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Source code for galaxy.managers.model_stores
from typing import Optional
from galaxy import model
from galaxy.exceptions import RequestParameterInvalidException
from galaxy.jobs.manager import JobManager
from galaxy.managers.context import ProvidesUserContext
from galaxy.managers.histories import HistoryManager
from galaxy.managers.users import UserManager
from galaxy.model.scoped_session import galaxy_scoped_session
from galaxy.model.store import (
ImportDiscardedDataType,
ImportOptions,
ObjectImportTracker,
source_to_import_store,
)
from galaxy.schema.schema import HistoryContentType
from galaxy.schema.tasks import (
GenerateHistoryContentDownload,
GenerateHistoryDownload,
GenerateInvocationDownload,
ImportModelStoreTaskRequest,
SetupHistoryExportJob,
WriteHistoryContentTo,
WriteHistoryTo,
WriteInvocationTo,
)
from galaxy.structured_app import MinimalManagerApp
from galaxy.web.short_term_storage import (
ShortTermStorageMonitor,
storage_context,
)
[docs]class ModelStoreUserContext(ProvidesUserContext):
[docs] def __init__(self, app: MinimalManagerApp, user: model.User) -> None:
self._app = app
self._user = user
@property
def app(self):
return self._app
@property
def url_builder(self):
raise NotImplementedError("URL builder not available in ModelStore context.")
[docs] def set_user(self, user):
raise NotImplementedError("Cannot change user from ModelStore context.")
user = property(get_user, set_user)
[docs]class ModelStoreManager:
[docs] def __init__(
self,
app: MinimalManagerApp,
history_manager: HistoryManager,
sa_session: galaxy_scoped_session,
job_manager: JobManager,
short_term_storage_monitor: ShortTermStorageMonitor,
user_manager: UserManager,
):
self._app = app
self._sa_session = sa_session
self._job_manager = job_manager
self._history_manager = history_manager
self._short_term_storage_monitor = short_term_storage_monitor
self._user_manager = user_manager
[docs] def setup_history_export_job(self, request: SetupHistoryExportJob):
history_id = request.history_id
job_id = request.job_id
include_hidden = request.include_hidden
include_deleted = request.include_deleted
store_directory = request.store_directory
history = self._sa_session.query(model.History).get(history_id)
# symlink files on export, on worker files will tarred up in a dereferenced manner.
with model.store.DirectoryModelExportStore(
store_directory, app=self._app, export_files="symlink"
) as export_store:
export_store.export_history(history, include_hidden=include_hidden, include_deleted=include_deleted)
job = self._sa_session.query(model.Job).get(job_id)
job.state = model.Job.states.NEW
self._sa_session.flush()
self._job_manager.enqueue(job)
[docs] def prepare_history_download(self, request: GenerateHistoryDownload):
model_store_format = request.model_store_format
history = self._history_manager.by_id(request.history_id)
export_files = "symlink" if request.include_files else None
include_hidden = request.include_hidden
include_deleted = request.include_deleted
with storage_context(
request.short_term_storage_request_id, self._short_term_storage_monitor
) as short_term_storage_target:
with model.store.get_export_store_factory(self._app, model_store_format, export_files=export_files)(
short_term_storage_target.path
) as export_store:
export_store.export_history(history, include_hidden=include_hidden, include_deleted=include_deleted)
[docs] def prepare_history_content_download(self, request: GenerateHistoryContentDownload):
model_store_format = request.model_store_format
export_files = "symlink" if request.include_files else None
with storage_context(
request.short_term_storage_request_id, self._short_term_storage_monitor
) as short_term_storage_target:
with model.store.get_export_store_factory(self._app, model_store_format, export_files=export_files)(
short_term_storage_target.path
) as export_store:
if request.content_type == HistoryContentType.dataset:
hda = self._sa_session.query(model.HistoryDatasetAssociation).get(request.content_id)
export_store.add_dataset(hda)
else:
hdca = self._sa_session.query(model.HistoryDatasetCollectionAssociation).get(request.content_id)
export_store.export_collection(
hdca, include_hidden=request.include_hidden, include_deleted=request.include_deleted
)
[docs] def prepare_invocation_download(self, request: GenerateInvocationDownload):
model_store_format = request.model_store_format
export_files = "symlink" if request.include_files else None
with storage_context(
request.short_term_storage_request_id, self._short_term_storage_monitor
) as short_term_storage_target:
with model.store.get_export_store_factory(self._app, model_store_format, export_files=export_files)(
short_term_storage_target.path
) as export_store:
invocation = self._sa_session.query(model.WorkflowInvocation).get(request.invocation_id)
export_store.export_workflow_invocation(
invocation, include_hidden=request.include_hidden, include_deleted=request.include_deleted
)
[docs] def write_invocation_to(self, request: WriteInvocationTo):
model_store_format = request.model_store_format
export_files = "symlink" if request.include_files else None
target_uri = request.target_uri
user_context = self._build_user_context(request.user.user_id)
with model.store.get_export_store_factory(
self._app,
model_store_format,
export_files=export_files,
user_context=user_context,
)(target_uri) as export_store:
invocation = self._sa_session.query(model.WorkflowInvocation).get(request.invocation_id)
export_store.export_workflow_invocation(
invocation, include_hidden=request.include_hidden, include_deleted=request.include_deleted
)
[docs] def write_history_content_to(self, request: WriteHistoryContentTo):
model_store_format = request.model_store_format
export_files = "symlink" if request.include_files else None
target_uri = request.target_uri
user_context = self._build_user_context(request.user.user_id)
with model.store.get_export_store_factory(
self._app, model_store_format, export_files=export_files, user_context=user_context
)(target_uri) as export_store:
if request.content_type == HistoryContentType.dataset:
hda = self._sa_session.query(model.HistoryDatasetAssociation).get(request.content_id)
export_store.add_dataset(hda)
else:
hdca = self._sa_session.query(model.HistoryDatasetCollectionAssociation).get(request.content_id)
export_store.export_collection(
hdca, include_hidden=request.include_hidden, include_deleted=request.include_deleted
)
[docs] def write_history_to(self, request: WriteHistoryTo):
model_store_format = request.model_store_format
export_files = "symlink" if request.include_files else None
target_uri = request.target_uri
user_context = self._build_user_context(request.user.user_id)
with model.store.get_export_store_factory(
self._app, model_store_format, export_files=export_files, user_context=user_context
)(target_uri) as export_store:
history = self._history_manager.by_id(request.history_id)
export_store.export_history(
history, include_hidden=request.include_hidden, include_deleted=request.include_deleted
)
[docs] def import_model_store(self, request: ImportModelStoreTaskRequest):
import_options = ImportOptions(
allow_library_creation=request.for_library,
)
history_id = request.history_id
if history_id:
history = self._sa_session.query(model.History).get(history_id)
else:
history = None
user_context = self._build_user_context(request.user.user_id)
model_import_store = source_to_import_store(
request.source_uri,
self._app,
import_options,
model_store_format=request.model_store_format,
user_context=user_context,
)
new_history = history is None and not request.for_library
if new_history:
if not model_import_store.defines_new_history():
raise RequestParameterInvalidException("Supplied model store doesn't define new history to import.")
with model_import_store.target_history(legacy_history_naming=False) as new_history:
object_tracker = model_import_store.perform_import(new_history, new_history=True)
object_tracker.new_history = new_history
else:
object_tracker = model_import_store.perform_import(
history=history,
new_history=new_history,
)
return object_tracker
def _build_user_context(self, user_id: int):
user = self._user_manager.by_id(user_id)
user_context = ModelStoreUserContext(self._app, user)
return user_context
[docs]def create_objects_from_store(
app: MinimalManagerApp,
galaxy_user: Optional[model.User],
payload,
history: Optional[model.History] = None,
for_library: bool = False,
) -> ObjectImportTracker:
import_options = ImportOptions(
discarded_data=ImportDiscardedDataType.FORCE,
allow_library_creation=for_library,
)
user_context = ModelStoreUserContext(app, galaxy_user) if galaxy_user is not None else None
model_import_store = source_to_import_store(
payload.store_content_uri or payload.store_dict,
app=app,
import_options=import_options,
model_store_format=payload.model_store_format,
user_context=user_context,
)
new_history = history is None and not for_library
if new_history:
if not model_import_store.defines_new_history():
raise RequestParameterInvalidException("Supplied model store doesn't define new history to import.")
with model_import_store.target_history(legacy_history_naming=False) as new_history:
object_tracker = model_import_store.perform_import(new_history, new_history=True)
object_tracker.new_history = new_history
else:
object_tracker = model_import_store.perform_import(
history=history,
new_history=new_history,
)
return object_tracker