def _make_library_uploaded_dataset(self, trans, params, name, path, type, library_bunch, in_folder=None):
link_data_only = params.get('link_data_only', 'copy_files')
uuid_str = params.get('uuid', None)
file_type = params.get('file_type', None)
library_bunch.replace_dataset = None # not valid for these types of upload
uploaded_dataset = util.bunch.Bunch()
new_name = name
# Remove compressed file extensions, if any, but only if
# we're copying files into Galaxy's file space.
if link_data_only == 'copy_files':
if new_name.endswith('.gz'):
new_name = new_name.rstrip('.gz')
elif new_name.endswith('.zip'):
new_name = new_name.rstrip('.zip')
uploaded_dataset.name = new_name
uploaded_dataset.path = path
uploaded_dataset.type = type
uploaded_dataset.ext = None
uploaded_dataset.file_type = file_type
uploaded_dataset.dbkey = params.get('dbkey', None)
uploaded_dataset.to_posix_lines = params.get('to_posix_lines', None)
uploaded_dataset.space_to_tab = params.get('space_to_tab', None)
uploaded_dataset.tag_using_filenames = params.get('tag_using_filenames', False)
uploaded_dataset.purge_source = getattr(trans.app.config, 'ftp_upload_purge', True)
if in_folder:
uploaded_dataset.in_folder = in_folder
uploaded_dataset.data = upload_common.new_upload(trans, 'api', uploaded_dataset, library_bunch)
uploaded_dataset.link_data_only = link_data_only
uploaded_dataset.uuid = uuid_str
if link_data_only == 'link_to_files':
uploaded_dataset.data.link_to(path)
trans.sa_session.add_all((uploaded_dataset.data, uploaded_dataset.data.dataset))
trans.sa_session.flush()
return uploaded_dataset
def _make_library_uploaded_dataset(self, trans, params, name, path, type, library_bunch, in_folder=None):
link_data_only = params.get('link_data_only', 'copy_files')
uuid_str = params.get('uuid', None)
file_type = params.get('file_type', None)
library_bunch.replace_dataset = None # not valid for these types of upload
uploaded_dataset = util.bunch.Bunch()
new_name = name
# Remove compressed file extensions, if any, but only if
# we're copying files into Galaxy's file space.
if link_data_only == 'copy_files':
if new_name.endswith('.gz'):
new_name = new_name.rstrip('.gz')
elif new_name.endswith('.zip'):
new_name = new_name.rstrip('.zip')
uploaded_dataset.name = new_name
uploaded_dataset.path = path
uploaded_dataset.type = type
uploaded_dataset.ext = None
uploaded_dataset.file_type = file_type
uploaded_dataset.dbkey = params.get('dbkey', None)
uploaded_dataset.to_posix_lines = params.get('to_posix_lines', None)
uploaded_dataset.space_to_tab = params.get('space_to_tab', None)
uploaded_dataset.tag_using_filenames = params.get('tag_using_filenames', False)
uploaded_dataset.tags = params.get('tags', None)
uploaded_dataset.purge_source = getattr(trans.app.config, 'ftp_upload_purge', True)
if in_folder:
uploaded_dataset.in_folder = in_folder
uploaded_dataset.data = upload_common.new_upload(trans, 'api', uploaded_dataset, library_bunch)
uploaded_dataset.link_data_only = link_data_only
uploaded_dataset.uuid = uuid_str
if link_data_only == 'link_to_files':
uploaded_dataset.data.link_to(path)
trans.sa_session.add_all((uploaded_dataset.data, uploaded_dataset.data.dataset))
trans.sa_session.flush()
return uploaded_dataset
def _precreate_fetched_hdas(trans, history, target, outputs):
for item in target.get("elements", []):
name = item.get("name", None)
if name is None:
src = item.get("src", None)
if src == "url":
url = item.get("url")
if name is None:
name = url.split("/")[-1]
elif src == "path":
path = item["path"]
if name is None:
name = os.path.basename(path)
file_type = item.get("ext", "auto")
dbkey = item.get("dbkey", "?")
uploaded_dataset = Bunch(type='file',
name=name,
file_type=file_type,
dbkey=dbkey)
tag_list = item.get("tags", [])
data = upload_common.new_upload(trans,
'',
uploaded_dataset,
library_bunch=None,
history=history,
tag_list=tag_list)
outputs.append(data)
item["object_id"] = data.id
def make_library_uploaded_dataset(self,
trans,
params,
name,
path,
type,
library_bunch,
in_folder=None):
library_bunch.replace_dataset = None # not valid for these types of upload
uploaded_dataset = util.bunch.Bunch()
uploaded_dataset.name = name
uploaded_dataset.path = path
uploaded_dataset.type = type
uploaded_dataset.ext = None
uploaded_dataset.file_type = params.file_type
uploaded_dataset.dbkey = params.dbkey
uploaded_dataset.space_to_tab = params.space_to_tab
if in_folder:
uploaded_dataset.in_folder = in_folder
uploaded_dataset.data = upload_common.new_upload(
trans, uploaded_dataset, library_bunch)
if params.get('link_data_only', False):
uploaded_dataset.link_data_only = True
uploaded_dataset.data.file_name = os.path.abspath(path)
trans.sa_session.add(uploaded_dataset.data)
trans.sa_session.flush()
return uploaded_dataset
def create_dataset( name ):
ud = Bunch( name=name, file_type=None, dbkey=None )
if nonfile_params.get( 'folder_id', False ):
replace_id = nonfile_params.get( 'replace_id', None )
if replace_id not in [ None, 'None' ]:
replace_dataset = trans.sa_session.query( l.LibraryDataset ).get( int( replace_id ) )
else:
replace_dataset = None
library_bunch = upload_common.handle_library_params( trans, nonfile_params, nonfile_params.folder_id, replace_dataset )
else:
library_bunch = None
return upload_common.new_upload( trans, ud, library_bunch=library_bunch, state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD )
def create_dataset( name ):
ud = Bunch( name=name, file_type=None, dbkey=None )
if nonfile_params.get( 'folder_id', False ):
replace_id = nonfile_params.get( 'replace_id', None )
if replace_id not in [ None, 'None' ]:
replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) )
else:
replace_dataset = None
# FIXME: instead of passing params here ( chiech have been process by util.Params(), the original kwd
# should be passed so that complex objects that may have been included in the initial request remain.
library_bunch = upload_common.handle_library_params( trans, nonfile_params, nonfile_params.folder_id, replace_dataset )
else:
library_bunch = None
return upload_common.new_upload( trans, cntrller, ud, library_bunch=library_bunch, state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD )
def create_dataset( name ):
ud = Bunch( name=name, file_type=None, dbkey=None )
if nonfile_params.get( 'folder_id', False ):
replace_id = nonfile_params.get( 'replace_id', None )
if replace_id not in [ None, 'None' ]:
replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) )
else:
replace_dataset = None
# FIXME: instead of passing params here ( chiech have been process by util.Params(), the original kwd
# should be passed so that complex objects that may have been included in the initial request remain.
library_bunch = upload_common.handle_library_params( trans, nonfile_params, nonfile_params.folder_id, replace_dataset )
else:
library_bunch = None
return upload_common.new_upload( trans, cntrller, ud, library_bunch=library_bunch, state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD )
def _make_library_uploaded_dataset(self,
trans,
params,
name,
path,
type,
library_bunch,
in_folder=None):
link_data_only = params.get('link_data_only', 'copy_files')
uuid_str = params.get('uuid', None)
file_type = params.get('file_type', None)
library_bunch.replace_dataset = None # not valid for these types of upload
uploaded_dataset = util.bunch.Bunch()
new_name = name
# Remove compressed file extensions, if any, but only if
# we're copying files into Galaxy's file space.
if link_data_only == 'copy_files':
if new_name.endswith('.gz'):
new_name = new_name.rstrip('.gz')
elif new_name.endswith('.zip'):
new_name = new_name.rstrip('.zip')
uploaded_dataset.name = new_name
uploaded_dataset.path = path
uploaded_dataset.type = type
uploaded_dataset.ext = None
uploaded_dataset.file_type = file_type
uploaded_dataset.dbkey = params.get('dbkey', None)
uploaded_dataset.to_posix_lines = params.get('to_posix_lines', None)
uploaded_dataset.space_to_tab = params.get('space_to_tab', None)
uploaded_dataset.tag_using_filenames = params.get(
'tag_using_filenames', True)
if in_folder:
uploaded_dataset.in_folder = in_folder
uploaded_dataset.data = upload_common.new_upload(
trans, 'api', uploaded_dataset, library_bunch)
uploaded_dataset.link_data_only = link_data_only
uploaded_dataset.uuid = uuid_str
if link_data_only == 'link_to_files':
uploaded_dataset.data.file_name = os.path.abspath(path)
# Since we are not copying the file into Galaxy's managed
# default file location, the dataset should never be purgable.
uploaded_dataset.data.dataset.purgable = False
trans.sa_session.add_all(
(uploaded_dataset.data, uploaded_dataset.data.dataset))
trans.sa_session.flush()
return uploaded_dataset
def create_dataset(name):
ud = Bunch(name=name, file_type=None, dbkey=None)
if nonfile_params.get('folder_id', False):
replace_id = nonfile_params.get('replace_id', None)
if replace_id not in [None, 'None']:
replace_dataset = trans.sa_session.query(
l.LibraryDataset).get(int(replace_id))
else:
replace_dataset = None
library_bunch = upload_common.handle_library_params(
trans, nonfile_params, nonfile_params.folder_id,
replace_dataset)
else:
library_bunch = None
return upload_common.new_upload(
trans,
ud,
library_bunch=library_bunch,
state=trans.app.model.HistoryDatasetAssociation.states.UPLOAD)
def make_library_uploaded_dataset( self, trans, params, name, path, type, library_bunch, in_folder=None ):
library_bunch.replace_dataset = None # not valid for these types of upload
uploaded_dataset = util.bunch.Bunch()
uploaded_dataset.name = name
uploaded_dataset.path = path
uploaded_dataset.type = type
uploaded_dataset.ext = None
uploaded_dataset.file_type = params.file_type
uploaded_dataset.dbkey = params.dbkey
uploaded_dataset.space_to_tab = params.space_to_tab
if in_folder:
uploaded_dataset.in_folder = in_folder
uploaded_dataset.data = upload_common.new_upload( trans, uploaded_dataset, library_bunch )
if params.get( 'link_data_only', False ):
uploaded_dataset.link_data_only = True
uploaded_dataset.data.file_name = os.path.abspath( path )
trans.sa_session.add( uploaded_dataset.data )
trans.sa_session.flush()
return uploaded_dataset
def _precreate_fetched_hdas(trans, history, target, outputs):
for item in target.get("elements", []):
name = item.get("name", None)
if name is None:
src = item.get("src", None)
if src == "url":
url = item.get("url")
if name is None:
name = url.split("/")[-1]
elif src == "path":
path = item["path"]
if name is None:
name = os.path.basename(path)
file_type = item.get("ext", "auto")
dbkey = item.get("dbkey", "?")
uploaded_dataset = Bunch(
type='file', name=name, file_type=file_type, dbkey=dbkey
)
data = upload_common.new_upload(trans, '', uploaded_dataset, library_bunch=None, history=history)
outputs.append(data)
item["object_id"] = data.id
def _make_library_uploaded_dataset(self, trans, params, name, path, type, library_bunch, in_folder=None):
link_data_only = params.get('link_data_only', 'copy_files')
uuid_str = params.get('uuid', None)
file_type = params.get('file_type', None)
library_bunch.replace_dataset = None # not valid for these types of upload
uploaded_dataset = util.bunch.Bunch()
new_name = name
# Remove compressed file extensions, if any, but only if
# we're copying files into Galaxy's file space.
if link_data_only == 'copy_files':
if new_name.endswith('.gz'):
new_name = new_name.rstrip('.gz')
elif new_name.endswith('.zip'):
new_name = new_name.rstrip('.zip')
uploaded_dataset.name = new_name
uploaded_dataset.path = path
uploaded_dataset.type = type
uploaded_dataset.ext = None
uploaded_dataset.file_type = file_type
uploaded_dataset.dbkey = params.get('dbkey', None)
uploaded_dataset.to_posix_lines = params.get('to_posix_lines', None)
uploaded_dataset.space_to_tab = params.get('space_to_tab', None)
uploaded_dataset.tag_using_filenames = params.get('tag_using_filenames', True)
if in_folder:
uploaded_dataset.in_folder = in_folder
uploaded_dataset.data = upload_common.new_upload(trans, 'api', uploaded_dataset, library_bunch)
uploaded_dataset.link_data_only = link_data_only
uploaded_dataset.uuid = uuid_str
if link_data_only == 'link_to_files':
uploaded_dataset.data.file_name = os.path.abspath(path)
# Since we are not copying the file into Galaxy's managed
# default file location, the dataset should never be purgable.
uploaded_dataset.data.dataset.purgable = False
trans.sa_session.add_all((uploaded_dataset.data, uploaded_dataset.data.dataset))
trans.sa_session.flush()
return uploaded_dataset