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Source code for galaxy.webapps.base.controller
"""
Contains functionality needed in every web interface
"""
import logging
from six import string_types
from sqlalchemy import true
from webob.exc import (
HTTPBadRequest,
HTTPInternalServerError,
HTTPNotImplemented
)
from galaxy import (
exceptions,
model,
security,
util,
web
)
from galaxy.datatypes.interval import ChromatinInteractions
from galaxy.managers import (
api_keys,
base as managers_base,
configuration,
users,
workflows
)
from galaxy.model import (
ExtendedMetadata,
ExtendedMetadataIndex,
HistoryDatasetAssociation,
LibraryDatasetDatasetAssociation,
tags,
)
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.util.dictifiable import Dictifiable
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import (
error,
url_for
)
from galaxy.web.form_builder import (
AddressField,
CheckboxField,
PasswordField
)
from galaxy.workflow.modules import WorkflowModuleInjector
log = logging.getLogger(__name__)
# States for passing messages
SUCCESS, INFO, WARNING, ERROR = "done", "info", "warning", "error"
[docs]class BaseController(object):
"""
Base class for Galaxy web application controllers.
"""
[docs] def __init__(self, app):
"""Initialize an interface for application 'app'"""
self.app = app
self.sa_session = app.model.context
self.user_manager = users.UserManager(app)
[docs] def get_class(self, class_name):
""" Returns the class object that a string denotes. Without this method, we'd have to do eval(<class_name>). """
return managers_base.get_class(class_name)
[docs] def get_object(self, trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None):
"""
Convenience method to get a model object with the specified checks.
"""
return managers_base.get_object(trans, id, class_name, check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted)
# this should be here - but catching errors from sharable item controllers that *should* have SharableItemMixin
# but *don't* then becomes difficult
# def security_check( self, trans, item, check_ownership=False, check_accessible=False ):
# log.warning( 'BaseController.security_check: %s, %b, %b', str( item ), check_ownership, check_accessible )
# # meant to be overridden in SharableSecurityMixin
# return item
[docs] def get_user(self, trans, id, check_ownership=False, check_accessible=False, deleted=None):
return self.get_object(trans, id, 'User', check_ownership=False, check_accessible=False, deleted=deleted)
[docs] def get_group(self, trans, id, check_ownership=False, check_accessible=False, deleted=None):
return self.get_object(trans, id, 'Group', check_ownership=False, check_accessible=False, deleted=deleted)
[docs] def get_role(self, trans, id, check_ownership=False, check_accessible=False, deleted=None):
return self.get_object(trans, id, 'Role', check_ownership=False, check_accessible=False, deleted=deleted)
# ---- parsing query params
[docs] def encode_all_ids(self, trans, rval, recursive=False):
"""
Encodes all integer values in the dict rval whose keys are 'id' or end with '_id'
It might be useful to turn this in to a decorator
"""
return trans.security.encode_all_ids(rval, recursive=recursive)
[docs] def parse_filter_params(self, qdict, filter_attr_key='q', filter_value_key='qv', attr_op_split_char='-'):
"""
"""
# TODO: import DEFAULT_OP from FilterParser
DEFAULT_OP = 'eq'
if filter_attr_key not in qdict:
return []
# precondition: attrs/value pairs are in-order in the qstring
attrs = qdict.get(filter_attr_key)
if not isinstance(attrs, list):
attrs = [attrs]
# ops are strings placed after the attr strings and separated by a split char (e.g. 'create_time-lt')
# ops are optional and default to 'eq'
reparsed_attrs = []
ops = []
for attr in attrs:
op = DEFAULT_OP
if attr_op_split_char in attr:
# note: only split the last (e.g. q=community-tags-in&qv=rna yields ( 'community-tags', 'in', 'rna' )
attr, op = attr.rsplit(attr_op_split_char, 1)
ops.append(op)
reparsed_attrs.append(attr)
attrs = reparsed_attrs
values = qdict.get(filter_value_key, [])
if not isinstance(values, list):
values = [values]
# TODO: it may be more helpful to the consumer if we error on incomplete 3-tuples
# (instead of relying on zip to shorten)
return list(zip(attrs, ops, values))
[docs] def parse_limit_offset(self, qdict):
"""
"""
def _parse_pos_int(i):
try:
new_val = int(i)
if new_val >= 0:
return new_val
except (TypeError, ValueError):
pass
return None
limit = _parse_pos_int(qdict.get('limit', None))
offset = _parse_pos_int(qdict.get('offset', None))
return (limit, offset)
Root = BaseController
[docs]class BaseUIController(BaseController):
[docs] def get_object(self, trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None):
try:
return BaseController.get_object(self, trans, id, class_name,
check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted)
except exceptions.MessageException:
raise # handled in the caller
except Exception:
log.exception("Exception in get_object check for %s %s:", class_name, str(id))
raise Exception('Server error retrieving %s id ( %s ).' % (class_name, str(id)))
[docs] def message_exception(self, trans, message, sanitize=True):
trans.response.status = 400
return {'err_msg': util.sanitize_text(message) if sanitize else message}
[docs]class BaseAPIController(BaseController):
[docs] def get_object(self, trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None):
try:
return BaseController.get_object(self, trans, id, class_name,
check_ownership=check_ownership, check_accessible=check_accessible, deleted=deleted)
except exceptions.ItemDeletionException as e:
raise HTTPBadRequest(detail="Invalid %s id ( %s ) specified: %s" % (class_name, str(id), util.unicodify(e)))
except exceptions.MessageException as e:
raise HTTPBadRequest(detail=e.err_msg)
except Exception as e:
log.exception("Exception in get_object check for %s %s.", class_name, str(id))
raise HTTPInternalServerError(comment=util.unicodify(e))
[docs] def validate_in_users_and_groups(self, trans, payload):
"""
For convenience, in_users and in_groups can be encoded IDs or emails/group names in the API.
"""
def get_id(item, model_class, column):
try:
return trans.security.decode_id(item)
except Exception:
pass # maybe an email/group name
# this will raise if the item is invalid
return trans.sa_session.query(model_class).filter(column == item).first().id
new_in_users = []
new_in_groups = []
invalid = []
for item in util.listify(payload.get('in_users', [])):
try:
new_in_users.append(get_id(item, trans.app.model.User, trans.app.model.User.table.c.email))
except Exception:
invalid.append(item)
for item in util.listify(payload.get('in_groups', [])):
try:
new_in_groups.append(get_id(item, trans.app.model.Group, trans.app.model.Group.table.c.name))
except Exception:
invalid.append(item)
if invalid:
msg = "The following value(s) for associated users and/or groups could not be parsed: %s." % ', '.join(invalid)
msg += " Valid values are email addresses of users, names of groups, or IDs of both."
raise Exception(msg)
payload['in_users'] = list(map(str, new_in_users))
payload['in_groups'] = list(map(str, new_in_groups))
def _parse_serialization_params(self, kwd, default_view):
view = kwd.get('view', None)
keys = kwd.get('keys')
if isinstance(keys, string_types):
keys = keys.split(',')
return dict(view=view, keys=keys, default_view=default_view)
def _parse_order_by(self, manager, order_by_string):
ORDER_BY_SEP_CHAR = ','
if ORDER_BY_SEP_CHAR in order_by_string:
return [manager.parse_order_by(o) for o in order_by_string.split(ORDER_BY_SEP_CHAR)]
return manager.parse_order_by(order_by_string)
[docs]class JSAppLauncher(BaseUIController):
"""
A controller that launches JavaScript web applications.
"""
#: path to js app template
JS_APP_MAKO_FILEPATH = "/js-app.mako"
#: window-scoped js function to call to start the app (will be passed options, bootstrapped)
DEFAULT_ENTRY_FN = "app"
#: keys used when serializing current user for bootstrapped data
USER_BOOTSTRAP_KEYS = ('id', 'email', 'username', 'is_admin', 'tags_used',
'total_disk_usage', 'nice_total_disk_usage', 'quota_percent', 'preferences')
[docs] def __init__(self, app):
super(JSAppLauncher, self).__init__(app)
self.user_manager = users.UserManager(app)
self.user_serializer = users.CurrentUserSerializer(app)
self.config_serializer = configuration.ConfigSerializer(app)
self.admin_config_serializer = configuration.AdminConfigSerializer(app)
def _check_require_login(self, trans):
if self.app.config.require_login and self.user_manager.is_anonymous(trans.user):
# TODO: this doesn't properly redirect when login is done
# (see webapp __ensure_logged_in_user for the initial redirect - not sure why it doesn't redirect to login?)
login_url = web.url_for(controller="root", action="login")
trans.response.send_redirect(login_url)
[docs] @web.expose
def client(self, trans, **kwd):
"""
Endpoint for clientside routes. This ships the primary SPA client.
Should not be used with url_for -- see
(https://github.com/galaxyproject/galaxy/issues/1878) for why.
"""
self._check_require_login(trans)
return self._bootstrapped_client(trans, **kwd)
def _bootstrapped_client(self, trans, app_name='analysis', **kwd):
js_options = self._get_js_options(trans)
js_options['config'].update(self._get_extended_config(trans))
return self.template(trans, app_name, options=js_options, **kwd)
def _get_js_options(self, trans, root=None):
"""
Return a dictionary of session/site configuration/options to jsonify
and pass onto the js app.
Defaults to `config`, `user`, and the root url. Pass kwargs to update further.
"""
root = root or web.url_for('/')
js_options = {
'root' : root,
'user' : self.user_serializer.serialize(trans.user, self.USER_BOOTSTRAP_KEYS, trans=trans),
'config' : self._get_site_configuration(trans),
'params' : dict(trans.request.params),
'session_csrf_token' : trans.session_csrf_token,
}
return js_options
def _get_extended_config(self, trans):
config = {
'active_view' : 'analysis',
'enable_cloud_launch' : trans.app.config.get_bool('enable_cloud_launch', False),
'enable_webhooks' : True if trans.app.webhooks_registry.webhooks else False,
# TODO: next two should be redundant - why can't we build one from the other?
'toolbox' : trans.app.toolbox.to_dict(trans, in_panel=False),
'toolbox_in_panel' : trans.app.toolbox.to_dict(trans),
'message_box_visible' : trans.app.config.message_box_visible,
'show_inactivity_warning' : trans.app.config.user_activation_on and trans.user and not trans.user.active,
'tool_shed_urls' : list(trans.app.tool_shed_registry.tool_sheds.values()) if trans.app.tool_shed_registry else [],
'tool_dynamic_configs' : list(trans.app.toolbox.dynamic_conf_filenames())
}
# TODO: move to user
stored_workflow_menu_entries = config['stored_workflow_menu_entries'] = []
for menu_item in getattr(trans.user, 'stored_workflow_menu_entries', []):
stored_workflow_menu_entries.append({
'encoded_stored_workflow_id': trans.security.encode_id(menu_item.stored_workflow_id),
'stored_workflow': {
'name': util.unicodify(menu_item.stored_workflow.name)
}
})
return config
def _get_site_configuration(self, trans):
"""
Return a dictionary representing Galaxy's current configuration.
"""
try:
serializer = self.config_serializer
if self.user_manager.is_admin(trans.user, trans=trans):
serializer = self.admin_config_serializer
return serializer.serialize_to_view(self.app.config, view='all')
except Exception as exc:
log.exception(exc)
return {}
[docs] def template(self, trans, app_name, entry_fn='app', options=None, bootstrapped_data=None, masthead=True, **additional_options):
"""
Render and return the single page mako template that starts the app.
`app_name` (string): the first portion of the webpack bundle to as the app.
`entry_fn` (string): the name of the window-scope function that starts the
app. Defaults to 'app'.
`bootstrapped_data` (dict): (optional) update containing any more data
the app may need.
`masthead` (boolean): (optional, default=True) include masthead elements in
the initial page dom.
`additional_options` (kwargs): update to the options sent to the app.
"""
options = options or self._get_js_options(trans)
options.update(additional_options)
return trans.fill_template(
self.JS_APP_MAKO_FILEPATH,
js_app_name=app_name,
js_app_entry_fn=(entry_fn or self.DEFAULT_ENTRY_FN),
options=options,
bootstrapped=(bootstrapped_data or {}),
masthead=masthead
)
[docs]class Datatype(object):
"""Used for storing in-memory list of datatypes currently in the datatypes registry."""
[docs] def __init__(self, extension, dtype, type_extension, mimetype, display_in_upload):
self.extension = extension
self.dtype = dtype
self.type_extension = type_extension
self.mimetype = mimetype
self.display_in_upload = display_in_upload
#
# -- Mixins for working with Galaxy objects. --
#
[docs]class CreatesApiKeysMixin(object):
"""
Mixing centralizing logic for creating API keys for user objects.
Deprecated - please use api_keys.ApiKeyManager for new development.
"""
[docs] def create_api_key(self, trans, user):
return api_keys.ApiKeyManager(trans.app).create_api_key(user)
[docs]class SharableItemSecurityMixin(object):
""" Mixin for handling security for sharable items. """
[docs] def security_check(self, trans, item, check_ownership=False, check_accessible=False):
""" Security checks for an item: checks if (a) user owns item or (b) item is accessible to user. """
return managers_base.security_check(trans, item, check_ownership=check_ownership, check_accessible=check_accessible)
[docs]class ExportsHistoryMixin(object):
[docs] def serve_ready_history_export(self, trans, jeha):
assert jeha.ready
if jeha.compressed:
trans.response.set_content_type('application/x-gzip')
else:
trans.response.set_content_type('application/x-tar')
disposition = 'attachment; filename="%s"' % jeha.export_name
trans.response.headers["Content-Disposition"] = disposition
archive = trans.app.object_store.get_filename(jeha.dataset)
return open(archive, mode='rb')
[docs] def queue_history_export(self, trans, history, gzip=True, include_hidden=False, include_deleted=False):
# Convert options to booleans.
if isinstance(gzip, string_types):
gzip = (gzip in ['True', 'true', 'T', 't'])
if isinstance(include_hidden, string_types):
include_hidden = (include_hidden in ['True', 'true', 'T', 't'])
if isinstance(include_deleted, string_types):
include_deleted = (include_deleted in ['True', 'true', 'T', 't'])
# Run job to do export.
history_exp_tool = trans.app.toolbox.get_tool('__EXPORT_HISTORY__')
params = {
'history_to_export': history,
'compress': gzip,
'include_hidden': include_hidden,
'include_deleted': include_deleted
}
history_exp_tool.execute(trans, incoming=params, history=history, set_output_hid=True)
[docs]class ImportsHistoryMixin(object):
[docs] def queue_history_import(self, trans, archive_type, archive_source):
# Run job to do import.
history_imp_tool = trans.app.toolbox.get_tool('__IMPORT_HISTORY__')
incoming = {'__ARCHIVE_SOURCE__' : archive_source, '__ARCHIVE_TYPE__' : archive_type}
history_imp_tool.execute(trans, incoming=incoming)
[docs]class UsesLibraryMixin(object):
[docs] def get_library(self, trans, id, check_ownership=False, check_accessible=True):
l = self.get_object(trans, id, 'Library')
if check_accessible and not (trans.user_is_admin or trans.app.security_agent.can_access_library(trans.get_current_user_roles(), l)):
error("LibraryFolder is not accessible to the current user")
return l
[docs]class UsesLibraryMixinItems(SharableItemSecurityMixin):
[docs] def get_library_folder(self, trans, id, check_ownership=False, check_accessible=True):
return self.get_object(trans, id, 'LibraryFolder',
check_ownership=False, check_accessible=check_accessible)
[docs] def get_library_dataset_dataset_association(self, trans, id, check_ownership=False, check_accessible=True):
# Deprecated in lieu to galaxy.managers.lddas.LDDAManager.get() but not
# reusing that exactly because of subtle differences in exception handling
# logic (API controller override get_object to be slightly different).
return self.get_object(trans, id, 'LibraryDatasetDatasetAssociation',
check_ownership=False, check_accessible=check_accessible)
[docs] def get_library_dataset(self, trans, id, check_ownership=False, check_accessible=True):
return self.get_object(trans, id, 'LibraryDataset',
check_ownership=False, check_accessible=check_accessible)
# TODO: it makes no sense that I can get roles from a user but not user.is_admin()
# def can_user_add_to_library_item( self, trans, user, item ):
# if not user: return False
# return ( ( user.is_admin() )
# or ( trans.app.security_agent.can_add_library_item( user.all_roles(), item ) ) )
[docs] def can_current_user_add_to_library_item(self, trans, item):
if not trans.user:
return False
return (trans.user_is_admin or
trans.app.security_agent.can_add_library_item(trans.get_current_user_roles(), item))
[docs] def check_user_can_add_to_library_item(self, trans, item, check_accessible=True):
"""
Raise exception if user cannot add to the specified library item (i.e.
Folder). Can set check_accessible to False if folder was loaded with
this check.
"""
if not trans.user:
return False
current_user_roles = trans.get_current_user_roles()
if trans.user_is_admin:
return True
if check_accessible:
if not trans.app.security_agent.can_access_library_item(current_user_roles, item, trans.user):
raise exceptions.ItemAccessibilityException('You do not have access to the requested item')
if not trans.app.security_agent.can_add_library_item(trans.get_current_user_roles(), item):
# Slight misuse of ItemOwnershipException?
raise exceptions.ItemOwnershipException("User cannot add to library item.")
def _copy_hdca_to_library_folder(self, trans, hda_manager, from_hdca_id, folder_id, ldda_message=''):
"""
Fetches the collection identified by `from_hcda_id` and dispatches individual collection elements to
_copy_hda_to_library_folder
"""
hdca = trans.sa_session.query(trans.app.model.HistoryDatasetCollectionAssociation).get(from_hdca_id)
if hdca.collection.collection_type != 'list':
raise exceptions.NotImplemented('Cannot add nested collections to library. Please flatten your collection first.')
hdas = []
for element in hdca.collection.elements:
hdas.append((element.element_identifier, element.dataset_instance.id))
return [self._copy_hda_to_library_folder(trans,
hda_manager=hda_manager,
from_hda_id=hda_id,
folder_id=folder_id,
ldda_message=ldda_message,
element_identifier=element_identifier) for (element_identifier, hda_id) in hdas]
def _copy_hda_to_library_folder(self, trans, hda_manager, from_hda_id, folder_id, ldda_message='', element_identifier=None):
"""
Copies hda ``from_hda_id`` to library folder ``folder_id``, optionally
adding ``ldda_message`` to the new ldda's ``message``.
``library_contents.create`` will branch to this if called with 'from_hda_id'
in its payload.
"""
log.debug('_copy_hda_to_library_folder: %s' % (str((from_hda_id, folder_id, ldda_message))))
# PRECONDITION: folder_id has already been altered to remove the folder prefix ('F')
# TODO: allow name and other, editable ldda attrs?
if ldda_message:
ldda_message = sanitize_html(ldda_message)
# check permissions on (all three?) resources: hda, library, folder
# TODO: do we really need the library??
hda = hda_manager.get_owned(from_hda_id, trans.user, current_history=trans.history)
hda = hda_manager.error_if_uploading(hda)
folder = self.get_library_folder(trans, folder_id, check_accessible=True)
# TOOD: refactor to use check_user_can_add_to_library_item, eliminate boolean
# can_current_user_add_to_library_item.
if folder.parent_library.deleted:
raise exceptions.ObjectAttributeInvalidException('You cannot add datasets into deleted library. Undelete it first.')
if not self.can_current_user_add_to_library_item(trans, folder):
raise exceptions.InsufficientPermissionsException('You do not have proper permissions to add a dataset to this folder,')
ldda = self.copy_hda_to_library_folder(trans, hda, folder, ldda_message=ldda_message, element_identifier=element_identifier)
# I don't see a reason why hdas copied into libraries should not be visible.
# If there is, refactor `ldda.visible = True` to do this only when adding HDCAs.
ldda.visible = True
ldda.update_parent_folder_update_times()
trans.sa_session.flush()
ldda_dict = ldda.to_dict()
rval = trans.security.encode_dict_ids(ldda_dict)
update_time = ldda.update_time.strftime("%Y-%m-%d %I:%M %p")
rval['update_time'] = update_time
return rval
[docs] def copy_hda_to_library_folder(self, trans, hda, library_folder, roles=None, ldda_message='', element_identifier=None):
# PRECONDITION: permissions for this action on hda and library_folder have been checked
roles = roles or []
# this code was extracted from library_common.add_history_datasets_to_library
# TODO: refactor library_common.add_history_datasets_to_library to use this for each hda to copy
# create the new ldda and apply the folder perms to it
ldda = hda.to_library_dataset_dataset_association(trans, target_folder=library_folder,
roles=roles, ldda_message=ldda_message, element_identifier=element_identifier)
self._apply_library_folder_permissions_to_ldda(trans, library_folder, ldda)
self._apply_hda_permissions_to_ldda(trans, hda, ldda)
# TODO:?? not really clear on how permissions are being traded here
# seems like hda -> ldda permissions should be set in to_library_dataset_dataset_association
# then they get reset in _apply_library_folder_permissions_to_ldda
# then finally, re-applies hda -> ldda for missing actions in _apply_hda_permissions_to_ldda??
return ldda
def _apply_library_folder_permissions_to_ldda(self, trans, library_folder, ldda):
"""
Copy actions/roles from library folder to an ldda (and its library_dataset).
"""
# PRECONDITION: permissions for this action on library_folder and ldda have been checked
security_agent = trans.app.security_agent
security_agent.copy_library_permissions(trans, library_folder, ldda)
security_agent.copy_library_permissions(trans, library_folder, ldda.library_dataset)
return security_agent.get_permissions(ldda)
def _apply_hda_permissions_to_ldda(self, trans, hda, ldda):
"""
Copy actions/roles from hda to ldda.library_dataset (and then ldda) if ldda
doesn't already have roles for the given action.
"""
# PRECONDITION: permissions for this action on hda and ldda have been checked
# Make sure to apply any defined dataset permissions, allowing the permissions inherited from the
# library_dataset to over-ride the same permissions on the dataset, if they exist.
security_agent = trans.app.security_agent
dataset_permissions_dict = security_agent.get_permissions(hda.dataset)
library_dataset = ldda.library_dataset
library_dataset_actions = [permission.action for permission in library_dataset.actions]
# except that: if DATASET_MANAGE_PERMISSIONS exists in the hda.dataset permissions,
# we need to instead apply those roles to the LIBRARY_MANAGE permission to the library dataset
dataset_manage_permissions_action = security_agent.get_action('DATASET_MANAGE_PERMISSIONS').action
library_manage_permissions_action = security_agent.get_action('LIBRARY_MANAGE').action
# TODO: test this and remove if in loop below
# TODO: doesn't handle action.action
# if dataset_manage_permissions_action in dataset_permissions_dict:
# managing_roles = dataset_permissions_dict.pop( dataset_manage_permissions_action )
# dataset_permissions_dict[ library_manage_permissions_action ] = managing_roles
flush_needed = False
for action, dataset_permissions_roles in dataset_permissions_dict.items():
if isinstance(action, security.Action):
action = action.action
# alter : DATASET_MANAGE_PERMISSIONS -> LIBRARY_MANAGE (see above)
if action == dataset_manage_permissions_action:
action = library_manage_permissions_action
# TODO: generalize to util.update_dict_without_overwrite
# add the hda actions & roles to the library_dataset
# NOTE: only apply an hda perm if it's NOT set in the library_dataset perms (don't overwrite)
if action not in library_dataset_actions:
for role in dataset_permissions_roles:
ldps = trans.model.LibraryDatasetPermissions(action, library_dataset, role)
ldps = [ldps] if not isinstance(ldps, list) else ldps
for ldp in ldps:
trans.sa_session.add(ldp)
flush_needed = True
if flush_needed:
trans.sa_session.flush()
# finally, apply the new library_dataset to its associated ldda (must be the same)
security_agent.copy_library_permissions(trans, library_dataset, ldda)
return security_agent.get_permissions(ldda)
[docs]class UsesVisualizationMixin(UsesLibraryMixinItems):
"""
Mixin for controllers that use Visualization objects.
"""
[docs] def get_visualization(self, trans, id, check_ownership=True, check_accessible=False):
"""
Get a Visualization from the database by id, verifying ownership.
"""
# Load workflow from database
try:
visualization = trans.sa_session.query(trans.model.Visualization).get(trans.security.decode_id(id))
except TypeError:
visualization = None
if not visualization:
error("Visualization not found")
else:
return self.security_check(trans, visualization, check_ownership, check_accessible)
[docs] def get_visualizations_by_user(self, trans, user, order_by=None, query_only=False):
"""
Return query or query results of visualizations filtered by a user.
Set `order_by` to a column or list of columns to change the order
returned. Defaults to `DEFAULT_ORDER_BY`.
Set `query_only` to return just the query for further filtering or
processing.
"""
# TODO: move into model (as class attr)
DEFAULT_ORDER_BY = [model.Visualization.title]
if not order_by:
order_by = DEFAULT_ORDER_BY
if not isinstance(order_by, list):
order_by = [order_by]
query = trans.sa_session.query(model.Visualization)
query = query.filter(model.Visualization.user == user)
if order_by:
query = query.order_by(*order_by)
if query_only:
return query
return query.all()
[docs] def get_published_visualizations(self, trans, exclude_user=None, order_by=None, query_only=False):
"""
Return query or query results for published visualizations optionally excluding
the user in `exclude_user`.
Set `order_by` to a column or list of columns to change the order
returned. Defaults to `DEFAULT_ORDER_BY`.
Set `query_only` to return just the query for further filtering or
processing.
"""
DEFAULT_ORDER_BY = [model.Visualization.title]
if not order_by:
order_by = DEFAULT_ORDER_BY
if not isinstance(order_by, list):
order_by = [order_by]
query = trans.sa_session.query(model.Visualization)
query = query.filter(model.Visualization.published == true())
if exclude_user:
query = query.filter(model.Visualization.user != exclude_user)
if order_by:
query = query.order_by(*order_by)
if query_only:
return query
return query.all()
# TODO: move into model (to_dict)
[docs] def get_visualization_summary_dict(self, visualization):
"""
Return a set of summary attributes for a visualization in dictionary form.
NOTE: that encoding ids isn't done here should happen at the caller level.
"""
# TODO: deleted
# TODO: importable
return {
'id' : visualization.id,
'title' : visualization.title,
'type' : visualization.type,
'dbkey' : visualization.dbkey,
}
[docs] def get_visualization_dict(self, visualization):
"""
Return a set of detailed attributes for a visualization in dictionary form.
The visualization's latest_revision is returned in its own sub-dictionary.
NOTE: that encoding ids isn't done here should happen at the caller level.
"""
return {
'model_class': 'Visualization',
'id' : visualization.id,
'title' : visualization.title,
'type' : visualization.type,
'user_id' : visualization.user.id,
'dbkey' : visualization.dbkey,
'slug' : visualization.slug,
# to_dict only the latest revision (allow older to be fetched elsewhere)
'latest_revision' : self.get_visualization_revision_dict(visualization.latest_revision),
'revisions' : [r.id for r in visualization.revisions],
}
[docs] def get_visualization_revision_dict(self, revision):
"""
Return a set of detailed attributes for a visualization in dictionary form.
NOTE: that encoding ids isn't done here should happen at the caller level.
"""
return {
'model_class' : 'VisualizationRevision',
'id' : revision.id,
'visualization_id' : revision.visualization.id,
'title' : revision.title,
'dbkey' : revision.dbkey,
'config' : revision.config,
}
[docs] def import_visualization(self, trans, id, user=None):
"""
Copy the visualization with the given id and associate the copy
with the given user (defaults to trans.user).
Raises `ItemAccessibilityException` if `user` is not passed and
the current user is anonymous, and if the visualization is not `importable`.
Raises `ItemDeletionException` if the visualization has been deleted.
"""
# default to trans.user, error if anon
if not user:
if not trans.user:
raise exceptions.ItemAccessibilityException("You must be logged in to import Galaxy visualizations")
user = trans.user
# check accessibility
visualization = self.get_visualization(trans, id, check_ownership=False)
if not visualization.importable:
raise exceptions.ItemAccessibilityException("The owner of this visualization has disabled imports via this link.")
if visualization.deleted:
raise exceptions.ItemDeletionException("You can't import this visualization because it has been deleted.")
# copy vis and alter title
# TODO: need to handle custom db keys.
imported_visualization = visualization.copy(user=user, title="imported: " + visualization.title)
trans.sa_session.add(imported_visualization)
trans.sa_session.flush()
return imported_visualization
[docs] def create_visualization(self, trans, type, title="Untitled Visualization", slug=None,
dbkey=None, annotation=None, config={}, save=True):
"""
Create visualiation and first revision.
"""
visualization = self._create_visualization(trans, title, type, dbkey, slug, annotation, save)
# TODO: handle this error structure better either in _create or here
if isinstance(visualization, dict):
err_dict = visualization
raise ValueError(err_dict['title_err'] or err_dict['slug_err'])
# Create and save first visualization revision
revision = trans.model.VisualizationRevision(visualization=visualization, title=title,
config=config, dbkey=dbkey)
visualization.latest_revision = revision
if save:
session = trans.sa_session
session.add(revision)
session.flush()
return visualization
[docs] def add_visualization_revision(self, trans, visualization, config, title, dbkey):
"""
Adds a new `VisualizationRevision` to the given `visualization` with
the given parameters and set its parent visualization's `latest_revision`
to the new revision.
"""
# precondition: only add new revision on owned vis's
# TODO:?? should we default title, dbkey, config? to which: visualization or latest_revision?
revision = trans.model.VisualizationRevision(visualization, title, dbkey, config)
visualization.latest_revision = revision
# TODO:?? does this automatically add revision to visualzation.revisions?
trans.sa_session.add(revision)
trans.sa_session.flush()
return revision
[docs] def save_visualization(self, trans, config, type, id=None, title=None, dbkey=None, slug=None, annotation=None):
session = trans.sa_session
# Create/get visualization.
if not id:
# Create new visualization.
vis = self._create_visualization(trans, title, type, dbkey, slug, annotation)
else:
decoded_id = trans.security.decode_id(id)
vis = session.query(trans.model.Visualization).get(decoded_id)
# TODO: security check?
# Create new VisualizationRevision that will be attached to the viz
vis_rev = trans.model.VisualizationRevision()
vis_rev.visualization = vis
# do NOT alter the dbkey
vis_rev.dbkey = vis.dbkey
# do alter the title and config
vis_rev.title = title
# -- Validate config. --
if vis.type == 'trackster':
def unpack_track(track_dict):
""" Unpack a track from its json. """
dataset_dict = track_dict['dataset']
return {
"dataset_id": trans.security.decode_id(dataset_dict['id']),
"hda_ldda": dataset_dict.get('hda_ldda', 'hda'),
"track_type": track_dict['track_type'],
"prefs": track_dict['prefs'],
"mode": track_dict['mode'],
"filters": track_dict['filters'],
"tool_state": track_dict['tool_state']
}
def unpack_collection(collection_json):
""" Unpack a collection from its json. """
unpacked_drawables = []
drawables = collection_json['drawables']
for drawable_json in drawables:
if 'track_type' in drawable_json:
drawable = unpack_track(drawable_json)
else:
drawable = unpack_collection(drawable_json)
unpacked_drawables.append(drawable)
return {
"obj_type": collection_json['obj_type'],
"drawables": unpacked_drawables,
"prefs": collection_json.get('prefs', []),
"filters": collection_json.get('filters', None)
}
# TODO: unpack and validate bookmarks:
def unpack_bookmarks(bookmarks_json):
return bookmarks_json
# Unpack and validate view content.
view_content = unpack_collection(config['view'])
bookmarks = unpack_bookmarks(config['bookmarks'])
vis_rev.config = {"view": view_content, "bookmarks": bookmarks}
# Viewport from payload
if 'viewport' in config:
chrom = config['viewport']['chrom']
start = config['viewport']['start']
end = config['viewport']['end']
overview = config['viewport']['overview']
vis_rev.config["viewport"] = {'chrom': chrom, 'start': start, 'end': end, 'overview': overview}
else:
# Default action is to save the config as is with no validation.
vis_rev.config = config
vis.latest_revision = vis_rev
session.add(vis_rev)
session.flush()
encoded_id = trans.security.encode_id(vis.id)
return {"vis_id": encoded_id, "url": url_for(controller='visualization', action=vis.type, id=encoded_id)}
[docs] def get_tool_def(self, trans, hda):
""" Returns definition of an interactive tool for an HDA. """
# Get dataset's job.
job = None
for job_output_assoc in hda.creating_job_associations:
job = job_output_assoc.job
break
if not job:
return None
tool = trans.app.toolbox.get_tool(job.tool_id, tool_version=job.tool_version)
if not tool:
return None
# Tool must have a Trackster configuration.
if not tool.trackster_conf:
return None
# -- Get tool definition and add input values from job. --
tool_dict = tool.to_dict(trans, io_details=True)
tool_param_values = dict([(p.name, p.value) for p in job.parameters])
tool_param_values = tool.params_from_strings(tool_param_values, trans.app, ignore_errors=True)
# Only get values for simple inputs for now.
inputs_dict = [i for i in tool_dict['inputs'] if i['type'] not in ['data', 'hidden_data', 'conditional']]
for t_input in inputs_dict:
# Add value to tool.
if 'name' in t_input:
name = t_input['name']
if name in tool_param_values:
value = tool_param_values[name]
if isinstance(value, Dictifiable):
value = value.to_dict()
t_input['value'] = value
return tool_dict
[docs] def get_visualization_config(self, trans, visualization):
""" Returns a visualization's configuration. Only works for trackster visualizations right now. """
config = None
if visualization.type in ['trackster', 'genome']:
# Unpack Trackster config.
latest_revision = visualization.latest_revision
bookmarks = latest_revision.config.get('bookmarks', [])
def pack_track(track_dict):
dataset_id = track_dict['dataset_id']
hda_ldda = track_dict.get('hda_ldda', 'hda')
dataset_id = trans.security.encode_id(dataset_id)
dataset = self.get_hda_or_ldda(trans, hda_ldda, dataset_id)
try:
prefs = track_dict['prefs']
except KeyError:
prefs = {}
track_data_provider = trans.app.data_provider_registry.get_data_provider(trans,
original_dataset=dataset,
source='data')
return {
"track_type": dataset.datatype.track_type,
"dataset": trans.security.encode_dict_ids(dataset.to_dict()),
"prefs": prefs,
"mode": track_dict.get('mode', 'Auto'),
"filters": track_dict.get('filters', {'filters' : track_data_provider.get_filters()}),
"tool": self.get_tool_def(trans, dataset),
"tool_state": track_dict.get('tool_state', {})
}
def pack_collection(collection_dict):
drawables = []
for drawable_dict in collection_dict['drawables']:
if 'track_type' in drawable_dict:
drawables.append(pack_track(drawable_dict))
else:
drawables.append(pack_collection(drawable_dict))
return {
'obj_type': collection_dict['obj_type'],
'drawables': drawables,
'prefs': collection_dict.get('prefs', []),
'filters': collection_dict.get('filters', {})
}
def encode_dbkey(dbkey):
"""
Encodes dbkey as needed. For now, prepends user's public name
to custom dbkey keys.
"""
encoded_dbkey = dbkey
user = visualization.user
if 'dbkeys' in user.preferences and str(dbkey) in user.preferences['dbkeys']:
encoded_dbkey = "%s:%s" % (user.username, dbkey)
return encoded_dbkey
# Set tracks.
tracks = []
if 'tracks' in latest_revision.config:
# Legacy code.
for track_dict in visualization.latest_revision.config['tracks']:
tracks.append(pack_track(track_dict))
elif 'view' in latest_revision.config:
for drawable_dict in visualization.latest_revision.config['view']['drawables']:
if 'track_type' in drawable_dict:
tracks.append(pack_track(drawable_dict))
else:
tracks.append(pack_collection(drawable_dict))
config = {"title": visualization.title,
"vis_id": trans.security.encode_id(visualization.id),
"tracks": tracks,
"bookmarks": bookmarks,
"chrom": "",
"dbkey": encode_dbkey(visualization.dbkey)}
if 'viewport' in latest_revision.config:
config['viewport'] = latest_revision.config['viewport']
else:
# Default action is to return config unaltered.
latest_revision = visualization.latest_revision
config = latest_revision.config
return config
[docs] def get_new_track_config(self, trans, dataset):
"""
Returns track configuration dict for a dataset.
"""
# Get data provider.
track_data_provider = trans.app.data_provider_registry.get_data_provider(trans, original_dataset=dataset)
# Get track definition.
return {
"track_type": dataset.datatype.track_type,
"name": dataset.name,
"dataset": trans.security.encode_dict_ids(dataset.to_dict()),
"prefs": {},
"filters": {'filters' : track_data_provider.get_filters()},
"tool": self.get_tool_def(trans, dataset),
"tool_state": {}
}
[docs] def get_hda_or_ldda(self, trans, hda_ldda, dataset_id):
""" Returns either HDA or LDDA for hda/ldda and id combination. """
if hda_ldda == "hda":
return self.get_hda(trans, dataset_id, check_ownership=False, check_accessible=True)
else:
return self.get_library_dataset_dataset_association(trans, dataset_id)
[docs] def get_hda(self, trans, dataset_id, check_ownership=True, check_accessible=False, check_state=True):
"""
Get an HDA object by id performing security checks using
the current transaction.
Deprecated in lieu to galaxy.managers.hdas.HDAManager.get_accessible(decoded_id, user)
"""
try:
dataset_id = trans.security.decode_id(dataset_id)
except (AttributeError, TypeError):
raise HTTPBadRequest("Invalid dataset id: %s." % str(dataset_id))
try:
data = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(int(dataset_id))
except Exception:
raise HTTPBadRequest("Invalid dataset id: %s." % str(dataset_id))
if not data:
raise HTTPBadRequest("Invalid dataset id: %s." % str(dataset_id))
if check_ownership:
# Verify ownership.
user = trans.get_user()
if not user:
error("Must be logged in to manage Galaxy items")
if data.history.user != user:
error("%s is not owned by current user" % data.__class__.__name__)
if check_accessible:
current_user_roles = trans.get_current_user_roles()
if not trans.app.security_agent.can_access_dataset(current_user_roles, data.dataset):
error("You are not allowed to access this dataset")
if check_state and data.state == trans.model.Dataset.states.UPLOAD:
return trans.show_error_message("Please wait until this dataset finishes uploading " +
"before attempting to view it.")
return data
# -- Helper functions --
def _create_visualization(self, trans, title, type, dbkey=None, slug=None, annotation=None, save=True):
""" Create visualization but not first revision. Returns Visualization object. """
user = trans.get_user()
# Error checking.
title_err = slug_err = ""
if not title:
title_err = "visualization name is required"
elif slug and not managers_base.is_valid_slug(slug):
slug_err = "visualization identifier must consist of only lowercase letters, numbers, and the '-' character"
elif slug and trans.sa_session.query(trans.model.Visualization).filter_by(user=user, slug=slug, deleted=False).first():
slug_err = "visualization identifier must be unique"
if title_err or slug_err:
return {'title_err': title_err, 'slug_err': slug_err}
# Create visualization
visualization = trans.model.Visualization(user=user, title=title, dbkey=dbkey, type=type)
if slug:
visualization.slug = slug
else:
self.create_item_slug(trans.sa_session, visualization)
if annotation:
annotation = sanitize_html(annotation)
# TODO: if this is to stay in the mixin, UsesAnnotations should be added to the superclasses
# right now this is depending on the classes that include this mixin to have UsesAnnotations
self.add_item_annotation(trans.sa_session, trans.user, visualization, annotation)
if save:
session = trans.sa_session
session.add(visualization)
session.flush()
return visualization
def _get_genome_data(self, trans, dataset, dbkey=None):
"""
Returns genome-wide data for dataset if available; if not, message is returned.
"""
rval = None
# Get data sources.
data_sources = dataset.get_datasources(trans)
query_dbkey = dataset.dbkey
if query_dbkey == "?":
query_dbkey = dbkey
chroms_info = self.app.genomes.chroms(trans, dbkey=query_dbkey)
# If there are no messages (messages indicate data is not ready/available), get data.
messages_list = [data_source_dict['message'] for data_source_dict in data_sources.values()]
message = self._get_highest_priority_msg(messages_list)
if message:
rval = message
else:
# HACK: chromatin interactions tracks use data as source.
source = 'index'
if isinstance(dataset.datatype, ChromatinInteractions):
source = 'data'
data_provider = trans.app.data_provider_registry.get_data_provider(trans,
original_dataset=dataset,
source=source)
# HACK: pass in additional params which are used for only some
# types of data providers; level, cutoffs used for summary tree,
# num_samples for BBI, and interchromosomal used for chromatin interactions.
rval = data_provider.get_genome_data(chroms_info,
level=4, detail_cutoff=0, draw_cutoff=0,
num_samples=150,
interchromosomal=True)
return rval
# FIXME: this method probably belongs down in the model.Dataset class.
def _get_highest_priority_msg(self, message_list):
"""
Returns highest priority message from a list of messages.
"""
return_message = None
# For now, priority is: job error (dict), no converter, pending.
for message in message_list:
if message is not None:
if isinstance(message, dict):
return_message = message
break
elif message == "no converter":
return_message = message
elif return_message is None and message == "pending":
return_message = message
return return_message
[docs]class UsesStoredWorkflowMixin(SharableItemSecurityMixin, UsesAnnotations):
""" Mixin for controllers that use StoredWorkflow objects. """
[docs] def get_stored_workflow(self, trans, id, check_ownership=True, check_accessible=False):
""" Get a StoredWorkflow from the database by id, verifying ownership. """
# Load workflow from database
workflow_contents_manager = workflows.WorkflowsManager(self.app)
workflow = workflow_contents_manager.get_stored_workflow(trans=trans, workflow_id=id)
if not workflow:
error("Workflow not found")
else:
self.security_check(trans, workflow, check_ownership, check_accessible)
# Older workflows may be missing slugs, so set them here.
if not workflow.slug:
self.create_item_slug(trans.sa_session, workflow)
trans.sa_session.flush()
return workflow
[docs] def get_stored_workflow_steps(self, trans, stored_workflow):
""" Restores states for a stored workflow's steps. """
module_injector = WorkflowModuleInjector(trans)
for step in stored_workflow.latest_workflow.steps:
try:
module_injector.inject(step, exact_tools=False)
except exceptions.ToolMissingException:
pass
def _import_shared_workflow(self, trans, stored):
""" Imports a shared workflow """
# Copy workflow.
imported_stored = model.StoredWorkflow()
imported_stored.name = "imported: " + stored.name
workflow = stored.latest_workflow.copy()
workflow.stored_workflow = imported_stored
imported_stored.latest_workflow = workflow
imported_stored.user = trans.user
# Save new workflow.
session = trans.sa_session
session.add(imported_stored)
session.flush()
# Copy annotations.
self.copy_item_annotation(session, stored.user, stored, imported_stored.user, imported_stored)
for order_index, step in enumerate(stored.latest_workflow.steps):
self.copy_item_annotation(session, stored.user, step,
imported_stored.user, imported_stored.latest_workflow.steps[order_index])
session.flush()
return imported_stored
def _workflow_from_dict(self, trans, data, source=None, add_to_menu=False, publish=False, exact_tools=True, fill_defaults=False):
"""
Creates a workflow from a dict. Created workflow is stored in the database and returned.
"""
# TODO: replace this method with direct access to manager.
workflow_contents_manager = workflows.WorkflowContentsManager(self.app)
raw_workflow_description = workflow_contents_manager.ensure_raw_description(data)
created_workflow = workflow_contents_manager.build_workflow_from_raw_description(
trans,
raw_workflow_description,
source=source,
add_to_menu=add_to_menu,
publish=publish,
exact_tools=exact_tools,
fill_defaults=fill_defaults,
)
return created_workflow.stored_workflow, created_workflow.missing_tools
def _workflow_to_dict(self, trans, stored):
"""
Converts a workflow to a dict of attributes suitable for exporting.
"""
workflow_contents_manager = workflows.WorkflowContentsManager(self.app)
return workflow_contents_manager.workflow_to_dict(
trans,
stored,
)
[docs]class UsesFormDefinitionsMixin(object):
"""Mixin for controllers that use Galaxy form objects."""
[docs] def get_all_forms(self, trans, all_versions=False, filter=None, form_type='All'):
"""
Return all the latest forms from the form_definition_current table
if all_versions is set to True. Otherwise return all the versions
of all the forms from the form_definition table.
"""
if all_versions:
return trans.sa_session.query(trans.app.model.FormDefinition)
if filter:
fdc_list = trans.sa_session.query(trans.app.model.FormDefinitionCurrent).filter_by(**filter)
else:
fdc_list = trans.sa_session.query(trans.app.model.FormDefinitionCurrent)
if form_type == 'All':
return [fdc.latest_form for fdc in fdc_list]
else:
return [fdc.latest_form for fdc in fdc_list if fdc.latest_form.type == form_type]
[docs] def save_widget_field(self, trans, field_obj, widget_name, **kwd):
# Save a form_builder field object
params = util.Params(kwd)
if isinstance(field_obj, trans.model.UserAddress):
field_obj.desc = util.restore_text(params.get('%s_short_desc' % widget_name, ''))
field_obj.name = util.restore_text(params.get('%s_name' % widget_name, ''))
field_obj.institution = util.restore_text(params.get('%s_institution' % widget_name, ''))
field_obj.address = util.restore_text(params.get('%s_address' % widget_name, ''))
field_obj.city = util.restore_text(params.get('%s_city' % widget_name, ''))
field_obj.state = util.restore_text(params.get('%s_state' % widget_name, ''))
field_obj.postal_code = util.restore_text(params.get('%s_postal_code' % widget_name, ''))
field_obj.country = util.restore_text(params.get('%s_country' % widget_name, ''))
field_obj.phone = util.restore_text(params.get('%s_phone' % widget_name, ''))
trans.sa_session.add(field_obj)
trans.sa_session.flush()
[docs] def get_form_values(self, trans, user, form_definition, **kwd):
'''
Returns the name:value dictionary containing all the form values
'''
params = util.Params(kwd)
values = {}
for field in form_definition.fields:
field_type = field['type']
field_name = field['name']
input_value = params.get(field_name, '')
if field_type == AddressField.__name__:
input_text_value = util.restore_text(input_value)
if input_text_value == 'new':
# Save this new address in the list of this user's addresses
user_address = trans.model.UserAddress(user=user)
self.save_widget_field(trans, user_address, field_name, **kwd)
trans.sa_session.refresh(user)
field_value = int(user_address.id)
elif input_text_value in ['', 'none', 'None', None]:
field_value = ''
else:
field_value = int(input_text_value)
elif field_type == CheckboxField.__name__:
field_value = CheckboxField.is_checked(input_value)
elif field_type == PasswordField.__name__:
field_value = kwd.get(field_name, '')
else:
field_value = util.restore_text(input_value)
values[field_name] = field_value
return values
[docs]class SharableMixin(object):
""" Mixin for a controller that manages an item that can be shared. """
manager = None
serializer = None
# -- Implemented methods. --
def _is_valid_slug(self, slug):
""" Returns true if slug is valid. """
return managers_base.is_valid_slug(slug)
[docs] @web.expose
@web.require_login("modify Galaxy items")
def set_slug_async(self, trans, id, new_slug):
item = self.get_item(trans, id)
if item:
# Only update slug if slug is not already in use.
if trans.sa_session.query(item.__class__).filter_by(user=item.user, slug=new_slug).count() == 0:
item.slug = new_slug
trans.sa_session.flush()
return item.slug
def _make_item_accessible(self, sa_session, item):
""" Makes item accessible--viewable and importable--and sets item's slug.
Does not flush/commit changes, however. Item must have name, user,
importable, and slug attributes. """
item.importable = True
self.create_item_slug(sa_session, item)
[docs] def create_item_slug(self, sa_session, item):
""" Create/set item slug. Slug is unique among user's importable items
for item's class. Returns true if item's slug was set/changed; false
otherwise.
"""
cur_slug = item.slug
# Setup slug base.
if cur_slug is None or cur_slug == "":
# Item can have either a name or a title.
if hasattr(item, 'name'):
item_name = item.name
elif hasattr(item, 'title'):
item_name = item.title
slug_base = util.ready_name_for_url(item_name.lower())
else:
slug_base = cur_slug
# Using slug base, find a slug that is not taken. If slug is taken,
# add integer to end.
new_slug = slug_base
count = 1
# Ensure unique across model class and user and don't include this item
# in the check in case it has previously been assigned a valid slug.
while sa_session.query(item.__class__).filter(item.__class__.user == item.user, item.__class__.slug == new_slug, item.__class__.id != item.id).count() != 0:
# Slug taken; choose a new slug based on count. This approach can
# handle numerous items with the same name gracefully.
new_slug = '%s-%i' % (slug_base, count)
count += 1
# Set slug and return.
item.slug = new_slug
return item.slug == cur_slug
[docs] @web.legacy_expose_api
def sharing(self, trans, id, payload=None, **kwd):
skipped = False
class_name = self.manager.model_class.__name__
item = self.get_object(trans, id, class_name, check_ownership=True, check_accessible=True, deleted=False)
if payload and payload.get("action"):
action = payload.get("action")
if action == "make_accessible_via_link":
self._make_item_accessible(trans.sa_session, item)
if hasattr(item, "has_possible_members") and item.has_possible_members and payload.get("make_members_public", False):
shared, skipped = self._make_members_public(trans, item)
elif action == "make_accessible_and_publish":
self._make_item_accessible(trans.sa_session, item)
if hasattr(item, "has_possible_members") and item.has_possible_members and payload.get("make_members_public", False):
shared, skipped = self._make_members_public(trans, item)
item.published = True
elif action == "publish":
if item.importable:
item.published = True
if hasattr(item, "has_possible_members") and item.has_possible_members and payload.get("make_members_public", False):
shared, skipped = self._make_members_public(trans, item)
else:
raise exceptions.MessageException("%s not importable." % class_name)
elif action == "disable_link_access":
item.importable = False
elif action == "unpublish":
item.published = False
elif action == "disable_link_access_and_unpublish":
item.importable = item.published = False
elif action == "unshare_user":
user = trans.sa_session.query(trans.app.model.User).get(self.decode_id(payload.get("user_id")))
class_name_lc = class_name.lower()
ShareAssociation = getattr(trans.app.model, "%sUserShareAssociation" % class_name)
usas = trans.sa_session.query(ShareAssociation).filter_by(**{"user": user, class_name_lc: item}).all()
if not usas:
raise exceptions.MessageException("%s was not shared with user." % class_name)
for usa in usas:
trans.sa_session.delete(usa)
trans.sa_session.add(item)
trans.sa_session.flush()
if item.importable and not item.slug:
self._make_item_accessible(trans.sa_session, item)
item_dict = self.serializer.serialize_to_view(item,
user=trans.user, trans=trans, default_view="sharing")
item_dict["users_shared_with"] = [{"id": self.app.security.encode_id(a.user.id), "email": a.user.email} for a in item.users_shared_with]
if skipped:
item_dict["skipped"] = True
return item_dict
def _make_members_public(self, trans, item):
""" Make the non-purged datasets in history public
Performs pemissions check.
"""
# TODO eventually we should handle more classes than just History
skipped = False
for hda in item.activatable_datasets:
dataset = hda.dataset
if not trans.app.security_agent.dataset_is_public(dataset):
if trans.app.security_agent.can_manage_dataset(trans.user.all_roles(), dataset):
try:
trans.app.security_agent.make_dataset_public(hda.dataset)
except Exception:
log.warning("Unable to make dataset with id: %s public", dataset.id)
skipped = True
else:
log.warning("User without permissions tried to make dataset with id: %s public", dataset.id)
skipped = True
return item, skipped
# -- Abstract methods. --
[docs] @web.expose
def display_by_username_and_slug(self, trans, username, slug):
""" Display item by username and slug. """
raise NotImplementedError()
[docs] @web.json
@web.require_login("get item name and link")
def get_name_and_link_async(self, trans, id=None):
""" Returns item's name and link. """
raise NotImplementedError()
[docs] @web.expose
@web.require_login("get item content asynchronously")
def get_item_content_async(self, trans, id):
""" Returns item content in HTML format. """
raise NotImplementedError()
[docs]class UsesQuotaMixin(object):
[docs] def get_quota(self, trans, id, check_ownership=False, check_accessible=False, deleted=None):
return self.get_object(trans, id, 'Quota', check_ownership=False, check_accessible=False, deleted=deleted)
[docs]class UsesTagsMixin(SharableItemSecurityMixin):
def _get_user_tags(self, trans, item_class_name, id):
user = trans.user
tagged_item = self._get_tagged_item(trans, item_class_name, id)
return [tag for tag in tagged_item.tags if tag.user == user]
def _get_tagged_item(self, trans, item_class_name, id, check_ownership=True):
tagged_item = self.get_object(trans, id, item_class_name, check_ownership=check_ownership, check_accessible=True)
return tagged_item
def _remove_items_tag(self, trans, item_class_name, id, tag_name):
"""Remove a tag from an item."""
user = trans.user
tagged_item = self._get_tagged_item(trans, item_class_name, id)
deleted = tagged_item and self.get_tag_handler(trans).remove_item_tag(trans, user, tagged_item, tag_name)
trans.sa_session.flush()
return deleted
def _apply_item_tag(self, trans, item_class_name, id, tag_name, tag_value=None):
user = trans.user
tagged_item = self._get_tagged_item(trans, item_class_name, id)
tag_assoc = self.get_tag_handler(trans).apply_item_tag(user, tagged_item, tag_name, tag_value)
trans.sa_session.flush()
return tag_assoc
def _get_item_tag_assoc(self, trans, item_class_name, id, tag_name):
user = trans.user
tagged_item = self._get_tagged_item(trans, item_class_name, id)
log.debug("In get_item_tag_assoc with tagged_item %s" % tagged_item)
return self.get_tag_handler(trans)._get_item_tag_assoc(user, tagged_item, tag_name)
[docs] def set_tags_from_list(self, trans, item, new_tags_list, user=None):
tag_handler = tags.GalaxyTagHandler(trans.app.model.context)
return tag_handler.set_tags_from_list(user, item, new_tags_list)
[docs] def get_user_tags_used(self, trans, user=None):
"""
Return a list of distinct 'user_tname:user_value' strings that the
given user has used.
user defaults to trans.user.
Returns an empty list if no user is given and trans.user is anonymous.
"""
# TODO: for lack of a UsesUserMixin - placing this here - maybe into UsesTags, tho
user = user or trans.user
if not user:
return []
# get all the taggable model TagAssociations
tag_models = [v.tag_assoc_class for v in trans.app.tag_handler.item_tag_assoc_info.values()]
# create a union of subqueries for each for this user - getting only the tname and user_value
all_tags_query = None
for tag_model in tag_models:
subq = (trans.sa_session.query(tag_model.user_tname, tag_model.user_value)
.filter(tag_model.user == trans.user))
all_tags_query = subq if all_tags_query is None else all_tags_query.union(subq)
# if nothing init'd the query, bail
if all_tags_query is None:
return []
# boil the tag tuples down into a sorted list of DISTINCT name:val strings
tags = all_tags_query.distinct().all()
tags = [((name + ':' + val) if val else name) for name, val in tags]
return sorted(tags)
[docs]class UsesExtendedMetadataMixin(SharableItemSecurityMixin):
""" Mixin for getting and setting item extended metadata. """
[docs] def get_item_extended_metadata_obj(self, trans, item):
"""
Given an item object (such as a LibraryDatasetDatasetAssociation), find the object
of the associated extended metadata
"""
if item.extended_metadata:
return item.extended_metadata
return None
[docs] def set_item_extended_metadata_obj(self, trans, item, extmeta_obj, check_writable=False):
if item.__class__ == LibraryDatasetDatasetAssociation:
if not check_writable or trans.app.security_agent.can_modify_library_item(trans.get_current_user_roles(), item, trans.user):
item.extended_metadata = extmeta_obj
trans.sa_session.flush()
if item.__class__ == HistoryDatasetAssociation:
history = None
if check_writable:
history = self.security_check(trans, item, check_ownership=True, check_accessible=True)
else:
history = self.security_check(trans, item, check_ownership=False, check_accessible=True)
if history:
item.extended_metadata = extmeta_obj
trans.sa_session.flush()
[docs] def unset_item_extended_metadata_obj(self, trans, item, check_writable=False):
if item.__class__ == LibraryDatasetDatasetAssociation:
if not check_writable or trans.app.security_agent.can_modify_library_item(trans.get_current_user_roles(), item, trans.user):
item.extended_metadata = None
trans.sa_session.flush()
if item.__class__ == HistoryDatasetAssociation:
history = None
if check_writable:
history = self.security_check(trans, item, check_ownership=True, check_accessible=True)
else:
history = self.security_check(trans, item, check_ownership=False, check_accessible=True)
if history:
item.extended_metadata = None
trans.sa_session.flush()
[docs] def create_extended_metadata(self, trans, extmeta):
"""
Create/index an extended metadata object. The returned object is
not associated with any items
"""
ex_meta = ExtendedMetadata(extmeta)
trans.sa_session.add(ex_meta)
trans.sa_session.flush()
for path, value in self._scan_json_block(extmeta):
meta_i = ExtendedMetadataIndex(ex_meta, path, value)
trans.sa_session.add(meta_i)
trans.sa_session.flush()
return ex_meta
[docs] def delete_extended_metadata(self, trans, item):
if item.__class__ == ExtendedMetadata:
trans.sa_session.delete(item)
trans.sa_session.flush()
def _scan_json_block(self, meta, prefix=""):
"""
Scan a json style data structure, and emit all fields and their values.
Example paths
Data
{ "data" : [ 1, 2, 3 ] }
Path:
/data == [1,2,3]
/data/[0] == 1
"""
if isinstance(meta, dict):
for a in meta:
for path, value in self._scan_json_block(meta[a], prefix + "/" + a):
yield path, value
elif isinstance(meta, list):
for i, a in enumerate(meta):
for path, value in self._scan_json_block(a, prefix + "[%d]" % (i)):
yield path, value
else:
# BUG: Everything is cast to string, which can lead to false positives
# for cross type comparisions, ie "True" == True
yield prefix, ("%s" % (meta)).encode("utf8", errors='replace')
# ---- Utility methods -------------------------------------------------------
[docs]def sort_by_attr(seq, attr):
"""
Sort the sequence of objects by object's attribute
Arguments:
seq - the list or any sequence (including immutable one) of objects to sort.
attr - the name of attribute to sort by
"""
# Use the "Schwartzian transform"
# Create the auxiliary list of tuples where every i-th tuple has form
# (seq[i].attr, i, seq[i]) and sort it. The second item of tuple is needed not
# only to provide stable sorting, but mainly to eliminate comparison of objects
# (which can be expensive or prohibited) in case of equal attribute values.
intermed = [(getattr(v, attr), i, v) for i, v in enumerate(seq)]
intermed.sort()
return [_[-1] for _ in intermed]