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Source code for galaxy.webapps.tool_shed.controllers.admin
import logging
import tool_shed.grids.admin_grids as admin_grids
from galaxy import (
util,
web
)
from galaxy.util import inflector
from galaxy.web.base.controller import BaseUIController
from galaxy.web.framework.helpers import grids
from tool_shed.metadata import repository_metadata_manager
from tool_shed.util import (
metadata_util,
repository_util,
shed_util_common as suc
)
from tool_shed.util.admin_util import Admin
from tool_shed.util.web_util import escape
log = logging.getLogger(__name__)
[docs]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)
[docs] @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)
[docs] @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)
[docs] @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)
[docs] @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))
[docs] @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))
[docs] @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)
[docs] @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)
[docs] @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)
[docs] @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)
[docs] @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)
[docs] @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'))
[docs] @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'))
[docs] @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'))
[docs] @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'))