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 UserRequestsGrid( RequestsGrid ):
operations = [ operation for operation in RequestsGrid.operations ]
operations.append( grids.GridOperation( "Edit", allow_multiple=False, condition=( lambda item: item.is_unsubmitted and not item.deleted ) ) )
operations.append( grids.GridOperation( "Delete", allow_multiple=True, condition=( lambda item: item.is_new and not item.deleted ) ) )
operations.append( grids.GridOperation( "Undelete", allow_multiple=True, condition=( lambda item: item.deleted ) ) )
def apply_query_filter( self, trans, query, **kwd ):
return query.filter_by( user=trans.user )
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 AdminRequestsGrid(RequestsGrid):
class UserColumn(grids.TextColumn):
def get_value(self, trans, grid, request):
return escape(request.user.email)
# Grid definition
columns = [col for col in RequestsGrid.columns]
columns.append(UserColumn("User", model_class=model.User, key='username'))
operations = [operation for operation in RequestsGrid.operations]
operations.append(
grids.GridOperation("Edit",
allow_multiple=False,
condition=(lambda item: not item.deleted)))
operations.append(
grids.GridOperation(
"Reject",
allow_multiple=False,
condition=(lambda item: not item.deleted and item.is_submitted)))
operations.append(
grids.GridOperation("Delete",
allow_multiple=True,
condition=(lambda item: not item.deleted)))
operations.append(
grids.GridOperation("Undelete", condition=(lambda item: item.deleted)))
global_actions = [
grids.GridAction(
"Create new request",
dict(controller='requests_common',
action='create_request',
cntrller='requests_admin'))
]
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 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['__route_name__'] = 'saved_visualization'
url_kwargs['visualization_name'] = item.type
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("Build", 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")
)
operations = [
grids.GridOperation("Open", allow_multiple=False, url_args=get_url_args),
grids.GridOperation("Edit Attributes", allow_multiple=False, url_args=dict(controller="", action='visualizations/edit')),
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), url_args=dict(action='sharing')),
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 AdminRepositoryListGrid(RepositoryListGrid):
operations = [operation for operation in RepositoryListGrid.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 = []
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 UserOpenIDGrid(grids.Grid):
use_panels = False
title = "OpenIDs linked to your account"
model_class = model.UserOpenID
template = '/user/openid_manage.mako'
default_filter = {"openid": "All"}
default_sort_key = "-create_time"
columns = [
grids.TextColumn("OpenID URL",
key="openid",
link=(lambda x: dict(action='openid_auth',
login_button="Login",
openid_url=x.openid
if not x.provider else '',
openid_provider=x.provider,
auto_associate=True))),
grids.GridColumn("Created", key="create_time", format=time_ago),
]
operations = [
grids.GridOperation("Delete", async_compatible=True),
]
def build_initial_query(self, trans, **kwd):
return trans.sa_session.query(
self.model_class).filter(self.model_class.user_id == trans.user.id)
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 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 PageListGrid( grids.Grid ):
# Grid definition
use_panels = True
title = "Pages"
model_class = model.Page
default_filter = { "published" : "All"}
default_sort_key = "-create_time"
columns = [
grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="standard" ),
PublicURLColumn( "Public URL" ),
grids.GridColumn( "Published", key="published", format=format_bool, filterable="standard" ),
grids.GridColumn( "Created", key="create_time", format=time_ago ),
grids.GridColumn( "Last Updated", key="update_time", format=time_ago ),
]
global_actions = [
grids.GridAction( "Add new page", dict( action='create' ) )
]
operations = [
grids.GridOperation( "View", allow_multiple=False, url_args=dict( action='display') ),
grids.GridOperation( "Edit name/id", allow_multiple=False, url_args=dict( action='edit') ),
grids.GridOperation( "Edit content", allow_multiple=False, url_args=dict( action='edit_content') ),
grids.GridOperation( "Delete" ),
grids.GridOperation( "Publish", condition=( lambda item: not item.published ) ),
grids.GridOperation( "Unpublish", condition=( lambda item: item.published ) ),
]
def apply_default_filter( self, trans, query, **kwargs ):
return query.filter_by( user=trans.user, 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 SharedHistoryListGrid(grids.Grid):
# Custom column types
class DatasetsByStateColumn(grids.GridColumn):
def get_value(self, trans, grid, history):
rval = ''
for state in ('ok', 'running', 'queued', 'error'):
total = sum(1 for d in history.active_datasets if d.state == state)
if total:
rval += f'<div class="count-box state-color-{state}">{total}</div>'
return rval
class SharedByColumn(grids.GridColumn):
def get_value(self, trans, grid, history):
return escape(history.user.email)
# Grid definition
title = "Histories shared with you by others"
model_class = model.History
default_sort_key = "-update_time"
columns = [
grids.GridColumn("Name", key="name", attach_popup=True),
DatasetsByStateColumn("Datasets", sortable=False),
grids.GridColumn("Created", key="create_time", format=time_ago),
grids.GridColumn("Last Updated", key="update_time", format=time_ago),
SharedByColumn("Shared by", key="user_id")
]
operations = [
grids.GridOperation("View", allow_multiple=False, url_args=dict(controller="", action="histories/view")),
grids.GridOperation("Copy", allow_multiple=False),
grids.GridOperation("Unshare", allow_multiple=False)
]
def build_initial_query(self, trans, **kwargs):
return trans.sa_session.query(self.model_class).join('users_shared_with')
def apply_query_filter(self, trans, query, **kwargs):
return query.filter(model.HistoryUserShareAssociation.user == trans.user)
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 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 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
def browse_libraries(self, trans, **kwd):
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "browse":
return trans.response.send_redirect(
web.url_for(controller='library_common',
action='browse_library',
cntrller='library_admin',
**kwd))
elif operation == "delete":
return self.delete_library(trans, **kwd)
elif operation == "undelete":
return self.undelete_library(trans, **kwd)
self.library_list_grid.operations = []
if 'f-deleted' in kwd:
if kwd['f-deleted'] != 'All':
if galaxy.util.string_as_bool(kwd['f-deleted']):
# We're viewing deleted data libraries, so add a GridOperation
# enabling one or more of them to be undeleted.
self.library_list_grid.operations = [
grids.GridOperation(
"Undelete",
condition=(lambda item: item.deleted),
allow_multiple=True,
allow_popup=False,
url_args=dict(webapp="galaxy"))
]
else:
# We're viewing active data libraries, so add a GridOperation
# enabling one or more of them to be deleted.
self.library_list_grid.operations = [
grids.GridOperation(
"Delete",
condition=(lambda item: not item.deleted),
allow_multiple=True,
allow_popup=False,
url_args=dict(webapp="galaxy"))
]
else:
# We're viewing active data libraries, so add a GridOperation
# enabling one or more of them to be deleted.
self.library_list_grid.operations = [
grids.GridOperation("Delete",
condition=(lambda item: not item.deleted),
allow_multiple=True,
allow_popup=False,
url_args=dict(webapp="galaxy"))
]
if 'f-free-text-search' in kwd:
search_term = kwd["f-free-text-search"]
if trans.app.config.enable_lucene_library_search:
indexed_search_enabled = True
search_url = trans.app.config.config_dict.get(
"fulltext_find_url", "")
if search_url:
status, message, lddas = lucene_search(
trans, 'library_admin', search_term, search_url, **kwd)
elif trans.app.config.enable_whoosh_library_search:
indexed_search_enabled = True
status, message, lddas = whoosh_search(trans, 'library_admin',
search_term, **kwd)
else:
indexed_search_enabled = False
if indexed_search_enabled:
comptypes = get_comptypes(trans)
show_deleted = galaxy.util.string_as_bool(
kwd.get('show_deleted', False))
use_panels = galaxy.util.string_as_bool(
kwd.get('use_panels', False))
return trans.fill_template(
'/library/common/library_dataset_search_results.mako',
cntrller='library_admin',
search_term=search_term,
comptypes=comptypes,
lddas=lddas,
show_deleted=show_deleted,
use_panels=use_panels,
message=escape(message),
status=escape(status))
# Render the list view
return self.library_list_grid(trans, **kwd)
class AdminGalaxy( BaseUIController, Admin, AdminActions, UsesQuotaMixin, QuotaParamParser ):
user_list_grid = UserListGrid()
role_list_grid = RoleListGrid()
group_list_grid = GroupListGrid()
quota_list_grid = QuotaListGrid()
tool_version_list_grid = ToolVersionListGrid()
delete_operation = grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ), allow_multiple=True )
undelete_operation = grids.GridOperation( "Undelete", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True )
purge_operation = grids.GridOperation( "Purge", condition=( lambda item: item.deleted and not item.purged ), allow_multiple=True )
@web.expose
@web.require_admin
def quotas( self, trans, **kwargs ):
if 'operation' in kwargs:
operation = kwargs.pop('operation').lower()
if operation == "quotas":
return self.quota( trans, **kwargs )
if operation == "create":
return self.create_quota( trans, **kwargs )
if operation == "delete":
return self.mark_quota_deleted( trans, **kwargs )
if operation == "undelete":
return self.undelete_quota( trans, **kwargs )
if operation == "purge":
return self.purge_quota( trans, **kwargs )
if operation == "change amount":
return self.edit_quota( trans, **kwargs )
if operation == "manage users and groups":
return self.manage_users_and_groups_for_quota( trans, **kwargs )
if operation == "rename":
return self.rename_quota( trans, **kwargs )
if operation == "edit":
return self.edit_quota( trans, **kwargs )
# Render the list view
return self.quota_list_grid( trans, **kwargs )
@web.expose
@web.require_admin
def create_quota( self, trans, **kwd ):
params = self.get_quota_params( kwd )
if params.get( 'create_quota_button', False ):
try:
quota, message = self._create_quota( params )
return trans.response.send_redirect( web.url_for( controller='admin',
action='quotas',
webapp=params.webapp,
message=sanitize_text( message ),
status='done' ) )
except MessageException as e:
params.message = str( e )
params.status = 'error'
in_users = map( int, params.in_users )
in_groups = map( int, params.in_groups )
new_in_users = []
new_in_groups = []
for user in trans.sa_session.query( trans.app.model.User ) \
.filter( trans.app.model.User.table.c.deleted == expression.false() ) \
.order_by( trans.app.model.User.table.c.email ):
if user.id in in_users:
new_in_users.append( ( user.id, user.email ) )
else:
params.out_users.append( ( user.id, user.email ) )
for group in trans.sa_session.query( trans.app.model.Group ) \
.filter( trans.app.model.Group.table.c.deleted == expression.false() ) \
.order_by( trans.app.model.Group.table.c.name ):
if group.id in in_groups:
new_in_groups.append( ( group.id, group.name ) )
else:
params.out_groups.append( ( group.id, group.name ) )
return trans.fill_template( '/admin/quota/quota_create.mako',
webapp=params.webapp,
name=params.name,
description=params.description,
amount=params.amount,
operation=params.operation,
default=params.default,
in_users=new_in_users,
out_users=params.out_users,
in_groups=new_in_groups,
out_groups=params.out_groups,
message=params.message,
status=params.status )
@web.expose
@web.require_admin
def rename_quota( self, trans, **kwd ):
quota, params = self._quota_op( trans, 'rename_quota_button', self._rename_quota, kwd )
if not quota:
return
return trans.fill_template( '/admin/quota/quota_rename.mako',
id=params.id,
name=params.name or quota.name,
description=params.description or quota.description,
webapp=params.webapp,
message=params.message,
status=params.status )
@web.expose
@web.require_admin
def manage_users_and_groups_for_quota( self, trans, **kwd ):
quota, params = self._quota_op( trans, 'quota_members_edit_button', self._manage_users_and_groups_for_quota, kwd )
if not quota:
return
in_users = []
out_users = []
in_groups = []
out_groups = []
for user in trans.sa_session.query( trans.app.model.User ) \
.filter( trans.app.model.User.table.c.deleted == expression.false() ) \
.order_by( trans.app.model.User.table.c.email ):
if user in [ x.user for x in quota.users ]:
in_users.append( ( user.id, user.email ) )
else:
out_users.append( ( user.id, user.email ) )
for group in trans.sa_session.query( trans.app.model.Group ) \
.filter( trans.app.model.Group.table.c.deleted == expression.false()) \
.order_by( trans.app.model.Group.table.c.name ):
if group in [ x.group for x in quota.groups ]:
in_groups.append( ( group.id, group.name ) )
else:
out_groups.append( ( group.id, group.name ) )
return trans.fill_template( '/admin/quota/quota.mako',
id=params.id,
name=quota.name,
in_users=in_users,
out_users=out_users,
in_groups=in_groups,
out_groups=out_groups,
webapp=params.webapp,
message=params.message,
status=params.status )
@web.expose
@web.require_admin
def edit_quota( self, trans, **kwd ):
quota, params = self._quota_op( trans, 'edit_quota_button', self._edit_quota, kwd )
if not quota:
return
return trans.fill_template( '/admin/quota/quota_edit.mako',
id=params.id,
operation=params.operation or quota.operation,
display_amount=params.amount or quota.display_amount,
webapp=params.webapp,
message=params.message,
status=params.status )
@web.expose
@web.require_admin
def set_quota_default( self, trans, **kwd ):
quota, params = self._quota_op( trans, 'set_default_quota_button', self._set_quota_default, kwd )
if not quota:
return
if params.default:
default = params.default
elif quota.default:
default = quota.default[0].type
else:
default = "no"
return trans.fill_template( '/admin/quota/quota_set_default.mako',
id=params.id,
default=default,
webapp=params.webapp,
message=params.message,
status=params.status )
@web.expose
@web.require_admin
def unset_quota_default( self, trans, **kwd ):
quota, params = self._quota_op( trans, True, self._unset_quota_default, kwd )
if not quota:
return
return trans.response.send_redirect( web.url_for( controller='admin',
action='quotas',
webapp=params.webapp,
message=sanitize_text( params.message ),
status='error' ) )
@web.expose
@web.require_admin
def mark_quota_deleted( self, trans, **kwd ):
quota, params = self._quota_op( trans, True, self._mark_quota_deleted, kwd, listify=True )
if not quota:
return
return trans.response.send_redirect( web.url_for( controller='admin',
action='quotas',
webapp=params.webapp,
message=sanitize_text( params.message ),
status='error' ) )
@web.expose
@web.require_admin
def undelete_quota( self, trans, **kwd ):
quota, params = self._quota_op( trans, True, self._undelete_quota, kwd, listify=True )
if not quota:
return
return trans.response.send_redirect( web.url_for( controller='admin',
action='quotas',
webapp=params.webapp,
message=sanitize_text( params.message ),
status='error' ) )
@web.expose
@web.require_admin
def purge_quota( self, trans, **kwd ):
quota, params = self._quota_op( trans, True, self._purge_quota, kwd, listify=True )
if not quota:
return
return trans.response.send_redirect( web.url_for( controller='admin',
action='quotas',
webapp=params.webapp,
message=sanitize_text( params.message ),
status='error' ) )
def _quota_op( self, trans, do_op, op_method, kwd, listify=False ):
params = self.get_quota_params( kwd )
if listify:
quota = []
messages = []
for id in galaxy.util.listify( params.id ):
try:
quota.append( self.get_quota( trans, id ) )
except MessageException as e:
messages.append( str( e ) )
if messages:
return None, trans.response.send_redirect( web.url_for( controller='admin',
action='quotas',
webapp=params.webapp,
message=sanitize_text( ', '.join( messages ) ),
status='error' ) )
else:
try:
quota = self.get_quota( trans, params.id, deleted=False )
except MessageException as e:
return None, trans.response.send_redirect( web.url_for( controller='admin',
action='quotas',
webapp=params.webapp,
message=sanitize_text( str( e ) ),
status='error' ) )
if do_op is True or ( do_op is not False and params.get( do_op, False ) ):
try:
message = op_method( quota, params )
return None, trans.response.send_redirect( web.url_for( controller='admin',
action='quotas',
webapp=params.webapp,
message=sanitize_text( message ),
status='done' ) )
except MessageException as e:
params.message = e.err_msg
params.status = e.type
return quota, params
@web.expose
@web.require_admin
def impersonate( self, trans, email=None, **kwd ):
if not trans.app.config.allow_user_impersonation:
return trans.show_error_message( "User impersonation is not enabled in this instance of Galaxy." )
message = ''
status = 'done'
emails = None
if email is not None:
user = trans.sa_session.query( trans.app.model.User ).filter_by( email=email ).first()
if user:
trans.handle_user_logout()
trans.handle_user_login(user)
message = 'You are now logged in as %s, <a target="_top" href="%s">return to the home page</a>' % ( email, url_for( controller='root' ) )
emails = []
else:
message = 'Invalid user selected'
status = 'error'
if emails is None:
emails = [ u.email for u in trans.sa_session.query( trans.app.model.User ).enable_eagerloads( False ).all() ]
return trans.fill_template( 'admin/impersonate.mako', emails=emails, message=message, status=status )
def check_for_tool_dependencies( self, trans, migration_stage ):
# Get the 000x_tools.xml file associated with migration_stage.
tools_xml_file_path = os.path.abspath( os.path.join( trans.app.config.root, 'scripts', 'migrate_tools', '%04d_tools.xml' % migration_stage ) )
tree = galaxy.util.parse_xml( tools_xml_file_path )
root = tree.getroot()
tool_shed = root.get( 'name' )
shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed )
repo_name_dependency_tups = []
if shed_url:
for elem in root:
if elem.tag == 'repository':
tool_dependencies = []
tool_dependencies_dict = {}
repository_name = elem.get( 'name' )
changeset_revision = elem.get( 'changeset_revision' )
params = dict( name=repository_name, owner='devteam', changeset_revision=changeset_revision )
pathspec = [ 'repository', 'get_tool_dependencies' ]
text = url_get( shed_url, password_mgr=self.app.tool_shed_registry.url_auth( shed_url ), pathspec=pathspec, params=params )
if text:
tool_dependencies_dict = encoding_util.tool_shed_decode( text )
for dependency_key, requirements_dict in tool_dependencies_dict.items():
tool_dependency_name = requirements_dict[ 'name' ]
tool_dependency_version = requirements_dict[ 'version' ]
tool_dependency_type = requirements_dict[ 'type' ]
tool_dependency_readme = requirements_dict.get( 'readme', '' )
tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) )
repo_name_dependency_tups.append( ( repository_name, tool_dependencies ) )
return repo_name_dependency_tups
@web.expose
@web.require_admin
def review_tool_migration_stages( self, trans, **kwd ):
message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) )
status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
migration_stages_dict = odict()
migration_modules = []
migration_scripts_dir = os.path.abspath( os.path.join( trans.app.config.root, 'lib', 'tool_shed', 'galaxy_install', 'migrate', 'versions' ) )
migration_scripts_dir_contents = os.listdir( migration_scripts_dir )
for item in migration_scripts_dir_contents:
if os.path.isfile( os.path.join( migration_scripts_dir, item ) ) and item.endswith( '.py' ):
module = item.replace( '.py', '' )
migration_modules.append( module )
if migration_modules:
migration_modules.sort()
# Remove the 0001_tools.py script since it is the seed.
migration_modules = migration_modules[ 1: ]
# Reverse the list so viewing will be newest to oldest.
migration_modules.reverse()
for migration_module in migration_modules:
migration_stage = int( migration_module.replace( '_tools', '' ) )
repo_name_dependency_tups = self.check_for_tool_dependencies( trans, migration_stage )
open_file_obj, file_name, description = imp.find_module( migration_module, [ migration_scripts_dir ] )
imported_module = imp.load_module( 'upgrade', open_file_obj, file_name, description )
migration_info = imported_module.__doc__
open_file_obj.close()
migration_stages_dict[ migration_stage ] = ( migration_info, repo_name_dependency_tups )
return trans.fill_template( 'admin/review_tool_migration_stages.mako',
migration_stages_dict=migration_stages_dict,
message=message,
status=status )
@web.expose
@web.require_admin
def tool_errors( self, trans, **kwd ):
return trans.fill_template('admin/tool_errors.mako', tool_errors=global_tool_errors.error_stack)
@web.expose
@web.require_admin
def view_datatypes_registry( self, trans, **kwd ):
message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) )
status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
return trans.fill_template( 'admin/view_datatypes_registry.mako', message=message, status=status )
@web.expose
@web.require_admin
def view_tool_data_tables( self, trans, **kwd ):
message = escape( galaxy.util.restore_text( kwd.get( 'message', '' ) ) )
status = galaxy.util.restore_text( kwd.get( 'status', 'done' ) )
return trans.fill_template( 'admin/view_data_tables_registry.mako', message=message, status=status )
@web.expose
@web.require_admin
def display_applications( self, trans, **kwd ):
return trans.fill_template( 'admin/view_display_applications.mako', display_applications=trans.app.datatypes_registry.display_applications )
@web.expose
@web.require_admin
def reload_display_application( self, trans, **kwd ):
galaxy.queue_worker.send_control_task(trans.app,
'reload_display_application',
noop_self=True,
kwargs={'display_application_ids': kwd.get( 'id' )} )
reloaded, failed = trans.app.datatypes_registry.reload_display_applications( kwd.get( 'id' ) )
if not reloaded and failed:
return trans.show_error_message( 'Unable to reload any of the %i requested display applications ("%s").'
% ( len( failed ), '", "'.join( failed ) ) )
if failed:
return trans.show_warn_message( 'Reloaded %i display applications ("%s"), but failed to reload %i display applications ("%s").'
% ( len( reloaded ), '", "'.join( reloaded ), len( failed ), '", "'.join( failed ) ) )
if not reloaded:
return trans.show_warn_message( 'You need to request at least one display application to reload.' )
return trans.show_ok_message( 'Reloaded %i requested display applications ("%s").' % ( len( reloaded ), '", "'.join( reloaded ) ) )
@web.expose
@web.require_admin
def recalculate_user_disk_usage( self, trans, **kwd ):
user_id = kwd.get( 'id', None )
user = trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( user_id ) )
if not user:
return trans.show_error_message( "User not found for id (%s)" % sanitize_text( str( user_id ) ) )
current = user.get_disk_usage()
user.calculate_and_set_disk_usage()
new = user.get_disk_usage()
if new in ( current, None ):
message = 'Usage is unchanged at %s.' % nice_size( current )
else:
message = 'Usage has changed by %s to %s.' % ( nice_size( new - current ), nice_size( new ) )
return trans.response.send_redirect( web.url_for( controller='admin',
action='users',
message=sanitize_text( message ),
status='info' ) )
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
class GroupListGrid( grids.Grid ):
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, group ):
return escape(group.name)
class StatusColumn( grids.GridColumn ):
def get_value( self, trans, grid, group ):
if group.deleted:
return "deleted"
return ""
class RolesColumn( grids.GridColumn ):
def get_value( self, trans, grid, group ):
if group.roles:
return len( group.roles )
return 0
class UsersColumn( grids.GridColumn ):
def get_value( self, trans, grid, group ):
if group.members:
return len( group.members )
return 0
# Grid definition
title = "Groups"
model_class = model.Group
template = '/admin/dataset_security/group/grid.mako'
default_sort_key = "name"
columns = [
NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="Manage users and roles", id=item.id, webapp="galaxy" ) ),
model_class=model.Group,
attach_popup=True,
filterable="advanced" ),
UsersColumn( "Users", attach_popup=False ),
RolesColumn( "Roles", 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 group", dict( controller='admin', action='groups', operation='create', webapp="galaxy" ) )
]
operations = [ grids.GridOperation( "Rename",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="rename_group" ) ),
grids.GridOperation( "Delete",
condition=( lambda item: not item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="mark_group_deleted" ) ),
grids.GridOperation( "Undelete",
condition=( lambda item: item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="undelete_group" ) ),
grids.GridOperation( "Purge",
condition=( lambda item: item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="purge_group" ) ) ]
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 RoleListGrid( grids.Grid ):
class NameColumn( grids.TextColumn ):
def get_value( self, trans, grid, role ):
return escape(role.name)
class DescriptionColumn( grids.TextColumn ):
def get_value( self, trans, grid, role ):
if role.description:
return escape(role.description)
return ''
class TypeColumn( grids.TextColumn ):
def get_value( self, trans, grid, role ):
return role.type
class StatusColumn( grids.GridColumn ):
def get_value( self, trans, grid, role ):
if role.deleted:
return "deleted"
return ""
class GroupsColumn( grids.GridColumn ):
def get_value( self, trans, grid, role ):
if role.groups:
return len( role.groups )
return 0
class UsersColumn( grids.GridColumn ):
def get_value( self, trans, grid, role ):
if role.users:
return len( role.users )
return 0
# Grid definition
title = "Roles"
model_class = model.Role
template = '/admin/dataset_security/role/grid.mako'
default_sort_key = "name"
columns = [
NameColumn( "Name",
key="name",
link=( lambda item: dict( operation="Manage users and groups", id=item.id, webapp="galaxy" ) ),
model_class=model.Role,
attach_popup=True,
filterable="advanced" ),
DescriptionColumn( "Description",
key='description',
model_class=model.Role,
attach_popup=False,
filterable="advanced" ),
TypeColumn( "Type",
key='type',
model_class=model.Role,
attach_popup=False,
filterable="advanced" ),
GroupsColumn( "Groups", attach_popup=False ),
UsersColumn( "Users", 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 role", dict( controller='admin', action='roles', operation='create' ) )
]
operations = [ grids.GridOperation( "Edit",
condition=( lambda item: not item.deleted ),
allow_multiple=False,
url_args=dict( webapp="galaxy", action="rename_role" ) ),
grids.GridOperation( "Delete",
condition=( lambda item: not item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="mark_role_deleted" ) ),
grids.GridOperation( "Undelete",
condition=( lambda item: item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="undelete_role" ) ),
grids.GridOperation( "Purge",
condition=( lambda item: item.deleted ),
allow_multiple=True,
url_args=dict( webapp="galaxy", action="purge_role" ) ) ]
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
def apply_query_filter( self, trans, query, **kwargs ):
return query.filter( model.Role.type != model.Role.types.PRIVATE )
class AdminController(BaseUIController, Admin):
user_list_grid = admin_grids.UserGrid()
role_list_grid = admin_grids.RoleGrid()
group_list_grid = admin_grids.GroupGrid()
manage_category_grid = admin_grids.ManageCategoryGrid()
repository_grid = admin_grids.AdminRepositoryGrid()
repository_metadata_grid = admin_grids.RepositoryMetadataGrid()
delete_operation = grids.GridOperation(
"Delete",
condition=(lambda item: not item.deleted),
allow_multiple=True)
undelete_operation = grids.GridOperation(
"Undelete",
condition=(lambda item: item.deleted and not item.purged),
allow_multiple=True)
purge_operation = grids.GridOperation(
"Purge",
condition=(lambda item: item.deleted and not item.purged),
allow_multiple=True)
@web.expose
@web.require_admin
def browse_repositories(self, trans, **kwd):
# We add parameters to the keyword dict in this method in order to rename the param
# with an "f-" prefix, simulating filtering by clicking a search link. We have
# to take this approach because the "-" character is illegal in HTTP requests.
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "view_or_manage_repository":
return trans.response.send_redirect(
web.url_for(controller='repository',
action='browse_repositories',
**kwd))
elif operation == "edit_repository":
return trans.response.send_redirect(
web.url_for(controller='repository',
action='edit_repository',
**kwd))
elif operation == "repositories_by_user":
# Eliminate the current filters if any exist.
for k, v in list(kwd.items()):
if k.startswith('f-'):
del kwd[k]
if 'user_id' in kwd:
user = suc.get_user(trans.app, kwd['user_id'])
kwd['f-email'] = user.email
del kwd['user_id']
else:
# The received id is the repository id, so we need to get the id of the user
# that uploaded the repository.
repository_id = kwd.get('id', None)
repository = repository_util.get_repository_in_tool_shed(
trans.app, repository_id)
kwd['f-email'] = repository.user.email
elif operation == "repositories_by_category":
# Eliminate the current filters if any exist.
for k, v in list(kwd.items()):
if k.startswith('f-'):
del kwd[k]
category_id = kwd.get('id', None)
category = suc.get_category(trans.app, category_id)
kwd['f-Category.name'] = category.name
elif operation == "receive email alerts":
if kwd['id']:
kwd['caller'] = 'browse_repositories'
return trans.response.send_redirect(
web.url_for(controller='repository',
action='set_email_alerts',
**kwd))
else:
del kwd['operation']
elif operation == 'delete':
return self.delete_repository(trans, **kwd)
elif operation == "undelete":
return self.undelete_repository(trans, **kwd)
# The changeset_revision_select_field in the RepositoryGrid performs a refresh_on_change
# which sends in request parameters like changeset_revison_1, changeset_revision_2, etc. One
# of the many select fields on the grid performed the refresh_on_change, so we loop through
# all of the received values to see which value is not the repository tip. If we find it, we
# know the refresh_on_change occurred, and we have the necessary repository id and change set
# revision to pass on.
for k, v in kwd.items():
changeset_revision_str = 'changeset_revision_'
if k.startswith(changeset_revision_str):
repository_id = trans.security.encode_id(
int(k.lstrip(changeset_revision_str)))
repository = repository_util.get_repository_in_tool_shed(
trans.app, repository_id)
if repository.tip(trans.app) != v:
return trans.response.send_redirect(
web.url_for(controller='repository',
action='browse_repositories',
operation='view_or_manage_repository',
id=trans.security.encode_id(repository.id),
changeset_revision=v))
# Render the list view
return self.repository_grid(trans, **kwd)
@web.expose
@web.require_admin
def browse_repository_metadata(self, trans, **kwd):
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "delete":
return self.delete_repository_metadata(trans, **kwd)
if operation == "view_or_manage_repository_revision":
# The received id is a RepositoryMetadata object id, so we need to get the
# associated Repository and redirect to view_or_manage_repository with the
# changeset_revision.
repository_metadata = metadata_util.get_repository_metadata_by_id(
trans.app, kwd['id'])
repository = repository_metadata.repository
kwd['id'] = trans.security.encode_id(repository.id)
kwd['changeset_revision'] = repository_metadata.changeset_revision
kwd['operation'] = 'view_or_manage_repository'
return trans.response.send_redirect(
web.url_for(controller='repository',
action='browse_repositories',
**kwd))
return self.repository_metadata_grid(trans, **kwd)
@web.expose
@web.require_admin
def create_category(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
name = kwd.get('name', '').strip()
description = kwd.get('description', '').strip()
if kwd.get('create_category_button', False):
if not name or not description:
message = 'Enter a valid name and a description'
status = 'error'
elif suc.get_category_by_name(trans.app, name):
message = 'A category with that name already exists'
status = 'error'
else:
# Create the category
category = trans.app.model.Category(name=name,
description=description)
trans.sa_session.add(category)
trans.sa_session.flush()
# Update the Tool Shed's repository registry.
trans.app.repository_registry.add_category_entry(category)
message = "Category '%s' has been created" % escape(
category.name)
status = 'done'
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=message,
status=status))
return trans.fill_template(
'/webapps/tool_shed/category/create_category.mako',
name=name,
description=description,
message=message,
status=status)
@web.expose
@web.require_admin
def delete_repository(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
id = kwd.get('id', None)
if id:
# Deleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
ids = util.listify(id)
count = 0
deleted_repositories = ""
for repository_id in ids:
repository = repository_util.get_repository_in_tool_shed(
trans.app, repository_id)
if repository:
if not repository.deleted:
# Mark all installable repository_metadata records as not installable.
for repository_metadata in repository.downloadable_revisions:
repository_metadata.downloadable = False
trans.sa_session.add(repository_metadata)
# Mark the repository admin role as deleted.
repository_admin_role = repository.admin_role
if repository_admin_role is not None:
repository_admin_role.deleted = True
trans.sa_session.add(repository_admin_role)
repository.deleted = True
trans.sa_session.add(repository)
trans.sa_session.flush()
# Update the repository registry.
trans.app.repository_registry.remove_entry(repository)
count += 1
deleted_repositories += " %s " % repository.name
if count:
message = "Deleted %d %s: %s" % (
count, inflector.cond_plural(
len(ids), "repository"), escape(deleted_repositories))
else:
message = "All selected repositories were already marked deleted."
else:
message = "No repository ids received for deleting."
status = 'error'
trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repositories',
message=util.sanitize_text(message),
status=status))
@web.expose
@web.require_admin
def delete_repository_metadata(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
for repository_metadata_id in ids:
repository_metadata = metadata_util.get_repository_metadata_by_id(
trans.app, repository_metadata_id)
trans.sa_session.delete(repository_metadata)
trans.sa_session.flush()
count += 1
if count:
message = "Deleted %d repository metadata %s" % (
count, inflector.cond_plural(len(ids), "record"))
else:
message = "No repository metadata ids received for deleting."
status = 'error'
trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repository_metadata',
message=util.sanitize_text(message),
status=status))
@web.expose
@web.require_admin
def edit_category(self, trans, **kwd):
'''Handle requests to edit TS category name or description'''
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
id = kwd.get('id', None)
if not id:
message = "No category ids received for editing"
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=message,
status='error'))
category = suc.get_category(trans.app, id)
original_category_name = str(category.name)
original_category_description = str(category.description)
if kwd.get('edit_category_button', False):
flush_needed = False
new_name = kwd.get('name', '').strip()
new_description = kwd.get('description', '').strip()
if original_category_name != new_name:
if not new_name:
message = 'Enter a valid name'
status = 'error'
elif original_category_name != new_name and suc.get_category_by_name(
trans.app, new_name):
message = 'A category with that name already exists'
status = 'error'
else:
category.name = new_name
flush_needed = True
if original_category_description != new_description:
category.description = new_description
if not flush_needed:
flush_needed = True
if flush_needed:
trans.sa_session.add(category)
trans.sa_session.flush()
if original_category_name != new_name:
# Update the Tool Shed's repository registry.
trans.app.repository_registry.edit_category_entry(
original_category_name, new_name)
message = "The information has been saved for category '%s'" % escape(
category.name)
status = 'done'
return trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=message,
status=status))
return trans.fill_template(
'/webapps/tool_shed/category/edit_category.mako',
category=category,
message=message,
status=status)
@web.expose
@web.require_admin
def manage_categories(self, trans, **kwd):
if 'f-free-text-search' in kwd:
# Trick to enable searching repository name, description from the CategoryGrid.
# What we've done is rendered the search box for the RepositoryGrid on the grid.mako
# template for the CategoryGrid. See ~/templates/webapps/tool_shed/category/grid.mako.
# Since we are searching repositories and not categories, redirect to browse_repositories().
return trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repositories',
**kwd))
if 'operation' in kwd:
operation = kwd['operation'].lower()
if operation == "create":
return trans.response.send_redirect(
web.url_for(controller='admin',
action='create_category',
**kwd))
elif operation == "delete":
return trans.response.send_redirect(
web.url_for(controller='admin',
action='mark_category_deleted',
**kwd))
elif operation == "undelete":
return trans.response.send_redirect(
web.url_for(controller='admin',
action='undelete_category',
**kwd))
elif operation == "purge":
return trans.response.send_redirect(
web.url_for(controller='admin',
action='purge_category',
**kwd))
elif operation == "edit":
return trans.response.send_redirect(
web.url_for(controller='admin',
action='edit_category',
**kwd))
return self.manage_category_grid(trans, **kwd)
@web.expose
@web.require_admin
def regenerate_statistics(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
if 'regenerate_statistics_button' in kwd:
trans.app.shed_counter.generate_statistics()
message = "Successfully regenerated statistics"
return trans.fill_template('/webapps/tool_shed/admin/statistics.mako',
message=message,
status=status)
@web.expose
@web.require_admin
def manage_role_associations(self, trans, **kwd):
"""Manage users, groups and repositories associated with a role."""
role_id = kwd.get('id', None)
role = repository_util.get_role_by_id(trans.app, role_id)
# We currently only have a single role associated with a repository, the repository admin role.
repository_role_association = role.repositories[0]
repository = repository_role_association.repository
associations_dict = repository_util.handle_role_associations(
trans.app, role, repository, **kwd)
in_users = associations_dict.get('in_users', [])
out_users = associations_dict.get('out_users', [])
in_groups = associations_dict.get('in_groups', [])
out_groups = associations_dict.get('out_groups', [])
message = associations_dict.get('message', '')
status = associations_dict.get('status', 'done')
return trans.fill_template('/webapps/tool_shed/role/role.mako',
in_admin_controller=True,
repository=repository,
role=role,
in_users=in_users,
out_users=out_users,
in_groups=in_groups,
out_groups=out_groups,
message=message,
status=status)
@web.expose
@web.require_admin
def reset_metadata_on_selected_repositories_in_tool_shed(
self, trans, **kwd):
rmm = repository_metadata_manager.RepositoryMetadataManager(
trans.app, trans.user)
if 'reset_metadata_on_selected_repositories_button' in kwd:
message, status = rmm.reset_metadata_on_selected_repositories(
**kwd)
else:
message = escape(util.restore_text(kwd.get('message', '')))
status = kwd.get('status', 'done')
repositories_select_field = rmm.build_repository_ids_select_field(
name='repository_ids',
multiple=True,
display='checkboxes',
my_writable=False)
return trans.fill_template(
'/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako',
repositories_select_field=repositories_select_field,
message=message,
status=status)
@web.expose
@web.require_admin
def undelete_repository(self, trans, **kwd):
message = escape(kwd.get('message', ''))
id = kwd.get('id', None)
if id:
# Undeleting multiple items is currently not allowed (allow_multiple=False), so there will only be 1 id.
ids = util.listify(id)
count = 0
undeleted_repositories = ""
for repository_id in ids:
repository = repository_util.get_repository_in_tool_shed(
trans.app, repository_id)
if repository:
if repository.deleted:
# Inspect all repository_metadata records to determine those that are installable, and mark
# them accordingly.
for repository_metadata in repository.metadata_revisions:
metadata = repository_metadata.metadata
if metadata:
if metadata_util.is_downloadable(metadata):
repository_metadata.downloadable = True
trans.sa_session.add(repository_metadata)
# Mark the repository admin role as not deleted.
repository_admin_role = repository.admin_role
if repository_admin_role is not None:
repository_admin_role.deleted = False
trans.sa_session.add(repository_admin_role)
repository.deleted = False
trans.sa_session.add(repository)
trans.sa_session.flush()
if not repository.deprecated:
# Update the repository registry.
trans.app.repository_registry.add_entry(repository)
count += 1
undeleted_repositories += " %s" % repository.name
if count:
message = "Undeleted %d %s: %s" % (
count, inflector.cond_plural(
count, "repository"), undeleted_repositories)
else:
message = "No selected repositories were marked deleted, so they could not be undeleted."
else:
message = "No repository ids received for undeleting."
trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repositories',
message=util.sanitize_text(message),
status='done'))
@web.expose
@web.require_admin
def mark_category_deleted(self, trans, **kwd):
# TODO: We should probably eliminate the Category.deleted column since it really makes no
# sense to mark a category as deleted (category names and descriptions can be changed instead).
# If we do this, and the following 2 methods can be eliminated.
message = escape(kwd.get('message', ''))
id = kwd.get('id', None)
if id:
ids = util.listify(id)
message = "Deleted %d categories: " % len(ids)
for category_id in ids:
category = suc.get_category(trans.app, category_id)
category.deleted = True
trans.sa_session.add(category)
trans.sa_session.flush()
# Update the Tool Shed's repository registry.
trans.app.repository_registry.remove_category_entry(category)
message += " %s " % escape(category.name)
else:
message = "No category ids received for deleting."
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=util.sanitize_text(message),
status='done'))
@web.expose
@web.require_admin
def purge_category(self, trans, **kwd):
# This method should only be called for a Category that has previously been deleted.
# Purging a deleted Category deletes all of the following from the database:
# - RepoitoryCategoryAssociations where category_id == Category.id
message = escape(kwd.get('message', ''))
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
purged_categories = ""
message = "Purged %d categories: " % len(ids)
for category_id in ids:
category = suc.get_category(trans.app, category_id)
if category.deleted:
# Delete RepositoryCategoryAssociations
for rca in category.repositories:
trans.sa_session.delete(rca)
trans.sa_session.flush()
purged_categories += " %s " % category.name
message = "Purged %d categories: %s" % (count,
escape(purged_categories))
else:
message = "No category ids received for purging."
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=util.sanitize_text(message),
status='done'))
@web.expose
@web.require_admin
def undelete_category(self, trans, **kwd):
message = escape(kwd.get('message', ''))
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
undeleted_categories = ""
for category_id in ids:
category = suc.get_category(trans.app, category_id)
if category.deleted:
category.deleted = False
trans.sa_session.add(category)
trans.sa_session.flush()
# Update the Tool Shed's repository registry.
trans.app.repository_registry.add_category_entry(category)
count += 1
undeleted_categories += " %s" % category.name
message = "Undeleted %d categories: %s" % (
count, escape(undeleted_categories))
else:
message = "No category ids received for undeleting."
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=util.sanitize_text(message),
status='done'))
class RepositoryMetadataGrid(grids.Grid):
class IdColumn(grids.IntegerColumn):
def get_value(self, trans, grid, repository_metadata):
return repository_metadata.id
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, repository_metadata):
return escape(repository_metadata.repository.name)
class OwnerColumn(grids.TextColumn):
def get_value(self, trans, grid, repository_metadata):
return escape(repository_metadata.repository.user.username)
class RevisionColumn(grids.TextColumn):
def get_value(self, trans, grid, repository_metadata):
repository = repository_metadata.repository
return hg_util.get_revision_label(
trans.app,
repository,
repository_metadata.changeset_revision,
include_date=True,
include_hash=True)
class ToolsColumn(grids.TextColumn):
def get_value(self, trans, grid, repository_metadata):
tools_str = '0'
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
if 'tools' in metadata:
# We used to display the following, but grid was too cluttered.
# for tool_metadata_dict in metadata[ 'tools' ]:
# tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] )
return '%d' % len(metadata['tools'])
return tools_str
class DatatypesColumn(grids.TextColumn):
def get_value(self, trans, grid, repository_metadata):
datatypes_str = '0'
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
if 'datatypes' in metadata:
# We used to display the following, but grid was too cluttered.
# for datatype_metadata_dict in metadata[ 'datatypes' ]:
# datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ]
return '%d' % len(metadata['datatypes'])
return datatypes_str
class WorkflowsColumn(grids.TextColumn):
def get_value(self, trans, grid, repository_metadata):
workflows_str = '0'
if repository_metadata:
metadata = repository_metadata.metadata
if metadata:
if 'workflows' in metadata:
# We used to display the following, but grid was too cluttered.
# workflows_str += '<b>Workflows:</b><br/>'
# metadata[ 'workflows' ] is a list of tuples where each contained tuple is
# [ <relative path to the .ga file in the repository>, <exported workflow dict> ]
# workflow_tups = metadata[ 'workflows' ]
# workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ]
# for workflow_metadata_dict in workflow_metadata_dicts:
# workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ]
return '%d' % len(metadata['workflows'])
return workflows_str
class DeletedColumn(grids.BooleanColumn):
def get_value(self, trans, grid, repository_metadata):
if repository_metadata.repository.deleted:
return 'yes'
return ''
class DeprecatedColumn(grids.BooleanColumn):
def get_value(self, trans, grid, repository_metadata):
if repository_metadata.repository.deprecated:
return 'yes'
return ''
class MaliciousColumn(grids.BooleanColumn):
def get_value(self, trans, grid, repository_metadata):
if repository_metadata.malicious:
return 'yes'
return ''
# Grid definition
title = "Repository Metadata"
model_class = model.RepositoryMetadata
default_sort_key = "name"
use_hide_message = False
columns = [
IdColumn("Id", visible=False, attach_popup=False),
NameColumn(
"Name",
key="name",
model_class=model.Repository,
link=(lambda item: dict(
operation="view_or_manage_repository_revision", id=item.id)),
attach_popup=True),
OwnerColumn("Owner", attach_popup=False),
RevisionColumn("Revision", attach_popup=False),
ToolsColumn("Tools", attach_popup=False),
DatatypesColumn("Datatypes", attach_popup=False),
WorkflowsColumn("Workflows", attach_popup=False),
DeletedColumn("Deleted", attach_popup=False),
DeprecatedColumn("Deprecated", attach_popup=False),
MaliciousColumn("Malicious", attach_popup=False)
]
columns.append(
grids.MulticolFilterColumn("Search repository name",
cols_to_filter=[columns[1]],
key="free-text-search",
visible=False,
filterable="standard"))
operations = [
grids.GridOperation(
"Delete",
allow_multiple=False,
allow_popup=True,
async_compatible=False,
confirm=
"Repository metadata records cannot be recovered after they are deleted. Click OK to delete the selected items."
)
]
standard_filters = []
default_filter = {}
use_paging = False
def build_initial_query(self, trans, **kwd):
return trans.sa_session.query(model.RepositoryMetadata) \
.join(model.Repository.table)
class UserGrid(grids.Grid):
class UserLoginColumn(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 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 StatusColumn(grids.GridColumn):
def get_value(self, trans, grid, user):
if user.purged:
return "purged"
elif user.deleted:
return "deleted"
return ""
class EmailColumn(grids.GridColumn):
def filter(self, trans, user, query, column_filter):
if column_filter == 'All':
return query
return query.filter(
and_(model.Tool.table.c.user_id == model.User.table.c.id,
model.User.table.c.email == column_filter))
title = "Users"
model_class = model.User
default_sort_key = "email"
columns = [
UserLoginColumn(
"Email",
key="email",
link=(lambda item: dict(operation="information", id=item.id)),
attach_popup=True,
filterable="advanced"),
UserNameColumn("User Name",
key="username",
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),
# Columns that are valid for filtering but are not visible.
EmailColumn("Email", key="email", visible=False)
]
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'))
]
operations = [
grids.GridOperation(
"Manage Roles and Groups",
condition=(lambda item: not item.deleted),
allow_multiple=False,
url_args=dict(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(action="reset_user_password"))
]
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'))
]
use_paging = False
def get_current_item(self, trans, **kwargs):
return trans.user
class RoleGrid(grids.Grid):
class NameColumn(grids.TextColumn):
def get_value(self, trans, grid, role):
return escape(str(role.name))
class DescriptionColumn(grids.TextColumn):
def get_value(self, trans, grid, role):
if role.description:
return str(role.description)
return ''
class TypeColumn(grids.TextColumn):
def get_value(self, trans, grid, role):
return str(role.type)
class StatusColumn(grids.GridColumn):
def get_value(self, trans, grid, role):
if role.deleted:
return "deleted"
return ""
class GroupsColumn(grids.GridColumn):
def get_value(self, trans, grid, role):
if role.groups:
return len(role.groups)
return 0
class RepositoriesColumn(grids.GridColumn):
def get_value(self, trans, grid, role):
if role.repositories:
return len(role.repositories)
return 0
class UsersColumn(grids.GridColumn):
def get_value(self, trans, grid, role):
if role.users:
return len(role.users)
return 0
title = "Roles"
model_class = model.Role
default_sort_key = "name"
columns = [
NameColumn("Name",
key="name",
link=(lambda item: dict(
operation="Manage role associations", id=item.id)),
attach_popup=True,
filterable="advanced"),
DescriptionColumn("Description",
key='description',
attach_popup=False,
filterable="advanced"),
GroupsColumn("Groups", attach_popup=False),
RepositoriesColumn("Repositories", attach_popup=False),
UsersColumn("Users", 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]],
key="free-text-search",
visible=False,
filterable="standard"))
global_actions = [
grids.GridAction(
"Add new role",
dict(controller='admin', action='roles', operation='create'))
]
# Repository admin roles currently do not have any operations since they are managed automatically based
# on other events. For example, if a repository is renamed, its associated admin role is automatically
# renamed accordingly and if a repository is deleted its associated admin role is automatically deleted.
operations = [
grids.GridOperation("Rename",
condition=(lambda item: not item.deleted and
not item.is_repository_admin_role),
allow_multiple=False,
url_args=dict(action="rename_role")),
grids.GridOperation("Delete",
condition=(lambda item: not item.deleted and
not item.is_repository_admin_role),
allow_multiple=True,
url_args=dict(action="mark_role_deleted")),
grids.GridOperation("Undelete",
condition=(lambda item: item.deleted and not item.
is_repository_admin_role),
allow_multiple=True,
url_args=dict(action="undelete_role")),
grids.GridOperation("Purge",
condition=(lambda item: item.deleted and not item.
is_repository_admin_role),
allow_multiple=True,
url_args=dict(action="purge_role"))
]
standard_filters = [
grids.GridColumnFilter("Active", args=dict(deleted=False)),
grids.GridColumnFilter("Deleted", args=dict(deleted=True)),
grids.GridColumnFilter("All", args=dict(deleted='All'))
]
use_paging = False
def apply_query_filter(self, trans, query, **kwd):
return query.filter(model.Role.type != model.Role.types.PRIVATE)
