class RepositoriesReviewedByMeGrid(RepositoriesWithReviewsGrid):
# This grid filters out repositories that have been marked as either deprecated or deleted.
columns = [
RepositoriesWithReviewsGrid.NameColumn(
"Repository name",
key="name",
link=(lambda item: dict(operation="view_or_manage_repository",
id=item.id)),
attach_popup=True),
RepositoriesWithReviewsGrid.UserColumn("Owner", attach_popup=False),
RepositoriesWithReviewsGrid.WithReviewsRevisionColumn(
"Reviewed revisions"),
RepositoriesWithReviewsGrid.ReviewersColumn("Reviewers",
attach_popup=False),
RepositoriesWithReviewsGrid.RatingColumn("Rating", attach_popup=False),
RepositoriesWithReviewsGrid.ApprovedColumn("Approved",
attach_popup=False)
]
columns.append(
grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
def build_initial_query(self, trans, **kwd):
return trans.sa_session.query( model.Repository ) \
.filter( and_( model.Repository.table.c.deleted == False,
model.Repository.table.c.deprecated == False ) ) \
.join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \
.filter( model.RepositoryReview.table.c.user_id == trans.user.id ) \
.join( ( model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id ) ) \
.outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \
.outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) )
class LibraryDatasetsSelectionGrid(grids.Grid):
available_tracks = None
title = "Add Datasets"
model_class = model.LibraryDatasetDatasetAssociation
default_filter = {"deleted": "False"}
default_sort_key = "-id"
columns = [
grids.GridColumn("Id", key="id"),
grids.TextColumn("Name",
key="name",
model_class=model.LibraryDatasetDatasetAssociation),
grids.TextColumn("Type",
key="extension",
model_class=model.LibraryDatasetDatasetAssociation),
]
columns.append(
grids.MulticolFilterColumn("Search name and filetype",
cols_to_filter=[columns[1], columns[2]],
key="free-text-search",
visible=False,
filterable="standard"))
def build_initial_query(self, trans, **kwargs):
return trans.sa_session.query(self.model_class).join(
model.Dataset.table)
def apply_query_filter(self, trans, query, **kwargs):
if self.available_tracks is None:
self.available_tracks = trans.app.datatypes_registry.get_available_tracks(
)
return query.filter(model.LibraryDatasetDatasetAssociation.user == trans.user) \
.filter(model.LibraryDatasetDatasetAssociation.extension.in_(self.available_tracks)) \
.filter(model.Dataset.state == model.Dataset.states.OK) \
.filter(model.LibraryDatasetDatasetAssociation.deleted == false()) \
.filter(model.LibraryDatasetDatasetAssociation.visible == true())
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 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 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 InteractiveToolEntryPointListGrid(grids.Grid):
use_panels = True
title = "Available InteractiveTools"
model_class = model.InteractiveToolEntryPoint
default_filter = {"name": "All"}
default_sort_key = "-update_time"
columns = [
EntryPointLinkColumn("Name", filterable="advanced"),
JobStatusColumn("Job Info", key="job_state", model_class=model.Job),
grids.GridColumn("Created", key="created_time", format=time_ago),
grids.GridColumn("Last Updated", key="modified_time", format=time_ago),
]
columns.append(
grids.MulticolFilterColumn(
"Search",
cols_to_filter=[columns[0]],
key="free-text-search", visible=False, filterable="standard"
)
)
operations = [
grids.GridOperation("Stop", condition=(lambda item: item.active), async_compatible=False),
]
def build_initial_query(self, trans, **kwargs):
# Get list of user's active InteractiveTools
return trans.app.interactivetool_manager.get_nonterminal_for_user_by_trans(trans)
class StoredWorkflowAllPublishedGrid(grids.Grid):
title = "Published Workflows"
model_class = model.StoredWorkflow
default_sort_key = "update_time"
default_filter = dict(public_url="All", username="******", tags="All")
columns = [
grids.PublicURLColumn("Name", key="name", filterable="advanced", attach_popup=True),
grids.OwnerAnnotationColumn("Annotation",
key="annotation",
model_annotation_association_class=model.StoredWorkflowAnnotationAssociation,
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.StoredWorkflowTagAssociation,
filterable="advanced", grid_name="PublicWorkflowListGrid"),
grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago)
]
columns.append(
grids.MulticolFilterColumn(
"Search name, annotation, owner, and tags",
cols_to_filter=[columns[0], columns[1], columns[2], columns[4]],
key="free-text-search", visible=False, filterable="standard"
)
)
operations = [
grids.GridOperation(
'Run',
condition=(lambda item: not item.deleted),
allow_multiple=False,
url_args=dict(controller='workflows', action="run")
),
grids.GridOperation(
"Import",
condition=(lambda item: not item.deleted),
allow_multiple=False,
url_args=dict(action="imp")
),
grids.GridOperation(
"Save as File",
condition=(lambda item: not item.deleted),
allow_multiple=False,
url_args=dict(action="export_to_file")
),
]
num_rows_per_page = 50
use_paging = True
def build_initial_query(self, trans, **kwargs):
# See optimization description comments and TODO for tags in matching public histories query.
# In addition to that - be sure to lazyload the latest_workflow - it isn't needed and it causes all
# of its steps to be eagerly loaded.
return trans.sa_session.query(self.model_class).join("user").options(lazyload("latest_workflow"), eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
def apply_query_filter(self, trans, query, **kwargs):
# A public workflow is published, has a slug, and is not deleted.
return query.filter(
self.model_class.published == expression.true()).filter(
self.model_class.slug.isnot(None)).filter(
self.model_class.deleted == expression.false())
class PageAllPublishedGrid(grids.Grid):
# Grid definition
use_panels = True
title = "Published Pages"
model_class = model.Page
default_sort_key = "update_time"
default_filter = dict(title="All", username="******")
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):
# See optimization description comments and TODO for tags in matching public histories query.
return trans.sa_session.query(self.model_class).join("user").options(eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
def apply_query_filter(self, trans, query, **kwargs):
return query.filter(self.model_class.deleted == false()).filter(self.model_class.published == true())
class FormsGrid( grids.Grid ):
# Custom column types
class NameColumn( grids.TextColumn ):
def get_value(self, trans, grid, form):
return form.latest_form.name
class DescriptionColumn( grids.TextColumn ):
def get_value(self, trans, grid, form):
return form.latest_form.desc
class TypeColumn( grids.TextColumn ):
def get_value(self, trans, grid, form):
return form.latest_form.type
class DeletedColumn( grids.GridColumn ):
def get_accepted_filters( self ):
""" Returns a list of accepted filters for this column. """
accepted_filter_labels_and_vals = { "active" : "False", "deleted" : "True", "all": "All" }
accepted_filters = []
for label, val in accepted_filter_labels_and_vals.items():
args = { self.key: val }
accepted_filters.append( grids.GridColumnFilter( label, args) )
return accepted_filters
# Grid definition
title = "Forms"
template = "admin/forms/grid.mako"
model_class = model.FormDefinitionCurrent
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = dict( deleted="False" )
columns = [
NameColumn( "Name",
key="name",
model_class=model.FormDefinition,
link=( lambda item: iff( item.deleted, None, dict( operation="view", id=item.id ) ) ),
attach_popup=True,
filterable="advanced" ),
DescriptionColumn( "Description",
key='desc',
model_class=model.FormDefinition,
filterable="advanced" ),
TypeColumn( "Type" ),
DeletedColumn( "Deleted",
key="deleted",
visible=False,
filterable="advanced" )
]
columns.append( grids.MulticolFilterColumn( "Search",
cols_to_filter=[ columns[0], columns[1] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
operations = [
grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: not item.deleted ) ),
grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: not item.deleted ) ),
grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ),
]
global_actions = [
grids.GridAction( "Create new form", dict( controller='forms',
action='new' ) )
]
class LibraryListGrid( grids.Grid ):
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, library ):
return library.name
class DescriptionColumn( grids.TextColumn ):
def get_value( self, trans, grid, library ):
if library.description:
return library.description
return ''
# Grid definition
title = "Data Libraries"
model_class = model.Library
template='/library/grid.mako'
default_sort_key = "name"
columns = [
NameColumn( "Data library name",
key="name",
link=( lambda library: dict( operation="browse", id=library.id ) ),
attach_popup=False,
filterable="advanced" ),
DescriptionColumn( "Data library description",
key="description",
attach_popup=False,
filterable="advanced" ),
]
columns.append( grids.MulticolFilterColumn( "search dataset name, info, message, dbkey",
cols_to_filter=[ columns[0], columns[1] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
standard_filters = []
default_filter = dict( name="All", description="All", deleted="False", purged="False" )
num_rows_per_page = 50
preserve_state = False
use_paging = True
def build_initial_query( self, trans, **kwargs ):
return trans.sa_session.query( self.model_class ).filter( self.model_class.table.c.deleted == False )
def apply_query_filter( self, trans, query, **kwd ):
current_user_role_ids = [ role.id for role in trans.get_current_user_roles() ]
library_access_action = trans.app.security_agent.permitted_actions.LIBRARY_ACCESS.action
restricted_library_ids = [ lp.library_id for lp in trans.sa_session.query( trans.model.LibraryPermissions ) \
.filter( trans.model.LibraryPermissions.table.c.action == library_access_action ) \
.distinct() ]
accessible_restricted_library_ids = [ lp.library_id for lp in trans.sa_session.query( trans.model.LibraryPermissions ) \
.filter( and_( trans.model.LibraryPermissions.table.c.action == library_access_action,
trans.model.LibraryPermissions.table.c.role_id.in_( current_user_role_ids ) ) ) ]
if not trans.user:
# Filter to get only public libraries, a library whose id
# is not in restricted_library_ids is a public library
return query.filter( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ) )
else:
# Filter to get libraries accessible by the current user, get both
# public libraries and restricted libraries accessible by the current user.
return query.filter( or_( not_( trans.model.Library.table.c.id.in_( restricted_library_ids ) ),
trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) )
class RepositoriesWithoutReviewsGrid(RepositoriesWithReviewsGrid):
# This grid filters out repositories that have been marked as deprecated.
title = "Repositories with no reviews"
columns = [
RepositoriesWithReviewsGrid.NameColumn(
"Repository name",
key="name",
link=(lambda item: dict(operation="view_or_manage_repository",
id=item.id)),
attach_popup=True),
RepositoriesWithReviewsGrid.DescriptionColumn("Synopsis",
key="description",
attach_popup=False),
RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn(
"Revisions for review"),
RepositoriesWithReviewsGrid.UserColumn("Owner", attach_popup=False)
]
columns.append(
grids.MulticolFilterColumn("Search repository name, description",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation("Inspect repository revisions",
allow_multiple=False,
condition=(lambda item: not item.deleted),
async_compatible=False)
]
def build_initial_query(self, trans, **kwd):
return trans.sa_session.query( model.Repository ) \
.filter( and_( model.Repository.table.c.deprecated == False,
model.Repository.reviews == None ) ) \
.join( model.User.table )
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="******" )
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 FormsGrid(grids.Grid):
# Custom column types
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, form):
return escape(form.latest_form.name)
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, form):
return escape(form.latest_form.desc)
class TypeColumn(grids.TextColumn):
def get_value(self, trans, grid, form):
return form.latest_form.type
# Grid definition
title = "Forms"
template = "admin/forms/grid.mako"
model_class = model.FormDefinitionCurrent
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = True
default_filter = dict(deleted="False")
columns = [
NameColumn("Name",
key="name",
model_class=model.FormDefinition,
link=(lambda item: iff(item.deleted, None, dict(operation="view_latest_form_definition",
id=item.id))),
attach_popup=True,
filterable="advanced"),
DescriptionColumn("Description",
key='desc',
model_class=model.FormDefinition,
filterable="advanced"),
TypeColumn("Type"),
grids.DeletedColumn("Deleted",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0], columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation("Edit", allow_multiple=False, condition=(lambda item: not item.deleted)),
grids.GridOperation("Delete", allow_multiple=True, condition=(lambda item: not item.deleted)),
grids.GridOperation("Undelete", condition=(lambda item: item.deleted)),
]
global_actions = [
grids.GridAction("Create new form", dict(controller='forms', action='create_form_definition'))
]
def build_initial_query(self, trans, **kwargs):
return trans.sa_session.query(self.model_class).join(model.FormDefinition, self.model_class.latest_form_id == model.FormDefinition.id)
class StoredWorkflowListGrid(grids.Grid):
class StepsColumn(grids.GridColumn):
def get_value(self, trans, grid, workflow):
return len(workflow.latest_workflow.steps)
# Grid definition
use_panels = True
title = "Saved Workflows"
model_class = model.StoredWorkflow
default_filter = {"name": "All", "tags": "All"}
default_sort_key = "-update_time"
columns = [
grids.TextColumn("Name",
key="name",
attach_popup=True,
filterable="advanced"),
grids.IndividualTagsColumn(
"Tags",
"tags",
model_tag_association_class=model.StoredWorkflowTagAssociation,
filterable="advanced",
grid_name="StoredWorkflowListGrid"),
StepsColumn("Steps"),
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[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation("Edit",
allow_multiple=False,
condition=(lambda item: not item.deleted),
async_compatible=False),
grids.GridOperation("Run",
condition=(lambda item: not item.deleted),
async_compatible=False),
grids.GridOperation("Copy",
condition=(lambda item: not item.deleted),
async_compatible=False),
grids.GridOperation("Rename",
condition=(lambda item: not item.deleted),
async_compatible=False),
grids.GridOperation("Sharing",
condition=(lambda item: not item.deleted),
async_compatible=False),
grids.GridOperation("Delete",
condition=(lambda item: item.deleted),
async_compatible=True),
]
def apply_query_filter(self, trans, query, **kwargs):
return query.filter_by(user=trans.user, deleted=False)
class LibraryListGrid( grids.Grid ):
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, library ):
return library.name
class DescriptionColumn( grids.TextColumn ):
def get_value( self, trans, grid, library ):
if library.description:
return library.description
return ''
class StatusColumn( grids.GridColumn ):
def get_value( self, trans, grid, library ):
if library.purged:
return "purged"
elif library.deleted:
return "deleted"
return ""
# Grid definition
title = "Data Libraries"
model_class = model.Library
template='/admin/library/grid.mako'
default_sort_key = "name"
columns = [
NameColumn( "Data library name",
key="name",
link=( lambda library: dict( operation="browse", id=library.id ) ),
attach_popup=False,
filterable="advanced" ),
DescriptionColumn( "Data library description",
key="description",
attach_popup=False,
filterable="advanced" ),
grids.GridColumn( "Created", key="create_time", format=time_ago ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
StatusColumn( "Status", attach_popup=False ),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" )
]
columns.append( grids.MulticolFilterColumn( "search dataset name, info, message, dbkey",
cols_to_filter=[ columns[0], columns[1] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
global_actions = [
grids.GridAction( "Create new data library", dict( controller='library_admin', action='create_library' ) )
]
standard_filters = [
grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ),
grids.GridColumnFilter( "Purged", args=dict( purged=True ) ),
grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
]
default_filter = dict( name="All", description="All", deleted="False", purged="False" )
num_rows_per_page = 50
preserve_state = False
use_paging = True
class VisualizationListGrid( grids.Grid ):
def get_url_args( item ):
"""
Returns dictionary used to create item link.
"""
url_kwargs = dict( controller='visualization', id=item.id )
#TODO: hack to build link to saved visualization - need trans in this function instead in order to do
#link_data = trans.app.visualizations_registry.get_visualizations( trans, item )
if item.type in registry.VisualizationsRegistry.BUILT_IN_VISUALIZATIONS:
url_kwargs[ 'action' ] = item.type
else:
url_kwargs[ 'action' ] = 'saved'
return url_kwargs
def get_display_name( self, trans, item ):
if trans.app.visualizations_registry and item.type in trans.app.visualizations_registry.plugins:
plugin = trans.app.visualizations_registry.plugins[ item.type ]
return plugin.config.get( 'name', item.type )
return item.type
# Grid definition
title = "Saved Visualizations"
model_class = model.Visualization
default_sort_key = "-update_time"
default_filter = dict( title="All", deleted="False", tags="All", sharing="All" )
columns = [
grids.TextColumn( "Title", key="title", attach_popup=True, link=get_url_args ),
grids.TextColumn( "Type", method='get_display_name' ),
grids.TextColumn( "Dbkey", key="dbkey" ),
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( "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( "Create new visualization", dict( action='create' ), inbound=True )
]
operations = [
grids.GridOperation( "Open", allow_multiple=False, url_args=get_url_args ),
grids.GridOperation( "Open in Circster", allow_multiple=False, condition=( lambda item: item.type == 'trackster' ), url_args=dict( action='circster' ) ),
grids.GridOperation( "Edit Attributes", allow_multiple=False, url_args=dict( action='edit'), inbound=True),
grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted )),
grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), confirm="Are you sure you want to delete this visualization?" ),
]
def apply_query_filter( self, trans, query, **kwargs ):
return query.filter_by( user=trans.user, deleted=False )
class ToolVersionListGrid(grids.Grid):
class ToolIdColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_version):
toolbox = trans.app.toolbox
if toolbox.has_tool(tool_version.tool_id, exact=True):
link = url_for(controller='tool_runner',
tool_id=tool_version.tool_id)
link_str = '<a href="%s">' % link
return '<div class="count-box state-color-ok">%s%s</a></div>' % (
link_str, tool_version.tool_id)
return tool_version.tool_id
class ToolVersionsColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_version):
tool_ids_str = ''
toolbox = trans.app.toolbox
for tool_id in tool_version.get_version_ids(trans.app):
if toolbox.has_tool(tool_id, exact=True):
link = url_for(controller='tool_runner',
tool_id=tool_version.tool_id)
link_str = '<a href="%s">' % link
tool_ids_str += '<div class="count-box state-color-ok">%s%s</a></div><br/>' % (
link_str, tool_id)
else:
tool_ids_str += '%s<br/>' % tool_id
return tool_ids_str
# Grid definition
title = "Tool versions"
model_class = install_model.ToolVersion
template = '/admin/tool_version/grid.mako'
default_sort_key = "tool_id"
columns = [
ToolIdColumn("Tool id", key='tool_id', attach_popup=False),
ToolVersionsColumn("Version lineage by tool id (parent/child ordered)")
]
columns.append(
grids.MulticolFilterColumn("Search tool id",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
global_actions = []
operations = []
standard_filters = []
default_filter = {}
num_rows_per_page = 50
preserve_state = False
use_paging = True
def build_initial_query(self, trans, **kwd):
return trans.install_model.context.query(self.model_class)
class AdminRepositoryGrid(RepositoryGrid):
class DeletedColumn(grids.BooleanColumn):
def get_value(self, trans, grid, repository):
if repository.deleted:
return 'yes'
return ''
columns = [
RepositoryGrid.NameColumn(
"Name",
key="name",
link=(lambda item: dict(operation="view_or_manage_repository",
id=item.id)),
attach_popup=True),
RepositoryGrid.HeadsColumn("Heads"),
RepositoryGrid.UserColumn(
"Owner",
model_class=model.User,
link=(lambda item: dict(operation="repositories_by_user",
id=item.id)),
attach_popup=False,
key="User.username"),
RepositoryGrid.DeprecatedColumn("Deprecated",
key="deprecated",
attach_popup=False),
# Columns that are valid for filtering but are not visible.
DeletedColumn("Deleted", key="deleted", attach_popup=False)
]
columns.append(
grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [operation for operation in RepositoryGrid.operations]
operations.append(
grids.GridOperation("Delete",
allow_multiple=False,
condition=(lambda item: not item.deleted),
async_compatible=False))
operations.append(
grids.GridOperation("Undelete",
allow_multiple=False,
condition=(lambda item: item.deleted),
async_compatible=False))
standard_filters = []
default_filter = {}
def build_initial_query(self, trans, **kwd):
return trans.sa_session.query(model.Repository) \
.join(model.User.table)
class HistoryDatasetsSelectionGrid(grids.Grid):
class DbKeyColumn(grids.GridColumn):
def filter(self, trans, user, query, dbkey):
""" Filter by dbkey through a raw SQL b/c metadata is a BLOB. """
dbkey_user, dbkey = decode_dbkey(dbkey)
dbkey = dbkey.replace("'", "\\'")
return query.filter(or_(text("metadata like '%%\"dbkey\": [\"%s\"]%%'" % dbkey,
"metadata like '%%\"dbkey\": \"%s\"%%'" % dbkey)))
class HistoryColumn(grids.GridColumn):
def get_value(self, trans, grid, hda):
return escape(hda.history.name)
def sort(self, trans, query, ascending, column_name=None):
"""Sort query using this column."""
return grids.GridColumn.sort(self, trans, query, ascending, column_name="history_id")
available_tracks = None
title = "Add Datasets"
model_class = model.HistoryDatasetAssociation
default_filter = {"deleted": "False", "shared": "All"}
default_sort_key = "-hid"
columns = [
grids.GridColumn("Id", key="hid"),
grids.TextColumn("Name", key="name", model_class=model.HistoryDatasetAssociation),
grids.TextColumn("Type", key="extension", model_class=model.HistoryDatasetAssociation),
grids.TextColumn("history_id", key="history_id", model_class=model.HistoryDatasetAssociation, visible=False),
HistoryColumn("History", key="history", visible=True),
DbKeyColumn("Build", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=True, sortable=False)
]
columns.append(
grids.MulticolFilterColumn("Search name and filetype", cols_to_filter=[columns[1], columns[2]],
key="free-text-search", visible=False, filterable="standard")
)
def build_initial_query(self, trans, **kwargs):
return trans.sa_session.query(self.model_class).join(model.History.table).join(model.Dataset.table)
def apply_query_filter(self, trans, query, **kwargs):
if self.available_tracks is None:
self.available_tracks = trans.app.datatypes_registry.get_available_tracks()
return query.filter(model.History.user == trans.user) \
.filter(model.HistoryDatasetAssociation.extension.in_(self.available_tracks)) \
.filter(model.Dataset.state == model.Dataset.states.OK) \
.filter(model.HistoryDatasetAssociation.deleted == false()) \
.filter(model.HistoryDatasetAssociation.visible == true())
class RepositoriesReadyForReviewGrid(RepositoriesWithoutReviewsGrid):
# Repositories that are ready for human review are those that either:
# 1) Have no tools
# 2) Have tools that have been proven to be functionally correct within Galaxy.
# This grid filters out repositories that have been marked as either deprecated or deleted.
title = "Repositories ready for review"
columns = [
RepositoriesWithoutReviewsGrid.NameColumn(
"Repository name",
key="name",
link=(lambda item: dict(operation="view_or_manage_repository",
id=item.id)),
attach_popup=True),
RepositoriesWithoutReviewsGrid.DescriptionColumn("Synopsis",
key="description",
attach_popup=False),
RepositoriesWithoutReviewsGrid.WithoutReviewsRevisionColumn(
"Revisions for review"),
RepositoriesWithoutReviewsGrid.UserColumn("Owner",
model_class=model.User,
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 = [
grids.GridOperation("Inspect repository revisions",
allow_multiple=False,
condition=(lambda item: not item.deleted),
async_compatible=False)
]
def build_initial_query(self, trans, **kwd):
return trans.sa_session.query( model.Repository ) \
.filter( and_( model.Repository.table.c.deleted == False,
model.Repository.table.c.deprecated == False,
model.Repository.reviews == None ) ) \
.join( model.RepositoryMetadata.table ) \
.filter( and_( model.RepositoryMetadata.table.c.downloadable == True,
or_( model.RepositoryMetadata.table.c.includes_tools == False,
and_( model.RepositoryMetadata.table.c.includes_tools == True,
model.RepositoryMetadata.table.c.tools_functionally_correct == True ) ) ) ) \
.join( model.User.table )
class VisualizationListGrid( grids.Grid ):
def get_url_args( item ):
"""
Returns dictionary used to create item link.
"""
controller = "visualization"
action = item.type
if item.type == "phyloviz":
controller = "phyloviz"
action = "visualization"
return dict( controller=controller, action=action, id=item.id )
# Grid definition
title = "Saved Visualizations"
model_class = model.Visualization
default_sort_key = "-update_time"
default_filter = dict( title="All", deleted="False", tags="All", sharing="All" )
columns = [
grids.TextColumn( "Title", key="title", attach_popup=True, link=get_url_args ),
grids.TextColumn( "Type", key="type" ),
grids.TextColumn( "Dbkey", key="dbkey" ),
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( "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( "Create new visualization", dict( action='create' ) )
]
operations = [
grids.GridOperation( "Open", allow_multiple=False, url_args=get_url_args ),
grids.GridOperation( "Open in Circster", allow_multiple=False, condition=( lambda item: item.type == 'trackster' ), url_args=dict( action='circster' ) ),
grids.GridOperation( "Edit Attributes", allow_multiple=False, url_args=dict( action='edit') ),
grids.GridOperation( "Copy", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False, url_args=dict( action='copy') ),
grids.GridOperation( "Share or Publish", allow_multiple=False, condition=( lambda item: not item.deleted ), async_compatible=False ),
grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), async_compatible=True, confirm="Are you sure you want to delete this visualization?" ),
]
def apply_query_filter( self, trans, query, **kwargs ):
return query.filter_by( user=trans.user, deleted=False )
class HistoryAllPublishedGrid(grids.Grid):
class NameURLColumn(grids.PublicURLColumn, NameColumn):
pass
title = "Published Histories"
model_class = model.History
default_sort_key = "update_time"
default_filter = dict(public_url="All", username="******", tags="All")
use_paging = True
num_rows_per_page = 50
columns = [
NameURLColumn("Name", key="name", filterable="advanced"),
grids.OwnerAnnotationColumn("Annotation", key="annotation", model_annotation_association_class=model.HistoryAnnotationAssociation, 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.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid"),
grids.ReverseSortColumn("Last Updated", key="update_time", format=time_ago)
]
columns.append(
grids.MulticolFilterColumn(
"Search name, 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):
# TODO: Tags are still loaded one at a time, consider doing this all at once:
# - eagerload would keep everything in one query but would explode the number of rows and potentially
# result in unneeded info transferred over the wire.
# - subqueryload("tags").subqueryload("tag") would probably be better under postgres but I'd
# like some performance data against a big database first - might cause problems?
# - Pull down only username from associated User table since that is all that is used
# (can be used during search). Need join in addition to the eagerload since it is used in
# the .count() query which doesn't respect the eagerload options (could eliminate this with #5523).
# - Undefer average_rating column to prevent loading individual ratings per-history.
# - Eager load annotations - this causes a left join which might be inefficient if there were
# potentially many items per history (like if joining HDAs for instance) but there should only
# be at most one so this is fine.
return trans.sa_session.query(self.model_class).join("user").options(eagerload("user").load_only("username"), eagerload("annotations"), undefer("average_rating"))
def apply_query_filter(self, trans, query, **kwargs):
# 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 != null()).filter(self.model_class.deleted == false())
class PageListGrid( grids.Grid ):
# Custom column.
class URLColumn( grids.PublicURLColumn ):
def get_value( self, trans, grid, item ):
return url_for(controller='page', 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 = "-update_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 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 HistoryDatasetsSelectionGrid( grids.Grid ):
# Grid definition.
available_tracks = None
title = "Add Datasets"
template = "tracks/history_datasets_select_grid.mako"
model_class = model.HistoryDatasetAssociation
default_filter = { "deleted" : "False" , "shared" : "All" }
default_sort_key = "-hid"
use_async = True
use_paging = False
columns = [
grids.GridColumn( "Id", key="hid" ),
grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation ),
grids.TextColumn( "Filetype", key="extension", model_class=model.HistoryDatasetAssociation ),
HistoryColumn( "History", key="history", visible=False ),
DbKeyColumn( "Dbkey", key="dbkey", model_class=model.HistoryDatasetAssociation, visible=True, sortable=False )
]
columns.append(
grids.MulticolFilterColumn( "Search name and filetype", cols_to_filter=[ columns[1], columns[2] ],
key="free-text-search", visible=False, filterable="standard" )
)
def get_current_item( self, trans, **kwargs ):
"""
Current item for grid is the history being queried. This is a bit
of hack since current_item typically means the current item in the grid.
"""
return model.History.get( trans.security.decode_id( kwargs[ 'f-history' ] ) )
def build_initial_query( self, trans, **kwargs ):
return trans.sa_session.query( self.model_class ).join( model.History.table ).join( model.Dataset.table )
def apply_query_filter( self, trans, query, **kwargs ):
if self.available_tracks is None:
self.available_tracks = trans.app.datatypes_registry.get_available_tracks()
return query.filter( model.HistoryDatasetAssociation.extension.in_(self.available_tracks) ) \
.filter( model.Dataset.state == model.Dataset.states.OK ) \
.filter( model.HistoryDatasetAssociation.deleted == False ) \
.filter( model.HistoryDatasetAssociation.visible == True )
class ReviewedRepositoriesIOwnGrid(RepositoriesWithReviewsGrid):
title = "Reviewed repositories I own"
columns = [
RepositoriesWithReviewsGrid.NameColumn(
"Repository name",
key="name",
link=(lambda item: dict(operation="view_or_manage_repository",
id=item.id)),
attach_popup=True),
RepositoriesWithReviewsGrid.WithReviewsRevisionColumn(
"Reviewed revisions"),
RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn(
"Revisions for review"),
RepositoriesWithReviewsGrid.ReviewersColumn("Reviewers",
attach_popup=False),
RepositoryGrid.DeprecatedColumn("Deprecated")
]
columns.append(
grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation("Inspect repository revisions",
allow_multiple=False,
condition=(lambda item: not item.deleted),
async_compatible=False)
]
def build_initial_query(self, trans, **kwd):
return trans.sa_session.query( model.Repository ) \
.join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \
.filter( model.Repository.table.c.user_id == trans.user.id ) \
.join( ( model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id ) ) \
.outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \
.outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) )
class DataTransferGrid(grids.Grid):
# Custom column types
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, sample_dataset):
return escape(sample_dataset.name)
class SizeColumn(grids.TextColumn):
def get_value(self, trans, grid, sample_dataset):
return sample_dataset.size
class StatusColumn(grids.TextColumn):
def get_value(self, trans, grid, sample_dataset):
return sample_dataset.status
class ExternalServiceColumn(grids.TextColumn):
def get_value(self, trans, grid, sample_dataset):
try:
return escape(sample_dataset.external_service.name)
except:
return 'None'
# Grid definition
title = "Sample Datasets"
template = "admin/requests/sample_datasets_grid.mako"
model_class = model.SampleDataset
default_sort_key = "-create_time"
num_rows_per_page = 50
preserve_state = True
use_paging = False
columns = [
NameColumn("Name",
link=(lambda item: dict(operation="view", id=item.id)),
attach_popup=True,
filterable="advanced"),
SizeColumn("Size", filterable="advanced"),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
ExternalServiceColumn(
'External service',
link=(lambda item: dict(operation="view_external_service",
id=item.external_service.id)),
),
StatusColumn("Transfer Status",
filterable="advanced",
label_id_prefix='datasetTransferStatus-'),
]
columns.append(
grids.MulticolFilterColumn("Search",
cols_to_filter=[columns[0]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation(
"Transfer",
allow_multiple=True,
condition=(lambda item: item.status in
[model.SampleDataset.transfer_status.NOT_STARTED])),
grids.GridOperation(
"Rename",
allow_multiple=True,
allow_popup=False,
condition=(lambda item: item.status in
[model.SampleDataset.transfer_status.NOT_STARTED])),
grids.GridOperation(
"Delete",
allow_multiple=True,
condition=(lambda item: item.status in
[model.SampleDataset.transfer_status.NOT_STARTED]))
]
def apply_query_filter(self, trans, query, **kwd):
sample_id = kwd.get('sample_id', None)
if not sample_id:
return query
return query.filter_by(sample_id=trans.security.decode_id(sample_id))
class InstalledRepositoryGrid(grids.Grid):
class ToolShedStatusColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
if tool_shed_repository.tool_shed_status:
tool_shed_status_str = ''
if tool_shed_repository.is_deprecated_in_tool_shed:
tool_shed_status_str += generate_deprecated_repository_img_str(
include_mouse_over=True)
if tool_shed_repository.is_latest_installable_revision:
tool_shed_status_str += generate_latest_revision_img_str(
include_mouse_over=True)
if tool_shed_repository.revision_update_available:
tool_shed_status_str += generate_revision_updates_img_str(
include_mouse_over=True)
if tool_shed_repository.upgrade_available:
tool_shed_status_str += generate_revision_upgrades_img_str(
include_mouse_over=True)
if tool_shed_repository.includes_workflows:
tool_shed_status_str += generate_includes_workflows_img_str(
include_mouse_over=True)
else:
tool_shed_status_str = generate_unknown_img_str(
include_mouse_over=True)
return tool_shed_status_str
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return str(tool_shed_repository.name)
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return util.unicodify(tool_shed_repository.description)
class OwnerColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return str(tool_shed_repository.owner)
class RevisionColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return str(tool_shed_repository.changeset_revision)
class StatusColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return suc.get_tool_shed_repository_status_label(
trans.app, tool_shed_repository)
class ToolShedColumn(grids.TextColumn):
def get_value(self, trans, grid, tool_shed_repository):
return tool_shed_repository.tool_shed
class DeletedColumn(grids.DeletedColumn):
def get_accepted_filters(self):
""" Returns a list of accepted filters for this column. """
accepted_filter_labels_and_vals = {
"Active": "False",
"Deactivated or uninstalled": "True",
"All": "All"
}
accepted_filters = []
for label, val in accepted_filter_labels_and_vals.items():
args = {self.key: val}
accepted_filters.append(grids.GridColumnFilter(label, args))
return accepted_filters
# Grid definition
title = "Installed tool shed repositories"
model_class = tool_shed_install.ToolShedRepository
template = '/admin/tool_shed_repository/grid.mako'
default_sort_key = "name"
columns = [
ToolShedStatusColumn(label=""),
NameColumn(
label="Name",
key="name",
link=(lambda item: iff(
item.status in [
tool_shed_install.ToolShedRepository.installation_status.
CLONING
], None, dict(operation="manage_repository", id=item.id))),
attach_popup=True),
DescriptionColumn(label="Description"),
OwnerColumn(label="Owner"),
RevisionColumn(label="Revision"),
StatusColumn(label="Installation Status", filterable="advanced"),
ToolShedColumn(label="Tool shed"),
# Columns that are valid for filtering but are not visible.
DeletedColumn(label="Status",
key="deleted",
visible=False,
filterable="advanced")
]
columns.append(
grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
global_actions = [
grids.GridAction(
label="Update tool shed status",
url_args=dict(
controller='admin_toolshed',
action='update_tool_shed_status_for_installed_repository',
all_installed_repositories=True),
inbound=False)
]
operations = [ grids.GridOperation( label="Update tool shed status",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='update tool shed status' ) ),
grids.GridOperation( label="Get updates",
condition=( lambda item: \
not item.deleted and \
item.revision_update_available and \
item.status not in \
[ tool_shed_install.ToolShedRepository.installation_status.ERROR,
tool_shed_install.ToolShedRepository.installation_status.NEW ] ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='get updates' ) ),
grids.GridOperation( label="Install latest revision",
condition=( lambda item: item.upgrade_available ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='install latest revision' ) ),
grids.GridOperation( label="Install",
condition=( lambda item: \
not item.deleted and \
item.status == tool_shed_install.ToolShedRepository.installation_status.NEW ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='manage_repository',
operation='install' ) ),
grids.GridOperation( label="Deactivate or uninstall",
condition=( lambda item: \
not item.deleted and \
item.status != tool_shed_install.ToolShedRepository.installation_status.NEW ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='deactivate or uninstall' ) ),
grids.GridOperation( label="Reset to install",
condition=( lambda item: \
( item.status == tool_shed_install.ToolShedRepository.installation_status.ERROR ) ),
allow_multiple=False,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='reset to install' ) ),
grids.GridOperation( label="Activate or reinstall",
condition=( lambda item: item.deleted ),
allow_multiple=False,
target=None,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='activate or reinstall' ) ),
grids.GridOperation( label="Purge",
condition=( lambda item: item.is_new ),
allow_multiple=False,
target=None,
url_args=dict( controller='admin_toolshed',
action='browse_repositories',
operation='purge' ) ) ]
standard_filters = []
default_filter = dict(deleted="False")
num_rows_per_page = 50
preserve_state = False
use_paging = False
def build_initial_query(self, trans, **kwd):
return trans.install_model.context.query( self.model_class ) \
.order_by( self.model_class.table.c.tool_shed,
self.model_class.table.c.name,
self.model_class.table.c.owner,
self.model_class.table.c.ctx_rev )
@property
def legend(self):
legend_str = '%s Updates are available in the Tool Shed for this revision<br/>' % generate_revision_updates_img_str(
)
legend_str += '%s A newer installable revision is available for this repository<br/>' % generate_revision_upgrades_img_str(
)
legend_str += '%s This is the latest installable revision of this repository<br/>' % generate_latest_revision_img_str(
)
legend_str += '%s This repository is deprecated in the Tool Shed<br/>' % generate_deprecated_repository_img_str(
)
legend_str += '%s This repository contains exported workflows<br/>' % generate_includes_workflows_img_str(
)
legend_str += '%s Unable to get information from the Tool Shed<br/>' % generate_unknown_img_str(
)
return legend_str
class QuotaListGrid( grids.Grid ):
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, quota ):
return escape(quota.name)
class DescriptionColumn( grids.TextColumn ):
def get_value( self, trans, grid, quota ):
if quota.description:
return escape(quota.description)
return ''
class AmountColumn( grids.TextColumn ):
def get_value( self, trans, grid, quota ):
return quota.operation + quota.display_amount
class StatusColumn( grids.GridColumn ):
def get_value( self, trans, grid, quota ):
if quota.deleted:
return "deleted"
elif quota.default:
return "<strong>default for %s users</strong>" % quota.default[0].type
return ""
class UsersColumn( grids.GridColumn ):
def get_value( self, trans, grid, quota ):
if quota.users:
return len( quota.users )
return 0
class GroupsColumn( grids.GridColumn ):
def get_value( self, trans, grid, quota ):
if quota.groups:
return len( quota.groups )
return 0
# Grid definition
title = "Quotas"
model_class = model.Quota
template = '/admin/quota/grid.mako'
default_sort_key = "name"
columns = [
NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="Change amount", id=item.id, webapp="galaxy" ) ),
model_class=model.Quota,
attach_popup=True,
filterable="advanced" ),
DescriptionColumn( "Description",
key='description',
model_class=model.Quota,
attach_popup=False,
filterable="advanced" ),
AmountColumn( "Amount",
key='amount',
model_class=model.Quota,
attach_popup=False,
filterable="advanced" ),
UsersColumn( "Users", attach_popup=False ),
GroupsColumn( "Groups", attach_popup=False ),
StatusColumn( "Status", attach_popup=False ),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" )
]
columns.append( grids.MulticolFilterColumn( "Search",
cols_to_filter=[ columns[0], columns[1], columns[2] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
global_actions = [
grids.GridAction( "Add new quota", dict( controller='admin', action='quotas', operation='create' ) )
]
operations = [ grids.GridOperation( "Rename",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="rename_quota" ) ),
grids.GridOperation( "Change amount",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="edit_quota" ) ),
grids.GridOperation( "Manage users and groups",
condition=( lambda item: not item.default and not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="manage_users_and_groups_for_quota" ) ),
grids.GridOperation( "Set as different type of default",
condition=( lambda item: item.default ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="set_quota_default" ) ),
grids.GridOperation( "Set as default",
condition=( lambda item: not item.default and not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="set_quota_default" ) ),
grids.GridOperation( "Unset as default",
condition=( lambda item: item.default and not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="unset_quota_default" ) ),
grids.GridOperation( "Delete",
condition=( lambda item: not item.deleted and not item.default ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="mark_quota_deleted" ) ),
grids.GridOperation( "Undelete",
condition=( lambda item: item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="undelete_quota" ) ),
grids.GridOperation( "Purge",
condition=( lambda item: item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="purge_quota" ) ) ]
standard_filters = [
grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ),
grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
]
num_rows_per_page = 50
preserve_state = False
use_paging = True
class UserListGrid( grids.Grid ):
class EmailColumn( grids.TextColumn ):
def get_value( self, trans, grid, user ):
return escape(user.email)
class UserNameColumn( grids.TextColumn ):
def get_value( self, trans, grid, user ):
if user.username:
return escape(user.username)
return 'not set'
class StatusColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
if user.purged:
return "purged"
elif user.deleted:
return "deleted"
return ""
class GroupsColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
if user.groups:
return len( user.groups )
return 0
class RolesColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
if user.roles:
return len( user.roles )
return 0
class ExternalColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
if user.external:
return 'yes'
return 'no'
class LastLoginColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
if user.galaxy_sessions:
return self.format( user.galaxy_sessions[ 0 ].update_time )
return 'never'
class TimeCreatedColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
return user.create_time.strftime('%x')
class ActivatedColumn( grids.GridColumn ):
def get_value( self, trans, grid, user ):
if user.active:
return 'Y'
else:
return 'N'
# Grid definition
title = "Users"
model_class = model.User
template = '/admin/user/grid.mako'
default_sort_key = "email"
columns = [
EmailColumn( "Email",
key="email",
model_class=model.User,
link=( lambda item: dict( operation="information", id=item.id, webapp="galaxy" ) ),
attach_popup=True,
filterable="advanced",
target="top" ),
UserNameColumn( "User Name",
key="username",
model_class=model.User,
attach_popup=False,
filterable="advanced" ),
GroupsColumn( "Groups", attach_popup=False ),
RolesColumn( "Roles", attach_popup=False ),
ExternalColumn( "External", attach_popup=False ),
LastLoginColumn( "Last Login", format=time_ago ),
StatusColumn( "Status", attach_popup=False ),
TimeCreatedColumn( "Created", attach_popup=False ),
ActivatedColumn( "Activated", attach_popup=False ),
# Columns that are valid for filtering but are not visible.
grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" )
]
columns.append( grids.MulticolFilterColumn( "Search",
cols_to_filter=[ columns[0], columns[1] ],
key="free-text-search",
visible=False,
filterable="standard" ) )
global_actions = [
grids.GridAction( "Create new user", dict( controller='admin', action='users', operation='create', webapp="galaxy" ) )
]
operations = [
grids.GridOperation( "Manage Roles and Groups",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="manage_roles_and_groups_for_user" ) ),
grids.GridOperation( "Reset Password",
condition=( lambda item: not item.deleted ),
allow_multiple=True,
allow_popup=False,
url_args=dict( webapp="galaxy", action="reset_user_password" ) ),
grids.GridOperation( "Recalculate Disk Usage",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="recalculate_user_disk_usage" ) )
]
standard_filters = [
grids.GridColumnFilter( "Active", args=dict( deleted=False ) ),
grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ),
grids.GridColumnFilter( "Purged", args=dict( purged=True ) ),
grids.GridColumnFilter( "All", args=dict( deleted='All' ) )
]
num_rows_per_page = 50
preserve_state = False
use_paging = True
def get_current_item( self, trans, **kwargs ):
return trans.user
