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Annotations for published items: (1) added annotations to pages; (2) added annotation column to all published item grids; (3) refactored annotation code out of base controller and into its own mixin.

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This commit is contained in:
Jeremy Goecks
2010-02-22 13:56:51 -05:00
parent 9d7974a3cb
commit 7e96a18c68
10 changed files with 118 additions and 21 deletions
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lib/galaxy/model/__init__.py
+3
View File
@@ -1567,6 +1567,9 @@ class StoredWorkflowAnnotationAssociation( object ):
class WorkflowStepAnnotationAssociation( object ):
pass
class PageAnnotationAssociation( object ):
pass
class UserPreference ( object ):
def __init__( self, name=None, value=None ):
self.name = name
lib/galaxy/model/mapping.py
+12 -1
View File
@@ -814,6 +814,12 @@ WorkflowStepAnnotationAssociation.table = Table( "workflow_step_annotation_assoc
Column( "workflow_step_id", Integer, ForeignKey( "workflow_step.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "annotation", TEXT, index=True) )
PageAnnotationAssociation.table = Table( "page_annotation_association", metadata,
Column( "id", Integer, primary_key=True ),
Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "annotation", TEXT, index=True) )
# User tables.
@@ -1304,7 +1310,8 @@ assign_mapper( context, Page, Page.table,
latest_revision=relation( PageRevision, post_update=True,
primaryjoin=( Page.table.c.latest_revision_id == PageRevision.table.c.id ),
lazy=False ),
tags=relation(PageTagAssociation, order_by=PageTagAssociation.table.c.id, backref="pages")
tags=relation(PageTagAssociation, order_by=PageTagAssociation.table.c.id, backref="pages"),
annotations=relation( PageAnnotationAssociation, order_by=PageAnnotationAssociation.table.c.id, backref="pages" )
) )
# Set up proxy so that
@@ -1377,6 +1384,10 @@ assign_mapper( context, WorkflowStepAnnotationAssociation, WorkflowStepAnnotatio
properties=dict( workflow_step=relation( WorkflowStep ), user=relation( User ) )
)
assign_mapper( context, PageAnnotationAssociation, PageAnnotationAssociation.table,
properties=dict( page=relation( Page ), user=relation( User ) )
)
assign_mapper( context, UserPreference, UserPreference.table,
properties = {}
)
lib/galaxy/model/migrate/versions/0040_page_annotations.py
+42
View File
@@ -0,0 +1,42 @@
"""
Migration script to (a) create tables for annotating pages.
"""
from sqlalchemy import *
from sqlalchemy.orm import *
from migrate import *
from migrate.changeset import *
import logging
log = logging.getLogger( __name__ )
metadata = MetaData( migrate_engine )
db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
PageAnnotationAssociation_table = Table( "page_annotation_association", metadata,
Column( "id", Integer, primary_key=True ),
Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ),
Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ),
Column( "annotation", TEXT, index=True) )
def upgrade():
print __doc__
metadata.reflect()
# Create history_annotation_association table.
try:
PageAnnotationAssociation_table.create()
except Exception, e:
print str(e)
log.debug( "Creating page_annotation_association table failed: %s" % str( e ) )
def downgrade():
metadata.reflect()
# Drop page_annotation_association table.
try:
PageAnnotationAssociation_table.drop()
except Exception, e:
print str(e)
log.debug( "Dropping page_annotation_association table failed: %s" % str( e ) )
lib/galaxy/web/base/controller.py
+6 -2
View File
@@ -41,6 +41,10 @@ class BaseController( object ):
item_class = None
return item_class
Root = BaseController
class UsesAnnotations:
""" Mixin for getting and setting item annotations. """
def get_item_annotation_str( self, db_session, user, item ):
""" Returns a user's annotation string for an item. """
annotation_obj = self.get_item_annotation_obj( db_session, user, item )
@@ -67,6 +71,8 @@ class BaseController( object ):
annotation_assoc = annotation_assoc.filter_by( stored_workflow=item )
elif item.__class__ == model.WorkflowStep:
annotation_assoc = annotation_assoc.filter_by( workflow_step=item )
elif item.__class__ == model.Page:
annotation_assoc = annotation_assoc.filter_by( page=item )
return annotation_assoc.first()
def add_item_annotation( self, trans, item, annotation ):
@@ -89,8 +95,6 @@ class BaseController( object ):
# Set annotation.
annotation_assoc.annotation = annotation
return True
Root = BaseController
class SharableItemSecurity:
""" Mixin for handling security for sharable items. """
lib/galaxy/web/controllers/dataset.py
+1 -1
View File
@@ -110,7 +110,7 @@ class HistoryDatasetAssociationListGrid( grids.Grid ):
# a user relation.
return query.select_from( model.HistoryDatasetAssociation.table.join( model.History.table ) ).filter( model.History.user == trans.user )
class DatasetInterface( BaseController, UsesHistoryDatasetAssociation ):
class DatasetInterface( BaseController, UsesAnnotations, UsesHistoryDatasetAssociation ):
stored_list_grid = HistoryDatasetAssociationListGrid()
lib/galaxy/web/controllers/history.py
+2 -1
View File
@@ -128,6 +128,7 @@ class HistoryAllPublishedGrid( grids.Grid ):
use_async = True
columns = [
NameURLColumn( "Name", key="name", model_class=model.History, filterable="advanced" ),
grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.History, model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ),
grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ),
grids.CommunityTagsColumn( "Community Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago )
@@ -146,7 +147,7 @@ class HistoryAllPublishedGrid( grids.Grid ):
# A public history is published, has a slug, and is not deleted.
return query.filter( self.model_class.published == True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False )
class HistoryController( BaseController, Sharable, UsesHistory ):
class HistoryController( BaseController, Sharable, UsesAnnotations, UsesHistory ):
@web.expose
def index( self, trans ):
return ""
lib/galaxy/web/controllers/page.py
+17 -7
View File
@@ -45,7 +45,7 @@ class PageListGrid( grids.Grid ):
]
operations = [
grids.DisplayByUsernameAndSlugGridOperation( "View", allow_multiple=False ),
grids.GridOperation( "Edit name/id", allow_multiple=False, url_args=dict( action='edit') ),
grids.GridOperation( "Edit attributes", allow_multiple=False, url_args=dict( action='edit') ),
grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ),
grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
grids.GridOperation( "Delete" ),
@@ -63,6 +63,7 @@ class PageAllPublishedGrid( grids.Grid ):
default_filter = dict( title="All", username="All" )
columns = [
grids.PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced"),
grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ),
grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ),
grids.CommunityTagsColumn( "Community Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago )
@@ -70,7 +71,7 @@ class PageAllPublishedGrid( grids.Grid ):
columns.append(
grids.MulticolFilterColumn(
"Search",
cols_to_filter=[ columns[0], columns[1], columns[2] ],
cols_to_filter=[ columns[0], columns[1], columns[2], columns[3] ],
key="free-text-search", visible=False, filterable="standard" )
)
def build_initial_query( self, session ):
@@ -285,7 +286,7 @@ class _PageContentProcessor( _BaseHTMLProcessor ):
# Default behavior:
_BaseHTMLProcessor.unknown_endtag( self, tag )
class PageController( BaseController, Sharable, UsesHistory, UsesStoredWorkflow, UsesHistoryDatasetAssociation ):
class PageController( BaseController, Sharable, UsesAnnotations, UsesHistory, UsesStoredWorkflow, UsesHistoryDatasetAssociation ):
_page_list = PageListGrid()
_all_published_list = PageAllPublishedGrid()
@@ -385,7 +386,7 @@ class PageController( BaseController, Sharable, UsesHistory, UsesStoredWorkflow,
@web.expose
@web.require_login( "create pages" )
def edit( self, trans, id, page_title="", page_slug="" ):
def edit( self, trans, id, page_title="", page_slug="", page_annotation="" ):
"""
Create a new page
"""
@@ -395,7 +396,7 @@ class PageController( BaseController, Sharable, UsesHistory, UsesStoredWorkflow,
page = session.query( model.Page ).get( id )
user = trans.user
assert page.user == user
page_title_err = page_slug_err = ""
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"
@@ -403,17 +404,24 @@ class PageController( BaseController, Sharable, UsesHistory, UsesStoredWorkflow,
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 or trans.sa_session.query( model.Page ).filter_by( user=user, slug=page_slug, deleted=False ).first():
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, 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.get_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 )
@@ -422,7 +430,9 @@ class PageController( BaseController, Sharable, UsesHistory, UsesStoredWorkflow,
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.""" ),
the '-' character.""" )
.add_text( "page_annotation", "Page annotation", value=page_annotation, error=page_annotation_err,
help="A description of or notes about the page. Annotation is shown alongside published pages."),
template="page/create.mako" )
@web.expose
lib/galaxy/web/controllers/root.py
+1 -1
View File
@@ -10,7 +10,7 @@ from galaxy.model.orm import *
log = logging.getLogger( __name__ )
class RootController( BaseController, UsesHistory ):
class RootController( BaseController, UsesHistory, UsesAnnotations ):
@web.expose
def default(self, trans, target1=None, target2=None, **kwd):
lib/galaxy/web/controllers/workflow.py
+2 -1
View File
@@ -60,6 +60,7 @@ class StoredWorkflowAllPublishedGrid( grids.Grid ):
use_async = True
columns = [
grids.PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ),
grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.StoredWorkflow, model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ),
grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ),
grids.CommunityTagsColumn( "Community Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago )
@@ -78,7 +79,7 @@ class StoredWorkflowAllPublishedGrid( grids.Grid ):
# A public workflow is published, has a slug, and is not deleted.
return query.filter( self.model_class.published==True ).filter( self.model_class.slug != None ).filter( self.model_class.deleted == False )
class WorkflowController( BaseController, Sharable, UsesStoredWorkflow ):
class WorkflowController( BaseController, Sharable, UsesStoredWorkflow, UsesAnnotations ):
stored_list_grid = StoredWorkflowListGrid()
published_list_grid = StoredWorkflowAllPublishedGrid()
lib/galaxy/web/framework/helpers/grids.py
+32 -7
View File
@@ -1,6 +1,7 @@
from galaxy.model import *
from galaxy.model.orm import *
from galaxy.web.base import controller
from galaxy.web.framework.helpers import iff
from galaxy.tags.tag_handler import TagHandler
from galaxy.web import url_for
@@ -341,22 +342,46 @@ class TextColumn( GridColumn ):
elif column_filter:
query = query.filter( self.get_filter( user, column_filter ) )
return query
def get_filter( self, user, column_filter ):
""" Returns a SQLAlchemy criterion derived from column_filter. """
model_class_key_field = getattr( self.model_class, self.key )
def get_filter( self, user, column_filter ):
""" Returns a SQLAlchemy criterion derived from column_filter. """
if isinstance( column_filter, basestring ):
return func.lower( model_class_key_field ).like( "%" + column_filter.lower() + "%" )
return self.get_single_filter( user, column_filter )
elif isinstance( column_filter, list ):
clause_list = []
for filter in column_filter:
clause_list.append( func.lower( model_class_key_field ).like( "%" + filter.lower() + "%" ) )
clause_list.append( self.get_single_filter( user, filter ) )
return and_( *clause_list )
def get_single_filter( self, user, a_filter ):
""" Returns a SQLAlchemy criterion derived for a single filter. Single filter is the most basic filter--usually a string--and cannot be a list. """
model_class_key_field = getattr( self.model_class, self.key )
return func.lower( model_class_key_field ).like( "%" + a_filter.lower() + "%" )
class OwnerAnnotationColumn( TextColumn, controller.UsesAnnotations ):
""" Column that displays and filters item owner's annotations. """
def __init__( self, col_name, key, model_class, model_annotation_association_class, filterable ):
GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable )
self.sortable = False
self.model_annotation_association_class = model_annotation_association_class
def get_value( self, trans, grid, item ):
""" Returns item annotation. """
annotation = self.get_item_annotation_str( trans.sa_session, item.user, item )
return iff( annotation, annotation, "" )
def get_single_filter( self, user, a_filter ):
""" Filter by annotation and annotation owner. """
return self.model_class.annotations.any(
and_( func.lower( self.model_annotation_association_class.annotation ).like( "%" + a_filter.lower() + "%" ),
# TODO: not sure why, to filter by owner's annotations, we have to do this rather than
# 'self.model_class.user==self.model_annotation_association_class.user'
self.model_annotation_association_class.table.c.user_id==self.model_class.table.c.user_id ) )
class CommunityTagsColumn( TextColumn ):
""" Column that supports community tags. """
def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ):
GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable)
GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable )
self.model_tag_association_class = model_tag_association_class
# Tags cannot be sorted.
self.sortable = False