Source code for galaxy.webapps.galaxy.api.users

"""
API operations on User objects.
"""
import json
import logging
import re
from collections import OrderedDict

import six
from markupsafe import escape
from sqlalchemy import (
    false,
    or_,
    true
)

from galaxy import (
    exceptions,
    util,
    web
)
from galaxy.exceptions import ObjectInvalid
from galaxy.managers import users
from galaxy.security.validate_user_input import (
    validate_email,
    validate_password,
    validate_publicname
)
from galaxy.tools.toolbox.filters import FilterFactory
from galaxy.util import (
    docstring_trim,
    listify
)
from galaxy.web import (
    expose_api,
    expose_api_anonymous
)
from galaxy.web.form_builder import AddressField
from galaxy.webapps.base.controller import (
    BaseAPIController,
    BaseUIController,
    CreatesApiKeysMixin,
    UsesFormDefinitionsMixin,
    UsesTagsMixin
)


log = logging.getLogger(__name__)


[docs]class UserAPIController(BaseAPIController, UsesTagsMixin, CreatesApiKeysMixin, BaseUIController, UsesFormDefinitionsMixin):
[docs] def __init__(self, app): super(UserAPIController, self).__init__(app) self.user_manager = users.UserManager(app) self.user_serializer = users.UserSerializer(app) self.user_deserializer = users.UserDeserializer(app)
[docs] @expose_api def index(self, trans, deleted='False', f_email=None, f_name=None, f_any=None, **kwd): """ GET /api/users GET /api/users/deleted Displays a collection (list) of users. :param deleted: (optional) If true, show deleted users :type deleted: bool :param f_email: (optional) An email address to filter on. (Non-admin users can only use this if ``expose_user_email`` is ``True`` in galaxy.ini) :type f_email: str :param f_name: (optional) A username to filter on. (Non-admin users can only use this if ``expose_user_name`` is ``True`` in galaxy.ini) :type f_name: str :param f_any: (optional) Filter on username OR email. (Non-admin users can use this, the email filter and username filter will only be active if their corresponding ``expose_user_*`` is ``True`` in galaxy.ini) :type f_any: str """ rval = [] query = trans.sa_session.query(trans.app.model.User) deleted = util.string_as_bool(deleted) if f_email and (trans.user_is_admin or trans.app.config.expose_user_email): query = query.filter(trans.app.model.User.email.like("%%%s%%" % f_email)) if f_name and (trans.user_is_admin or trans.app.config.expose_user_name): query = query.filter(trans.app.model.User.username.like("%%%s%%" % f_name)) if f_any: if trans.user_is_admin: query = query.filter(or_( trans.app.model.User.email.like("%%%s%%" % f_any), trans.app.model.User.username.like("%%%s%%" % f_any) )) else: if trans.app.config.expose_user_email and trans.app.config.expose_user_name: query = query.filter(or_( trans.app.model.User.email.like("%%%s%%" % f_any), trans.app.model.User.username.like("%%%s%%" % f_any) )) elif trans.app.config.expose_user_email: query = query.filter(trans.app.model.User.email.like("%%%s%%" % f_any)) elif trans.app.config.expose_user_name: query = query.filter(trans.app.model.User.username.like("%%%s%%" % f_any)) if deleted: query = query.filter(trans.app.model.User.table.c.deleted == true()) # only admins can see deleted users if not trans.user_is_admin: return [] else: query = query.filter(trans.app.model.User.table.c.deleted == false()) # special case: user can see only their own user # special case2: if the galaxy admin has specified that other user email/names are # exposed, we don't want special case #1 if not trans.user_is_admin and not trans.app.config.expose_user_name and not trans.app.config.expose_user_email: item = trans.user.to_dict(value_mapper={'id': trans.security.encode_id}) return [item] for user in query: item = user.to_dict(value_mapper={'id': trans.security.encode_id}) # If NOT configured to expose_email, do not expose email UNLESS the user is self, or # the user is an admin if user is not trans.user and not trans.user_is_admin: expose_keys = ["id"] if trans.app.config.expose_user_name: expose_keys.append("username") if trans.app.config.expose_user_email: expose_keys.append("email") new_item = {} for key, value in item.items(): if key in expose_keys: new_item[key] = value item = new_item # TODO: move into api_values rval.append(item) return rval
[docs] @expose_api_anonymous def show(self, trans, id, deleted='False', **kwd): """ GET /api/users/{encoded_id} GET /api/users/deleted/{encoded_id} GET /api/users/current Displays information about a user. """ deleted = util.string_as_bool(deleted) try: # user is requesting data about themselves if id == "current": # ...and is anonymous - return usage and quota (if any) if not trans.user: item = self.anon_user_api_value(trans) return item # ...and is logged in - return full else: user = trans.user else: user = self.get_user(trans, id, deleted=deleted) # check that the user is requesting themselves (and they aren't del'd) unless admin if not trans.user_is_admin: assert trans.user == user assert not user.deleted except exceptions.ItemDeletionException: raise except Exception: raise exceptions.RequestParameterInvalidException('Invalid user id specified', id=id) return self.user_serializer.serialize_to_view(user, view='detailed')
[docs] @expose_api def create(self, trans, payload, **kwd): """ POST /api/users Creates a new Galaxy user. """ if not trans.app.config.allow_user_creation and not trans.user_is_admin: raise exceptions.ConfigDoesNotAllowException('User creation is not allowed in this Galaxy instance') if trans.app.config.use_remote_user and trans.user_is_admin: user = trans.get_or_create_remote_user(remote_user_email=payload['remote_user_email']) elif trans.user_is_admin: username = payload['username'] email = payload['email'] password = payload['password'] message = "\n".join([validate_email(trans, email), validate_password(trans, password, password), validate_publicname(trans, username)]).rstrip() if message: raise exceptions.RequestParameterInvalidException(message) else: user = self.user_manager.create(email=email, username=username, password=password) else: raise exceptions.NotImplemented() item = user.to_dict(view='element', value_mapper={'id': trans.security.encode_id, 'total_disk_usage': float}) return item
[docs] @expose_api def update(self, trans, id, payload, **kwd): """ update( self, trans, id, payload, **kwd ) * PUT /api/users/{id} updates the values for the item with the given ``id`` :type id: str :param id: the encoded id of the item to update :type payload: dict :param payload: a dictionary of new attribute values :rtype: dict :returns: an error object if an error occurred or a dictionary containing the serialized item after any changes """ current_user = trans.user user_to_update = self.user_manager.by_id(self.decode_id(id)) # only allow updating other users if they're admin editing_someone_else = current_user != user_to_update is_admin = trans.api_inherit_admin or self.user_manager.is_admin(current_user) if editing_someone_else and not is_admin: raise exceptions.InsufficientPermissionsException('you are not allowed to update that user', id=id) self.user_deserializer.deserialize(user_to_update, payload, user=current_user, trans=trans) return self.user_serializer.serialize_to_view(user_to_update, view='detailed')
[docs] @expose_api @web.require_admin def delete(self, trans, id, **kwd): """ DELETE /api/users/{id} delete the user with the given ``id`` :param id: the encoded id of the user to delete :type id: str :param purge: (optional) if True, purge the user :type purge: bool """ user = self.get_user(trans, id) purge = util.string_as_bool(kwd.get('purge', False)) if purge: log.debug("Purging user %s" % user) self.user_manager.purge(user) else: self.user_manager.delete(user) return self.user_serializer.serialize_to_view(user, view='detailed')
[docs] @expose_api @web.require_admin def undelete(self, trans, id, **kwd): """ POST /api/users/deleted/{id}/undelete Undelete the user with the given ``id`` :param id: the encoded id of the user to be undeleted :type id: str """ user = self.get_user(trans, id) self.user_manager.undelete(user) return self.user_serializer.serialize_to_view(user, view='detailed')
# TODO: move to more basal, common resource than this
[docs] def anon_user_api_value(self, trans): """Return data for an anonymous user, truncated to only usage and quota_percent""" usage = trans.app.quota_agent.get_usage(trans) percent = trans.app.quota_agent.get_percent(trans=trans, usage=usage) return {'total_disk_usage': int(usage), 'nice_total_disk_usage': util.nice_size(usage), 'quota_percent': percent}
def _get_extra_user_preferences(self, trans): """ Reads the file user_preferences_extra_conf.yml to display admin defined user informations """ return trans.app.config.user_preferences_extra['preferences'] def _build_extra_user_pref_inputs(self, preferences, user): """ Build extra user preferences inputs list. Add values to the fields if present """ if not preferences: return [] extra_pref_inputs = list() # Build sections for different categories of inputs for item, value in preferences.items(): if value is not None: for input in value["inputs"]: help = input.get('help', '') required = 'Required' if util.string_as_bool(input.get('required')) else '' if help: input['help'] = "%s %s" % (help, required) else: input['help'] = required field = item + '|' + input['name'] for data_item in user.extra_preferences: if field in data_item: input['value'] = user.extra_preferences[data_item] extra_pref_inputs.append({'type': 'section', 'title': value['description'], 'name': item, 'expanded': True, 'inputs': value['inputs']}) return extra_pref_inputs
[docs] @expose_api def get_information(self, trans, id, **kwd): """ GET /api/users/{id}/information/inputs Return user details such as username, email, addresses etc. :param id: the encoded id of the user :type id: str """ user = self._get_user(trans, id) email = user.email username = user.username inputs = list() inputs.append({ 'id': 'email_input', 'name': 'email', 'type': 'text', 'label': 'Email address', 'value': email, 'help': 'If you change your email address you will receive an activation link in the new mailbox and you have to activate your account by visiting it.'}) if trans.webapp.name == 'galaxy': inputs.append({ 'id': 'name_input', 'name': 'username', 'type': 'text', 'label': 'Public name', 'value': username, 'help': 'Your public name is an identifier that will be used to generate addresses for information you share publicly. Public names must be at least three characters in length and contain only lower-case letters, numbers, and the "-" character.'}) info_form_models = self.get_all_forms(trans, filter=dict(deleted=False), form_type=trans.app.model.FormDefinition.types.USER_INFO) if info_form_models: info_form_id = trans.security.encode_id(user.values.form_definition.id) if user.values else None info_field = { 'type': 'conditional', 'name': 'info', 'cases': [], 'test_param': { 'name': 'form_id', 'label': 'User type', 'type': 'select', 'value': info_form_id, 'help': '', 'data': [] } } for f in info_form_models: values = None if info_form_id == trans.security.encode_id(f.id) and user.values: values = user.values.content info_form = f.to_dict(user=user, values=values, security=trans.security) info_field['test_param']['data'].append({'label': info_form['name'], 'value': info_form['id']}) info_field['cases'].append({'value': info_form['id'], 'inputs': info_form['inputs']}) inputs.append(info_field) address_inputs = [{'type': 'hidden', 'name': 'id', 'hidden': True}] for field in AddressField.fields(): address_inputs.append({'type': 'text', 'name': field[0], 'label': field[1], 'help': field[2]}) address_repeat = {'title': 'Address', 'name': 'address', 'type': 'repeat', 'inputs': address_inputs, 'cache': []} address_values = [address.to_dict(trans) for address in user.addresses] for address in address_values: address_cache = [] for input in address_inputs: input_copy = input.copy() input_copy['value'] = address.get(input['name']) address_cache.append(input_copy) address_repeat['cache'].append(address_cache) inputs.append(address_repeat) # Build input sections for extra user preferences extra_user_pref = self._build_extra_user_pref_inputs(self._get_extra_user_preferences(trans), user) for item in extra_user_pref: inputs.append(item) else: if user.active_repositories: inputs.append(dict(id='name_input', name='username', label='Public name:', type='hidden', value=username, help='You cannot change your public name after you have created a repository in this tool shed.')) else: inputs.append(dict(id='name_input', name='username', label='Public name:', type='text', value=username, help='Your public name provides a means of identifying you publicly within this tool shed. Public names must be at least three characters in length and contain only lower-case letters, numbers, and the "-" character. You cannot change your public name after you have created a repository in this tool shed.')) return { 'email': email, 'username': username, 'addresses': [address.to_dict(trans) for address in user.addresses], 'inputs': inputs, }
[docs] @expose_api def set_information(self, trans, id, payload={}, **kwd): """ PUT /api/users/{id}/information/inputs Save a user's email, username, addresses etc. :param id: the encoded id of the user :type id: str :param payload: data with new settings :type payload: dict """ user = self._get_user(trans, id) # Update email if 'email' in payload: email = payload.get('email') message = self._validate_email(email) or validate_email(trans, email, user) if message: raise exceptions.RequestParameterInvalidException(message) if user.email != email: # Update user email and user's private role name which must match private_role = trans.app.security_agent.get_private_user_role(user) private_role.name = email private_role.description = 'Private role for ' + email user.email = email trans.sa_session.add(user) trans.sa_session.add(private_role) trans.sa_session.flush() if trans.app.config.user_activation_on: # Deactivate the user if email was changed and activation is on. user.active = False if self.user_manager.send_activation_email(trans, user.email, user.username): message = 'The login information has been updated with the changes.<br>Verification email has been sent to your new email address. Please verify it by clicking the activation link in the email.<br>Please check your spam/trash folder in case you cannot find the message.' else: message = 'Unable to send activation email, please contact your local Galaxy administrator.' if trans.app.config.error_email_to is not None: message += ' Contact: %s' % trans.app.config.error_email_to raise exceptions.InternalServerError(message) # Update public name if 'username' in payload: username = payload.get('username') message = self._validate_publicname(username) or validate_publicname(trans, username, user) if message: raise exceptions.RequestParameterInvalidException(message) if user.username != username: user.username = username # Update user custom form user_info_form_id = payload.get('info|form_id') if user_info_form_id: prefix = 'info|' user_info_form = trans.sa_session.query(trans.app.model.FormDefinition).get(trans.security.decode_id(user_info_form_id)) user_info_values = {} for item in payload: if item.startswith(prefix): user_info_values[item[len(prefix):]] = payload[item] form_values = trans.model.FormValues(user_info_form, user_info_values) trans.sa_session.add(form_values) user.values = form_values # Update values for extra user preference items extra_user_pref_data = dict() extra_pref_keys = self._get_extra_user_preferences(trans) if extra_pref_keys is not None: for key in extra_pref_keys: key_prefix = key + '|' for item in payload: if item.startswith(key_prefix): # Show error message if the required field is empty if payload[item] == "": # Raise an exception when a required field is empty while saving the form keys = item.split("|") section = extra_pref_keys[keys[0]] for input in section['inputs']: if input['name'] == keys[1] and input['required']: raise exceptions.ObjectAttributeMissingException("Please fill the required field") extra_user_pref_data[item] = payload[item] user.preferences["extra_user_preferences"] = json.dumps(extra_user_pref_data) # Update user addresses address_dicts = {} address_count = 0 for item in payload: match = re.match(r'^address_(?P<index>\d+)\|(?P<attribute>\S+)', item) if match: groups = match.groupdict() index = int(groups['index']) attribute = groups['attribute'] address_dicts[index] = address_dicts.get(index) or {} address_dicts[index][attribute] = payload[item] address_count = max(address_count, index + 1) user.addresses = [] for index in range(0, address_count): d = address_dicts[index] if d.get('id'): try: user_address = trans.sa_session.query(trans.app.model.UserAddress).get(trans.security.decode_id(d['id'])) except Exception as e: raise exceptions.ObjectNotFound('Failed to access user address (%s). %s' % (d['id'], e)) else: user_address = trans.model.UserAddress() trans.log_event('User address added') for field in AddressField.fields(): if str(field[2]).lower() == 'required' and not d.get(field[0]): raise exceptions.ObjectAttributeMissingException('Address %s: %s (%s) required.' % (index + 1, field[1], field[0])) setattr(user_address, field[0], str(d.get(field[0], ''))) user_address.user = user user.addresses.append(user_address) trans.sa_session.add(user_address) trans.sa_session.add(user) trans.sa_session.flush() trans.log_event('User information added') return {'message': 'User information has been saved.'}
[docs] @expose_api def set_favorite(self, trans, id, object_type, payload={}, **kwd): """Add the object to user's favorites PUT /api/users/{id}/favorites/{object_type} :param id: the encoded id of the user :type id: str :param object_type: the object type that users wants to favorite :type object_type: str :param object_id: the id of an object that users wants to favorite :type object_id: str """ self._validate_favorite_object_type(object_type) user = self._get_user(trans, id) favorites = json.loads(user.preferences['favorites']) if 'favorites' in user.preferences else {} if object_type == 'tools': tool_id = payload.get('object_id') tool = self.app.toolbox.get_tool(tool_id) if not tool: raise exceptions.ObjectNotFound("Could not find tool with id '%s'." % tool_id) if not tool.allow_user_access(user): raise exceptions.AuthenticationFailed("Access denied for tool with id '%s'." % tool_id) if 'tools' in favorites: favorite_tools = favorites['tools'] else: favorite_tools = [] if tool_id not in favorite_tools: favorite_tools.append(tool_id) favorites['tools'] = favorite_tools user.preferences['favorites'] = json.dumps(favorites) trans.sa_session.flush() return favorites
[docs] @expose_api def remove_favorite(self, trans, id, object_type, object_id, payload={}, **kwd): """Remove the object from user's favorites DELETE /api/users/{id}/favorites/{object_type}/{object_id:.*?} :param id: the encoded id of the user :type id: str :param object_type: the object type that users wants to favorite :type object_type: str :param object_id: the id of an object that users wants to remove from favorites :type object_id: str """ self._validate_favorite_object_type(object_type) user = self._get_user(trans, id) favorites = json.loads(user.preferences['favorites']) if 'favorites' in user.preferences else {} if object_type == 'tools': if 'tools' in favorites: favorite_tools = favorites['tools'] if object_id in favorite_tools: del favorite_tools[favorite_tools.index(object_id)] favorites['tools'] = favorite_tools user.preferences['favorites'] = json.dumps(favorites) trans.sa_session.flush() else: raise exceptions.ObjectNotFound('Given object is not in the list of favorites') return favorites
def _validate_favorite_object_type(self, object_type): if object_type in ['tools']: pass else: raise exceptions.ObjectAttributeInvalidException("This type is not supported. Given object_type: %s" % object_type) def _validate_email(self, email): ''' Validate email and username using regex ''' if email == '' or not isinstance(email, six.string_types): return 'Please provide your email address.' if not re.match(r'^(([^<>()[\]\.,;:\s@"]+(\.[^<>()[\]\.,;:\s@"]+)*)|(".+"))@((\[[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}\.[0-9]{1,3}])|(([a-zA-Z\-0-9]+\.)+[a-zA-Z]{2,}))$', email): return 'Please provide your valid email address.' if len(email) > 255: return 'Email cannot be more than 255 characters in length.' def _validate_publicname(self, username): if not re.match(r'^[a-z0-9\-]{3,255}$', username): return 'Public name must contain only lowercase letters, numbers and "-". It also has to be shorter than 255 characters but longer than 2.'
[docs] @expose_api def get_password(self, trans, id, payload={}, **kwd): """ Return available password inputs. """ return {'inputs': [{'name': 'current', 'type': 'password', 'label': 'Current password'}, {'name': 'password', 'type': 'password', 'label': 'New password'}, {'name': 'confirm', 'type': 'password', 'label': 'Confirm password'}]}
[docs] @expose_api def set_password(self, trans, id, payload={}, **kwd): """ Allows to the logged-in user to change own password. """ user, message = self.user_manager.change_password(trans, id=id, **payload) if user is None: raise exceptions.AuthenticationRequired(message) return {"message": "Password has been changed."}
[docs] @expose_api def get_permissions(self, trans, id, payload={}, **kwd): """ Get the user's default permissions for the new histories """ user = self._get_user(trans, id) roles = user.all_roles() inputs = [] for index, action in trans.app.model.Dataset.permitted_actions.items(): inputs.append({'type': 'select', 'multiple': True, 'optional': True, 'name': index, 'label': action.action, 'help': action.description, 'options': list(set((r.name, r.id) for r in roles)), 'value': [a.role.id for a in user.default_permissions if a.action == action.action]}) return {'inputs': inputs}
[docs] @expose_api def set_permissions(self, trans, id, payload={}, **kwd): """ Set the user's default permissions for the new histories """ user = self._get_user(trans, id) permissions = {} for index, action in trans.app.model.Dataset.permitted_actions.items(): action_id = trans.app.security_agent.get_action(action.action).action permissions[action_id] = [trans.sa_session.query(trans.app.model.Role).get(x) for x in (payload.get(index) or [])] trans.app.security_agent.user_set_default_permissions(user, permissions) return {'message': 'Permissions have been saved.'}
[docs] @expose_api def get_toolbox_filters(self, trans, id, payload={}, **kwd): """ API call for fetching toolbox filters data. Toolbox filters are specified in galaxy.ini. The user can activate them and the choice is stored in user_preferences. """ user = self._get_user(trans, id) filter_types = self._get_filter_types(trans) saved_values = {} for name, value in user.preferences.items(): if name in filter_types: saved_values[name] = listify(value, do_strip=True) inputs = [] errors = {} factory = FilterFactory(trans.app.toolbox) for filter_type in filter_types: self._add_filter_inputs(factory, filter_types, inputs, errors, filter_type, saved_values) return {'inputs': inputs, 'errors': errors}
[docs] @expose_api def set_toolbox_filters(self, trans, id, payload={}, **kwd): """ API call to update toolbox filters data. """ user = self._get_user(trans, id) filter_types = self._get_filter_types(trans) for filter_type in filter_types: new_filters = [] for prefixed_name in payload: if payload.get(prefixed_name) == 'true' and prefixed_name.startswith(filter_type): prefix = filter_type + '|' new_filters.append(prefixed_name[len(prefix):]) user.preferences[filter_type] = ','.join(new_filters) trans.sa_session.add(user) trans.sa_session.flush() return {'message': 'Toolbox filters have been saved.'}
def _add_filter_inputs(self, factory, filter_types, inputs, errors, filter_type, saved_values): filter_inputs = list() filter_values = saved_values.get(filter_type, []) filter_config = filter_types[filter_type]['config'] filter_title = filter_types[filter_type]['title'] for filter_name in filter_config: function = factory.build_filter_function(filter_name) if function is None: errors['%s|%s' % (filter_type, filter_name)] = 'Filter function not found.' short_description, description = None, None doc_string = docstring_trim(function.__doc__) split = doc_string.split('\n\n') if split: short_description = split[0] if len(split) > 1: description = split[1] else: log.warning('No description specified in the __doc__ string for %s.' % filter_name) filter_inputs.append({ 'type': 'boolean', 'name': filter_name, 'label': short_description or filter_name, 'help': description or 'No description available.', 'value': 'true' if filter_name in filter_values else 'false' }) if filter_inputs: inputs.append({'type': 'section', 'title': filter_title, 'name': filter_type, 'expanded': True, 'inputs': filter_inputs}) def _get_filter_types(self, trans): return OrderedDict([('toolbox_tool_filters', {'title': 'Tools', 'config': trans.app.config.user_tool_filters}), ('toolbox_section_filters', {'title': 'Sections', 'config': trans.app.config.user_tool_section_filters}), ('toolbox_label_filters', {'title': 'Labels', 'config': trans.app.config.user_tool_label_filters})])
[docs] @expose_api def api_key(self, trans, id, payload={}, **kwd): """ Create API key. """ user = self._get_user(trans, id) return self.create_api_key(trans, user)
[docs] @expose_api def get_api_key(self, trans, id, payload={}, **kwd): """ Get API key inputs. """ user = self._get_user(trans, id) return self._build_inputs_api_key(user)
[docs] @expose_api def set_api_key(self, trans, id, payload={}, **kwd): """ Get API key inputs with new API key. """ user = self._get_user(trans, id) self.create_api_key(trans, user) return self._build_inputs_api_key(user, message='Generated a new web API key.')
def _build_inputs_api_key(self, user, message=''): """ Build API key inputs. """ inputs = [{'name': 'api-key', 'type': 'text', 'label': 'Current API key:', 'value': user.api_keys[0].key if user.api_keys else 'Not available.', 'readonly': True, 'help': ' An API key will allow you to access via web API. Please note that this key acts as an alternate means to access your account and should be treated with the same care as your login password.'}] return {'message': message, 'inputs': inputs}
[docs] @expose_api def get_communication(self, trans, id, payload={}, **kwd): """ Build communication server inputs. """ user = self._get_user(trans, id) return {'inputs': [{'name': 'enable', 'type': 'boolean', 'label': 'Enable communication', 'value': user.preferences.get('communication_server', 'false')}]}
[docs] @expose_api def set_communication(self, trans, id, payload={}, **kwd): """ Allows the user to activate/deactivate the communication server. """ user = self._get_user(trans, id) enable = payload.get('enable', 'false') if enable == 'true': message = 'Your communication server has been activated.' else: message = 'Your communication server has been disabled.' user.preferences['communication_server'] = enable trans.sa_session.add(user) trans.sa_session.flush() return {'message': message}
[docs] @expose_api def get_custom_builds(self, trans, id, payload={}, **kwd): """ GET /api/users/{id}/custom_builds Returns collection of custom builds. :param id: the encoded id of the user :type id: str """ user = self._get_user(trans, id) dbkeys = json.loads(user.preferences['dbkeys']) if 'dbkeys' in user.preferences else {} update = False for key in dbkeys: dbkey = dbkeys[key] if 'count' not in dbkey and 'linecount' in dbkey: chrom_count_dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(dbkey['linecount']) if chrom_count_dataset.state == trans.app.model.Job.states.OK: chrom_count = int(open(chrom_count_dataset.file_name).readline()) dbkey['count'] = chrom_count update = True if update: user.preferences['dbkeys'] = json.dumps(dbkeys) dbkey_collection = [] for key, attributes in dbkeys.items(): attributes['id'] = key dbkey_collection.append(attributes) return dbkey_collection
[docs] @expose_api def add_custom_builds(self, trans, id, key, payload={}, **kwd): """ PUT /api/users/{id}/custom_builds/{key} Add new custom build. :param id: the encoded id of the user :type id: str :param id: custom build key :type id: str :param payload: data with new build details :type payload: dict """ user = self._get_user(trans, id) dbkeys = json.loads(user.preferences['dbkeys']) if 'dbkeys' in user.preferences else {} name = payload.get('name') len_type = payload.get('len|type') len_value = payload.get('len|value') if len_type not in ['file', 'fasta', 'text'] or not len_value: raise exceptions.RequestParameterInvalidException('Please specify a valid data source type.') if not name or not key: raise exceptions.RequestParameterMissingException('You must specify values for all the fields.') elif key in dbkeys: raise exceptions.DuplicatedIdentifierException('There is already a custom build with that key. Delete it first if you want to replace it.') else: # Have everything needed; create new build. build_dict = {'name': name} if len_type in ['text', 'file']: # Create new len file new_len = trans.app.model.HistoryDatasetAssociation(extension='len', create_dataset=True, sa_session=trans.sa_session) trans.sa_session.add(new_len) new_len.name = name new_len.visible = False new_len.state = trans.app.model.Job.states.OK new_len.info = 'custom build .len file' try: trans.app.object_store.create(new_len.dataset) except ObjectInvalid: raise exceptions.InternalServerError('Unable to create output dataset: object store is full.') trans.sa_session.flush() counter = 0 lines_skipped = 0 f = open(new_len.file_name, 'w') # LEN files have format: # <chrom_name><tab><chrom_length> for line in len_value.split('\n'): # Splits at the last whitespace in the line lst = line.strip().rsplit(None, 1) if not lst or len(lst) < 2: lines_skipped += 1 continue chrom, length = lst[0], lst[1] try: length = int(length) except ValueError: lines_skipped += 1 continue if chrom != escape(chrom): build_dict['message'] = 'Invalid chromosome(s) with HTML detected and skipped.' lines_skipped += 1 continue counter += 1 f.write('%s\t%s\n' % (chrom, length)) f.close() build_dict['len'] = new_len.id build_dict['count'] = counter else: build_dict['fasta'] = trans.security.decode_id(len_value) dataset = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get(build_dict['fasta']) try: new_len = dataset.get_converted_dataset(trans, 'len') new_linecount = new_len.get_converted_dataset(trans, 'linecount') build_dict['len'] = new_len.id build_dict['linecount'] = new_linecount.id except Exception: raise exceptions.ToolExecutionError('Failed to convert dataset.') dbkeys[key] = build_dict user.preferences['dbkeys'] = json.dumps(dbkeys) trans.sa_session.flush() return build_dict
[docs] @expose_api def delete_custom_builds(self, trans, id, key, payload={}, **kwd): """ DELETE /api/users/{id}/custom_builds/{key} Delete a custom build. :param id: the encoded id of the user :type id: str :param id: custom build key to be deleted :type id: str """ user = self._get_user(trans, id) dbkeys = json.loads(user.preferences['dbkeys']) if 'dbkeys' in user.preferences else {} if key and key in dbkeys: del dbkeys[key] user.preferences['dbkeys'] = json.dumps(dbkeys) trans.sa_session.flush() return {'message': 'Deleted %s.' % key} else: raise exceptions.ObjectNotFound('Could not find and delete build (%s).' % key)
def _get_user(self, trans, id): user = self.get_user(trans, id) if not user: raise exceptions.RequestParameterInvalidException('Invalid user (%s).' % id) if user != trans.user and not trans.user_is_admin: raise exceptions.InsufficientPermissionsException('Access denied.') return user