def undelete_group(self, trans, **kwd):
id = kwd.get('id', None)
if not id:
message = "No group ids received for undeleting"
trans.response.send_redirect(
web.url_for(controller='admin',
action='groups',
message=message,
status='error'))
ids = util.listify(id)
count = 0
undeleted_groups = ""
for group_id in ids:
group = get_group(trans, group_id)
if not group.deleted:
message = "Group '%s' has not been deleted, so it cannot be undeleted." % group.name
trans.response.send_redirect(
web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status='error'))
group.deleted = False
trans.sa_session.add(group)
trans.sa_session.flush()
count += 1
undeleted_groups += " %s" % group.name
message = "Undeleted %d groups: %s" % (count, undeleted_groups)
trans.response.send_redirect(
web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status='done'))
def undelete_role(self, trans, **kwd):
id = kwd.get('id', None)
if not id:
message = "No role ids received for undeleting"
trans.response.send_redirect(
web.url_for(controller='admin',
action='roles',
message=message,
status='error'))
ids = util.listify(id)
count = 0
undeleted_roles = ""
for role_id in ids:
role = get_role(trans, role_id)
if not role.deleted:
message = "Role '%s' has not been deleted, so it cannot be undeleted." % role.name
trans.response.send_redirect(
web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='error'))
role.deleted = False
trans.sa_session.add(role)
trans.sa_session.flush()
count += 1
undeleted_roles += " %s" % role.name
message = "Undeleted %d roles: %s" % (count, undeleted_roles)
trans.response.send_redirect(
web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='done'))
def download_dataset_from_folder( self, trans, cntrller, obj_id, library_id=None, **kwd ):
"""Catches the dataset id and displays file contents as directed"""
# id must refer to a LibraryDatasetDatasetAssociation object
ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( obj_id )
if not ldda.dataset:
msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str( obj_id )
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_library',
obj_id=library_id,
msg=util.sanitize_text( msg ),
messagetype='error' ) )
mime = trans.app.datatypes_registry.get_mimetype_by_extension( ldda.extension.lower() )
trans.response.set_content_type( mime )
fStat = os.stat( ldda.file_name )
trans.response.headers[ 'Content-Length' ] = int( fStat.st_size )
valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
fname = ldda.name
fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ]
trans.response.headers[ "Content-Disposition" ] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % ( str( obj_id ), fname )
try:
return open( ldda.file_name )
except:
msg = 'This dataset contains no content'
return trans.response.send_redirect( web.url_for( controller=cntrller,
action='browse_library',
obj_id=library_id,
msg=util.sanitize_text( msg ),
messagetype='error' ) )
def undelete_user(self, trans, **kwd):
id = kwd.get('id', None)
if not id:
message = "No user ids received for undeleting"
trans.response.send_redirect(
web.url_for(controller='admin',
action='users',
message=message,
status='error'))
ids = util.listify(id)
count = 0
undeleted_users = ""
for user_id in ids:
user = get_user(trans, user_id)
if not user.deleted:
message = "User '%s' has not been deleted, so it cannot be undeleted." % user.email
trans.response.send_redirect(
web.url_for(controller='admin',
action='users',
message=util.sanitize_text(message),
status='error'))
user.deleted = False
trans.sa_session.add(user)
trans.sa_session.flush()
count += 1
undeleted_users += " %s" % user.email
message = "Undeleted %d users: %s" % (count, undeleted_users)
trans.response.send_redirect(
web.url_for(controller='admin',
action='users',
message=util.sanitize_text(message),
status='done'))
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 ) ) )
engine = None
if trans.app.config.database_connection:
engine = trans.app.config.database_connection.split(':')[0]
if engine not in ( 'postgres', 'postgresql' ):
done = False
while not done:
current = user.get_disk_usage()
new = user.calculate_disk_usage()
trans.sa_session.refresh( user )
# make sure usage didn't change while calculating, set done
if user.get_disk_usage() == current:
done = True
if new not in (current, None):
user.set_disk_usage( new )
trans.sa_session.add( user )
trans.sa_session.flush()
else:
# We can use the lightning fast pgcalc!
current = user.get_disk_usage()
new = pgcalc( self.sa_session, user.id )
# yes, still a small race condition between here and the flush
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' ) )
def undelete_user(self, trans, **kwd):
id = kwd.get('id', None)
if not id:
message = "No user ids received for undeleting"
trans.response.send_redirect(web.url_for(controller='admin',
action='users',
message=message,
status='error'))
ids = util.listify(id)
count = 0
undeleted_users = ""
for user_id in ids:
user = get_user(trans, user_id)
if not user.deleted:
message = "User '%s' has not been deleted, so it cannot be undeleted." % user.email
trans.response.send_redirect(web.url_for(controller='admin',
action='users',
message=util.sanitize_text(message),
status='error'))
user.deleted = False
trans.sa_session.add(user)
trans.sa_session.flush()
count += 1
undeleted_users += " %s" % user.email
message = "Undeleted %d users: %s" % (count, undeleted_users)
trans.response.send_redirect(web.url_for(controller='admin',
action='users',
message=util.sanitize_text(message),
status='done'))
def undelete_group(self, trans, **kwd):
id = kwd.get('id', None)
if not id:
message = "No group ids received for undeleting"
trans.response.send_redirect(web.url_for(controller='admin',
action='groups',
message=message,
status='error'))
ids = util.listify(id)
count = 0
undeleted_groups = ""
for group_id in ids:
group = get_group(trans, group_id)
if not group.deleted:
message = "Group '%s' has not been deleted, so it cannot be undeleted." % group.name
trans.response.send_redirect(web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status='error'))
group.deleted = False
trans.sa_session.add(group)
trans.sa_session.flush()
count += 1
undeleted_groups += " %s" % group.name
message = "Undeleted %d groups: %s" % (count, undeleted_groups)
trans.response.send_redirect(web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status='done'))
def purge_group(self, trans, **kwd):
# This method should only be called for a Group that has previously been deleted.
# Purging a deleted Group simply deletes all UserGroupAssociations and GroupRoleAssociations.
id = kwd.get('id', None)
if not id:
message = "No group ids received for purging"
trans.response.send_redirect(web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status='error'))
ids = util.listify(id)
message = "Purged %d groups: " % len(ids)
for group_id in ids:
group = get_group(trans, group_id)
if not group.deleted:
# We should never reach here, but just in case there is a bug somewhere...
message = "Group '%s' has not been deleted, so it cannot be purged." % group.name
trans.response.send_redirect(web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status='error'))
# Delete UserGroupAssociations
for uga in group.users:
trans.sa_session.delete(uga)
# Delete GroupRoleAssociations
for gra in group.roles:
trans.sa_session.delete(gra)
trans.sa_session.flush()
message += " %s " % group.name
trans.response.send_redirect(web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status='done'))
def undelete_role(self, trans, **kwd):
id = kwd.get('id', None)
if not id:
message = "No role ids received for undeleting"
trans.response.send_redirect(web.url_for(controller='admin',
action='roles',
message=message,
status='error'))
ids = util.listify(id)
count = 0
undeleted_roles = ""
for role_id in ids:
role = get_role(trans, role_id)
if not role.deleted:
message = "Role '%s' has not been deleted, so it cannot be undeleted." % role.name
trans.response.send_redirect(web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='error'))
role.deleted = False
trans.sa_session.add(role)
trans.sa_session.flush()
count += 1
undeleted_roles += " %s" % role.name
message = "Undeleted %d roles: %s" % (count, undeleted_roles)
trans.response.send_redirect(web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='done'))
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 ) ) )
engine = None
if trans.app.config.database_connection:
engine = trans.app.config.database_connection.split(':')[0]
if engine not in ( 'postgres', 'postgresql' ):
done = False
while not done:
current = user.get_disk_usage()
new = user.calculate_disk_usage()
trans.sa_session.refresh( user )
# make sure usage didn't change while calculating, set done
if user.get_disk_usage() == current:
done = True
if new not in (current, None):
user.set_disk_usage( new )
trans.sa_session.add( user )
trans.sa_session.flush()
else:
# We can use the lightning fast pgcalc!
current = user.get_disk_usage()
new = pgcalc( self.sa_session, user.id )
# yes, still a small race condition between here and the flush
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' ) )
def purge_role(self, trans, **kwd):
# This method should only be called for a Role that has previously been deleted.
# Purging a deleted Role deletes all of the following from the database:
# - UserRoleAssociations where role_id == Role.id
# - DefaultUserPermissions where role_id == Role.id
# - DefaultHistoryPermissions where role_id == Role.id
# - GroupRoleAssociations where role_id == Role.id
# - DatasetPermissionss where role_id == Role.id
id = kwd.get('id', None)
if not id:
message = "No role ids received for purging"
trans.response.send_redirect(
web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='error'))
ids = util.listify(id)
message = "Purged %d roles: " % len(ids)
for role_id in ids:
role = get_role(trans, role_id)
if not role.deleted:
message = "Role '%s' has not been deleted, so it cannot be purged." % role.name
trans.response.send_redirect(
web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='error'))
# Delete UserRoleAssociations
for ura in role.users:
user = trans.sa_session.query(trans.app.model.User).get(
ura.user_id)
# Delete DefaultUserPermissions for associated users
for dup in user.default_permissions:
if role == dup.role:
trans.sa_session.delete(dup)
# Delete DefaultHistoryPermissions for associated users
for history in user.histories:
for dhp in history.default_permissions:
if role == dhp.role:
trans.sa_session.delete(dhp)
trans.sa_session.delete(ura)
# Delete GroupRoleAssociations
for gra in role.groups:
trans.sa_session.delete(gra)
# Delete DatasetPermissionss
for dp in role.dataset_actions:
trans.sa_session.delete(dp)
trans.sa_session.flush()
message += " %s " % role.name
trans.response.send_redirect(
web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='done'))
def purge_role(self, trans, **kwd):
# This method should only be called for a Role that has previously been deleted.
# Purging a deleted Role deletes all of the following from the database:
# - UserRoleAssociations where role_id == Role.id
# - DefaultUserPermissions where role_id == Role.id
# - DefaultHistoryPermissions where role_id == Role.id
# - GroupRoleAssociations where role_id == Role.id
# - DatasetPermissionss where role_id == Role.id
id = kwd.get('id', None)
if not id:
message = "No role ids received for purging"
trans.response.send_redirect(web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='error'))
ids = util.listify(id)
message = "Purged %d roles: " % len(ids)
for role_id in ids:
role = get_role(trans, role_id)
if not role.deleted:
message = "Role '%s' has not been deleted, so it cannot be purged." % role.name
trans.response.send_redirect(web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='error'))
# Delete UserRoleAssociations
for ura in role.users:
user = trans.sa_session.query(trans.app.model.User).get(ura.user_id)
# Delete DefaultUserPermissions for associated users
for dup in user.default_permissions:
if role == dup.role:
trans.sa_session.delete(dup)
# Delete DefaultHistoryPermissions for associated users
for history in user.histories:
for dhp in history.default_permissions:
if role == dhp.role:
trans.sa_session.delete(dhp)
trans.sa_session.delete(ura)
# Delete GroupRoleAssociations
for gra in role.groups:
trans.sa_session.delete(gra)
# Delete DatasetPermissionss
for dp in role.dataset_actions:
trans.sa_session.delete(dp)
trans.sa_session.flush()
message += " %s " % role.name
trans.response.send_redirect(web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='done'))
def undelete_category(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
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, category_id)
if category.deleted:
category.deleted = False
trans.sa_session.add(category)
trans.sa_session.flush()
count += 1
undeleted_categories += " %s" % category.name
message = "Undeleted %d categories: %s" % (count,
undeleted_categories)
else:
message = "No category ids received for undeleting."
status = 'error'
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=util.sanitize_text(message),
status='done'))
def delete_repository_metadata(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
id = kwd.get('id', None)
if id:
ids = util.listify(id)
count = 0
for repository_metadata_id in ids:
repository_metadata = suc.get_repository_metadata_by_id(
trans, 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))
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'))
def user_per_month(self, trans, **kwd):
params = util.Params(kwd)
message = ''
email = util.restore_text(params.get('email', ''))
specs = sorter('date', kwd)
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
q = sa.select(
(self.select_month(model.Job.table.c.create_time).label('date'),
sa.func.count(model.Job.table.c.id).label('total_jobs')),
whereclause=sa.and_(
model.Job.table.c.session_id == model.GalaxySession.table.c.id,
model.GalaxySession.table.c.user_id == model.User.table.c.id,
model.User.table.c.email == email),
from_obj=[sa.join(model.Job.table, model.User.table)],
group_by=self.group_by_month(model.Job.table.c.create_time),
order_by=[_order])
jobs = []
for row in q.execute():
jobs.append((row.date.strftime("%Y-%m"), row.total_jobs,
row.date.strftime("%B"), row.date.strftime("%Y")))
return trans.fill_template('/webapps/reports/jobs_user_per_month.mako',
order=order,
arrow=arrow,
sort_id=sort_id,
id=kwd.get('id'),
email=util.sanitize_text(email),
jobs=jobs,
message=message)
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 = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
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 " % category.name
else:
message = "No category ids received for deleting."
status = 'error'
trans.response.send_redirect( web.url_for( controller='admin',
action='manage_categories',
message=util.sanitize_text( message ),
status='done' ) )
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"
)
)
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,
)
)
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 = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
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, purged_categories )
else:
message = "No category ids received for purging."
status = 'error'
trans.response.send_redirect( web.url_for( controller='admin',
action='manage_categories',
message=util.sanitize_text( message ),
status='done' ) )
def undelete_category( self, trans, **kwd ):
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
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, undeleted_categories )
else:
message = "No category ids received for undeleting."
status = 'error'
trans.response.send_redirect( web.url_for( controller='admin',
action='manage_categories',
message=util.sanitize_text( message ),
status='done' ) )
def user_per_month(self, trans, **kwd):
params = util.Params(kwd)
message = ''
specs = sorter('date', kwd)
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
email = util.restore_text(params.get('email', ''))
user_id = trans.security.decode_id(params.get('id', ''))
q = sa.select(
(self.select_month(
model.StoredWorkflow.table.c.create_time).label('date'),
sa.func.count(
model.StoredWorkflow.table.c.id).label('total_workflows')),
whereclause=model.StoredWorkflow.table.c.user_id == user_id,
from_obj=[model.StoredWorkflow.table],
group_by=self.group_by_month(
model.StoredWorkflow.table.c.create_time),
order_by=[_order])
workflows = []
for row in q.execute():
workflows.append(
(row.date.strftime("%Y-%m"), row.total_workflows,
row.date.strftime("%B"), row.date.strftime("%Y")))
return trans.fill_template(
'/webapps/reports/workflows_user_per_month.mako',
email=util.sanitize_text(email),
order=order,
arrow=arrow,
sort_id=sort_id,
workflows=workflows,
message=message)
def undelete_repository( self, trans, **kwd ):
params = util.Params( kwd )
message = util.restore_text( params.get( 'message', '' ) )
status = params.get( 'status', 'done' )
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 = suc.get_repository_in_tool_shed( trans, repository_id )
if repository.deleted:
repository.deleted = False
trans.sa_session.add( repository )
trans.sa_session.flush()
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."
status = 'error'
trans.response.send_redirect( web.url_for( controller='admin',
action='browse_repositories',
message=util.sanitize_text( message ),
status='done' ) )
def user_per_month(self, trans, **kwd):
params = util.Params(kwd)
message = ''
specs = sorter('date', kwd)
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
email = util.restore_text(params.get('email', ''))
user_id = trans.security.decode_id(params.get('id', ''))
q = sa.select(
(self.select_month(
model.StoredWorkflow.table.c.create_time).label('date'),
sa.func.count(
model.StoredWorkflow.table.c.id).label('total_workflows')),
whereclause=model.StoredWorkflow.table.c.user_id == user_id,
from_obj=[model.StoredWorkflow.table],
group_by=self.group_by_month(
model.StoredWorkflow.table.c.create_time),
order_by=[_order])
all_workflows_user_month = sa.select(
(self.select_day(
model.StoredWorkflow.table.c.create_time).label('date'),
model.StoredWorkflow.table.c.id),
whereclause=model.StoredWorkflow.table.c.user_id == user_id,
from_obj=[model.StoredWorkflow.table])
trends = dict()
for workflow in all_workflows_user_month.execute():
workflow_day = int(workflow.date.strftime("%-d")) - 1
workflow_month = int(workflow.date.strftime("%-m"))
workflow_month_name = workflow.date.strftime("%B")
workflow_year = workflow.date.strftime("%Y")
key = str(workflow_month_name + workflow_year)
try:
trends[key][workflow_day] += 1
except KeyError:
workflow_year = int(workflow_year)
wday, day_range = calendar.monthrange(workflow_year,
workflow_month)
trends[key] = [0] * day_range
trends[key][workflow_day] += 1
workflows = []
for row in q.execute():
workflows.append(
(row.date.strftime("%Y-%m"), row.total_workflows,
row.date.strftime("%B"), row.date.strftime("%Y")))
return trans.fill_template(
'/webapps/reports/workflows_user_per_month.mako',
email=util.sanitize_text(email),
order=order,
arrow=arrow,
sort_id=sort_id,
trends=trends,
workflows=workflows,
message=message)
def delete_repository( self, trans, **kwd ):
message = 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 = suc.get_repository_in_tool_shed( trans, 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 )
repository.deleted = True
trans.sa_session.add( repository )
trans.sa_session.flush()
count += 1
deleted_repositories += " %s " % repository.name
if count:
message = "Deleted %d %s: %s" % ( count, inflector.cond_plural( len( ids ), "repository" ), 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 ) )
def user_per_month(self, trans, **kwd):
params = util.Params(kwd)
message = ''
email = util.restore_text(params.get('email', ''))
user_id = trans.security.decode_id(params.get('id', ''))
q = sa.select((sa.func.date_trunc(
'month', sa.func.date(
model.Request.table.c.create_time)).label('date'),
sa.func.count(model.Request.table.c.id).label('total')),
whereclause=model.Request.table.c.user_id == user_id,
from_obj=[model.Request.table],
group_by=[
sa.func.date_trunc(
'month',
sa.func.date(model.Request.table.c.create_time))
],
order_by=[sa.desc('date')])
requests = []
for row in q.execute():
requests.append((row.date.strftime("%Y-%m"), row.total,
row.date.strftime("%B"), row.date.strftime("%Y")))
return trans.fill_template(
'/webapps/reports/requests_user_per_month.mako',
email=util.sanitize_text(email),
requests=requests,
message=message)
def user_per_month( self, trans, **kwd ):
params = util.Params( kwd )
message = ''
email = util.restore_text( params.get( 'email', '' ) )
specs = sorter( 'date', kwd )
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
q = sa.select( ( self.select_month( model.Job.table.c.create_time ).label( 'date' ),
sa.func.count( model.Job.table.c.id ).label( 'total_jobs' ) ),
whereclause=sa.and_( model.Job.table.c.session_id == model.GalaxySession.table.c.id,
model.GalaxySession.table.c.user_id == model.User.table.c.id,
model.User.table.c.email == email ),
from_obj=[ sa.join( model.Job.table, model.User.table ) ],
group_by=self.group_by_month( model.Job.table.c.create_time ),
order_by=[ _order ] )
jobs = []
for row in q.execute():
jobs.append( ( row.date.strftime( "%Y-%m" ),
row.total_jobs,
row.date.strftime( "%B" ),
row.date.strftime( "%Y" ) ) )
return trans.fill_template( '/webapps/reports/jobs_user_per_month.mako',
order=order,
arrow=arrow,
sort_id=sort_id,
id=kwd.get('id'),
email=util.sanitize_text( email ),
jobs=jobs, message=message )
def user_per_month( self, trans, **kwd ):
params = util.Params( kwd )
message = ''
specs = sorter( 'date', kwd )
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
email = util.restore_text( params.get( 'email', '' ) )
user_id = trans.security.decode_id( params.get( 'id', '' ) )
q = sa.select( ( self.select_month( model.StoredWorkflow.table.c.create_time ).label( 'date' ),
sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ),
whereclause=model.StoredWorkflow.table.c.user_id == user_id,
from_obj=[ model.StoredWorkflow.table ],
group_by=self.group_by_month( model.StoredWorkflow.table.c.create_time ),
order_by=[ _order ] )
workflows = []
for row in q.execute():
workflows.append( ( row.date.strftime( "%Y-%m" ),
row.total_workflows,
row.date.strftime( "%B" ),
row.date.strftime( "%Y" ) ) )
return trans.fill_template( '/webapps/reports/workflows_user_per_month.mako',
email=util.sanitize_text( email ),
order=order,
arrow=arrow,
sort_id=sort_id,
workflows=workflows,
message=message )
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', ''))
status = kwd.get('status', 'done')
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 " % category.name
else:
message = "No category ids received for deleting."
status = 'error'
trans.response.send_redirect(
web.url_for(controller='admin',
action='manage_categories',
message=util.sanitize_text(message),
status='done'))
def undelete_repository(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
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 = suc.get_repository_in_tool_shed(
trans, repository_id)
if repository.deleted:
repository.deleted = False
trans.sa_session.add(repository)
trans.sa_session.flush()
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."
status = 'error'
trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repositories',
message=util.sanitize_text(message),
status='done'))
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' ) )
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'))
def user_per_month(self, trans, **kwd):
params = util.Params(kwd)
message = ''
email = util.restore_text(params.get('email', ''))
q = sa.select(
(sa.func.date_trunc(
'month', sa.func.date(
model.Job.table.c.create_time)).label('date'),
sa.func.count(model.Job.table.c.id).label('total_jobs')),
whereclause=sa.and_(
model.Job.table.c.session_id == model.GalaxySession.table.c.id,
model.GalaxySession.table.c.user_id == model.User.table.c.id,
model.User.table.c.email == email),
from_obj=[sa.join(model.Job.table, model.User.table)],
group_by=[
sa.func.date_trunc('month',
sa.func.date(model.Job.table.c.create_time))
],
order_by=[sa.desc('date')])
jobs = []
for row in q.execute():
jobs.append((row.date.strftime("%Y-%m"), row.total_jobs,
row.date.strftime("%B"), row.date.strftime("%Y")))
return trans.fill_template('/webapps/reports/jobs_user_per_month.mako',
email=util.sanitize_text(email),
jobs=jobs,
message=message)
def upload_empty( self, trans, controller, library_id, folder_id, err_code, err_msg ):
msg = err_code + err_msg
return trans.response.send_redirect( web.url_for( controller=controller,
action='library_dataset_dataset_association',
library_id=library_id,
folder_id=folder_id,
msg=util.sanitize_text( msg ),
messagetype='error' ) )
def purge_library( self, trans, **kwd ):
# TODO: change this function to purge_library_item, behaving similar to delete_library_item
# assuming we want the ability to purge libraries.
# This function is currently only used by the functional tests.
params = util.Params( kwd )
library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( params.id ) )
def purge_folder( library_folder ):
for lf in library_folder.folders:
purge_folder( lf )
trans.sa_session.refresh( library_folder )
for library_dataset in library_folder.datasets:
trans.sa_session.refresh( library_dataset )
ldda = library_dataset.library_dataset_dataset_association
if ldda:
trans.sa_session.refresh( ldda )
dataset = ldda.dataset
trans.sa_session.refresh( dataset )
# If the dataset is not associated with any additional undeleted folders, then we can delete it.
# We don't set dataset.purged to True here because the cleanup_datasets script will do that for
# us, as well as removing the file from disk.
#if not dataset.deleted and len( dataset.active_library_associations ) <= 1: # This is our current ldda
dataset.deleted = True
ldda.deleted = True
trans.sa_session.add_all( ( dataset, ldda ) )
library_dataset.deleted = True
trans.sa_session.add( library_dataset )
library_folder.deleted = True
library_folder.purged = True
trans.sa_session.add( library_folder )
trans.sa_session.flush()
if not library.deleted:
message = "Library '%s' has not been marked deleted, so it cannot be purged" % ( library.name )
return trans.response.send_redirect( web.url_for( controller='library_admin',
action='browse_libraries',
message=util.sanitize_text( message ),
status='error' ) )
else:
purge_folder( library.root_folder )
library.purged = True
trans.sa_session.add( library )
trans.sa_session.flush()
message = "Library '%s' and all of its contents have been purged, datasets will be removed from disk via the cleanup_datasets script" % library.name
return trans.response.send_redirect( web.url_for( controller='library_admin',
action='browse_libraries',
message=util.sanitize_text( message ),
status='done' ) )
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 user_per_month(self, trans, **kwd):
params = util.Params(kwd)
message = ''
email = util.restore_text(params.get('email', ''))
specs = sorter('date', kwd)
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
q = sa.select(
(self.select_month(model.Job.table.c.create_time).label('date'),
sa.func.count(model.Job.table.c.id).label('total_jobs')),
whereclause=model.User.table.c.email == email,
from_obj=[sa.join(model.Job.table, model.User.table)],
group_by=self.group_by_month(model.Job.table.c.create_time),
order_by=[_order])
all_jobs_per_user = sa.select(
(model.Job.table.c.create_time.label('date'),
model.Job.table.c.id.label('job_id')),
whereclause=sa.and_(model.User.table.c.email == email),
from_obj=[sa.join(model.Job.table, model.User.table)])
trends = dict()
for job in all_jobs_per_user.execute():
job_day = int(job.date.strftime("%-d")) - 1
job_month = int(job.date.strftime("%-m"))
job_month_name = job.date.strftime("%B")
job_year = job.date.strftime("%Y")
key = str(job_month_name + job_year)
try:
trends[key][job_day] += 1
except KeyError:
job_year = int(job_year)
wday, day_range = calendar.monthrange(job_year, job_month)
trends[key] = [0] * day_range
trends[key][job_day] += 1
jobs = []
for row in q.execute():
jobs.append((row.date.strftime("%Y-%m"), row.total_jobs,
row.date.strftime("%B"), row.date.strftime("%Y")))
return trans.fill_template('/webapps/reports/jobs_user_per_month.mako',
order=order,
arrow=arrow,
sort_id=sort_id,
id=kwd.get('id'),
trends=trends,
email=util.sanitize_text(email),
jobs=jobs,
message=message)
def user_per_month(self, trans, **kwd):
params = util.Params(kwd)
message = ''
email = util.restore_text(params.get('email', ''))
specs = sorter('date', kwd)
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
q = sa.select((self.select_month(model.Job.table.c.create_time).label('date'),
sa.func.count(model.Job.table.c.id).label('total_jobs')),
whereclause=model.User.table.c.email == email,
from_obj=[sa.join(model.Job.table, model.User.table)],
group_by=self.group_by_month(model.Job.table.c.create_time),
order_by=[_order])
all_jobs_per_user = sa.select((model.Job.table.c.create_time.label('date'),
model.Job.table.c.id.label('job_id')),
whereclause=sa.and_(model.User.table.c.email == email),
from_obj=[sa.join(model.Job.table, model.User.table)])
trends = dict()
for job in all_jobs_per_user.execute():
job_day = int(job.date.strftime("%-d")) - 1
job_month = int(job.date.strftime("%-m"))
job_month_name = job.date.strftime("%B")
job_year = job.date.strftime("%Y")
key = str(job_month_name + job_year)
try:
trends[key][job_day] += 1
except KeyError:
job_year = int(job_year)
wday, day_range = calendar.monthrange(job_year, job_month)
trends[key] = [0] * day_range
trends[key][job_day] += 1
jobs = []
for row in q.execute():
jobs.append((row.date.strftime("%Y-%m"),
row.total_jobs,
row.date.strftime("%B"),
row.date.strftime("%Y")))
return trans.fill_template('/webapps/reports/jobs_user_per_month.mako',
order=order,
arrow=arrow,
sort_id=sort_id,
id=kwd.get('id'),
trends=trends,
email=util.sanitize_text(email),
jobs=jobs, message=message)
def create_role(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
name = util.restore_text(params.get('name', ''))
description = util.restore_text(params.get('description', ''))
in_users = util.listify(params.get('in_users', []))
out_users = util.listify(params.get('out_users', []))
in_groups = util.listify(params.get('in_groups', []))
out_groups = util.listify(params.get('out_groups', []))
create_group_for_role = params.get('create_group_for_role', '')
create_group_for_role_checked = CheckboxField.is_checked(create_group_for_role)
ok = True
if params.get('create_role_button', False):
if not name or not description:
message = "Enter a valid name and a description."
status = 'error'
ok = False
elif trans.sa_session.query(trans.app.model.Role).filter(trans.app.model.Role.table.c.name == name).first():
message = "Role names must be unique and a role with that name already exists, so choose another name."
status = 'error'
ok = False
else:
# Create the role
role, num_in_groups = trans.app.security_agent.create_role(
name, description, in_users, in_groups, create_group_for_role=create_group_for_role_checked)
message = "Role '%s' has been created with %d associated users and %d associated groups. " \
% (role.name, len(in_users), num_in_groups)
if create_group_for_role_checked:
message += 'One of the groups associated with this role is the newly created group with the same name.'
trans.response.send_redirect(web.url_for(controller='admin',
action='roles',
message=util.sanitize_text(message),
status='done'))
if ok:
for user in trans.sa_session.query(trans.app.model.User) \
.filter(trans.app.model.User.table.c.deleted == false()) \
.order_by(trans.app.model.User.table.c.email):
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 == false()) \
.order_by(trans.app.model.Group.table.c.name):
out_groups.append((group.id, group.name))
return trans.fill_template('/webapps/tool_shed/admin/dataset_security/role/role_create.mako',
name=name,
description=description,
in_users=in_users,
out_users=out_users,
in_groups=in_groups,
out_groups=out_groups,
create_group_for_role_checked=create_group_for_role_checked,
message=message,
status=status)
def manage_users_and_roles_for_group(self, trans, **kwd):
params = util.Params(kwd)
message = util.restore_text(params.get('message', ''))
status = params.get('status', 'done')
group = get_group(trans, params.id)
if params.get('group_roles_users_edit_button', False):
in_roles = [
trans.sa_session.query(trans.app.model.Role).get(x)
for x in util.listify(params.in_roles)
]
in_users = [
trans.sa_session.query(trans.app.model.User).get(x)
for x in util.listify(params.in_users)
]
trans.app.security_agent.set_entity_group_associations(
groups=[group], roles=in_roles, users=in_users)
trans.sa_session.refresh(group)
message += "Group '%s' has been updated with %d associated roles and %d associated users" % (
group.name, len(in_roles), len(in_users))
trans.response.send_redirect(
web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status=status))
in_roles = []
out_roles = []
in_users = []
out_users = []
for role in trans.sa_session.query(trans.app.model.Role) \
.filter(trans.app.model.Role.table.c.deleted == false()) \
.order_by(trans.app.model.Role.table.c.name):
if role in [x.role for x in group.roles]:
in_roles.append((role.id, role.name))
else:
out_roles.append((role.id, role.name))
for user in trans.sa_session.query(trans.app.model.User) \
.filter(trans.app.model.User.table.c.deleted == false()) \
.order_by(trans.app.model.User.table.c.email):
if user in [x.user for x in group.users]:
in_users.append((user.id, user.email))
else:
out_users.append((user.id, user.email))
message += 'Group %s is currently associated with %d roles and %d users' % (
group.name, len(in_roles), len(in_users))
return trans.fill_template(
'/webapps/tool_shed/admin/dataset_security/group/group.mako',
group=group,
in_roles=in_roles,
out_roles=out_roles,
in_users=in_users,
out_users=out_users,
message=message,
status=status)
def user_per_month( self, trans, **kwd ):
params = util.Params( kwd )
message = ''
specs = sorter( 'date', kwd )
sort_id = specs.sort_id
order = specs.order
arrow = specs.arrow
_order = specs.exc_order
email = util.restore_text( params.get( 'email', '' ) )
user_id = trans.security.decode_id( params.get( 'id', '' ) )
q = sa.select( ( self.select_month( model.StoredWorkflow.table.c.create_time ).label( 'date' ),
sa.func.count( model.StoredWorkflow.table.c.id ).label( 'total_workflows' ) ),
whereclause=model.StoredWorkflow.table.c.user_id == user_id,
from_obj=[ model.StoredWorkflow.table ],
group_by=self.group_by_month( model.StoredWorkflow.table.c.create_time ),
order_by=[ _order ] )
all_workflows_user_month = sa.select( ( self.select_day( model.StoredWorkflow.table.c.create_time ).label( 'date' ),
model.StoredWorkflow.table.c.id ),
whereclause=model.StoredWorkflow.table.c.user_id == user_id,
from_obj=[ model.StoredWorkflow.table ] )
trends = dict()
for workflow in all_workflows_user_month.execute():
workflow_day = int(workflow.date.strftime("%-d")) - 1
workflow_month = int(workflow.date.strftime("%-m"))
workflow_month_name = workflow.date.strftime("%B")
workflow_year = workflow.date.strftime("%Y")
key = str( workflow_month_name + workflow_year)
try:
trends[key][workflow_day] += 1
except KeyError:
workflow_year = int(workflow_year)
wday, day_range = calendar.monthrange(workflow_year, workflow_month)
trends[key] = [0] * day_range
trends[key][workflow_day] += 1
workflows = []
for row in q.execute():
workflows.append( ( row.date.strftime( "%Y-%m" ),
row.total_workflows,
row.date.strftime( "%B" ),
row.date.strftime( "%Y" ) ) )
return trans.fill_template( '/webapps/reports/workflows_user_per_month.mako',
email=util.sanitize_text( email ),
order=order,
arrow=arrow,
sort_id=sort_id,
trends=trends,
workflows=workflows,
message=message )
def download_dataset_from_folder(self,
trans,
cntrller,
obj_id,
library_id=None,
**kwd):
"""Catches the dataset id and displays file contents as directed"""
# id must refer to a LibraryDatasetDatasetAssociation object
ldda = trans.sa_session.query(
trans.app.model.LibraryDatasetDatasetAssociation).get(obj_id)
if not ldda.dataset:
msg = 'Invalid LibraryDatasetDatasetAssociation id %s received for file downlaod' % str(
obj_id)
return trans.response.send_redirect(
web.url_for(controller=cntrller,
action='browse_library',
obj_id=library_id,
msg=util.sanitize_text(msg),
messagetype='error'))
mime = trans.app.datatypes_registry.get_mimetype_by_extension(
ldda.extension.lower())
trans.response.set_content_type(mime)
fStat = os.stat(ldda.file_name)
trans.response.headers['Content-Length'] = int(fStat.st_size)
valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
fname = ldda.name
fname = ''.join(c in valid_chars and c or '_' for c in fname)[0:150]
trans.response.headers[
"Content-Disposition"] = "attachment; filename=GalaxyLibraryDataset-%s-[%s]" % (
str(obj_id), fname)
try:
return open(ldda.file_name)
except:
msg = 'This dataset contains no content'
return trans.response.send_redirect(
web.url_for(controller=cntrller,
action='browse_library',
obj_id=library_id,
msg=util.sanitize_text(msg),
messagetype='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
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, e:
params.message = str( e )
params.status = 'error'
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",
)
)
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, e:
params.message = str( e )
params.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
def list(self, trans, **kwargs):
"""List all available histories"""
current_history = trans.get_history()
message = kwargs.get('message')
status = kwargs.get('status')
if 'operation' in kwargs:
operation = kwargs['operation'].lower()
history_ids = listify(kwargs.get('id', []))
# Display no message by default
status, message = None, None
# Load the histories and ensure they all belong to the current user
histories = []
for history_id in history_ids:
history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)
if history:
# Ensure history is owned by current user
if history.user_id is not None and trans.user:
assert trans.user.id == history.user_id, "History does not belong to current user"
histories.append(history)
else:
log.warning("Invalid history id '%r' passed to list", history_id)
if histories:
if operation == "switch":
status, message = self._list_switch(trans, histories)
# Take action to update UI to reflect history switch. If
# grid is using panels, it is standalone and hence a redirect
# to root is needed; if grid is not using panels, it is nested
# in the main Galaxy UI and refreshing the history frame
# is sufficient.
use_panels = kwargs.get('use_panels', False) == 'True'
if use_panels:
return trans.response.send_redirect(url_for("/"))
else:
kwargs['refresh_frames'] = ['history']
elif operation in ("delete", "delete permanently"):
status, message = self._list_delete(trans, histories, purge=(operation == "delete permanently"))
if current_history in histories:
# Deleted the current history, so a new, empty history was
# created automatically, and we need to refresh the history frame
kwargs['refresh_frames'] = ['history']
elif operation == "undelete":
status, message = self._list_undelete(trans, histories)
trans.sa_session.flush()
# Render the list view
if message and status:
kwargs['message'] = sanitize_text(message)
kwargs['status'] = status
return self.stored_list_grid(trans, **kwargs)
def undelete_repository(self, trans, **kwd):
message = escape(kwd.get('message', ''))
status = kwd.get('status', 'done')
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 = suc.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."
status = 'error'
trans.response.send_redirect(
web.url_for(controller='admin',
action='browse_repositories',
message=util.sanitize_text(message),
status='done'))
def purge_group(self, trans, **kwd):
# This method should only be called for a Group that has previously been deleted.
# Purging a deleted Group simply deletes all UserGroupAssociations and GroupRoleAssociations.
id = kwd.get('id', None)
if not id:
message = "No group ids received for purging"
trans.response.send_redirect(
web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status='error'))
ids = util.listify(id)
message = "Purged %d groups: " % len(ids)
for group_id in ids:
group = get_group(trans, group_id)
if not group.deleted:
# We should never reach here, but just in case there is a bug somewhere...
message = "Group '%s' has not been deleted, so it cannot be purged." % group.name
trans.response.send_redirect(
web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status='error'))
# Delete UserGroupAssociations
for uga in group.users:
trans.sa_session.delete(uga)
# Delete GroupRoleAssociations
for gra in group.roles:
trans.sa_session.delete(gra)
trans.sa_session.flush()
message += " %s " % group.name
trans.response.send_redirect(
web.url_for(controller='admin',
action='groups',
message=util.sanitize_text(message),
status='done'))
def create_form(self, trans, payload=None, **kwd):
if trans.request.method == 'GET':
fd_types = sorted(trans.app.model.FormDefinition.types.items())
return {
'title' : 'Create new form',
'submit_title' : 'Create',
'inputs' : [{
'name' : 'name',
'label' : 'Name'
}, {
'name' : 'desc',
'label' : 'Description'
}, {
'name' : 'type',
'type' : 'select',
'options' : [('None', 'none')] + [(ft[1], ft[1]) for ft in fd_types],
'label' : 'Type'
}, {
'name' : 'csv_file',
'label' : 'Import from CSV',
'type' : 'upload',
'help' : 'Import fields from CSV-file with the following format: Label, Help, Type, Value, Options, Required=True/False.'
}]
}
else:
# csv-file format: label, helptext, type, default, selectlist, required '''
csv_file = payload.get('csv_file')
index = 0
if csv_file:
lines = csv_file.splitlines()
for line in lines:
row = line.split(',')
if len(row) >= 6:
prefix = 'fields_%i|' % index
payload['%s%s' % (prefix, 'name')] = '%i_imported_field' % (index + 1)
payload['%s%s' % (prefix, 'label')] = row[0]
payload['%s%s' % (prefix, 'helptext')] = row[1]
payload['%s%s' % (prefix, 'type')] = row[2]
payload['%s%s' % (prefix, 'default')] = row[3]
payload['%s%s' % (prefix, 'selectlist')] = row[4].split(',')
payload['%s%s' % (prefix, 'required')] = row[5].lower() == 'true'
index = index + 1
new_form, message = self.save_form_definition(trans, None, payload)
if new_form is None:
return self.message_exception(trans, message)
imported = (' with %i imported fields' % index) if index > 0 else ''
message = 'The form \'%s\' has been created%s.' % (payload.get('name'), imported)
return {'message': util.sanitize_text(message)}
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 = suc.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"
)
)
def create_form(self, trans, payload=None, **kwd):
if trans.request.method == 'GET':
fd_types = sorted(trans.app.model.FormDefinition.types.items())
return {
'title' : 'Create new form',
'submit_title' : 'Create',
'inputs' : [{
'name' : 'name',
'label' : 'Name'
}, {
'name' : 'desc',
'label' : 'Description'
}, {
'name' : 'type',
'type' : 'select',
'options' : [('None', 'none')] + [(ft[1], ft[1]) for ft in fd_types],
'label' : 'Type'
}, {
'name' : 'csv_file',
'label' : 'Import from CSV',
'type' : 'upload',
'help' : 'Import fields from CSV-file with the following format: Label, Help, Type, Value, Options, Required=True/False.'
}]
}
else:
# csv-file format: label, helptext, type, default, selectlist, required '''
csv_file = payload.get('csv_file')
index = 0
if csv_file:
lines = csv_file.splitlines()
for line in lines:
row = line.split(',')
if len(row) >= 6:
prefix = 'fields_%i|' % index
payload['%s%s' % (prefix, 'name')] = '%i_imported_field' % (index + 1)
payload['%s%s' % (prefix, 'label')] = row[0]
payload['%s%s' % (prefix, 'helptext')] = row[1]
payload['%s%s' % (prefix, 'type')] = row[2]
payload['%s%s' % (prefix, 'default')] = row[3]
payload['%s%s' % (prefix, 'selectlist')] = row[4].split(',')
payload['%s%s' % (prefix, 'required')] = row[5].lower() == 'true'
index = index + 1
new_form, message = self.save_form_definition(trans, None, payload)
if new_form is None:
return self.message_exception(trans, message)
imported = (' with %i imported fields' % index) if index > 0 else ''
message = 'The form \'%s\' has been created%s.' % (payload.get('name'), imported)
return {'message': util.sanitize_text(message)}
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, 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' ) )
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, 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' ) )
def forms_list(self, trans, payload=None, **kwd):
message = kwd.get('message', '')
status = kwd.get('status', '')
if 'operation' in kwd:
id = kwd.get('id')
if not id:
return self.message_exception(trans, 'Invalid form id (%s) received.' % str(id))
ids = util.listify(id)
operation = kwd['operation'].lower()
if operation == 'delete':
message, status = self._delete_form(trans, ids)
elif operation == 'undelete':
message, status = self._undelete_form(trans, ids)
if message and status:
kwd['message'] = util.sanitize_text(message)
kwd['status'] = status
return self.forms_grid(trans, **kwd)