mako b/templates/grid_base.mako
index 7ea91674f0d..45d4e7d2ce8 100644
--- a/templates/grid_base.mako
+++ b/templates/grid_base.mako
@@ -116,8 +116,8 @@
async_ops['${operation.label.lower()}'] = "True";
%endfor
- // Initialize grid controls
- function init_grid_controls() {
+ // Init operation buttons.
+ function init_operation_buttons() {
// Initialize operation buttons.
$('input[name=operation]:submit').each(function() {
$(this).click( function() {
@@ -132,6 +132,11 @@
do_operation(webapp, operation_name, item_ids);
});
});
+ };
+
+ // Initialize grid controls
+ function init_grid_controls() {
+ init_operation_buttons();
// Initialize submit image elements.
$('.submit-image').each( function() {
@@ -569,6 +574,7 @@
// Init grid.
init_grid_elements();
+ init_operation_buttons();
make_popup_menus();
// Hide loading overlay.
@@ -577,7 +583,7 @@
// Show message if there is one.
var message = $.trim( parsed_response_text[2] );
if (message != "") {
- $('#grid-message').html( message );
+ $('#grid-message').html( message ).show();
setTimeout( function() { $('#grid-message').hide(); }, 5000);
}
}
@@ -738,7 +744,7 @@
%if grid.global_actions:
- %else:
- <% module = step.module %>
-
- -
- %if len( grid.global_actions ) < 4:
+ %if len( grid.global_actions ) < 3:
%for action in grid.global_actions:
- ${action.label} %endfor @@ -771,6 +777,7 @@ show_item_checkboxes = True %>
-
- Step ${int(step.order_index)+1}: ${module.name}
- % if step.annotations:
-
+#
#
#So, for example, if your add_scores.loc began like this:
#
-#hg18 /galaxy/data/hg18/misc/phyloP
+#hg18 /galaxy/data/hg18/misc/phyloP44way.primate.bw
#
-#then your /galaxy/data/hg18/misc/phyloP directory would need to contain
-#the following gzipped files, among others:
+#then your /galaxy/data/hg18/misc/ directory would need to contain a
+#BigWig file named phyloP44way.primate.bw, among others:
#
-#-rw-r--r-- 1 g2data g2data 161981190 2010-03-19 12:48 chr10.phyloP44way.primate.wigFix.gz
-#-rw-r--r-- 1 g2data g2data 54091 2010-03-19 12:56 chr10_random.phyloP44way.primate.wigFix.gz
-#-rw-r--r-- 1 g2data g2data 158621990 2010-03-19 12:46 chr11.phyloP44way.primate.wigFix.gz
+#-rw-r--r-- 1 g2data g2data 6057387572 Nov 23 10:11 phyloP44way.primate.bw
#
-#hg18 /galaxy/data/hg18/misc/phyloP
+#hg18 /galaxy/data/hg18/misc/phyloP44way.primate.bw
+#hg19 /galaxy/data/hg19/misc/phyloP46way.primate.bw
diff --git a/tool-data/gatk_annotations.txt.sample b/tool-data/gatk_annotations.txt.sample
new file mode 100644
index 00000000000..d089f6f3288
--- /dev/null
+++ b/tool-data/gatk_annotations.txt.sample
@@ -0,0 +1,30 @@
+#unique_id name gatk_value tools_valid_for
+AlleleBalance AlleleBalance AlleleBalance UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+AlleleBalanceBySample AlleleBalanceBySample AlleleBalanceBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+BaseCounts BaseCounts BaseCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+BaseQualityRankSumTest BaseQualityRankSumTest BaseQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+ChromosomeCounts ChromosomeCounts ChromosomeCounts UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+DepthOfCoverage DepthOfCoverage DepthOfCoverage UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+DepthPerAlleleBySample DepthPerAlleleBySample DepthPerAlleleBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+FisherStrand FisherStrand FisherStrand UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+GCContent GCContent GCContent UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+HaplotypeScore HaplotypeScore HaplotypeScore UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+HardyWeinberg HardyWeinberg HardyWeinberg UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+HomopolymerRun HomopolymerRun HomopolymerRun UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+InbreedingCoeff InbreedingCoeff InbreedingCoeff UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+IndelType IndelType IndelType UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+LowMQ LowMQ LowMQ UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+MVLikelihoodRatio MVLikelihoodRatio MVLikelihoodRatio UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+MappingQualityRankSumTest MappingQualityRankSumTest MappingQualityRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+MappingQualityZero MappingQualityZero MappingQualityZero UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+MappingQualityZeroBySample MappingQualityZeroBySample MappingQualityZeroBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+MappingQualityZeroFraction MappingQualityZeroFraction MappingQualityZeroFraction UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+NBaseCount NBaseCount NBaseCount UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+QualByDepth QualByDepth QualByDepth UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+RMSMappingQuality RMSMappingQuality RMSMappingQuality UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+ReadDepthAndAllelicFractionBySample ReadDepthAndAllelicFractionBySample ReadDepthAndAllelicFractionBySample UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+ReadPosRankSumTest ReadPosRankSumTest ReadPosRankSumTest UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+SampleList SampleList SampleList UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+SnpEff SnpEff SnpEff VariantAnnotator,VariantRecalibrator
+SpanningDeletions SpanningDeletions SpanningDeletions UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
+TechnologyComposition TechnologyComposition TechnologyComposition UnifiedGenotyper,VariantAnnotator,VariantRecalibrator
diff --git a/tool-data/gatk_sorted_picard_index.loc.sample b/tool-data/gatk_sorted_picard_index.loc.sample
new file mode 100644
index 00000000000..d21a7b0c968
--- /dev/null
+++ b/tool-data/gatk_sorted_picard_index.loc.sample
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Picard dict and associated files. You will need
+#to create these data files and then create a picard_index.loc file
+#similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The picard_index.loc
+#file has this format (longer white space is the TAB character):
+#
+#
+#
+#So, for example, if you had hg18 indexed and stored in
+#/depot/data2/galaxy/srma/hg18/,
+#then the srma_index.loc entry would look like this:
+#
+#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
+#
+#and your /depot/data2/galaxy/srma/hg18/ directory
+#would contain the following three files:
+#hg18.fa
+#hg18.dict
+#hg18.fa.fai
+#
+#The dictionary file for each reference (ex. hg18.dict) must be
+#created via Picard (http://picard.sourceforge.net). Note that
+#the dict file does not have the .fa extension although the
+#path list in the loc file does include it.
+#
diff --git a/tool-data/shared/igv/igv_build_sites.txt.sample b/tool-data/shared/igv/igv_build_sites.txt.sample
new file mode 100644
index 00000000000..ae08070dcbf
--- /dev/null
+++ b/tool-data/shared/igv/igv_build_sites.txt.sample
@@ -0,0 +1,4 @@
+#site_id site_name site_url dbkey ivg_build_name
+web_link_main web current http://www.broadinstitute.org/igv/projects/current/igv.php hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
+#web_jnlp_1.5 web 1.5 http://www.broadinstitute.org/igvdata/jws/prod hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
+local_default local http://localhost:60151/load hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
\ No newline at end of file
diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 80af7fe1b34..a1606baff73 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -5,6 +5,7 @@
+
+
@@ -64,11 +68,12 @@
+
-
+
+
-
+
-
-
+
+
+
+
-
-
-->
-
-
-
-
-
-
-
-
-
+
+
-
+
+
-
-
-
-
+
+ -->
diff --git a/tool_data_table_conf.xml.sample b/tool_data_table_conf.xml.sample
index 869eb8c52de..952ee2cf3e0 100644
--- a/tool_data_table_conf.xml.sample
+++ b/tool_data_table_conf.xml.sample
@@ -65,11 +65,26 @@
value, name, path
+
+
+
+
+
+
+
${step.annotations[0].annotation}
- % endif
+ %else:
+ <% module = step.module %>
+
+
+
%endif
@@ -411,10 +439,12 @@ if wf_parms:
%endfor
%else:
+ %if history_id is None:
+ Step ${int(step.order_index)+1}: ${module.name}
+ % if step.annotations:
+
${step.annotations[0].annotation}
+ % endif
<%
@@ -397,7 +425,7 @@ if wf_parms:
if not type_filter:
type_filter = ['data']
%>
- ${do_inputs( module.get_runtime_inputs(type_filter), step.state.inputs, errors.get( step.id, dict() ), "", step )}
+ ${do_inputs( module.get_runtime_inputs(type_filter), step.state.inputs, errors.get( step.id, dict() ), "", step, None, used_accumulator )}
named:
+ %endif %endif diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py index 928c8d65fd0..a559fa4498e 100644 --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -455,16 +455,27 @@ class TwillTestCase( unittest.TestCase ): self.home() # Functions associated with datasets (history items) and meta data - def get_job_stderr( self, id ): - self.visit_page( "dataset/stderr?id=%s" % id ) - return self.last_page() + def _get_job_stream_output( self, hda_id, stream, format ): + self.visit_page( "datasets/%s/%s" % ( self.security.encode_id( hda_id ), stream ) ) + output = self.last_page() + if format: + msg = "---------------------- >> begin tool %s << -----------------------\n" % stream + msg += output + "\n" + msg += "----------------------- >> end tool %s << ------------------------\n" % stream + else: + msg = output + return msg + + def get_job_stdout( self, hda_id, format=False ): + return self._get_job_stream_output( hda_id, 'stdout', format ) + + def get_job_stderr( self, hda_id, format=False ): + return self._get_job_stream_output( hda_id, 'stderr', format ) def _assert_dataset_state( self, elem, state ): if elem.get( 'state' ) != state: errmsg = "Expecting dataset state '%s', but state is '%s'. Dataset blurb: %s\n\n" % ( state, elem.get('state'), elem.text.strip() ) - errmsg += "---------------------- >> begin tool stderr << -----------------------\n" - errmsg += self.get_job_stderr( elem.get( 'id' ) ) + "\n" - errmsg += "----------------------- >> end tool stderr << ------------------------\n" + errmsg += self.get_job_stderr( elem.get( 'id' ), format=True ) raise AssertionError( errmsg ) def check_metadata_for_string( self, patt, hid=None ): @@ -1224,7 +1235,7 @@ class TwillTestCase( unittest.TestCase ): tc.fv( "1", "password", password ) tc.fv( "1", "confirm", password ) tc.submit( "reset_user_password_button" ) - self.check_page_for_string( "Passwords reset for 1 users" ) + self.check_page_for_string( "Passwords reset for 1 user." ) self.home() def mark_user_deleted( self, user_id, email='' ): """Mark a user as deleted""" @@ -2278,7 +2289,7 @@ class TwillTestCase( unittest.TestCase ): item_desc = 'Dataset' else: item_desc = item_type.capitalize() - check_str = "%s '%s' has been marked deleted" % ( item_desc, item_name ) + check_str = "marked deleted" self.check_page_for_string( check_str ) self.home() def undelete_library_item( self, cntrller, library_id, item_id, item_name, item_type='library_dataset' ): @@ -2290,7 +2301,7 @@ class TwillTestCase( unittest.TestCase ): item_desc = 'Dataset' else: item_desc = item_type.capitalize() - check_str = "%s '%s' has been marked undeleted" % ( item_desc, item_name ) + check_str = "marked undeleted" self.check_page_for_string( check_str ) self.home() def purge_library( self, library_id, library_name ): diff --git a/test/functional/test_library_features.py b/test/functional/test_library_features.py index 05e546efec8..8067f237fc8 100644 --- a/test/functional/test_library_features.py +++ b/test/functional/test_library_features.py @@ -137,7 +137,7 @@ class TestLibraryFeatures( TwillTestCase ): assert ldda2 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda2 from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda2.name, ldda2.message, admin_user.email ] ) + strings_displayed=[ ldda2.name, ldda2.message, 'bed' ] ) def test_050_add_2nd_public_dataset_to_folder2( self ): """Testing adding a 2nd public dataset folder2""" # Logged in as admin_user @@ -156,7 +156,7 @@ class TestLibraryFeatures( TwillTestCase ): assert ldda3 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda3 from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda3.name, ldda3.message, admin_user.email ] ) + strings_displayed=[ ldda3.name, ldda3.message, 'bed' ] ) def test_055_copy_dataset_from_history_to_subfolder( self ): """Testing copying a dataset from the current history to a subfolder""" # logged in as admin_user @@ -176,7 +176,7 @@ class TestLibraryFeatures( TwillTestCase ): assert ldda4 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda4 from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda4.name, ldda4.message, admin_user.email ] ) + strings_displayed=[ ldda4.name, ldda4.message, 'bed' ] ) def test_060_editing_dataset_attribute_info( self ): """Testing editing a library dataset's attribute information""" # logged in as admin_user @@ -299,11 +299,11 @@ class TestLibraryFeatures( TwillTestCase ): ldda_message = 'Uploaded all files in test-data/users/test1...' self.browse_library( 'library', self.security.encode_id( library1.id ), - strings_displayed=[ regular_user1.email, ldda_message, '1.fasta' ] ) + strings_displayed=[ 'fasta', ldda_message, '1.fasta' ] ) ldda_message = 'Uploaded all files in test-data/users/test3.../run1' self.browse_library( 'library', self.security.encode_id( library1.id ), - strings_displayed=[ regular_user3.email, ldda_message, '2.fasta' ] ) + strings_displayed=[ 'fasta', ldda_message, '2.fasta' ] ) def test_085_mark_ldda2_deleted( self ): """Testing marking ldda2 as deleted""" # Logged in as admin_user diff --git a/test/functional/test_library_security.py b/test/functional/test_library_security.py index 550f2089529..95994a40720 100644 --- a/test/functional/test_library_security.py +++ b/test/functional/test_library_security.py @@ -157,7 +157,7 @@ class TestLibrarySecurity( TwillTestCase ): assert ldda1 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda1 from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda1.name, ldda1.message, admin_user.email ] ) + strings_displayed=[ ldda1.name, ldda1.message, 'bed' ] ) def test_030_access_ldda1_with_private_role_restriction( self ): """Testing accessing ldda1 with a private role restriction""" # Logged in as admin_user @@ -262,20 +262,20 @@ class TestLibrarySecurity( TwillTestCase ): assert ldda2 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda2 from the database' self.browse_library( cntrller='library', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda2.name, ldda2.message, admin_user.email ] ) + strings_displayed=[ ldda2.name, ldda2.message, 'bed' ] ) def test_045_accessing_ldda2_with_role_associated_with_group_and_users( self ): """Testing accessing ldda2 with a role that is associated with a group and users""" # Logged in as admin_user # admin_user should be able to see 2.bed since she is associated with role2 self.browse_library( cntrller='library', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda2.name, ldda2.message, admin_user.email ] ) + strings_displayed=[ ldda2.name, ldda2.message, 'bed' ] ) self.logout() # regular_user1 should be able to see 2.bed since she is associated with group_two self.login( email = regular_user1.email ) self.browse_library( cntrller='library', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ folder1.name, ldda2.name, ldda2.message, admin_user.email ] ) + strings_displayed=[ folder1.name, ldda2.name, ldda2.message, 'bed' ] ) # Check the permissions on the dataset 2.bed - they are as folows: # DATASET_MANAGE_PERMISSIONS = test@bx.psu.edu # DATASET_ACCESS = Role2 @@ -356,7 +356,7 @@ class TestLibrarySecurity( TwillTestCase ): strings_displayed=[ "Upload a directory of files" ] ) self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ admin_user.email, ldda_message ] ) + strings_displayed=[ 'bed', ldda_message ] ) def test_055_change_permissions_on_datasets_uploaded_from_library_dir( self ): """Testing changing the permissions on datasets uploaded from a directory from the Admin view""" # logged in as admin_user diff --git a/test/functional/test_library_templates.py b/test/functional/test_library_templates.py index a016e1afc24..dad2a61f2af 100644 --- a/test/functional/test_library_templates.py +++ b/test/functional/test_library_templates.py @@ -181,7 +181,7 @@ class TestLibraryFeatures( TwillTestCase ): assert ldda1 is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda1 from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library1.id ), - strings_displayed=[ ldda1.name, ldda1.message, admin_user.email ] ) + strings_displayed=[ ldda1.name, ldda1.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library1.id ), @@ -308,7 +308,7 @@ class TestLibraryFeatures( TwillTestCase ): assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library2.id ), - strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) + strings_displayed=[ ldda.name, ldda.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library2.id ), @@ -363,8 +363,7 @@ class TestLibraryFeatures( TwillTestCase ): 'Option1' ] ) def test_100_add_ldda_to_folder3( self ): """ - Testing adding a new library dataset to library3's folder, - making sure the SelectField setting is correct on the upload form. + Testing adding a new library dataset to library3's folder, making sure the SelectField setting is correct on the upload form. """ filename = '3.bed' ldda_message = '3.bed message' @@ -381,7 +380,7 @@ class TestLibraryFeatures( TwillTestCase ): assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library3.id ), - strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) + strings_displayed=[ ldda.name, ldda.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library3.id ), @@ -404,7 +403,7 @@ class TestLibraryFeatures( TwillTestCase ): assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library3.id ), - strings_displayed=[ ldda.name, admin_user.email ] ) + strings_displayed=[ ldda.name, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library3.id ), @@ -453,8 +452,7 @@ class TestLibraryFeatures( TwillTestCase ): 'This text should be inherited' ] ) def test_120_add_ldda_to_folder4( self ): """ - Testing adding a new library dataset to library4's folder, - making sure the TextArea setting is correct on the upload form. + Testing adding a new library dataset to library4's folder, making sure the TextArea setting is correct on the upload form. """ filename = '4.bed' ldda_message = '4.bed message' @@ -471,7 +469,7 @@ class TestLibraryFeatures( TwillTestCase ): assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library4.id ), - strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) + strings_displayed=[ ldda.name, ldda.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library4.id ), @@ -519,8 +517,7 @@ class TestLibraryFeatures( TwillTestCase ): 'This text should be inherited' ] ) def test_140_add_ldda_to_folder5( self ): """ - Testing adding a new library dataset to library5's folder, - making sure the TextField setting is correct on the upload form. + Testing adding a new library dataset to library5's folder, making sure the TextField setting is correct on the upload form. """ # Logged in as admin_user filename = '5.bed' @@ -537,7 +534,7 @@ class TestLibraryFeatures( TwillTestCase ): assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library5.id ), - strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) + strings_displayed=[ ldda.name, ldda.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library5.id ), @@ -558,9 +555,7 @@ class TestLibraryFeatures( TwillTestCase ): field_default_1='%s default' % TextArea_form.name ) def test_150_add_ldda_to_library5( self ): """ - Testing adding a new library dataset to library5's folder, - making sure the TextField and new TextArea settings are - correct on the upload form. + Testing adding a new library dataset to library5's folder, making sure the TextField and new TextArea settings are correct on the upload form. """ filename = '6.bed' ldda_message = '6.bed message' @@ -579,7 +574,7 @@ class TestLibraryFeatures( TwillTestCase ): assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library5.id ), - strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) + strings_displayed=[ ldda.name, ldda.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library5.id ), @@ -626,8 +621,7 @@ class TestLibraryFeatures( TwillTestCase ): 'none' ] ) def test_170_add_ldda_to_folder6( self ): """ - Testing adding a new library dataset to library6's folder, - making sure the WorkflowField setting is correct on the upload form. + Testing adding a new library dataset to library6's folder, making sure the WorkflowField setting is correct on the upload form. """ # Logged in as admin_user filename = '7.bed' @@ -644,7 +638,7 @@ class TestLibraryFeatures( TwillTestCase ): assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', library_id=self.security.encode_id( library6.id ), - strings_displayed=[ ldda.name, ldda.message, admin_user.email ] ) + strings_displayed=[ ldda.name, ldda.message, 'bed' ] ) # Make sure the library template contents were correctly saved self.ldda_edit_info( 'library_admin', self.security.encode_id( library6.id ), diff --git a/test/functional/test_toolbox.py b/test/functional/test_toolbox.py index 68aa7f0a54e..3ea9e92886f 100644 --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -59,7 +59,7 @@ class ToolTestCase( TwillTestCase ): # See if we have a grouping.Repeat element repeat_name = None for input_name, input_value in testdef.tool.inputs_by_page[0].items(): - if isinstance( input_value, grouping.Repeat ): + if isinstance( input_value, grouping.Repeat ) and all_inputs.get( input_name, 1 ) not in [ 0, "0" ]: #default behavior is to test 1 repeat, for backwards compatibility repeat_name = input_name break #check if we need to verify number of outputs created dynamically by tool @@ -93,7 +93,12 @@ class ToolTestCase( TwillTestCase ): self.assertTrue( elem is not None ) elem_hid = elem.get( 'hid' ) elem_index += 1 - self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes ) + try: + self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds, attributes=attributes ) + except Exception, e: + print >>sys.stderr, self.get_job_stdout( elem.get( 'id' ), format=True ) + print >>sys.stderr, self.get_job_stderr( elem.get( 'id' ), format=True ) + raise self.delete_history( id=self.security.encode_id( latest_history.id ) ) def __expand_grouping( self, tool_inputs, declared_inputs, prefix='' ): diff --git a/test/functional/test_user_info.py b/test/functional/test_user_info.py index 82ca78ef953..0697475028d 100644 --- a/test/functional/test_user_info.py +++ b/test/functional/test_user_info.py @@ -206,7 +206,7 @@ class TestUserInfo( TwillTestCase ): self.edit_user_info( cntrller='user', password='testuser', new_password='testuser#',\ - strings_displayed_after_submit=[ 'The password has been changed.' ] ) + strings_displayed_after_submit=[ 'The password has been changed' ] ) self.logout() refresh( regular_user12 ) # Test logging in with new email and password diff --git a/tool-data/add_scores.loc.sample b/tool-data/add_scores.loc.sample index 1fc798bac11..7ff12ed2225 100644 --- a/tool-data/add_scores.loc.sample +++ b/tool-data/add_scores.loc.sample @@ -1,21 +1,20 @@ -#This is a sample file distributed with Galaxy that enables tools to use a -#directory of gzipped genome files for use with add_scores. You will need to -#supply these files and then create a add_scores.loc file similar to this one -#(store it in this directory) that points to the directories in which those -#files are stored. The add_scores.loc file has this format (white space -#characters are TAB characters): +#This is a sample file distributed with Galaxy that lists the BigWig files +#available for use with the add_scores (phyloP interspecies conservation +#scores) tool. You will need to supply these BigWig files and then create +#an add_scores.loc file similar to this one (store it in this directory) +#that lists their locations. The add_scores.loc file has the following +#format (white space characters are TAB characters): # -#| \n')
res.append(' |
\n' % pdfpath s += 'This always happens if single ended data was provided to this tool,\n' s += 'so please double check that your input data really is paired-end NGS data.
\n' s += 'If your input was paired data this may be a bug worth reporting to the galaxy-bugs list\n
' - stdouts = '' - logging.info(s) + logging.info(s) if len(stdouts) > 0: logging.info(stdouts) @@ -627,13 +650,13 @@ def __main__(): cl.append('READ_NAME_REGEX="%s"' % opts.readregex) # maximum offset between two duplicate clusters cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist) - pic.runPic(opts.jar, cl) + stdouts,rval = pic.runPic(opts.jar, cl) elif pic.picname == 'FixMateInformation': cl.append('I=%s' % opts.input) cl.append('O=%s' % tempout) cl.append('SORT_ORDER=%s' % opts.sortorder) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar,cl) haveTempout = True elif pic.picname == 'ReorderSam': @@ -649,14 +672,14 @@ def __main__(): # contig length discordance if opts.allow_contig_len_discord == 'true': cl.append('ALLOW_CONTIG_LENGTH_DISCORDANCE=true') - pic.runPic(opts.jar, cl) + stdouts,rval = pic.runPic(opts.jar, cl) haveTempout = True elif pic.picname == 'ReplaceSamHeader': cl.append('INPUT=%s' % opts.input) cl.append('OUTPUT=%s' % tempout) cl.append('HEADER=%s' % opts.header_file) - pic.runPic(opts.jar, cl) + stdouts,rval = pic.runPic(opts.jar, cl) haveTempout = True elif pic.picname == 'CalculateHsMetrics': @@ -673,7 +696,7 @@ def __main__(): cl.append('INPUT=%s' % os.path.abspath(opts.input)) cl.append('OUTPUT=%s' % pic.metricsOut) cl.append('TMP_DIR=%s' % opts.tmpdir) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar,cl) elif pic.picname == 'ValidateSamFile': import pysam @@ -682,7 +705,7 @@ def __main__(): stf = open(pic.log_filename,'w') tlog = None if opts.datatype == 'sam': # need to work with a bam - tlog,tempbam = pic.samToBam(opts.input,opts.outdir) + tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir) try: tlog = pic.sortSam(tempbam,sortedfile,opts.outdir) except: @@ -709,7 +732,7 @@ def __main__(): cl.append('IS_BISULFITE_SEQUENCED=true') if opts.ref <> None or opts.ref_file <> None: cl.append('R=%s' % ref_file_name) - pic.runPic(opts.jar,cl) + stdouts,rval = pic.runPic(opts.jar,cl) if opts.datatype == 'sam': pic.delme.append(tempbam) newsam = opts.output @@ -725,10 +748,12 @@ def __main__(): if haveTempout: # Some Picard tools produced a potentially intermediate bam file. # Either just move to final location or create sam - shutil.move(tempout, os.path.abspath(opts.output)) - + if os.path.exists(tempout): + shutil.move(tempout, os.path.abspath(opts.output)) if opts.htmlout <> None or doFix: # return a pretty html page pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines) - + if rval <> 0: + print >> sys.stderr, '## exit code=%d; stdout=%s' % (rval,stdouts) + # signal failure if __name__=="__main__": __main__() diff --git a/tools/picard/rgPicardASMetrics.xml b/tools/picard/rgPicardASMetrics.xml index 7b5080c38c3..76028c21e3c 100644 --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -1,12 +1,12 @@ -