/lib/galaxy/web/controllers/page.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 762 lines · 742 code · 5 blank · 15 comment · 23 complexity · e356920c48742dc2e12b84a0e86ade1a MD5 · raw file
- from galaxy import model
- from galaxy.model.item_attrs import *
- from galaxy.web.base.controller import *
- from galaxy.web.framework.helpers import time_ago, grids
- from galaxy.util.sanitize_html import sanitize_html, _BaseHTMLProcessor
- from galaxy.util.odict import odict
- from galaxy.util.json import from_json_string
- def format_bool( b ):
- if b:
- return "yes"
- else:
- return ""
- class PageListGrid( grids.Grid ):
- # Custom column.
- class URLColumn( grids.PublicURLColumn ):
- def get_value( self, trans, grid, item ):
- return url_for( action='display_by_username_and_slug', username=item.user.username, slug=item.slug )
-
- # Grid definition
- use_panels = True
- title = "Pages"
- model_class = model.Page
- default_filter = { "published" : "All", "tags" : "All", "title" : "All", "sharing" : "All" }
- default_sort_key = "-create_time"
- columns = [
- grids.TextColumn( "Title", key="title", attach_popup=True, filterable="advanced" ),
- URLColumn( "Public URL" ),
- grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ),
- grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ),
- grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ),
- grids.GridColumn( "Created", key="create_time", format=time_ago ),
- grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
- ]
- columns.append(
- grids.MulticolFilterColumn(
- "Search",
- cols_to_filter=[ columns[0], columns[2] ],
- key="free-text-search", visible=False, filterable="standard" )
- )
- global_actions = [
- grids.GridAction( "Add new page", dict( action='create' ) )
- ]
- operations = [
- grids.DisplayByUsernameAndSlugGridOperation( "View", allow_multiple=False ),
- grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ),
- grids.GridOperation( "Edit attributes", allow_multiple=False, url_args=dict( action='edit') ),
- grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
- grids.GridOperation( "Delete", confirm="Are you sure you want to delete this page?" ),
- ]
- def apply_query_filter( self, trans, query, **kwargs ):
- return query.filter_by( user=trans.user, deleted=False )
-
- class PageAllPublishedGrid( grids.Grid ):
- # Grid definition
- use_panels = True
- use_async = True
- title = "Published Pages"
- model_class = model.Page
- default_sort_key = "update_time"
- default_filter = dict( title="All", username="All" )
- columns = [
- grids.PublicURLColumn( "Title", key="title", filterable="advanced" ),
- grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ),
- grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced" ),
- grids.CommunityRatingColumn( "Community Rating", key="rating" ),
- grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ),
- grids.ReverseSortColumn( "Last Updated", key="update_time", format=time_ago )
- ]
- columns.append(
- grids.MulticolFilterColumn(
- "Search title, annotation, owner, and tags",
- cols_to_filter=[ columns[0], columns[1], columns[2], columns[4] ],
- key="free-text-search", visible=False, filterable="standard" )
- )
- def build_initial_query( self, trans, **kwargs ):
- # Join so that searching history.user makes sense.
- return trans.sa_session.query( self.model_class ).join( model.User.table )
- def apply_query_filter( self, trans, query, **kwargs ):
- return query.filter( self.model_class.deleted==False ).filter( self.model_class.published==True )
-
- class ItemSelectionGrid( grids.Grid ):
- """ Base class for pages' item selection grids. """
- # Custom columns.
- class NameColumn( grids.TextColumn ):
- def get_value(self, trans, grid, item):
- if hasattr( item, "get_display_name" ):
- return item.get_display_name()
- else:
- return item.name
- # Grid definition.
- template = "/page/select_items_grid.mako"
- async_template = "/page/select_items_grid_async.mako"
- default_filter = { "deleted" : "False" , "sharing" : "All" }
- default_sort_key = "-update_time"
- use_async = True
- use_paging = True
- num_rows_per_page = 10
-
- def apply_query_filter( self, trans, query, **kwargs ):
- return query.filter_by( user=trans.user )
-
- class HistorySelectionGrid( ItemSelectionGrid ):
- """ Grid for selecting histories. """
- # Grid definition.
- title = "Saved Histories"
- model_class = model.History
- columns = [
- ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ),
- grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"),
- grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
- # Columns that are valid for filtering but are not visible.
- grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ),
- grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ),
- ]
- columns.append(
- grids.MulticolFilterColumn(
- "Search",
- cols_to_filter=[ columns[0], columns[1] ],
- key="free-text-search", visible=False, filterable="standard" )
- )
-
- def apply_query_filter( self, trans, query, **kwargs ):
- return query.filter_by( user=trans.user, purged=False )
-
- class HistoryDatasetAssociationSelectionGrid( ItemSelectionGrid ):
- """ Grid for selecting HDAs. """
- # Grid definition.
- title = "Saved Datasets"
- model_class = model.HistoryDatasetAssociation
- columns = [
- ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ),
- grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"),
- grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
- # Columns that are valid for filtering but are not visible.
- grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ),
- grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ),
- ]
- columns.append(
- grids.MulticolFilterColumn(
- "Search",
- cols_to_filter=[ columns[0], columns[1] ],
- key="free-text-search", visible=False, filterable="standard" )
- )
- def apply_query_filter( self, trans, query, **kwargs ):
- # To filter HDAs by user, need to join HDA and History table and then filter histories by user. This is necessary because HDAs do not have
- # a user relation.
- return query.select_from( model.HistoryDatasetAssociation.table.join( model.History.table ) ).filter( model.History.user == trans.user )
-
-
- class WorkflowSelectionGrid( ItemSelectionGrid ):
- """ Grid for selecting workflows. """
- # Grid definition.
- title = "Saved Workflows"
- model_class = model.StoredWorkflow
- columns = [
- ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ),
- grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"),
- grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
- # Columns that are valid for filtering but are not visible.
- grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ),
- grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ),
- ]
- columns.append(
- grids.MulticolFilterColumn(
- "Search",
- cols_to_filter=[ columns[0], columns[1] ],
- key="free-text-search", visible=False, filterable="standard" )
- )
- class PageSelectionGrid( ItemSelectionGrid ):
- """ Grid for selecting pages. """
- # Grid definition.
- title = "Saved Pages"
- model_class = model.Page
- columns = [
- grids.TextColumn( "Title", key="title", filterable="advanced" ),
- grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced"),
- grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
- # Columns that are valid for filtering but are not visible.
- grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ),
- grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ),
- ]
- columns.append(
- grids.MulticolFilterColumn(
- "Search",
- cols_to_filter=[ columns[0], columns[1] ],
- key="free-text-search", visible=False, filterable="standard" )
- )
-
- class VisualizationSelectionGrid( ItemSelectionGrid ):
- """ Grid for selecting visualizations. """
- # Grid definition.
- title = "Saved Visualizations"
- model_class = model.Visualization
- columns = [
- grids.TextColumn( "Title", key="title", filterable="advanced" ),
- grids.TextColumn( "Type", key="type" ),
- grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ),
- grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ),
- grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
- ]
- columns.append(
- grids.MulticolFilterColumn(
- "Search",
- cols_to_filter=[ columns[0], columns[2] ],
- key="free-text-search", visible=False, filterable="standard" )
- )
-
- class _PageContentProcessor( _BaseHTMLProcessor ):
- """ Processes page content to produce HTML that is suitable for display. For now, processor renders embedded objects. """
-
- def __init__( self, trans, encoding, type, render_embed_html_fn ):
- _BaseHTMLProcessor.__init__( self, encoding, type)
- self.trans = trans
- self.ignore_content = False
- self.num_open_tags_for_ignore = 0
- self.render_embed_html_fn = render_embed_html_fn
-
- def unknown_starttag( self, tag, attrs ):
- """ Called for each start tag; attrs is a list of (attr, value) tuples. """
-
- # If ignoring content, just increment tag count and ignore.
- if self.ignore_content:
- self.num_open_tags_for_ignore += 1
- return
-
- # Not ignoring tag; look for embedded content.
- embedded_item = False
- for attribute in attrs:
- if ( attribute[0] == "class" ) and ( "embedded-item" in attribute[1].split(" ") ):
- embedded_item = True
- break
- # For embedded content, set ignore flag to ignore current content and add new content for embedded item.
- if embedded_item:
- # Set processing attributes to ignore content.
- self.ignore_content = True
- self.num_open_tags_for_ignore = 1
-
- # Insert content for embedded element.
- for attribute in attrs:
- name = attribute[0]
- if name == "id":
- # ID has form '<class_name>-<encoded_item_id>'
- item_class, item_id = attribute[1].split("-")
- embed_html = self.render_embed_html_fn( self.trans, item_class, item_id )
- self.pieces.append( embed_html )
- return
-
- # Default behavior: not ignoring and no embedded content.
- _BaseHTMLProcessor.unknown_starttag( self, tag, attrs )
-
- def handle_data( self, text ):
- """ Called for each block of plain text. """
- if self.ignore_content:
- return
- _BaseHTMLProcessor.handle_data( self, text )
-
- def unknown_endtag( self, tag ):
- """ Called for each end tag. """
-
- # If ignoring content, see if current tag is the end of content to ignore.
- if self.ignore_content:
- self.num_open_tags_for_ignore -= 1
- if self.num_open_tags_for_ignore == 0:
- # Done ignoring content.
- self.ignore_content = False
- return
-
- # Default behavior:
- _BaseHTMLProcessor.unknown_endtag( self, tag )
-
- class PageController( BaseUIController, Sharable, UsesAnnotations, UsesHistory,
- UsesStoredWorkflow, UsesHistoryDatasetAssociation, UsesVisualization, UsesItemRatings ):
-
- _page_list = PageListGrid()
- _all_published_list = PageAllPublishedGrid()
- _history_selection_grid = HistorySelectionGrid()
- _workflow_selection_grid = WorkflowSelectionGrid()
- _datasets_selection_grid = HistoryDatasetAssociationSelectionGrid()
- _page_selection_grid = PageSelectionGrid()
- _visualization_selection_grid = VisualizationSelectionGrid()
-
- @web.expose
- @web.require_login()
- def list( self, trans, *args, **kwargs ):
- """ List user's pages. """
- # Handle operation
- if 'operation' in kwargs and 'id' in kwargs:
- session = trans.sa_session
- operation = kwargs['operation'].lower()
- ids = util.listify( kwargs['id'] )
- for id in ids:
- item = session.query( model.Page ).get( trans.security.decode_id( id ) )
- if operation == "delete":
- item.deleted = True
- if operation == "share or publish":
- return self.sharing( trans, **kwargs )
- session.flush()
-
- # Build grid HTML.
- grid = self._page_list( trans, *args, **kwargs )
-
- # Build list of pages shared with user.
- shared_by_others = trans.sa_session \
- .query( model.PageUserShareAssociation ) \
- .filter_by( user=trans.get_user() ) \
- .join( model.Page.table ) \
- .filter( model.Page.deleted == False ) \
- .order_by( desc( model.Page.update_time ) ) \
- .all()
-
- # Render grid wrapped in panels
- return trans.fill_template( "page/index.mako", grid=grid, shared_by_others=shared_by_others )
-
- @web.expose
- def list_published( self, trans, *args, **kwargs ):
- grid = self._all_published_list( trans, *args, **kwargs )
- if 'async' in kwargs:
- return grid
- else:
- # Render grid wrapped in panels
- return trans.fill_template( "page/list_published.mako", grid=grid )
-
- @web.expose
- @web.require_login( "create pages" )
- def create( self, trans, page_title="", page_slug="", page_annotation="" ):
- """
- Create a new page
- """
- user = trans.get_user()
- page_title_err = page_slug_err = page_annotation_err = ""
- if trans.request.method == "POST":
- if not page_title:
- page_title_err = "Page name is required"
- elif not page_slug:
- page_slug_err = "Page id is required"
- elif not VALID_SLUG_RE.match( page_slug ):
- page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character"
- elif trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first():
- page_slug_err = "Page id must be unique"
- else:
- # Create the new stored page
- page = model.Page()
- page.title = page_title
- page.slug = page_slug
- page_annotation = sanitize_html( page_annotation, 'utf-8', 'text/html' )
- self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation )
- page.user = user
- # And the first (empty) page revision
- page_revision = model.PageRevision()
- page_revision.title = page_title
- page_revision.page = page
- page.latest_revision = page_revision
- page_revision.content = ""
- # Persist
- session = trans.sa_session
- session.add( page )
- session.flush()
- # Display the management page
- ## trans.set_message( "Page '%s' created" % page.title )
- return trans.response.send_redirect( web.url_for( action='list' ) )
- return trans.show_form(
- web.FormBuilder( web.url_for(), "Create new page", submit_text="Submit" )
- .add_text( "page_title", "Page title", value=page_title, error=page_title_err )
- .add_text( "page_slug", "Page identifier", value=page_slug, error=page_slug_err,
- help="""A unique identifier that will be used for
- public links to this page. A default is generated
- from the page title, but can be edited. This field
- must contain only lowercase letters, numbers, and
- the '-' character.""" )
- .add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err,
- help="A description of the page; annotation is shown alongside published pages."),
- template="page/create.mako" )
-
- @web.expose
- @web.require_login( "edit pages" )
- def edit( self, trans, id, page_title="", page_slug="", page_annotation="" ):
- """
- Edit a page's attributes.
- """
- encoded_id = id
- id = trans.security.decode_id( id )
- session = trans.sa_session
- page = session.query( model.Page ).get( id )
- user = trans.user
- assert page.user == user
- page_title_err = page_slug_err = page_annotation_err = ""
- if trans.request.method == "POST":
- if not page_title:
- page_title_err = "Page name is required"
- elif not page_slug:
- page_slug_err = "Page id is required"
- elif not VALID_SLUG_RE.match( page_slug ):
- page_slug_err = "Page identifier must consist of only lowercase letters, numbers, and the '-' character"
- elif page_slug != page.slug and trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first():
- page_slug_err = "Page id must be unique"
- elif not page_annotation:
- page_annotation_err = "Page annotation is required"
- else:
- page.title = page_title
- page.slug = page_slug
- page_annotation = sanitize_html( page_annotation, 'utf-8', 'text/html' )
- self.add_item_annotation( trans.sa_session, trans.get_user(), page, page_annotation )
- session.flush()
- # Redirect to page list.
- return trans.response.send_redirect( web.url_for( action='list' ) )
- else:
- page_title = page.title
- page_slug = page.slug
- page_annotation = self.get_item_annotation_str( trans.sa_session, trans.user, page )
- if not page_annotation:
- page_annotation = ""
- return trans.show_form(
- web.FormBuilder( web.url_for( id=encoded_id ), "Edit page attributes", submit_text="Submit" )
- .add_text( "page_title", "Page title", value=page_title, error=page_title_err )
- .add_text( "page_slug", "Page identifier", value=page_slug, error=page_slug_err,
- help="""A unique identifier that will be used for
- public links to this page. A default is generated
- from the page title, but can be edited. This field
- must contain only lowercase letters, numbers, and
- the '-' character.""" )
- .add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err,
- help="A description of the page; annotation is shown alongside published pages."),
- template="page/create.mako" )
-
- @web.expose
- @web.require_login( "edit pages" )
- def edit_content( self, trans, id ):
- """
- Render the main page editor interface.
- """
- id = trans.security.decode_id( id )
- page = trans.sa_session.query( model.Page ).get( id )
- assert page.user == trans.user
- return trans.fill_template( "page/editor.mako", page=page )
-
- @web.expose
- @web.require_login( "use Galaxy pages" )
- def sharing( self, trans, id, **kwargs ):
- """ Handle page sharing. """
- # Get session and page.
- session = trans.sa_session
- page = trans.sa_session.query( model.Page ).get( trans.security.decode_id( id ) )
- # Do operation on page.
- if 'make_accessible_via_link' in kwargs:
- self._make_item_accessible( trans.sa_session, page )
- elif 'make_accessible_and_publish' in kwargs:
- self._make_item_accessible( trans.sa_session, page )
- page.published = True
- elif 'publish' in kwargs:
- page.published = True
- elif 'disable_link_access' in kwargs:
- page.importable = False
- elif 'unpublish' in kwargs:
- page.published = False
- elif 'disable_link_access_and_unpublish' in kwargs:
- page.importable = page.published = False
- elif 'unshare_user' in kwargs:
- user = session.query( model.User ).get( trans.security.decode_id( kwargs['unshare_user' ] ) )
- if not user:
- error( "User not found for provided id" )
- association = session.query( model.PageUserShareAssociation ) \
- .filter_by( user=user, page=page ).one()
- session.delete( association )
- session.flush()
- return trans.fill_template( "/sharing_base.mako",
- item=page, use_panels=True )
-
- @web.expose
- @web.require_login( "use Galaxy pages" )
- def share( self, trans, id, email="", use_panels=False ):
- """ Handle sharing with an individual user. """
- msg = mtype = None
- page = trans.sa_session.query( model.Page ).get( trans.security.decode_id( id ) )
- if email:
- other = trans.sa_session.query( model.User ) \
- .filter( and_( model.User.table.c.email==email,
- model.User.table.c.deleted==False ) ) \
- .first()
- if not other:
- mtype = "error"
- msg = ( "User '%s' does not exist" % email )
- elif other == trans.get_user():
- mtype = "error"
- msg = ( "You cannot share a page with yourself" )
- elif trans.sa_session.query( model.PageUserShareAssociation ) \
- .filter_by( user=other, page=page ).count() > 0:
- mtype = "error"
- msg = ( "Page already shared with '%s'" % email )
- else:
- share = model.PageUserShareAssociation()
- share.page = page
- share.user = other
- session = trans.sa_session
- session.add( share )
- self.create_item_slug( session, page )
- session.flush()
- trans.set_message( "Page '%s' shared with user '%s'" % ( page.title, other.email ) )
- return trans.response.send_redirect( url_for( controller='page', action='sharing', id=id ) )
- return trans.fill_template( "/ind_share_base.mako",
- message = msg,
- messagetype = mtype,
- item=page,
- email=email,
- use_panels=use_panels )
-
- @web.expose
- @web.require_login()
- def save( self, trans, id, content, annotations ):
- id = trans.security.decode_id( id )
- page = trans.sa_session.query( model.Page ).get( id )
- assert page.user == trans.user
-
- # Sanitize content
- content = sanitize_html( content, 'utf-8', 'text/html' )
-
- # Add a new revision to the page with the provided content.
- page_revision = model.PageRevision()
- page_revision.title = page.title
- page_revision.page = page
- page.latest_revision = page_revision
- page_revision.content = content
-
- # Save annotations.
- annotations = from_json_string( annotations )
- for annotation_dict in annotations:
- item_id = trans.security.decode_id( annotation_dict[ 'item_id' ] )
- item_class = self.get_class( annotation_dict[ 'item_class' ] )
- item = trans.sa_session.query( item_class ).filter_by( id=item_id ).first()
- if not item:
- raise RuntimeError( "cannot find annotated item" )
- text = sanitize_html( annotation_dict[ 'text' ], 'utf-8', 'text/html' )
-
- # Add/update annotation.
- if item_id and item_class and text:
- # Get annotation association.
- annotation_assoc_class = eval( "model.%sAnnotationAssociation" % item_class.__name__ )
- annotation_assoc = trans.sa_session.query( annotation_assoc_class ).filter_by( user=trans.get_user() )
- if item_class == model.History.__class__:
- annotation_assoc = annotation_assoc.filter_by( history=item )
- elif item_class == model.HistoryDatasetAssociation.__class__:
- annotation_assoc = annotation_assoc.filter_by( hda=item )
- elif item_class == model.StoredWorkflow.__class__:
- annotation_assoc = annotation_assoc.filter_by( stored_workflow=item )
- elif item_class == model.WorkflowStep.__class__:
- annotation_assoc = annotation_assoc.filter_by( workflow_step=item )
- annotation_assoc = annotation_assoc.first()
- if not annotation_assoc:
- # Create association.
- annotation_assoc = annotation_assoc_class()
- item.annotations.append( annotation_assoc )
- annotation_assoc.user = trans.get_user()
- # Set annotation user text.
- annotation_assoc.annotation = text
- trans.sa_session.flush()
-
- @web.expose
- @web.require_login()
- def display( self, trans, id ):
- id = trans.security.decode_id( id )
- page = trans.sa_session.query( model.Page ).get( id )
- if not page:
- raise web.httpexceptions.HTTPNotFound()
- return self.display_by_username_and_slug( trans, page.user.username, page.slug )
- @web.expose
- def display_by_username_and_slug( self, trans, username, slug ):
- """ Display page based on a username and slug. """
- # Get page.
- session = trans.sa_session
- user = session.query( model.User ).filter_by( username=username ).first()
- page = trans.sa_session.query( model.Page ).filter_by( user=user, slug=slug, deleted=False ).first()
- if page is None:
- raise web.httpexceptions.HTTPNotFound()
- # Security check raises error if user cannot access page.
- self.security_check( trans, page, False, True)
-
- # Process page content.
- processor = _PageContentProcessor( trans, 'utf-8', 'text/html', self._get_embed_html )
- processor.feed( page.latest_revision.content )
-
- # Get rating data.
- user_item_rating = 0
- if trans.get_user():
- user_item_rating = self.get_user_item_rating( trans.sa_session, trans.get_user(), page )
- if user_item_rating:
- user_item_rating = user_item_rating.rating
- else:
- user_item_rating = 0
- ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, page )
-
- # Output is string, so convert to unicode for display.
- page_content = unicode( processor.output(), 'utf-8' )
- return trans.fill_template_mako( "page/display.mako", item=page, item_data=page_content,
- user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings,
- content_only=True )
-
- @web.expose
- @web.require_login( "use Galaxy pages" )
- def set_accessible_async( self, trans, id=None, accessible=False ):
- """ Set page's importable attribute and slug. """
- page = self.get_page( trans, id )
- # Only set if importable value would change; this prevents a change in the update_time unless attribute really changed.
- importable = accessible in ['True', 'true', 't', 'T'];
- if page.importable != importable:
- if importable:
- self._make_item_accessible( trans.sa_session, page )
- else:
- page.importable = importable
- trans.sa_session.flush()
- return
- @web.expose
- @web.require_login( "modify Galaxy items" )
- def set_slug_async( self, trans, id, new_slug ):
- page = self.get_page( trans, id )
- if page:
- page.slug = new_slug
- trans.sa_session.flush()
- return page.slug
-
- @web.expose
- @web.require_login( "rate items" )
- @web.json
- def rate_async( self, trans, id, rating ):
- """ Rate a page asynchronously and return updated community data. """
- page = self.get_page( trans, id, check_ownership=False, check_accessible=True )
- if not page:
- return trans.show_error_message( "The specified page does not exist." )
- # Rate page.
- page_rating = self.rate_item( trans.sa_session, trans.get_user(), page, rating )
- return self.get_ave_item_rating_data( trans.sa_session, page )
-
- @web.expose
- def get_embed_html_async( self, trans, id ):
- """ Returns HTML for embedding a workflow in a page. """
- # TODO: user should be able to embed any item he has access to. see display_by_username_and_slug for security code.
- page = self.get_page( trans, id )
- if page:
- return "Embedded Page '%s'" % page.title
- @web.expose
- @web.json
- @web.require_login( "use Galaxy pages" )
- def get_name_and_link_async( self, trans, id=None ):
- """ Returns page's name and link. """
- page = self.get_page( trans, id )
- if self.create_item_slug( trans.sa_session, page ):
- trans.sa_session.flush()
- return_dict = { "name" : page.title, "link" : url_for( action="display_by_username_and_slug", username=page.user.username, slug=page.slug ) }
- return return_dict
-
- @web.expose
- @web.require_login("select a history from saved histories")
- def list_histories_for_selection( self, trans, **kwargs ):
- """ Returns HTML that enables a user to select one or more histories. """
- # Render the list view
- return self._history_selection_grid( trans, **kwargs )
-
- @web.expose
- @web.require_login("select a workflow from saved workflows")
- def list_workflows_for_selection( self, trans, **kwargs ):
- """ Returns HTML that enables a user to select one or more workflows. """
- # Render the list view
- return self._workflow_selection_grid( trans, **kwargs )
-
- @web.expose
- @web.require_login("select a visualization from saved visualizations")
- def list_visualizations_for_selection( self, trans, **kwargs ):
- """ Returns HTML that enables a user to select one or more visualizations. """
- # Render the list view
- return self._visualization_selection_grid( trans, **kwargs )
-
- @web.expose
- @web.require_login("select a page from saved pages")
- def list_pages_for_selection( self, trans, **kwargs ):
- """ Returns HTML that enables a user to select one or more pages. """
- # Render the list view
- return self._page_selection_grid( trans, **kwargs )
-
- @web.expose
- @web.require_login("select a dataset from saved datasets")
- def list_datasets_for_selection( self, trans, **kwargs ):
- """ Returns HTML that enables a user to select one or more datasets. """
- # Render the list view
- return self._datasets_selection_grid( trans, **kwargs )
-
- @web.expose
- @web.require_login("get annotation table for history")
- def get_history_annotation_table( self, trans, id ):
- """ Returns HTML for an annotation table for a history. """
- history = self.get_history( trans, id, False, True )
-
- if history:
- datasets = self.get_history_datasets( trans, history )
- return trans.fill_template( "page/history_annotation_table.mako", history=history, datasets=datasets, show_deleted=False )
-
- @web.expose
- def get_editor_iframe( self, trans ):
- """ Returns the document for the page editor's iframe. """
- return trans.fill_template( "page/wymiframe.mako" )
-
- def get_page( self, trans, id, check_ownership=True, check_accessible=False ):
- """Get a page from the database by id."""
- # Load history from database
- id = trans.security.decode_id( id )
- page = trans.sa_session.query( model.Page ).get( id )
- if not page:
- err+msg( "Page not found" )
- else:
- return self.security_check( trans, page, check_ownership, check_accessible )
-
- def get_item( self, trans, id ):
- return self.get_page( trans, id )
-
- def _get_embed_html( self, trans, item_class, item_id ):
- """ Returns HTML for embedding an item in a page. """
- item_class = self.get_class( item_class )
- if item_class == model.History:
- history = self.get_history( trans, item_id, False, True )
- history.annotation = self.get_item_annotation_str( trans.sa_session, history.user, history )
- if history:
- datasets = self.get_history_datasets( trans, history )
- return trans.fill_template( "history/embed.mako", item=history, item_data=datasets )
- elif item_class == model.HistoryDatasetAssociation:
- dataset = self.get_dataset( trans, item_id, False, True )
- dataset.annotation = self.get_item_annotation_str( trans.sa_session, dataset.history.user, dataset )
- if dataset:
- data = self.get_data( dataset )
- return trans.fill_template( "dataset/embed.mako", item=dataset, item_data=data )
- elif item_class == model.StoredWorkflow:
- workflow = self.get_stored_workflow( trans, item_id, False, True )
- workflow.annotation = self.get_item_annotation_str( trans.sa_session, workflow.user, workflow )
- if workflow:
- self.get_stored_workflow_steps( trans, workflow )
- return trans.fill_template( "workflow/embed.mako", item=workflow, item_data=workflow.latest_workflow.steps )
- elif item_class == model.Visualization:
- visualization = self.get_visualization( trans, item_id, False, True )
- visualization.annotation = self.get_item_annotation_str( trans.sa_session, visualization.user, visualization )
- if visualization:
- return trans.fill_template( "visualization/embed.mako", item=visualization, item_data=None )
-
- elif item_class == model.Page:
- pass