def _load_role(self, trans, role_name):
"""
Method loads the role from the DB based on the given role name.
:param role_name: name of the role to load from the DB
:type role_name: string
:rtype: Role
:returns: the loaded Role object
:raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError
"""
try:
role = trans.sa_session.query(trans.app.model.Role).filter(
trans.model.Role.table.c.name == role_name).one()
except MultipleResultsFound:
raise exceptions.InconsistentDatabase(
'Multiple roles found with the same name. Name: ' +
str(role_name))
except NoResultFound:
raise exceptions.RequestParameterInvalidException(
'No role found with the name provided. Name: ' +
str(role_name))
except Exception, e:
raise exceptions.InternalServerError(
'Error loading from the database.' + str(e))
def get(self, trans, decoded_library_id, check_accessible=True):
"""
Get the library from the DB.
:param decoded_library_id: decoded library id
:type decoded_library_id: int
:param check_accessible: flag whether to check that user can access item
:type check_accessible: bool
:returns: the requested library
:rtype: galaxy.model.Library
"""
try:
library = trans.sa_session.query(trans.app.model.Library).filter(
trans.app.model.Library.table.c.id ==
decoded_library_id).one()
except MultipleResultsFound:
raise exceptions.InconsistentDatabase(
'Multiple libraries found with the same id.')
except NoResultFound:
raise exceptions.RequestParameterInvalidException(
'No library found with the id provided.')
except Exception as e:
raise exceptions.InternalServerError(
'Error loading from the database.' + str(e))
library = self.secure(trans, library, check_accessible)
return library
def get(self,
trans,
decoded_folder_id,
check_manageable=False,
check_accessible=True):
"""
Get the folder from the DB.
:param decoded_folder_id: decoded folder id
:type decoded_folder_id: int
:param check_manageable: flag whether the check that user can manage item
:type check_manageable: bool
:param check_accessible: flag whether to check that user can access item
:type check_accessible: bool
:returns: the requested folder
:rtype: LibraryFolder
"""
try:
folder = trans.sa_session.query(
trans.app.model.LibraryFolder).filter(
trans.app.model.LibraryFolder.table.c.id ==
decoded_folder_id).one()
except MultipleResultsFound:
raise exceptions.InconsistentDatabase(
'Multiple folders found with the same id.')
except NoResultFound:
raise exceptions.RequestParameterInvalidException(
'No folder found with the id provided.')
except Exception, e:
raise exceptions.InternalServerError(
'Error loading from the database.' + str(e))
def get_api_key(self, trans, **kwd):
"""
def get_api_key( self, trans, **kwd )
* GET /api/authenticate/baseauth
returns an API key for authenticated user based on BaseAuth headers
:returns: api_key in json format
:rtype: dict
:raises: ObjectNotFound, HTTPBadRequest
"""
email, password = self._decode_baseauth(
trans.environ.get('HTTP_AUTHORIZATION'))
user = trans.sa_session.query(trans.app.model.User).filter(
trans.app.model.User.table.c.email == email).all()
if len(user) == 0:
raise exceptions.ObjectNotFound('The user does not exist.')
elif len(user) > 1:
# DB is inconsistent and we have more users with the same email.
raise exceptions.InconsistentDatabase(
'An error occured, please contact your administrator.')
else:
user = user[0]
is_valid_user = self.app.auth_manager.check_password(
user, password)
if is_valid_user:
key = self.api_keys_manager.get_or_create_api_key(user)
return dict(api_key=key)
else:
raise exceptions.AuthenticationFailed('Invalid password.')
def workflow_request_to_run_config( work_request_context, workflow_invocation ):
param_types = model.WorkflowRequestInputParameter.types
history = workflow_invocation.history
replacement_dict = {}
inputs = {}
param_map = {}
copy_inputs_to_history = None
for parameter in workflow_invocation.input_parameters:
parameter_type = parameter.type
if parameter_type == param_types.REPLACEMENT_PARAMETERS:
replacement_dict[ parameter.name ] = parameter.value
elif parameter_type == param_types.META_PARAMETERS:
if parameter.name == "copy_inputs_to_history":
copy_inputs_to_history = (parameter.value == "true")
for input_association in workflow_invocation.input_datasets:
inputs[ input_association.workflow_step_id ] = input_association.dataset
for input_association in workflow_invocation.input_dataset_collections:
inputs[ input_association.workflow_step_id ] = input_association.dataset_collection
for input_association in workflow_invocation.input_step_parameters:
inputs[ input_association.workflow_step_id ] = input_association.parameter_value
if copy_inputs_to_history is None:
raise exceptions.InconsistentDatabase("Failed to find copy_inputs_to_history parameter loading workflow_invocation from database.")
workflow_run_config = WorkflowRunConfig(
target_history=history,
replacement_dict=replacement_dict,
inputs=inputs,
param_map=param_map,
copy_inputs_to_history=copy_inputs_to_history,
)
return workflow_run_config
def index( self, trans, library_id, **kwd ):
"""
index( self, trans, library_id, **kwd )
* GET /api/libraries/{library_id}/contents:
Returns a list of library files and folders.
.. note:: May be slow! Returns all content traversing recursively through all folders.
.. seealso:: :class:`galaxy.webapps.galaxy.api.FolderContentsController.index` for a non-recursive solution
:param library_id: the encoded id of the library
:type library_id: str
:returns: list of dictionaries of the form:
* id: the encoded id of the library item
* name: the 'library path'
or relationship of the library item to the root
* type: 'file' or 'folder'
* url: the url to get detailed information on the library item
:rtype: list
:raises: MalformedId, InconsistentDatabase, RequestParameterInvalidException, InternalServerError
"""
rval = []
current_user_roles = trans.get_current_user_roles()
def traverse( folder ):
admin = trans.user_is_admin()
rval = []
for subfolder in folder.active_folders:
if not admin:
can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder )
if (admin or can_access) and not subfolder.deleted:
subfolder.api_path = folder.api_path + '/' + subfolder.name
subfolder.api_type = 'folder'
rval.append( subfolder )
rval.extend( traverse( subfolder ) )
for ld in folder.datasets:
if not admin:
can_access = trans.app.security_agent.can_access_dataset(
current_user_roles,
ld.library_dataset_dataset_association.dataset
)
if (admin or can_access) and not ld.deleted:
ld.api_path = folder.api_path + '/' + ld.name
ld.api_type = 'file'
rval.append( ld )
return rval
try:
decoded_library_id = self.decode_id( library_id )
except Exception:
raise exceptions.MalformedId( 'Malformed library id ( %s ) specified, unable to decode.' % library_id )
try:
library = trans.sa_session.query( trans.app.model.Library ).filter( trans.app.model.Library.table.c.id == decoded_library_id ).one()
except MultipleResultsFound:
raise exceptions.InconsistentDatabase( 'Multiple libraries found with the same id.' )
except NoResultFound:
raise exceptions.RequestParameterInvalidException( 'No library found with the id provided.' )
except Exception, e:
raise exceptions.InternalServerError( 'Error loading from the database.' + str(e))
def _one_with_recast_errors(self, query):
"""
Call sqlalchemy's one and recast errors to serializable errors if any.
:raises exceptions.ObjectNotFound: if no model is found
:raises exceptions.InconsistentDatabase: if more than one model is found
"""
# overridden to raise serializable errors
try:
return query.one()
except sqlalchemy.orm.exc.NoResultFound:
raise exceptions.ObjectNotFound(self.model_class.__name__ + ' not found')
except sqlalchemy.orm.exc.MultipleResultsFound:
raise exceptions.InconsistentDatabase('found more than one ' + self.model_class.__name__)
def workflow_request_to_run_config(work_request_context, workflow_invocation):
param_types = model.WorkflowRequestInputParameter.types
history = workflow_invocation.history
replacement_dict = {}
inputs = {}
param_map = {}
resource_params = {}
copy_inputs_to_history = None
use_cached_job = False
for parameter in workflow_invocation.input_parameters:
parameter_type = parameter.type
if parameter_type == param_types.REPLACEMENT_PARAMETERS:
replacement_dict[parameter.name] = parameter.value
elif parameter_type == param_types.META_PARAMETERS:
if parameter.name == "copy_inputs_to_history":
copy_inputs_to_history = (parameter.value == "true")
if parameter.name == 'use_cached_job':
use_cached_job = (parameter.value == 'true')
elif parameter_type == param_types.RESOURCE_PARAMETERS:
resource_params[parameter.name] = parameter.value
elif parameter_type == param_types.STEP_PARAMETERS:
param_map[int(parameter.name)] = json.loads(parameter.value)
for input_association in workflow_invocation.input_datasets:
inputs[input_association.workflow_step_id] = input_association.dataset
for input_association in workflow_invocation.input_dataset_collections:
inputs[input_association.
workflow_step_id] = input_association.dataset_collection
for input_association in workflow_invocation.input_step_parameters:
parameter_value = input_association.parameter_value
inputs[input_association.workflow_step_id] = parameter_value
step_label = input_association.workflow_step.label
if step_label and step_label not in replacement_dict:
replacement_dict[step_label] = str(parameter_value)
if copy_inputs_to_history is None:
raise exceptions.InconsistentDatabase(
"Failed to find copy_inputs_to_history parameter loading workflow_invocation from database."
)
workflow_run_config = WorkflowRunConfig(
target_history=history,
replacement_dict=replacement_dict,
inputs=inputs,
param_map=param_map,
copy_inputs_to_history=copy_inputs_to_history,
use_cached_job=use_cached_job,
resource_params=resource_params,
)
return workflow_run_config
def get( self, trans, decoded_role_id):
"""
Method loads the role from the DB based on the given role id.
:param decoded_role_id: id of the role to load from the DB
:type decoded_role_id: int
:returns: the loaded Role object
:rtype: Role
:raises: InconsistentDatabase, RequestParameterInvalidException, InternalServerError
"""
try:
role = trans.sa_session.query( trans.app.model.Role ).filter( trans.model.Role.table.c.id == decoded_role_id ).one()
except MultipleResultsFound:
raise exceptions.InconsistentDatabase( 'Multiple roles found with the same id.' )
except NoResultFound:
raise exceptions.RequestParameterInvalidException( 'No role found with the id provided.' )
except Exception, e:
raise exceptions.InternalServerError( 'Error loading from the database.' + str(e) )
def index(self, trans, library_id, **kwd):
"""
GET /api/libraries/{library_id}/contents:
Return a list of library files and folders.
.. note:: This endpoint is slow for large libraries. Returns all content traversing recursively through all folders.
.. seealso:: :class:`galaxy.webapps.galaxy.api.FolderContentsController.index` for a faster non-recursive solution
:param library_id: the encoded id of the library
:type library_id: str
:returns: list of dictionaries of the form:
* id: the encoded id of the library item
* name: the 'library path'
or relationship of the library item to the root
* type: 'file' or 'folder'
* url: the url to get detailed information on the library item
:rtype: list
:raises: MalformedId, InconsistentDatabase, RequestParameterInvalidException, InternalServerError
"""
rval = []
current_user_roles = trans.get_current_user_roles()
def traverse(folder):
admin = trans.user_is_admin
rval = []
for subfolder in folder.active_folders:
if not admin:
can_access, folder_ids = trans.app.security_agent.check_folder_contents(
trans.user, current_user_roles, subfolder)
if (admin or can_access) and not subfolder.deleted:
subfolder.api_path = folder.api_path + '/' + subfolder.name
subfolder.api_type = 'folder'
rval.append(subfolder)
rval.extend(traverse(subfolder))
for ld in folder.datasets:
if not admin:
can_access = trans.app.security_agent.can_access_dataset(
current_user_roles,
ld.library_dataset_dataset_association.dataset)
if (admin or can_access) and not ld.deleted:
ld.api_path = folder.api_path + '/' + ld.name
ld.api_type = 'file'
rval.append(ld)
return rval
decoded_library_id = self.decode_id(library_id)
try:
library = trans.sa_session.query(trans.app.model.Library).filter(
trans.app.model.Library.table.c.id ==
decoded_library_id).one()
except MultipleResultsFound:
raise exceptions.InconsistentDatabase(
'Multiple libraries found with the same id.')
except NoResultFound:
raise exceptions.RequestParameterInvalidException(
'No library found with the id provided.')
except Exception as e:
raise exceptions.InternalServerError(
'Error loading from the database.' + util.unicodify(e))
if not (trans.user_is_admin
or trans.app.security_agent.can_access_library(
current_user_roles, library)):
raise exceptions.RequestParameterInvalidException(
'No library found with the id provided.')
encoded_id = 'F' + trans.security.encode_id(library.root_folder.id)
# appending root folder
rval.append(
dict(id=encoded_id,
type='folder',
name='/',
url=url_for('library_content',
library_id=library_id,
id=encoded_id)))
library.root_folder.api_path = ''
# appending all other items in the library recursively
for content in traverse(library.root_folder):
encoded_id = trans.security.encode_id(content.id)
if content.api_type == 'folder':
encoded_id = 'F' + encoded_id
rval.append(
dict(id=encoded_id,
type=content.api_type,
name=content.api_path,
url=url_for(
'library_content',
library_id=library_id,
id=encoded_id,
)))
return rval
def index( self, trans, folder_id, **kwd ):
"""
GET /api/folders/{encoded_folder_id}/contents
Displays a collection (list) of a folder's contents
(files and folders). Encoded folder ID is prepended
with 'F' if it is a folder as opposed to a data set
which does not have it. Full path is provided in
response as a separate object providing data for
breadcrumb path building.
:param folder_id: encoded ID of the folder which
contents should be library_dataset_dict
:type folder_id: encoded string
:param kwd: keyword dictionary with other params
:type kwd: dict
:returns: dictionary containing all items and metadata
:type: dict
:raises: MalformedId, InconsistentDatabase, ObjectNotFound,
InternalServerError
"""
deleted = kwd.get( 'include_deleted', 'missing' )
try:
deleted = util.asbool( deleted )
except ValueError:
deleted = False
if ( len( folder_id ) == 17 and folder_id.startswith( 'F' ) ):
try:
decoded_folder_id = trans.security.decode_id( folder_id[ 1: ] )
except TypeError:
raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( folder_id ) )
else:
raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( folder_id ) )
try:
folder = trans.sa_session.query( trans.app.model.LibraryFolder ).filter( trans.app.model.LibraryFolder.table.c.id == decoded_folder_id ).one()
except MultipleResultsFound:
raise exceptions.InconsistentDatabase( 'Multiple folders with same id found.' )
except NoResultFound:
raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) )
except Exception:
raise exceptions.InternalServerError( 'Error loading from the database.' )
current_user_roles = trans.get_current_user_roles()
# Special level of security on top of libraries.
if trans.app.security_agent.can_access_library( current_user_roles, folder.parent_library ):
pass
else:
if trans.user:
log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) )
else:
log.warning( "SECURITY: Anonymous user is trying to load restricted folder with ID of %s" % ( decoded_folder_id ) )
raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) )
# if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ):
# log.debug('folder parent id: ' + str(folder.parent_id))
# if folder.parent_id is None:
# try:
# library = trans.sa_session.query( trans.app.model.Library ).filter( trans.app.model.Library.table.c.root_folder_id == decoded_folder_id ).one()
# except Exception:
# raise exceptions.InternalServerError( 'Error loading from the database.' )
# if trans.app.security_agent.library_is_unrestricted( library ):
# pass
# else:
# if trans.user:
# log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) )
# else:
# log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) )
# raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) )
# else:
# if trans.user:
# log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, decoded_folder_id ) )
# else:
# log.debug('PARENT ID IS NOT NONE')
# log.warning( "SECURITY: Anonymous user without proper access rights is trying to load folder with ID of %s" % ( decoded_folder_id ) )
# raise exceptions.ObjectNotFound( 'Folder with the id provided ( %s ) was not found' % str( folder_id ) )
folder_contents = []
update_time = ''
create_time = ''
# Go through every accessible item (folders, datasets) in the folder and include its meta-data.
for content_item in self._load_folder_contents( trans, folder, deleted ):
return_item = {}
encoded_id = trans.security.encode_id( content_item.id )
update_time = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" )
create_time = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" )
if content_item.api_type == 'folder':
encoded_id = 'F' + encoded_id
# Check whether user can modify current folder
can_modify = False
if trans.user_is_admin():
can_modify = True
elif trans.user:
can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, folder )
return_item.update( dict( can_modify=can_modify ) )
if content_item.api_type == 'file':
# Is the dataset public or private?
# When both are False the dataset is 'restricted'
is_private = False
is_unrestricted = False
if trans.app.security_agent.dataset_is_public( content_item.library_dataset_dataset_association.dataset ):
is_unrestricted = True
else:
is_unrestricted = False
if trans.user:
is_private = trans.app.security_agent.dataset_is_private_to_user( trans, content_item )
# Can user manage the permissions on the dataset?
can_manage = False
if trans.user_is_admin():
can_manage = True
elif trans.user:
can_manage = trans.app.security_agent.can_manage_dataset( current_user_roles, content_item.library_dataset_dataset_association.dataset )
nice_size = util.nice_size( int( content_item.library_dataset_dataset_association.get_size() ) )
library_dataset_dict = content_item.to_dict()
return_item.update( dict( data_type=library_dataset_dict[ 'data_type' ],
date_uploaded=library_dataset_dict[ 'date_uploaded' ],
is_unrestricted=is_unrestricted,
is_private=is_private,
can_manage=can_manage,
file_size=nice_size ) )
# For every item include the default meta-data
return_item.update( dict( id=encoded_id,
type=content_item.api_type,
name=content_item.name,
update_time=update_time,
create_time=create_time,
deleted=content_item.deleted
) )
folder_contents.append( return_item )
# Return the reversed path so it starts with the library node.
full_path = self.build_path( trans, folder )[ ::-1 ]
# Check whether user can add items to the current folder
can_add_library_item = trans.user_is_admin() or trans.app.security_agent.can_add_library_item( current_user_roles, folder )
# Check whether user can modify current folder
can_modify_folder = trans.app.security_agent.can_modify_library_item( current_user_roles, folder )
metadata = dict( full_path=full_path,
can_add_library_item=can_add_library_item,
can_modify_folder=can_modify_folder )
folder_container = dict( metadata=metadata, folder_contents=folder_contents )
return folder_container
def create(self, trans, encoded_parent_folder_id, **kwd):
"""
create( self, trans, encoded_parent_folder_id, **kwd )
*POST /api/folders/{encoded_parent_folder_id}
Create a new folder object underneath the one specified in the parameters.
:param encoded_parent_folder_id: the parent folder's id (required)
:type encoded_parent_folder_id: an encoded id string (should be prefixed by 'F')
:param name: the name of the new folder (required)
:type name: str
:param description: the description of the new folder
:type description: str
:returns: information about newly created folder, notably including ID
:rtype: dictionary
:raises: RequestParameterMissingException, MalformedId, InternalServerError
"""
payload = kwd.get('payload', None)
if payload is None:
raise exceptions.RequestParameterMissingException(
"Missing required parameters 'encoded_parent_folder_id' and 'name'."
)
name = payload.get('name', None)
description = payload.get('description', '')
if encoded_parent_folder_id is None:
raise exceptions.RequestParameterMissingException(
"Missing required parameter 'encoded_parent_folder_id'.")
elif name is None:
raise exceptions.RequestParameterMissingException(
"Missing required parameter 'name'.")
# encoded_parent_folder_id should be prefixed by 'F'
encoded_parent_folder_id = self.__cut_the_prefix(
encoded_parent_folder_id)
try:
decoded_parent_folder_id = trans.security.decode_id(
encoded_parent_folder_id)
except ValueError:
raise exceptions.MalformedId(
"Malformed folder id ( %s ) specified, unable to decode" %
(str(id)))
try:
parent_folder = trans.sa_session.query(
trans.app.model.LibraryFolder).filter(
trans.app.model.LibraryFolder.table.c.id ==
decoded_parent_folder_id).one()
except MultipleResultsFound:
raise exceptions.InconsistentDatabase(
'Multiple folders found with the same id.')
except NoResultFound:
raise exceptions.RequestParameterInvalidException(
'No folder found with the id provided.')
except Exception, e:
raise exceptions.InternalServerError(
'Error loading from the database.' + str(e))