trans.response.status = status
return output
else:
rval = []
for k, v in output.items():
if ex_meta_payload is not None:
"""
If there is extended metadata, store it, attach it to the dataset, and index it
"""
ex_meta = ExtendedMetadata(ex_meta_payload)
trans.sa_session.add(ex_meta)
v.extended_metadata = ex_meta
trans.sa_session.add(v)
trans.sa_session.flush()
for path, value in self._scan_json_block(ex_meta_payload):
meta_i = ExtendedMetadataIndex(ex_meta, path, value)
trans.sa_session.add(meta_i)
trans.sa_session.flush()
if type(v) == trans.app.model.LibraryDatasetDatasetAssociation:
v = v.library_dataset
encoded_id = trans.security.encode_id(v.id)
if create_type == 'folder':
encoded_id = 'F' + encoded_id
rval.append(
dict(id=encoded_id,
name=v.name,
url=url_for('library_content',
library_id=library_id,
id=encoded_id)))
return rval
def create(self, trans, library_id, payload, **kwd):
"""
create( self, trans, library_id, payload, **kwd )
* POST /api/libraries/{library_id}/contents:
create a new library file or folder
To copy an HDA into a library send ``create_type`` of 'file' and
the HDA's encoded id in ``from_hda_id`` (and optionally ``ldda_message``).
To copy an HDCA into a library send ``create_type`` of 'file' and
the HDCA's encoded id in ``from_hdca_id`` (and optionally ``ldda_message``).
:type library_id: str
:param library_id: the encoded id of the library where to create the new item
:type payload: dict
:param payload: dictionary structure containing:
* folder_id: the encoded id of the parent folder of the new item
* create_type: the type of item to create ('file', 'folder' or 'collection')
* from_hda_id: (optional, only if create_type is 'file') the
encoded id of an accessible HDA to copy into the library
* ldda_message: (optional) the new message attribute of the LDDA created
* extended_metadata: (optional) sub-dictionary containing any extended
metadata to associate with the item
* upload_option: (optional) one of 'upload_file' (default), 'upload_directory' or 'upload_paths'
* server_dir: (optional, only if upload_option is
'upload_directory') relative path of the subdirectory of Galaxy
``library_import_dir`` to upload. All and only the files (i.e.
no subdirectories) contained in the specified directory will be
uploaded.
* filesystem_paths: (optional, only if upload_option is
'upload_paths' and the user is an admin) file paths on the
Galaxy server to upload to the library, one file per line
* link_data_only: (optional, only when upload_option is
'upload_directory' or 'upload_paths') either 'copy_files'
(default) or 'link_to_files'. Setting to 'link_to_files'
symlinks instead of copying the files
* name: (optional, only if create_type is 'folder') name of the
folder to create
* description: (optional, only if create_type is 'folder')
description of the folder to create
* tag_using_filename: (optional)
create tags on datasets using the file's original name
:returns: a dictionary describing the new item unless ``from_hdca_id`` is supplied,
in that case a list of such dictionaries is returned.
:rtype: object
"""
if 'create_type' not in payload:
trans.response.status = 400
return "Missing required 'create_type' parameter."
else:
create_type = payload.pop('create_type')
if create_type not in ('file', 'folder', 'collection'):
trans.response.status = 400
return "Invalid value for 'create_type' parameter ( %s ) specified." % create_type
if 'folder_id' not in payload:
trans.response.status = 400
return "Missing required 'folder_id' parameter."
else:
folder_id = payload.pop('folder_id')
class_name, folder_id = self.__decode_library_content_id(folder_id)
try:
# security is checked in the downstream controller
parent = self.get_library_folder(trans,
folder_id,
check_ownership=False,
check_accessible=False)
except Exception as e:
return str(e)
# The rest of the security happens in the library_common controller.
real_folder_id = trans.security.encode_id(parent.id)
# are we copying an HDA to the library folder?
# we'll need the id and any message to attach, then branch to that private function
from_hda_id, from_hdca_id, ldda_message = (payload.pop(
'from_hda_id',
None), payload.pop('from_hdca_id',
None), payload.pop('ldda_message', ''))
if create_type == 'file':
if from_hda_id:
return self._copy_hda_to_library_folder(
trans, self.hda_manager, self.decode_id(from_hda_id),
real_folder_id, ldda_message)
if from_hdca_id:
return self._copy_hdca_to_library_folder(
trans, self.hda_manager, self.decode_id(from_hdca_id),
real_folder_id, ldda_message)
# check for extended metadata, store it and pop it out of the param
# otherwise sanitize_param will have a fit
ex_meta_payload = payload.pop('extended_metadata', None)
# Now create the desired content object, either file or folder.
if create_type == 'file':
status, output = trans.webapp.controllers[
'library_common'].upload_library_dataset(
trans, 'api', library_id, real_folder_id, **payload)
elif create_type == 'folder':
status, output = trans.webapp.controllers[
'library_common'].create_folder(trans, 'api', real_folder_id,
library_id, **payload)
elif create_type == 'collection':
# Not delegating to library_common, so need to check access to parent
# folder here.
self.check_user_can_add_to_library_item(trans,
parent,
check_accessible=True)
create_params = api_payload_to_create_params(payload)
create_params['parent'] = parent
service = trans.app.dataset_collections_service
dataset_collection_instance = service.create(**create_params)
return [
dictify_dataset_collection_instance(
dataset_collection_instance,
security=trans.security,
parent=parent)
]
if status != 200:
trans.response.status = status
return output
else:
rval = []
for v in output.values():
if ex_meta_payload is not None:
# If there is extended metadata, store it, attach it to the dataset, and index it
ex_meta = ExtendedMetadata(ex_meta_payload)
trans.sa_session.add(ex_meta)
v.extended_metadata = ex_meta
trans.sa_session.add(v)
trans.sa_session.flush()
for path, value in self._scan_json_block(ex_meta_payload):
meta_i = ExtendedMetadataIndex(ex_meta, path, value)
trans.sa_session.add(meta_i)
trans.sa_session.flush()
if type(v) == trans.app.model.LibraryDatasetDatasetAssociation:
v = v.library_dataset
encoded_id = trans.security.encode_id(v.id)
if create_type == 'folder':
encoded_id = 'F' + encoded_id
rval.append(
dict(id=encoded_id,
name=v.name,
url=url_for('library_content',
library_id=library_id,
id=encoded_id)))
return rval
class LibraryContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ):
@web.expose_api
# TODO: Add parameter to only get top level of datasets/subfolders.
def index( self, trans, library_id, **kwd ):
"""
GET /api/libraries/{encoded_library_id}/contents
Displays a collection (list) of library contents (files and folders).
"""
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:
log.debug( "type(folder): %s" % type( folder ) )
log.debug( "type(api_path): %s; folder.api_path: %s" % ( type(folder.api_path), folder.api_path ) )
#log.debug( "attributes of folder: %s" % str(dir(folder)) )
ld.api_path = folder.api_path + '/' + ld.name
ld.api_type = 'file'
rval.append( ld )
return rval
try:
decoded_library_id = trans.security.decode_id( library_id )
except TypeError:
trans.response.status = 400
return "Malformed library id ( %s ) specified, unable to decode." % str( library_id )
try:
library = trans.sa_session.query( trans.app.model.Library ).get( decoded_library_id )
except:
library = None
if not library or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( current_user_roles, library ) ):
trans.response.status = 400
return "Invalid library id ( %s ) specified." % str( library_id )
log.debug( "Root folder type: %s" % type( library.root_folder ) )
encoded_id = 'F' + trans.security.encode_id( library.root_folder.id )
rval.append( dict( id = encoded_id,
type = 'folder',
name = '/',
url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) )
log.debug( "Root folder attributes: %s" % str(dir(library.root_folder)) )
library.root_folder.api_path = ''
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
@web.expose_api
def show( self, trans, id, library_id, **kwd ):
"""
GET /api/libraries/{encoded_library_id}/contents/{encoded_content_id}
Displays information about a library content (file or folder).
"""
class_name, content_id = self.__decode_library_content_id( trans, id )
if class_name == 'LibraryFolder':
content = self.get_library_folder( trans, content_id, check_ownership=False, check_accessible=True )
else:
content = self.get_library_dataset( trans, content_id, check_ownership=False, check_accessible=True )
return self.encode_all_ids( trans, content.get_api_value( view='element' ) )
@web.expose_api
def create( self, trans, library_id, payload, **kwd ):
"""
POST /api/libraries/{encoded_library_id}/contents
Creates a new library content item (file or folder).
"""
create_type = None
if 'create_type' not in payload:
trans.response.status = 400
return "Missing required 'create_type' parameter."
else:
create_type = payload.pop( 'create_type' )
if create_type not in ( 'file', 'folder' ):
trans.response.status = 400
return "Invalid value for 'create_type' parameter ( %s ) specified." % create_type
if 'folder_id' not in payload:
trans.response.status = 400
return "Missing requred 'folder_id' parameter."
else:
folder_id = payload.pop( 'folder_id' )
class_name, folder_id = self.__decode_library_content_id( trans, folder_id )
try:
# security is checked in the downstream controller
parent = self.get_library_folder( trans, folder_id, check_ownership=False, check_accessible=False )
except Exception, e:
return str( e )
# The rest of the security happens in the library_common controller.
real_folder_id = trans.security.encode_id( parent.id )
#check for extended metadata, store it and pop it out of the param
#otherwise sanitize_param will have a fit
ex_meta_payload = None
if 'extended_metadata' in payload:
ex_meta_payload = payload.pop('extended_metadata')
# Now create the desired content object, either file or folder.
if create_type == 'file':
status, output = trans.webapp.controllers['library_common'].upload_library_dataset( trans, 'api', library_id, real_folder_id, **payload )
elif create_type == 'folder':
status, output = trans.webapp.controllers['library_common'].create_folder( trans, 'api', real_folder_id, library_id, **payload )
if status != 200:
trans.response.status = status
return output
else:
rval = []
for k, v in output.items():
if ex_meta_payload is not None:
"""
If there is extended metadata, store it, attach it to the dataset, and index it
"""
ex_meta = ExtendedMetadata(ex_meta_payload)
trans.sa_session.add( ex_meta )
v.extended_metadata = ex_meta
trans.sa_session.add(v)
trans.sa_session.flush()
for path, value in self._scan_json_block(ex_meta_payload):
meta_i = ExtendedMetadataIndex(ex_meta, path, value)
trans.sa_session.add(meta_i)
trans.sa_session.flush()
if type( v ) == trans.app.model.LibraryDatasetDatasetAssociation:
v = v.library_dataset
encoded_id = trans.security.encode_id( v.id )
if create_type == 'folder':
encoded_id = 'F' + encoded_id
rval.append( dict( id = encoded_id,
name = v.name,
url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) )
return rval