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This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for galaxy.model.store
import abc
import contextlib
import datetime
import logging
import os
import shutil
import tarfile
import tempfile
from collections import defaultdict
from dataclasses import dataclass
from enum import Enum
from json import (
dump,
dumps,
load,
)
from tempfile import mkdtemp
from types import TracebackType
from typing import (
Any,
Callable,
cast,
Dict,
Iterable,
Iterator,
List,
Optional,
Set,
Tuple,
Type,
TYPE_CHECKING,
Union,
)
from bdbag import bdbag_api as bdb
from boltons.iterutils import remap
from pydantic import (
BaseModel,
ConfigDict,
)
from rocrate.model.computationalworkflow import (
ComputationalWorkflow,
WorkflowDescription,
)
from rocrate.rocrate import ROCrate
from sqlalchemy import select
from sqlalchemy.orm import joinedload
from sqlalchemy.orm.scoping import scoped_session
from sqlalchemy.sql import expression
from typing_extensions import Protocol
from galaxy.datatypes.registry import Registry
from galaxy.exceptions import (
MalformedContents,
ObjectNotFound,
RequestParameterInvalidException,
)
from galaxy.files import (
ConfiguredFileSources,
ProvidesUserFileSourcesUserContext,
)
from galaxy.files.uris import stream_url_to_file
from galaxy.model.base import (
ensure_object_added_to_session,
transaction,
)
from galaxy.model.mapping import GalaxyModelMapping
from galaxy.model.metadata import MetadataCollection
from galaxy.model.orm.util import (
add_object_to_object_session,
add_object_to_session,
get_object_session,
)
from galaxy.model.tags import GalaxyTagHandler
from galaxy.objectstore import (
BaseObjectStore,
ObjectStore,
persist_extra_files,
)
from galaxy.schema.bco import (
BioComputeObjectCore,
DescriptionDomain,
DescriptionDomainUri,
ErrorDomain,
InputAndOutputDomain,
InputAndOutputDomainUri,
InputSubdomainItem,
OutputSubdomainItem,
ParametricDomain,
ParametricDomainItem,
PipelineStep,
ProvenanceDomain,
UsabilityDomain,
XrefItem,
)
from galaxy.schema.bco.io_domain import Uri
from galaxy.schema.bco.util import (
extension_domains,
galaxy_execution_domain,
get_contributors,
write_to_file,
)
from galaxy.schema.schema import (
DatasetStateField,
ModelStoreFormat,
)
from galaxy.security.idencoding import IdEncodingHelper
from galaxy.util import (
FILENAME_VALID_CHARS,
in_directory,
safe_makedirs,
)
from galaxy.util.bunch import Bunch
from galaxy.util.compression_utils import CompressedFile
from galaxy.util.path import StrPath
from ._bco_convert_utils import (
bco_workflow_version,
SoftwarePrerequisiteTracker,
)
from .ro_crate_utils import WorkflowRunCrateProfileBuilder
from ..custom_types import json_encoder
from ..item_attrs import (
add_item_annotation,
get_item_annotation_str,
)
from ... import model
if TYPE_CHECKING:
from galaxy.managers.workflows import WorkflowContentsManager
from galaxy.model import (
HistoryItem,
ImplicitCollectionJobs,
)
from galaxy.model.tags import GalaxyTagHandlerSession
log = logging.getLogger(__name__)
ObjectKeyType = Union[str, int]
ATTRS_FILENAME_HISTORY = "history_attrs.txt"
ATTRS_FILENAME_DATASETS = "datasets_attrs.txt"
ATTRS_FILENAME_JOBS = "jobs_attrs.txt"
ATTRS_FILENAME_IMPLICIT_COLLECTION_JOBS = "implicit_collection_jobs_attrs.txt"
ATTRS_FILENAME_COLLECTIONS = "collections_attrs.txt"
ATTRS_FILENAME_EXPORT = "export_attrs.txt"
ATTRS_FILENAME_LIBRARIES = "libraries_attrs.txt"
ATTRS_FILENAME_LIBRARY_FOLDERS = "library_folders_attrs.txt"
ATTRS_FILENAME_INVOCATIONS = "invocation_attrs.txt"
ATTRS_FILENAME_CONVERSIONS = "implicit_dataset_conversions.txt"
TRACEBACK = "traceback.txt"
GALAXY_EXPORT_VERSION = "2"
DICT_STORE_ATTRS_KEY_HISTORY = "history"
DICT_STORE_ATTRS_KEY_DATASETS = "datasets"
DICT_STORE_ATTRS_KEY_COLLECTIONS = "collections"
DICT_STORE_ATTRS_KEY_CONVERSIONS = "implicit_dataset_conversions"
DICT_STORE_ATTRS_KEY_JOBS = "jobs"
DICT_STORE_ATTRS_KEY_IMPLICIT_COLLECTION_JOBS = "implicit_collection_jobs"
DICT_STORE_ATTRS_KEY_LIBRARIES = "libraries"
DICT_STORE_ATTRS_KEY_INVOCATIONS = "invocations"
JsonDictT = Dict[str, Any]
[docs]class StoreAppProtocol(Protocol):
"""Define the parts of a Galaxy-like app consumed by model store."""
datatypes_registry: Registry
object_store: BaseObjectStore
security: IdEncodingHelper
tag_handler: GalaxyTagHandler
model: GalaxyModelMapping
file_sources: ConfiguredFileSources
workflow_contents_manager: "WorkflowContentsManager"
[docs]class ImportDiscardedDataType(Enum):
# Don't allow discarded 'okay' datasets on import, datasets will be marked deleted.
FORBID = "forbid"
# Allow datasets to be imported as experimental DISCARDED datasets that are not deleted if file data unavailable.
ALLOW = "allow"
# Import all datasets as discarded regardless of whether file data is available in the store.
FORCE = "force"
[docs]class DatasetAttributeImportModel(BaseModel):
state: Optional[DatasetStateField] = None
deleted: Optional[bool] = None
purged: Optional[bool] = None
external_filename: Optional[str] = None
_extra_files_path: Optional[str] = None
file_size: Optional[int] = None
object_store_id: Optional[str] = None
total_size: Optional[int] = None
created_from_basename: Optional[str] = None
uuid: Optional[str] = None
model_config = ConfigDict(extra="ignore")
DEFAULT_DISCARDED_DATA_TYPE = ImportDiscardedDataType.FORBID
[docs]class ImportOptions:
allow_edit: bool
allow_library_creation: bool
allow_dataset_object_edit: bool
discarded_data: ImportDiscardedDataType
[docs] def __init__(
self,
allow_edit: bool = False,
allow_library_creation: bool = False,
allow_dataset_object_edit: Optional[bool] = None,
discarded_data: ImportDiscardedDataType = DEFAULT_DISCARDED_DATA_TYPE,
) -> None:
self.allow_edit = allow_edit
self.allow_library_creation = allow_library_creation
if allow_dataset_object_edit is None:
self.allow_dataset_object_edit = allow_edit
else:
self.allow_dataset_object_edit = allow_dataset_object_edit
self.discarded_data = discarded_data
[docs]class SessionlessContext:
[docs] def query(self, model_class: model.RepresentById) -> Bunch:
def find(obj_id):
return self.objects.get(model_class, {}).get(obj_id) or None
def filter_by(*args, **kwargs):
# TODO: Hack for history export archive, should support this too
return Bunch(first=lambda: next(iter(self.objects.get(model_class, {None: None}))))
return Bunch(find=find, get=find, filter_by=filter_by)
[docs] def get(self, model_class: model.RepresentById, primary_key: Any): # patch for SQLAlchemy 2.0 compatibility
return self.query(model_class).get(primary_key)
[docs]def replace_metadata_file(
metadata: Dict[str, Any],
dataset_instance: model.DatasetInstance,
sa_session: Union[SessionlessContext, scoped_session],
) -> Dict[str, Any]:
def remap_objects(p, k, obj):
if isinstance(obj, dict) and "model_class" in obj and obj["model_class"] == "MetadataFile":
metadata_file = model.MetadataFile(dataset=dataset_instance, uuid=obj["uuid"])
sa_session.add(metadata_file)
return (k, metadata_file)
return (k, obj)
return remap(metadata, remap_objects)
[docs]class ModelImportStore(metaclass=abc.ABCMeta):
app: Optional[StoreAppProtocol]
archive_dir: str
[docs] def __init__(
self,
import_options: Optional[ImportOptions] = None,
app: Optional[StoreAppProtocol] = None,
user: Optional[model.User] = None,
object_store: Optional[ObjectStore] = None,
tag_handler: Optional["GalaxyTagHandlerSession"] = None,
) -> None:
if object_store is None:
if app is not None:
object_store = app.object_store
self.object_store = object_store
self.app = app
if app is not None:
self.sa_session = app.model.session
self.sessionless = False
else:
self.sa_session = SessionlessContext()
self.sessionless = True
self.user = user
self.import_options = import_options or ImportOptions()
self.dataset_state_serialized = True
self.tag_handler = tag_handler
if self.defines_new_history():
self.import_history_encoded_id = self.new_history_properties().get("encoded_id")
else:
self.import_history_encoded_id = None
[docs] @abc.abstractmethod
def defines_new_history(self) -> bool:
"""Does this store define a new history to create."""
[docs] @abc.abstractmethod
def new_history_properties(self) -> Dict[str, Any]:
"""Dict of history properties if defines_new_history() is truthy."""
[docs] @abc.abstractmethod
def datasets_properties(self) -> List[Dict[str, Any]]:
"""Return a list of HDA properties."""
[docs] def library_properties(self) -> List[Dict[str, Any]]:
"""Return a list of library properties."""
return []
[docs] @abc.abstractmethod
def collections_properties(self) -> List[Dict[str, Any]]:
"""Return a list of HDCA properties."""
[docs] @abc.abstractmethod
def implicit_dataset_conversion_properties(self) -> List[Dict[str, Any]]:
"""Return a list of ImplicitlyConvertedDatasetAssociation properties."""
[docs] @abc.abstractmethod
def jobs_properties(self) -> List[Dict[str, Any]]:
"""Return a list of jobs properties."""
[docs] @abc.abstractmethod
def implicit_collection_jobs_properties(self) -> List[Dict[str, Any]]: ...
@property
@abc.abstractmethod
def object_key(self) -> str:
"""Key used to connect objects in metadata.
Legacy exports used 'hid' but associated objects may not be from the same history
and a history may contain multiple objects with the same 'hid'.
"""
@property
def file_source_root(self) -> Optional[str]:
"""Source of valid file data."""
return None
[docs] def trust_hid(self, obj_attrs: Dict[str, Any]) -> bool:
"""Trust HID when importing objects into a new History."""
return (
self.import_history_encoded_id is not None
and obj_attrs.get("history_encoded_id") == self.import_history_encoded_id
)
[docs] @contextlib.contextmanager
def target_history(
self, default_history: Optional[model.History] = None, legacy_history_naming: bool = True
) -> Iterator[Optional[model.History]]:
new_history = None
if self.defines_new_history():
history_properties = self.new_history_properties()
history_name = history_properties.get("name")
if history_name and legacy_history_naming:
history_name = f"imported from archive: {history_name}"
elif history_name:
pass # history_name = history_name
else:
history_name = "unnamed imported history"
# Create history.
new_history = model.History(name=history_name, user=self.user)
new_history.importing = True
hid_counter = history_properties.get("hid_counter")
genome_build = history_properties.get("genome_build")
# TODO: This seems like it shouldn't be imported, try to test and verify we can calculate this
# and get away without it. -John
if hid_counter:
new_history.hid_counter = hid_counter
if genome_build:
new_history.genome_build = genome_build
self._session_add(new_history)
self._flush()
if self.user:
add_item_annotation(self.sa_session, self.user, new_history, history_properties.get("annotation"))
history: Optional[model.History] = new_history
else:
history = default_history
yield history
if new_history is not None:
# Done importing.
new_history.importing = False
self._flush()
[docs] def perform_import(
self, history: Optional[model.History] = None, new_history: bool = False, job: Optional[model.Job] = None
) -> "ObjectImportTracker":
object_import_tracker = ObjectImportTracker()
datasets_attrs = self.datasets_properties()
collections_attrs = self.collections_properties()
self._import_datasets(object_import_tracker, datasets_attrs, history, new_history, job)
self._import_dataset_copied_associations(object_import_tracker, datasets_attrs)
self._import_libraries(object_import_tracker)
self._import_collection_instances(object_import_tracker, collections_attrs, history, new_history)
self._import_collection_implicit_input_associations(object_import_tracker, collections_attrs)
self._import_collection_copied_associations(object_import_tracker, collections_attrs)
self._import_implicit_dataset_conversions(object_import_tracker)
self._reassign_hids(object_import_tracker, history)
self._import_jobs(object_import_tracker, history)
self._import_implicit_collection_jobs(object_import_tracker)
self._import_workflow_invocations(object_import_tracker, history)
self._flush()
return object_import_tracker
def _attach_dataset_hashes(
self,
dataset_or_file_attrs: Dict[str, Any],
dataset_instance: model.DatasetInstance,
) -> None:
if "hashes" in dataset_or_file_attrs:
for hash_attrs in dataset_or_file_attrs["hashes"]:
hash_obj = model.DatasetHash()
hash_obj.hash_value = hash_attrs["hash_value"]
hash_obj.hash_function = hash_attrs["hash_function"]
hash_obj.extra_files_path = hash_attrs["extra_files_path"]
dataset_instance.dataset.hashes.append(hash_obj)
def _attach_dataset_sources(
self,
dataset_or_file_attrs: Dict[str, Any],
dataset_instance: model.DatasetInstance,
) -> None:
if "sources" in dataset_or_file_attrs:
for source_attrs in dataset_or_file_attrs["sources"]:
source_obj = model.DatasetSource()
source_obj.source_uri = source_attrs["source_uri"]
source_obj.transform = source_attrs["transform"]
source_obj.extra_files_path = source_attrs["extra_files_path"]
for hash_attrs in source_attrs["hashes"]:
hash_obj = model.DatasetSourceHash()
hash_obj.hash_value = hash_attrs["hash_value"]
hash_obj.hash_function = hash_attrs["hash_function"]
source_obj.hashes.append(hash_obj)
dataset_instance.dataset.sources.append(source_obj)
def _import_datasets(
self,
object_import_tracker: "ObjectImportTracker",
datasets_attrs: List[Dict[str, Any]],
history: Optional[model.History],
new_history: bool,
job: Optional[model.Job],
) -> None:
object_key = self.object_key
def handle_dataset_object_edit(dataset_instance, dataset_attrs):
if "dataset" in dataset_attrs:
assert self.import_options.allow_dataset_object_edit
dataset_attributes = DatasetAttributeImportModel(**dataset_attrs["dataset"]).model_dump(
exclude_unset=True,
)
for attribute, value in dataset_attributes.items():
setattr(dataset_instance.dataset, attribute, value)
self._attach_dataset_hashes(dataset_attrs["dataset"], dataset_instance)
self._attach_dataset_sources(dataset_attrs["dataset"], dataset_instance)
if "id" in dataset_attrs["dataset"] and self.import_options.allow_edit:
dataset_instance.dataset.id = dataset_attrs["dataset"]["id"]
for dataset_association in dataset_instance.dataset.history_associations:
if (
dataset_association is not dataset_instance
and dataset_association.extension == dataset_instance.extension
or dataset_association.extension == "auto"
):
copy_dataset_instance_metadata_attributes(
source=dataset_instance, target=dataset_association
)
if job:
dataset_instance.dataset.job_id = job.id
for dataset_attrs in datasets_attrs:
if "state" not in dataset_attrs:
self.dataset_state_serialized = False
if "id" in dataset_attrs and self.import_options.allow_edit and not self.sessionless:
model_class = getattr(model, dataset_attrs["model_class"])
dataset_instance: model.DatasetInstance = self.sa_session.get(model_class, dataset_attrs["id"])
attributes = [
"name",
"extension",
"info",
"blurb",
"peek",
"designation",
"visible",
"metadata",
"tool_version",
"validated_state",
"validated_state_message",
]
for attribute in attributes:
if attribute in dataset_attrs:
value = dataset_attrs[attribute]
if attribute == "metadata":
value = replace_metadata_file(value, dataset_instance, self.sa_session)
setattr(dataset_instance, attribute, value)
handle_dataset_object_edit(dataset_instance, dataset_attrs)
else:
metadata_deferred = dataset_attrs.get("metadata_deferred", False)
metadata = dataset_attrs.get("metadata")
if metadata is None and not metadata_deferred:
raise MalformedContents("metadata_deferred must be true if no metadata found in dataset attributes")
if metadata is None:
metadata = {"dbkey": "?"}
model_class = dataset_attrs.get("model_class", "HistoryDatasetAssociation")
if model_class == "HistoryDatasetAssociation":
# Create dataset and HDA.
dataset_instance = model.HistoryDatasetAssociation(
name=dataset_attrs["name"],
extension=dataset_attrs["extension"],
info=dataset_attrs["info"],
blurb=dataset_attrs["blurb"],
peek=dataset_attrs["peek"],
designation=dataset_attrs["designation"],
visible=dataset_attrs["visible"],
deleted=dataset_attrs.get("deleted", False),
dbkey=metadata["dbkey"],
tool_version=metadata.get("tool_version"),
metadata_deferred=metadata_deferred,
history=history,
create_dataset=True,
flush=False,
sa_session=self.sa_session,
)
dataset_instance._metadata = metadata
elif model_class == "LibraryDatasetDatasetAssociation":
# Create dataset and LDDA.
dataset_instance = model.LibraryDatasetDatasetAssociation(
name=dataset_attrs["name"],
extension=dataset_attrs["extension"],
info=dataset_attrs["info"],
blurb=dataset_attrs["blurb"],
peek=dataset_attrs["peek"],
designation=dataset_attrs["designation"],
visible=dataset_attrs["visible"],
deleted=dataset_attrs.get("deleted", False),
dbkey=metadata["dbkey"],
tool_version=metadata.get("tool_version"),
metadata_deferred=metadata_deferred,
user=self.user,
create_dataset=True,
flush=False,
sa_session=self.sa_session,
)
else:
raise Exception("Unknown dataset instance type encountered")
metadata = replace_metadata_file(metadata, dataset_instance, self.sa_session)
if self.sessionless:
dataset_instance._metadata_collection = MetadataCollection(
dataset_instance, session=self.sa_session
)
dataset_instance._metadata = metadata
else:
dataset_instance.metadata = metadata
self._attach_raw_id_if_editing(dataset_instance, dataset_attrs)
# Older style...
if "uuid" in dataset_attrs:
dataset_instance.dataset.uuid = dataset_attrs["uuid"]
if "dataset_uuid" in dataset_attrs:
dataset_instance.dataset.uuid = dataset_attrs["dataset_uuid"]
self._session_add(dataset_instance)
if model_class == "HistoryDatasetAssociation":
hda = cast(model.HistoryDatasetAssociation, dataset_instance)
# don't use add_history to manage HID handling across full import to try to preserve
# HID structure.
hda.history = history
if new_history and self.trust_hid(dataset_attrs):
hda.hid = dataset_attrs["hid"]
else:
object_import_tracker.requires_hid.append(hda)
else:
pass
# ldda = cast(model.LibraryDatasetDatasetAssociation, dataset_instance)
# ldda.user = self.user
file_source_root = self.file_source_root
# If dataset is in the dictionary - we will assert this dataset is tied to the Galaxy instance
# and the import options are configured for allowing editing the dataset (e.g. for metadata setting).
# Otherwise, we will check for "file" information instead of dataset information - currently this includes
# "file_name", "extra_files_path".
if "dataset" in dataset_attrs:
handle_dataset_object_edit(dataset_instance, dataset_attrs)
else:
file_name = dataset_attrs.get("file_name")
if file_name:
assert file_source_root
# Do security check and move/copy dataset data.
archive_path = os.path.abspath(os.path.join(file_source_root, file_name))
if os.path.islink(archive_path):
raise MalformedContents(f"Invalid dataset path: {archive_path}")
temp_dataset_file_name = os.path.realpath(archive_path)
if not in_directory(temp_dataset_file_name, file_source_root):
raise MalformedContents(f"Invalid dataset path: {temp_dataset_file_name}")
has_good_source = False
file_metadata = dataset_attrs.get("file_metadata") or {}
if "sources" in file_metadata:
for source_attrs in file_metadata["sources"]:
extra_files_path = source_attrs["extra_files_path"]
if extra_files_path is None:
has_good_source = True
discarded_data = self.import_options.discarded_data
dataset_state = dataset_attrs.get("state", dataset_instance.states.OK)
if dataset_state == dataset_instance.states.DEFERRED:
dataset_instance.state = dataset_instance.states.DEFERRED
dataset_instance.deleted = False
dataset_instance.purged = False
dataset_instance.dataset.deleted = False
dataset_instance.dataset.purged = False
elif (
not file_name
or not os.path.exists(temp_dataset_file_name)
or discarded_data is ImportDiscardedDataType.FORCE
):
is_discarded = not has_good_source
target_state = (
dataset_instance.states.DISCARDED if is_discarded else dataset_instance.states.DEFERRED
)
dataset_instance.state = target_state
deleted = is_discarded and (discarded_data == ImportDiscardedDataType.FORBID)
dataset_instance.deleted = deleted
dataset_instance.purged = deleted
dataset_instance.dataset.state = target_state
dataset_instance.dataset.deleted = deleted
dataset_instance.dataset.purged = deleted
else:
dataset_instance.state = dataset_state
if not self.object_store:
raise Exception(f"self.object_store is missing from {self}.")
self.object_store.update_from_file(
dataset_instance.dataset, file_name=temp_dataset_file_name, create=True
)
# Import additional files if present. Histories exported previously might not have this attribute set.
dataset_extra_files_path = dataset_attrs.get("extra_files_path", None)
if dataset_extra_files_path:
assert file_source_root
dataset_extra_files_path = os.path.join(file_source_root, dataset_extra_files_path)
persist_extra_files(self.object_store, dataset_extra_files_path, dataset_instance)
# Don't trust serialized file size
dataset_instance.dataset.file_size = None
dataset_instance.dataset.set_total_size() # update the filesize record in the database
if dataset_instance.deleted:
dataset_instance.dataset.deleted = True
self._attach_dataset_hashes(file_metadata, dataset_instance)
self._attach_dataset_sources(file_metadata, dataset_instance)
if "created_from_basename" in file_metadata:
dataset_instance.dataset.created_from_basename = file_metadata["created_from_basename"]
if model_class == "HistoryDatasetAssociation" and self.user:
add_item_annotation(self.sa_session, self.user, dataset_instance, dataset_attrs["annotation"])
tag_list = dataset_attrs.get("tags")
if tag_list:
if not self.tag_handler:
raise Exception(f"Missing self.tag_handler on {self}.")
self.tag_handler.set_tags_from_list(
user=self.user, item=dataset_instance, new_tags_list=tag_list, flush=False
)
if self.app:
# If dataset instance is discarded or deferred, don't attempt to regenerate
# metadata for it.
if dataset_instance.state == dataset_instance.states.OK:
regenerate_kwds: Dict[str, Any] = {}
if job:
regenerate_kwds["user"] = job.user
regenerate_kwds["session_id"] = job.session_id
elif history:
user = history.user
regenerate_kwds["user"] = user
if user is None:
regenerate_kwds["session_id"] = history.galaxy_sessions[0].galaxy_session.id
else:
regenerate_kwds["session_id"] = None
else:
# Need a user to run library jobs to generate metadata...
pass
if not self.import_options.allow_edit:
# external import, metadata files need to be regenerated (as opposed to extended metadata dataset import)
if self.app.datatypes_registry.set_external_metadata_tool:
self.app.datatypes_registry.set_external_metadata_tool.regenerate_imported_metadata_if_needed(
dataset_instance, history, **regenerate_kwds
)
else:
# Try to set metadata directly. @mvdbeek thinks we should only record the datasets
try:
if dataset_instance.has_metadata_files:
dataset_instance.datatype.set_meta(dataset_instance) # type:ignore[arg-type]
except Exception:
log.debug(f"Metadata setting failed on {dataset_instance}", exc_info=True)
dataset_instance.state = dataset_instance.dataset.states.FAILED_METADATA
if model_class == "HistoryDatasetAssociation":
if not isinstance(dataset_instance, model.HistoryDatasetAssociation):
raise Exception(
"Mismatch between model class and Python class, "
f"expected HistoryDatasetAssociation, got a {type(dataset_instance)}: {dataset_instance}"
)
if object_key in dataset_attrs:
object_import_tracker.hdas_by_key[dataset_attrs[object_key]] = dataset_instance
else:
assert "id" in dataset_attrs
object_import_tracker.hdas_by_id[dataset_attrs["id"]] = dataset_instance
else:
if not isinstance(dataset_instance, model.LibraryDatasetDatasetAssociation):
raise Exception(
"Mismatch between model class and Python class, "
f"expected LibraryDatasetDatasetAssociation, got a {type(dataset_instance)}: {dataset_instance}"
)
if object_key in dataset_attrs:
object_import_tracker.lddas_by_key[dataset_attrs[object_key]] = dataset_instance
else:
assert "id" in dataset_attrs
object_import_tracker.lddas_by_key[dataset_attrs["id"]] = dataset_instance
def _import_libraries(self, object_import_tracker: "ObjectImportTracker") -> None:
object_key = self.object_key
def import_folder(folder_attrs, root_folder=None):
if root_folder:
library_folder = root_folder
else:
name = folder_attrs["name"]
description = folder_attrs["description"]
genome_build = folder_attrs["genome_build"]
deleted = folder_attrs["deleted"]
library_folder = model.LibraryFolder(name=name, description=description, genome_build=genome_build)
library_folder.deleted = deleted
self._session_add(library_folder)
for sub_folder_attrs in folder_attrs.get("folders", []):
sub_folder = import_folder(sub_folder_attrs)
library_folder.add_folder(sub_folder)
for ld_attrs in folder_attrs.get("datasets", []):
ld = model.LibraryDataset(
folder=library_folder, name=ld_attrs["name"], info=ld_attrs["info"], order_id=ld_attrs["order_id"]
)
if "ldda" in ld_attrs:
ldda = object_import_tracker.lddas_by_key[ld_attrs["ldda"][object_key]]
ld.library_dataset_dataset_association = ldda
self._session_add(ld)
with transaction(self.sa_session):
self.sa_session.commit()
return library_folder
libraries_attrs = self.library_properties()
for library_attrs in libraries_attrs:
if (
library_attrs["model_class"] == "LibraryFolder"
and library_attrs.get("id")
and not self.sessionless
and self.import_options.allow_edit
):
library_folder = self.sa_session.get(model.LibraryFolder, library_attrs["id"])
import_folder(library_attrs, root_folder=library_folder)
else:
assert self.import_options.allow_library_creation
name = library_attrs["name"]
description = library_attrs["description"]
synopsis = library_attrs["synopsis"]
library = model.Library(name=name, description=description, synopsis=synopsis)
self._session_add(library)
object_import_tracker.libraries_by_key[library_attrs[object_key]] = library
if "root_folder" in library_attrs:
library.root_folder = import_folder(library_attrs["root_folder"])
def _import_collection_instances(
self,
object_import_tracker: "ObjectImportTracker",
collections_attrs: List[Dict[str, Any]],
history: Optional[model.History],
new_history: bool,
) -> None:
object_key = self.object_key
def import_collection(collection_attrs):
def materialize_elements(dc):
if "elements" not in collection_attrs:
return
elements_attrs = collection_attrs["elements"]
for element_attrs in elements_attrs:
dce = model.DatasetCollectionElement(
collection=dc,
element=model.DatasetCollectionElement.UNINITIALIZED_ELEMENT,
element_index=element_attrs["element_index"],
element_identifier=element_attrs["element_identifier"],
)
if "encoded_id" in element_attrs:
object_import_tracker.dces_by_key[element_attrs["encoded_id"]] = dce
if "hda" in element_attrs:
hda_attrs = element_attrs["hda"]
if object_key in hda_attrs:
hda_key = hda_attrs[object_key]
hdas_by_key = object_import_tracker.hdas_by_key
if hda_key in hdas_by_key:
hda = hdas_by_key[hda_key]
else:
raise KeyError(
f"Failed to find exported hda with key [{hda_key}] of type [{object_key}] in [{hdas_by_key}]"
)
else:
hda_id = hda_attrs["id"]
hdas_by_id = object_import_tracker.hdas_by_id
if hda_id not in hdas_by_id:
raise Exception(f"Failed to find HDA with id [{hda_id}] in [{hdas_by_id}]")
hda = hdas_by_id[hda_id]
dce.hda = hda
elif "child_collection" in element_attrs:
dce.child_collection = import_collection(element_attrs["child_collection"])
else:
raise Exception("Unknown collection element type encountered.")
dc.element_count = len(elements_attrs)
if "id" in collection_attrs and self.import_options.allow_edit and not self.sessionless:
dc = self.sa_session.get(model.DatasetCollection, collection_attrs["id"])
attributes = [
"collection_type",
"populated_state",
"populated_state_message",
"element_count",
]
for attribute in attributes:
if attribute in collection_attrs:
setattr(dc, attribute, collection_attrs.get(attribute))
materialize_elements(dc)
else:
# create collection
dc = model.DatasetCollection(collection_type=collection_attrs["type"])
dc.populated_state = collection_attrs["populated_state"]
dc.populated_state_message = collection_attrs.get("populated_state_message")
self._attach_raw_id_if_editing(dc, collection_attrs)
materialize_elements(dc)
self._session_add(dc)
return dc
history_sa_session = get_object_session(history)
for collection_attrs in collections_attrs:
if "collection" in collection_attrs:
dc = import_collection(collection_attrs["collection"])
if "id" in collection_attrs and self.import_options.allow_edit and not self.sessionless:
hdca = self.sa_session.get(model.HistoryDatasetCollectionAssociation, collection_attrs["id"])
# TODO: edit attributes...
else:
hdca = model.HistoryDatasetCollectionAssociation(
collection=dc,
visible=True,
name=collection_attrs["display_name"],
implicit_output_name=collection_attrs.get("implicit_output_name"),
)
self._attach_raw_id_if_editing(hdca, collection_attrs)
add_object_to_session(hdca, history_sa_session)
hdca.history = history
if new_history and self.trust_hid(collection_attrs):
hdca.hid = collection_attrs["hid"]
else:
object_import_tracker.requires_hid.append(hdca)
self._session_add(hdca)
if object_key in collection_attrs:
object_import_tracker.hdcas_by_key[collection_attrs[object_key]] = hdca
else:
assert "id" in collection_attrs
object_import_tracker.hdcas_by_id[collection_attrs["id"]] = hdca
else:
import_collection(collection_attrs)
def _attach_raw_id_if_editing(
self,
obj: model.RepresentById,
attrs: Dict[str, Any],
) -> None:
if self.sessionless and "id" in attrs and self.import_options.allow_edit:
obj.id = attrs["id"]
def _import_collection_implicit_input_associations(
self, object_import_tracker: "ObjectImportTracker", collections_attrs: List[Dict[str, Any]]
) -> None:
object_key = self.object_key
for collection_attrs in collections_attrs:
if "id" in collection_attrs:
# Existing object, not a new one, this property is immutable via model stores currently.
continue
hdca = object_import_tracker.hdcas_by_key[collection_attrs[object_key]]
if "implicit_input_collections" in collection_attrs:
implicit_input_collections = collection_attrs["implicit_input_collections"]
for implicit_input_collection in implicit_input_collections:
name = implicit_input_collection["name"]
input_collection_identifier = implicit_input_collection["input_dataset_collection"]
if input_collection_identifier in object_import_tracker.hdcas_by_key:
input_dataset_collection = object_import_tracker.hdcas_by_key[input_collection_identifier]
hdca.add_implicit_input_collection(name, input_dataset_collection)
def _import_dataset_copied_associations(
self, object_import_tracker: "ObjectImportTracker", datasets_attrs: List[Dict[str, Any]]
) -> None:
object_key = self.object_key
# Re-establish copied_from_history_dataset_association relationships so history extraction
# has a greater chance of working in this history, for reproducibility.
for dataset_attrs in datasets_attrs:
if "id" in dataset_attrs:
# Existing object, not a new one, this property is not immutable via model stores currently.
continue
dataset_key = dataset_attrs[object_key]
if dataset_key not in object_import_tracker.hdas_by_key:
continue
hda = object_import_tracker.hdas_by_key[dataset_key]
copied_from_chain = dataset_attrs.get("copied_from_history_dataset_association_id_chain", [])
copied_from_object_key = _copied_from_object_key(copied_from_chain, object_import_tracker.hdas_by_key)
if not copied_from_object_key:
continue
# Re-establish the chain if we can.
if copied_from_object_key in object_import_tracker.hdas_by_key:
hda.copied_from_history_dataset_association = object_import_tracker.hdas_by_key[copied_from_object_key]
else:
# We're at the end of the chain and this HDA was copied from an HDA
# outside the history. So when we find this job and are looking for inputs/outputs
# attach to this node... unless we've already encountered another dataset
# copied from that jobs output... in that case we are going to cheat and
# say this dataset was copied from that one. It wasn't in the original Galaxy
# instance but I think it is fine to pretend in order to create a DAG here.
hda_copied_from_sinks = object_import_tracker.hda_copied_from_sinks
if copied_from_object_key in hda_copied_from_sinks:
hda.copied_from_history_dataset_association = object_import_tracker.hdas_by_key[
hda_copied_from_sinks[copied_from_object_key]
]
else:
hda_copied_from_sinks[copied_from_object_key] = dataset_key
def _import_collection_copied_associations(
self, object_import_tracker: "ObjectImportTracker", collections_attrs: List[Dict[str, Any]]
) -> None:
object_key = self.object_key
# Re-establish copied_from_history_dataset_collection_association relationships so history extraction
# has a greater chance of working in this history, for reproducibility. Very similar to HDA code above
# see comments there.
for collection_attrs in collections_attrs:
if "id" in collection_attrs:
# Existing object, not a new one, this property is immutable via model stores currently.
continue
dataset_collection_key = collection_attrs[object_key]
if dataset_collection_key not in object_import_tracker.hdcas_by_key:
continue
hdca = object_import_tracker.hdcas_by_key[dataset_collection_key]
copied_from_chain = collection_attrs.get("copied_from_history_dataset_collection_association_id_chain", [])
copied_from_object_key = _copied_from_object_key(copied_from_chain, object_import_tracker.hdcas_by_key)
if not copied_from_object_key:
continue
# Re-establish the chain if we can, again see comments for hdas above for this to make more
# sense.
hdca_copied_from_sinks = object_import_tracker.hdca_copied_from_sinks
if copied_from_object_key in object_import_tracker.hdcas_by_key:
hdca.copied_from_history_dataset_collection_association = object_import_tracker.hdcas_by_key[
copied_from_object_key
]
else:
if copied_from_object_key in hdca_copied_from_sinks:
hdca.copied_from_history_dataset_collection_association = object_import_tracker.hdcas_by_key[
hdca_copied_from_sinks[copied_from_object_key]
]
else:
hdca_copied_from_sinks[copied_from_object_key] = dataset_collection_key
def _reassign_hids(self, object_import_tracker: "ObjectImportTracker", history: Optional[model.History]) -> None:
# assign HIDs for newly created objects that didn't match original history
requires_hid = object_import_tracker.requires_hid
requires_hid_len = len(requires_hid)
if requires_hid_len > 0 and not self.sessionless:
if not history:
raise Exception("Optional history is required here.")
for obj in requires_hid:
history.stage_addition(obj)
history.add_pending_items()
if object_import_tracker.copy_hid_for:
# in an if to avoid flush if unneeded
for from_dataset, to_dataset in object_import_tracker.copy_hid_for.items():
to_dataset.hid = from_dataset.hid
self._session_add(to_dataset)
self._flush()
def _import_workflow_invocations(
self, object_import_tracker: "ObjectImportTracker", history: Optional[model.History]
) -> None:
#
# Create jobs.
#
object_key = self.object_key
for workflow_key, workflow_path in self.workflow_paths():
workflows_directory = os.path.join(self.archive_dir, "workflows")
if not self.app:
raise Exception(f"Missing require self.app in {self}.")
workflow = self.app.workflow_contents_manager.read_workflow_from_path(
self.app, self.user, workflow_path, allow_in_directory=workflows_directory
)
object_import_tracker.workflows_by_key[workflow_key] = workflow
invocations_attrs = self.invocations_properties()
for invocation_attrs in invocations_attrs:
assert not self.import_options.allow_edit
imported_invocation = model.WorkflowInvocation()
imported_invocation.history = history
ensure_object_added_to_session(imported_invocation, object_in_session=history)
workflow_key = invocation_attrs["workflow"]
if workflow_key not in object_import_tracker.workflows_by_key:
raise Exception(f"Failed to find key {workflow_key} in {object_import_tracker.workflows_by_key.keys()}")
workflow = object_import_tracker.workflows_by_key[workflow_key]
imported_invocation.workflow = workflow
state = invocation_attrs["state"]
if state in model.WorkflowInvocation.non_terminal_states:
state = model.WorkflowInvocation.states.CANCELLED
imported_invocation.state = state
restore_times(imported_invocation, invocation_attrs)
self._session_add(imported_invocation)
self._flush()
def attach_workflow_step(imported_object, attrs):
order_index = attrs["order_index"]
imported_object.workflow_step = workflow.step_by_index(order_index) # noqa: B023
for step_attrs in invocation_attrs["steps"]:
imported_invocation_step = model.WorkflowInvocationStep()
imported_invocation_step.workflow_invocation = imported_invocation
ensure_object_added_to_session(imported_invocation, session=self.sa_session)
attach_workflow_step(imported_invocation_step, step_attrs)
restore_times(imported_invocation_step, step_attrs)
imported_invocation_step.action = step_attrs["action"]
# TODO: ensure terminal...
imported_invocation_step.state = step_attrs["state"]
if "job" in step_attrs:
job = object_import_tracker.jobs_by_key[step_attrs["job"][object_key]]
imported_invocation_step.job = job
ensure_object_added_to_session(imported_invocation_step, object_in_session=job)
elif "implicit_collection_jobs" in step_attrs:
icj = object_import_tracker.implicit_collection_jobs_by_key[
step_attrs["implicit_collection_jobs"][object_key]
]
imported_invocation_step.implicit_collection_jobs = icj
# TODO: handle step outputs...
output_dicts = step_attrs["outputs"]
step_outputs = []
for output_dict in output_dicts:
step_output = model.WorkflowInvocationStepOutputDatasetAssociation()
step_output.output_name = output_dict["output_name"]
dataset_link_attrs = output_dict["dataset"]
if dataset_link_attrs:
dataset = object_import_tracker.find_hda(dataset_link_attrs[object_key])
assert dataset
step_output.dataset = dataset
step_outputs.append(step_output)
imported_invocation_step.output_datasets = step_outputs
output_collection_dicts = step_attrs["output_collections"]
step_output_collections = []
for output_collection_dict in output_collection_dicts:
step_output_collection = model.WorkflowInvocationStepOutputDatasetCollectionAssociation()
step_output_collection.output_name = output_collection_dict["output_name"]
dataset_collection_link_attrs = output_collection_dict["dataset_collection"]
if dataset_collection_link_attrs:
dataset_collection = object_import_tracker.find_hdca(dataset_collection_link_attrs[object_key])
assert dataset_collection
step_output_collection.dataset_collection = dataset_collection
step_output_collections.append(step_output_collection)
imported_invocation_step.output_dataset_collections = step_output_collections
input_parameters = []
for input_parameter_attrs in invocation_attrs["input_parameters"]:
input_parameter = model.WorkflowRequestInputParameter()
input_parameter.value = input_parameter_attrs["value"]
input_parameter.name = input_parameter_attrs["name"]
input_parameter.type = input_parameter_attrs["type"]
input_parameter.workflow_invocation = imported_invocation
self._session_add(input_parameter)
input_parameters.append(input_parameter)
# invocation_attrs["input_parameters"] = input_parameters
step_states = []
for step_state_attrs in invocation_attrs["step_states"]:
step_state = model.WorkflowRequestStepState()
step_state.value = step_state_attrs["value"]
attach_workflow_step(step_state, step_state_attrs)
step_state.workflow_invocation = imported_invocation
self._session_add(step_state)
step_states.append(step_state)
input_step_parameters = []
for input_step_parameter_attrs in invocation_attrs["input_step_parameters"]:
input_step_parameter = model.WorkflowRequestInputStepParameter()
input_step_parameter.parameter_value = input_step_parameter_attrs["parameter_value"]
attach_workflow_step(input_step_parameter, input_step_parameter_attrs)
input_step_parameter.workflow_invocation = imported_invocation
self._session_add(input_step_parameter)
input_step_parameters.append(input_step_parameter)
input_datasets = []
for input_dataset_attrs in invocation_attrs["input_datasets"]:
input_dataset = model.WorkflowRequestToInputDatasetAssociation()
attach_workflow_step(input_dataset, input_dataset_attrs)
input_dataset.workflow_invocation = imported_invocation
input_dataset.name = input_dataset_attrs["name"]
dataset_link_attrs = input_dataset_attrs["dataset"]
if dataset_link_attrs:
dataset = object_import_tracker.find_hda(dataset_link_attrs[object_key])
assert dataset
input_dataset.dataset = dataset
self._session_add(input_dataset)
input_datasets.append(input_dataset)
input_dataset_collections = []
for input_dataset_collection_attrs in invocation_attrs["input_dataset_collections"]:
input_dataset_collection = model.WorkflowRequestToInputDatasetCollectionAssociation()
attach_workflow_step(input_dataset_collection, input_dataset_collection_attrs)
input_dataset_collection.workflow_invocation = imported_invocation
input_dataset_collection.name = input_dataset_collection_attrs["name"]
dataset_collection_link_attrs = input_dataset_collection_attrs["dataset_collection"]
if dataset_collection_link_attrs:
dataset_collection = object_import_tracker.find_hdca(dataset_collection_link_attrs[object_key])
assert dataset_collection
input_dataset_collection.dataset_collection = dataset_collection
self._session_add(input_dataset_collection)
input_dataset_collections.append(input_dataset_collection)
output_dataset_collections = []
for output_dataset_collection_attrs in invocation_attrs["output_dataset_collections"]:
output_dataset_collection = model.WorkflowInvocationOutputDatasetCollectionAssociation()
output_dataset_collection.workflow_invocation = imported_invocation
attach_workflow_step(output_dataset_collection, output_dataset_collection_attrs)
workflow_output = output_dataset_collection_attrs["workflow_output"]
label = workflow_output.get("label")
workflow_output = workflow.workflow_output_for(label)
output_dataset_collection.workflow_output = workflow_output
self._session_add(output_dataset_collection)
output_dataset_collections.append(output_dataset_collection)
output_datasets = []
for output_dataset_attrs in invocation_attrs["output_datasets"]:
output_dataset = model.WorkflowInvocationOutputDatasetAssociation()
output_dataset.workflow_invocation = imported_invocation
attach_workflow_step(output_dataset, output_dataset_attrs)
workflow_output = output_dataset_attrs["workflow_output"]
label = workflow_output.get("label")
workflow_output = workflow.workflow_output_for(label)
output_dataset.workflow_output = workflow_output
self._session_add(output_dataset)
output_datasets.append(output_dataset)
output_values = []
for output_value_attrs in invocation_attrs["output_values"]:
output_value = model.WorkflowInvocationOutputValue()
output_value.workflow_invocation = imported_invocation
output_value.value = output_value_attrs["value"]
attach_workflow_step(output_value, output_value_attrs)
workflow_output = output_value_attrs["workflow_output"]
label = workflow_output.get("label")
workflow_output = workflow.workflow_output_for(label)
output_value.workflow_output = workflow_output
self._session_add(output_value)
output_values.append(output_value)
if object_key in invocation_attrs:
object_import_tracker.invocations_by_key[invocation_attrs[object_key]] = imported_invocation
def _import_jobs(self, object_import_tracker: "ObjectImportTracker", history: Optional[model.History]) -> None:
self._flush()
object_key = self.object_key
_find_hda = object_import_tracker.find_hda
_find_hdca = object_import_tracker.find_hdca
_find_dce = object_import_tracker.find_dce
#
# Create jobs.
#
jobs_attrs = self.jobs_properties()
# Create each job.
history_sa_session = get_object_session(history)
for job_attrs in jobs_attrs:
if "id" in job_attrs and not self.sessionless:
# only thing we allow editing currently is associations for incoming jobs.
assert self.import_options.allow_edit
job = self.sa_session.get(model.Job, job_attrs["id"])
self._connect_job_io(job, job_attrs, _find_hda, _find_hdca, _find_dce) # type: ignore[attr-defined]
self._set_job_attributes(job, job_attrs, force_terminal=False) # type: ignore[attr-defined]
# Don't edit job
continue
imported_job = model.Job()
imported_job.id = cast(int, job_attrs.get("id"))
imported_job.user = self.user
add_object_to_session(imported_job, history_sa_session)
imported_job.history = history
imported_job.imported = True
imported_job.tool_id = job_attrs["tool_id"]
imported_job.tool_version = job_attrs["tool_version"]
self._set_job_attributes(imported_job, job_attrs, force_terminal=True) # type: ignore[attr-defined]
restore_times(imported_job, job_attrs)
self._session_add(imported_job)
# Connect jobs to input and output datasets.
params = self._normalize_job_parameters(imported_job, job_attrs, _find_hda, _find_hdca, _find_dce) # type: ignore[attr-defined]
for name, value in params.items():
# Transform parameter values when necessary.
imported_job.add_parameter(name, dumps(value))
self._connect_job_io(imported_job, job_attrs, _find_hda, _find_hdca, _find_dce) # type: ignore[attr-defined]
if object_key in job_attrs:
object_import_tracker.jobs_by_key[job_attrs[object_key]] = imported_job
def _import_implicit_dataset_conversions(self, object_import_tracker: "ObjectImportTracker") -> None:
implicit_dataset_conversion_attrs = self.implicit_dataset_conversion_properties()
for idc_attrs in implicit_dataset_conversion_attrs:
# I don't know what metadata_safe does per se... should we copy this property or
# just set it to False?
metadata_safe = False
idc = model.ImplicitlyConvertedDatasetAssociation(metadata_safe=metadata_safe, for_import=True)
idc.type = idc_attrs["file_type"]
if idc_attrs.get("parent_hda"):
idc.parent_hda = object_import_tracker.hdas_by_key[idc_attrs["parent_hda"]]
if idc_attrs.get("hda"):
idc.dataset = object_import_tracker.hdas_by_key[idc_attrs["hda"]]
# we have a the dataset and the parent, lets ensure they land up with the same HID
if idc.dataset and idc.parent_hda and idc.parent_hda in object_import_tracker.requires_hid:
try:
object_import_tracker.requires_hid.remove(idc.dataset)
except ValueError:
pass # we wanted to remove it anyway.
object_import_tracker.copy_hid_for[idc.parent_hda] = idc.dataset
self._session_add(idc)
def _import_implicit_collection_jobs(self, object_import_tracker: "ObjectImportTracker") -> None:
object_key = self.object_key
implicit_collection_jobs_attrs = self.implicit_collection_jobs_properties()
for icj_attrs in implicit_collection_jobs_attrs:
icj = model.ImplicitCollectionJobs()
icj.populated_state = icj_attrs["populated_state"]
icj.jobs = []
for order_index, job in enumerate(icj_attrs["jobs"]):
icja = model.ImplicitCollectionJobsJobAssociation()
add_object_to_object_session(icja, icj)
icja.implicit_collection_jobs = icj
if job in object_import_tracker.jobs_by_key:
job_instance = object_import_tracker.jobs_by_key[job]
add_object_to_object_session(icja, job_instance)
icja.job = job_instance
icja.order_index = order_index
icj.jobs.append(icja)
self._session_add(icja)
object_import_tracker.implicit_collection_jobs_by_key[icj_attrs[object_key]] = icj
self._session_add(icj)
def _session_add(self, obj: model.RepresentById) -> None:
self.sa_session.add(obj)
def _flush(self) -> None:
with transaction(self.sa_session):
self.sa_session.commit()
def _copied_from_object_key(
copied_from_chain: List[ObjectKeyType],
objects_by_key: Union[
Dict[ObjectKeyType, model.HistoryDatasetAssociation],
Dict[ObjectKeyType, model.HistoryDatasetCollectionAssociation],
],
) -> Optional[ObjectKeyType]:
if len(copied_from_chain) == 0:
return None
# Okay this gets fun, we need the last thing in the chain to reconnect jobs
# from outside the history to inputs/outputs in this history but there may
# be cycles in the chain that lead outside the original history, so just eliminate
# all IDs not from this history except the last one.
filtered_copied_from_chain = []
for i, copied_from_key in enumerate(copied_from_chain):
filter_id = (i != len(copied_from_chain) - 1) and (copied_from_key not in objects_by_key)
if not filter_id:
filtered_copied_from_chain.append(copied_from_key)
copied_from_chain = filtered_copied_from_chain
if len(copied_from_chain) == 0:
return None
copied_from_object_key = copied_from_chain[0]
return copied_from_object_key
[docs]class ObjectImportTracker:
"""Keep track of new and existing imported objects.
Needed to re-establish connections and such in multiple passes.
"""
libraries_by_key: Dict[ObjectKeyType, model.Library]
hdas_by_key: Dict[ObjectKeyType, model.HistoryDatasetAssociation]
hdas_by_id: Dict[int, model.HistoryDatasetAssociation]
hdcas_by_key: Dict[ObjectKeyType, model.HistoryDatasetCollectionAssociation]
hdcas_by_id: Dict[int, model.HistoryDatasetCollectionAssociation]
dces_by_key: Dict[ObjectKeyType, model.DatasetCollectionElement]
dces_by_id: Dict[int, model.DatasetCollectionElement]
lddas_by_key: Dict[ObjectKeyType, model.LibraryDatasetDatasetAssociation]
hda_copied_from_sinks: Dict[ObjectKeyType, ObjectKeyType]
hdca_copied_from_sinks: Dict[ObjectKeyType, ObjectKeyType]
jobs_by_key: Dict[ObjectKeyType, model.Job]
requires_hid: List["HistoryItem"]
copy_hid_for: Dict["HistoryItem", "HistoryItem"]
[docs] def __init__(self) -> None:
self.libraries_by_key = {}
self.hdas_by_key = {}
self.hdas_by_id = {}
self.hdcas_by_key = {}
self.hdcas_by_id = {}
self.dces_by_key = {}
self.dces_by_id = {}
self.lddas_by_key = {}
self.hda_copied_from_sinks = {}
self.hdca_copied_from_sinks = {}
self.jobs_by_key = {}
self.invocations_by_key: Dict[str, model.WorkflowInvocation] = {}
self.implicit_collection_jobs_by_key: Dict[str, ImplicitCollectionJobs] = {}
self.workflows_by_key: Dict[str, model.Workflow] = {}
self.requires_hid = []
self.copy_hid_for = {}
self.new_history: Optional[model.History] = None
[docs] def find_hda(
self, input_key: ObjectKeyType, hda_id: Optional[int] = None
) -> Optional[model.HistoryDatasetAssociation]:
hda = None
if input_key in self.hdas_by_key:
hda = self.hdas_by_key[input_key]
elif isinstance(input_key, int) and input_key in self.hdas_by_id:
# TODO: untangle this, I don't quite understand why we hdas_by_key and hdas_by_id
hda = self.hdas_by_id[input_key]
if input_key in self.hda_copied_from_sinks:
hda = self.hdas_by_key[self.hda_copied_from_sinks[input_key]]
return hda
[docs] def find_hdca(self, input_key: ObjectKeyType) -> Optional[model.HistoryDatasetCollectionAssociation]:
hdca = None
if input_key in self.hdcas_by_key:
hdca = self.hdcas_by_key[input_key]
elif isinstance(input_key, int) and input_key in self.hdcas_by_id:
hdca = self.hdcas_by_id[input_key]
if input_key in self.hdca_copied_from_sinks:
hdca = self.hdcas_by_key[self.hdca_copied_from_sinks[input_key]]
return hdca
[docs] def find_dce(self, input_key: ObjectKeyType) -> Optional[model.DatasetCollectionElement]:
dce = None
if input_key in self.dces_by_key:
dce = self.dces_by_key[input_key]
elif isinstance(input_key, int) and input_key in self.dces_by_id:
dce = self.dces_by_id[input_key]
return dce
[docs]def get_import_model_store_for_directory(
archive_dir: str, **kwd
) -> Union["DirectoryImportModelStore1901", "DirectoryImportModelStoreLatest"]:
traceback_file = os.path.join(archive_dir, TRACEBACK)
if not os.path.isdir(archive_dir):
raise Exception(
f"Could not find import model store for directory [{archive_dir}] (full path [{os.path.abspath(archive_dir)}])"
)
if os.path.exists(os.path.join(archive_dir, ATTRS_FILENAME_EXPORT)):
if os.path.exists(traceback_file):
with open(traceback_file) as tb:
raise FileTracebackException(traceback=tb.read())
return DirectoryImportModelStoreLatest(archive_dir, **kwd)
else:
return DirectoryImportModelStore1901(archive_dir, **kwd)
[docs]class DictImportModelStore(ModelImportStore):
object_key = "encoded_id"
[docs] def __init__(
self,
store_as_dict: Dict[str, Any],
**kwd,
) -> None:
self._store_as_dict = store_as_dict
super().__init__(**kwd)
self.archive_dir = ""
[docs] def defines_new_history(self) -> bool:
return DICT_STORE_ATTRS_KEY_HISTORY in self._store_as_dict
[docs] def new_history_properties(self) -> Dict[str, Any]:
return self._store_as_dict.get(DICT_STORE_ATTRS_KEY_HISTORY) or {}
[docs] def datasets_properties(
self,
) -> List[Dict[str, Any]]:
return self._store_as_dict.get(DICT_STORE_ATTRS_KEY_DATASETS) or []
[docs] def collections_properties(self) -> List[Dict[str, Any]]:
return self._store_as_dict.get(DICT_STORE_ATTRS_KEY_COLLECTIONS) or []
[docs] def implicit_dataset_conversion_properties(self) -> List[Dict[str, Any]]:
return self._store_as_dict.get(DICT_STORE_ATTRS_KEY_CONVERSIONS) or []
[docs] def library_properties(
self,
) -> List[Dict[str, Any]]:
return self._store_as_dict.get(DICT_STORE_ATTRS_KEY_LIBRARIES) or []
[docs] def jobs_properties(self) -> List[Dict[str, Any]]:
return self._store_as_dict.get(DICT_STORE_ATTRS_KEY_JOBS) or []
[docs] def implicit_collection_jobs_properties(self) -> List[Dict[str, Any]]:
return self._store_as_dict.get(DICT_STORE_ATTRS_KEY_IMPLICIT_COLLECTION_JOBS) or []
[docs] def invocations_properties(self) -> List[Dict[str, Any]]:
return self._store_as_dict.get(DICT_STORE_ATTRS_KEY_INVOCATIONS) or []
[docs]def get_import_model_store_for_dict(
as_dict: Dict[str, Any],
**kwd,
) -> DictImportModelStore:
return DictImportModelStore(as_dict, **kwd)
[docs]class BaseDirectoryImportModelStore(ModelImportStore):
@abc.abstractmethod
def _normalize_job_parameters(
self,
imported_job: model.Job,
job_attrs: Dict[str, Any],
_find_hda: Callable,
_find_hdca: Callable,
_find_dce: Callable,
) -> Dict[str, Any]: ...
@abc.abstractmethod
def _connect_job_io(
self,
imported_job: model.Job,
job_attrs: Dict[str, Any],
_find_hda: Callable,
_find_hdca: Callable,
_find_dce: Callable,
) -> None: ...
@property
def file_source_root(self) -> str:
return self.archive_dir
[docs] def defines_new_history(self) -> bool:
new_history_attributes = os.path.join(self.archive_dir, ATTRS_FILENAME_HISTORY)
return os.path.exists(new_history_attributes)
[docs] def new_history_properties(self) -> Dict[str, Any]:
new_history_attributes = os.path.join(self.archive_dir, ATTRS_FILENAME_HISTORY)
history_properties = load(open(new_history_attributes))
return history_properties
[docs] def datasets_properties(self) -> List[Dict[str, Any]]:
datasets_attrs_file_name = os.path.join(self.archive_dir, ATTRS_FILENAME_DATASETS)
datasets_attrs = load(open(datasets_attrs_file_name))
provenance_file_name = f"{datasets_attrs_file_name}.provenance"
if os.path.exists(provenance_file_name):
provenance_attrs = load(open(provenance_file_name))
datasets_attrs += provenance_attrs
return datasets_attrs
[docs] def collections_properties(self) -> List[Dict[str, Any]]:
return self._read_list_if_exists(ATTRS_FILENAME_COLLECTIONS)
[docs] def implicit_dataset_conversion_properties(self) -> List[Dict[str, Any]]:
return self._read_list_if_exists(ATTRS_FILENAME_CONVERSIONS)
[docs] def library_properties(
self,
) -> List[Dict[str, Any]]:
libraries_attrs = self._read_list_if_exists(ATTRS_FILENAME_LIBRARIES)
libraries_attrs.extend(self._read_list_if_exists(ATTRS_FILENAME_LIBRARY_FOLDERS))
return libraries_attrs
[docs] def jobs_properties(
self,
) -> List[Dict[str, Any]]:
return self._read_list_if_exists(ATTRS_FILENAME_JOBS)
[docs] def implicit_collection_jobs_properties(self) -> List[Dict[str, Any]]:
implicit_collection_jobs_attrs_file_name = os.path.join(
self.archive_dir, ATTRS_FILENAME_IMPLICIT_COLLECTION_JOBS
)
try:
return load(open(implicit_collection_jobs_attrs_file_name))
except FileNotFoundError:
return []
[docs] def invocations_properties(
self,
) -> List[Dict[str, Any]]:
return self._read_list_if_exists(ATTRS_FILENAME_INVOCATIONS)
[docs] def workflow_paths(self) -> Iterator[Tuple[str, str]]:
workflows_directory = os.path.join(self.archive_dir, "workflows")
if not os.path.exists(workflows_directory):
return
for name in os.listdir(workflows_directory):
if name.endswith(".ga") or name.endswith(".abstract.cwl") or name.endswith(".html"):
continue
assert name.endswith(".gxwf.yml")
workflow_key = name[0 : -len(".gxwf.yml")]
yield workflow_key, os.path.join(workflows_directory, name)
def _set_job_attributes(
self, imported_job: model.Job, job_attrs: Dict[str, Any], force_terminal: bool = False
) -> None:
ATTRIBUTES = (
"info",
"exit_code",
"traceback",
"job_messages",
"tool_stdout",
"tool_stderr",
"job_stdout",
"job_stderr",
"galaxy_version",
)
for attribute in ATTRIBUTES:
value = job_attrs.get(attribute)
if value is not None:
setattr(imported_job, attribute, value)
if "stdout" in job_attrs:
imported_job.tool_stdout = job_attrs.get("stdout")
imported_job.tool_stderr = job_attrs.get("stderr")
raw_state = job_attrs.get("state")
if force_terminal and raw_state and raw_state not in model.Job.terminal_states:
raw_state = model.Job.states.ERROR
if raw_state:
imported_job.set_state(raw_state)
def _read_list_if_exists(self, file_name: str, required: bool = False) -> List[Dict[str, Any]]:
file_name = os.path.join(self.archive_dir, file_name)
if os.path.exists(file_name):
attrs = load(open(file_name))
else:
if required:
raise Exception("Failed to find file [%s] in model store archive" % file_name)
attrs = []
return attrs
[docs]def restore_times(
model_object: Union[model.Job, model.WorkflowInvocation, model.WorkflowInvocationStep], attrs: Dict[str, Any]
) -> None:
try:
model_object.create_time = datetime.datetime.strptime(attrs["create_time"], "%Y-%m-%dT%H:%M:%S.%f")
except Exception:
pass
try:
model_object.update_time = datetime.datetime.strptime(attrs["update_time"], "%Y-%m-%dT%H:%M:%S.%f")
except Exception:
pass
[docs]class DirectoryImportModelStore1901(BaseDirectoryImportModelStore):
object_key = "hid"
[docs] def __init__(self, archive_dir: str, **kwd) -> None:
archive_dir = os.path.realpath(archive_dir)
# BioBlend previous to 17.01 exported histories with an extra subdir.
if not os.path.exists(os.path.join(archive_dir, ATTRS_FILENAME_HISTORY)):
for d in os.listdir(archive_dir):
if os.path.isdir(os.path.join(archive_dir, d)):
archive_dir = os.path.join(archive_dir, d)
break
self.archive_dir = archive_dir
super().__init__(**kwd)
def _connect_job_io(
self,
imported_job: model.Job,
job_attrs: Dict[str, Any],
_find_hda: Callable,
_find_hdca: Callable,
_find_dce: Callable,
) -> None:
for output_key in job_attrs["output_datasets"]:
output_hda = _find_hda(output_key)
if output_hda:
if not self.dataset_state_serialized:
# dataset state has not been serialized, get state from job
output_hda.state = imported_job.state
imported_job.add_output_dataset(output_hda.name, output_hda)
if "input_mapping" in job_attrs:
for input_name, input_key in job_attrs["input_mapping"].items():
input_hda = _find_hda(input_key)
if input_hda:
imported_job.add_input_dataset(input_name, input_hda)
def _normalize_job_parameters(
self,
imported_job: model.Job,
job_attrs: Dict[str, Any],
_find_hda: Callable,
_find_hdca: Callable,
_find_dce: Callable,
) -> Dict[str, Any]:
def remap_objects(p, k, obj):
if isinstance(obj, dict) and obj.get("__HistoryDatasetAssociation__", False):
imported_hda = _find_hda(obj[self.object_key])
if imported_hda:
return (k, {"src": "hda", "id": imported_hda.id})
return (k, obj)
params = job_attrs["params"]
params = remap(params, remap_objects)
return params
[docs] def trust_hid(self, obj_attrs: Dict[str, Any]) -> bool:
# We didn't do object tracking so we pretty much have to trust the HID and accept
# that it will be wrong a lot.
return True
[docs]class DirectoryImportModelStoreLatest(BaseDirectoryImportModelStore):
object_key = "encoded_id"
[docs] def __init__(self, archive_dir: str, **kwd) -> None:
archive_dir = os.path.realpath(archive_dir)
self.archive_dir = archive_dir
super().__init__(**kwd)
def _connect_job_io(
self,
imported_job: model.Job,
job_attrs: Dict[str, Any],
_find_hda: Callable,
_find_hdca: Callable,
_find_dce: Callable,
) -> None:
if imported_job.command_line is None:
imported_job.command_line = job_attrs.get("command_line")
if "input_dataset_mapping" in job_attrs:
for input_name, input_keys in job_attrs["input_dataset_mapping"].items():
input_keys = input_keys or []
for input_key in input_keys:
input_hda = _find_hda(input_key)
if input_hda:
imported_job.add_input_dataset(input_name, input_hda)
if "input_dataset_collection_mapping" in job_attrs:
for input_name, input_keys in job_attrs["input_dataset_collection_mapping"].items():
input_keys = input_keys or []
for input_key in input_keys:
input_hdca = _find_hdca(input_key)
if input_hdca:
imported_job.add_input_dataset_collection(input_name, input_hdca)
if "input_dataset_collection_element_mapping" in job_attrs:
for input_name, input_keys in job_attrs["input_dataset_collection_element_mapping"].items():
input_keys = input_keys or []
for input_key in input_keys:
input_dce = _find_dce(input_key)
if input_dce:
imported_job.add_input_dataset_collection_element(input_name, input_dce)
if "output_dataset_mapping" in job_attrs:
for output_name, output_keys in job_attrs["output_dataset_mapping"].items():
output_keys = output_keys or []
for output_key in output_keys:
output_hda = _find_hda(output_key)
if output_hda:
if not self.dataset_state_serialized:
# dataset state has not been serialized, get state from job
output_hda.state = imported_job.state
imported_job.add_output_dataset(output_name, output_hda)
if "output_dataset_collection_mapping" in job_attrs:
for output_name, output_keys in job_attrs["output_dataset_collection_mapping"].items():
output_keys = output_keys or []
for output_key in output_keys:
output_hdca = _find_hdca(output_key)
if output_hdca:
imported_job.add_output_dataset_collection(output_name, output_hdca)
def _normalize_job_parameters(
self,
imported_job: model.Job,
job_attrs: Dict[str, Any],
_find_hda: Callable,
_find_hdca: Callable,
_find_dce: Callable,
) -> Dict[str, Any]:
def remap_objects(p, k, obj):
if isinstance(obj, dict) and "src" in obj and obj["src"] in ["hda", "hdca", "dce"]:
if obj["src"] == "hda":
imported_hda = _find_hda(obj["id"])
if imported_hda:
new_id = imported_hda.id
else:
new_id = None
elif obj["src"] == "hdca":
imported_hdca = _find_hdca(obj["id"])
if imported_hdca:
new_id = imported_hdca.id
else:
new_id = None
elif obj["src"] == "dce":
imported_dce = _find_dce(obj["id"])
if imported_dce:
new_id = imported_dce.id
else:
new_id = None
else:
raise NotImplementedError()
new_obj = obj.copy()
if not new_id and self.import_options.allow_edit:
# We may not have exported all job parameters, such as dces,
# but we shouldn't set the object_id to none in that case.
new_id = obj["id"]
new_obj["id"] = new_id
return (k, new_obj)
return (k, obj)
params = job_attrs["params"]
params = remap(params, remap_objects)
return cast(Dict[str, Any], params)
[docs]class BagArchiveImportModelStore(DirectoryImportModelStoreLatest):
[docs] def __init__(self, bag_archive: str, **kwd) -> None:
archive_dir = tempfile.mkdtemp()
bdb.extract_bag(bag_archive, output_path=archive_dir)
# Why this line though...?
archive_dir = os.path.join(archive_dir, os.listdir(archive_dir)[0])
bdb.revert_bag(archive_dir)
super().__init__(archive_dir, **kwd)
[docs]class ModelExportStore(metaclass=abc.ABCMeta):
[docs] @abc.abstractmethod
def export_history(
self, history: model.History, include_hidden: bool = False, include_deleted: bool = False
) -> None:
"""Export history to store."""
[docs] @abc.abstractmethod
def export_library(
self, library: model.Library, include_hidden: bool = False, include_deleted: bool = False
) -> None:
"""Export library to store."""
[docs] @abc.abstractmethod
def export_library_folder(
self, library_folder: model.LibraryFolder, include_hidden: bool = False, include_deleted: bool = False
) -> None:
"""Export library folder to store."""
[docs] @abc.abstractmethod
def export_workflow_invocation(self, workflow_invocation, include_hidden=False, include_deleted=False):
"""Export workflow invocation to store."""
[docs] @abc.abstractmethod
def add_dataset_collection(
self, collection: Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]
):
"""Add Dataset Collection or HDCA to export store."""
[docs] @abc.abstractmethod
def add_dataset(self, dataset: model.DatasetInstance, include_files: bool = True):
"""
Add HDA to export store.
``include_files`` controls whether file contents are exported as well.
"""
@abc.abstractmethod
def __enter__(self):
"""Export store should be used as context manager."""
@abc.abstractmethod
def __exit__(self, exc_type, exc_val, exc_tb):
"""Export store should be used as context manager."""
[docs]class DirectoryModelExportStore(ModelExportStore):
app: Optional[StoreAppProtocol]
file_sources: Optional[ConfiguredFileSources]
[docs] def __init__(
self,
export_directory: StrPath,
app: Optional[StoreAppProtocol] = None,
file_sources: Optional[ConfiguredFileSources] = None,
for_edit: bool = False,
serialize_dataset_objects: Optional[bool] = None,
export_files: Optional[str] = None,
strip_metadata_files: bool = True,
serialize_jobs: bool = True,
user_context=None,
) -> None:
"""
:param export_directory: path to export directory. Will be created if it does not exist.
:param app: Galaxy App or app-like object. Must be provided if `for_edit` and/or `serialize_dataset_objects` are True
:param for_edit: Allow modifying existing HDA and dataset metadata during import.
:param serialize_dataset_objects: If True will encode IDs using the host secret. Defaults `for_edit`.
:param export_files: How files should be exported, can be 'symlink', 'copy' or None, in which case files
will not be serialized.
:param serialize_jobs: Include job data in model export. Not needed for set_metadata script.
"""
if not os.path.exists(export_directory):
os.makedirs(export_directory)
sessionless = False
if app is not None:
self.app = app
security = app.security
sessionless = False
if file_sources is None:
file_sources = app.file_sources
else:
sessionless = True
security = IdEncodingHelper(id_secret="randomdoesntmatter")
self.user_context = ProvidesUserFileSourcesUserContext(user_context)
self.file_sources = file_sources
self.serialize_jobs = serialize_jobs
self.sessionless = sessionless
self.security = security
self.export_directory = export_directory
self.serialization_options = model.SerializationOptions(
for_edit=for_edit,
serialize_dataset_objects=serialize_dataset_objects,
strip_metadata_files=strip_metadata_files,
serialize_files_handler=self,
)
self.export_files = export_files
self.included_datasets: Dict[model.DatasetInstance, Tuple[model.DatasetInstance, bool]] = {}
self.dataset_implicit_conversions: Dict[model.DatasetInstance, model.ImplicitlyConvertedDatasetAssociation] = {}
self.included_collections: List[Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]] = []
self.included_libraries: List[model.Library] = []
self.included_library_folders: List[model.LibraryFolder] = []
self.included_invocations: List[model.WorkflowInvocation] = []
self.collection_datasets: Set[int] = set()
self.collections_attrs: List[Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]] = []
self.dataset_id_to_path: Dict[int, Tuple[Optional[str], Optional[str]]] = {}
self.job_output_dataset_associations: Dict[int, Dict[str, model.DatasetInstance]] = {}
@property
def workflows_directory(self) -> str:
return os.path.join(self.export_directory, "workflows")
[docs] def serialize_files(self, dataset: model.DatasetInstance, as_dict: JsonDictT) -> None:
if self.export_files is None:
return None
add: Callable[[str, str], None]
if self.export_files == "symlink":
add = os.symlink
elif self.export_files == "copy":
def add(src, dest):
if os.path.isdir(src):
shutil.copytree(src, dest)
else:
shutil.copyfile(src, dest)
else:
raise Exception(f"Unknown export_files parameter type encountered {self.export_files}")
export_directory = self.export_directory
_, include_files = self.included_datasets[dataset]
if not include_files:
return
file_name, extra_files_path = None, None
try:
_file_name = dataset.get_file_name()
if os.path.exists(_file_name):
file_name = _file_name
except ObjectNotFound:
pass
if dataset.extra_files_path_exists():
extra_files_path = dataset.extra_files_path
else:
pass
dir_name = "datasets"
dir_path = os.path.join(export_directory, dir_name)
dataset_hid = as_dict["hid"]
assert dataset_hid, as_dict
if dataset.dataset.id in self.dataset_id_to_path:
file_name, extra_files_path = self.dataset_id_to_path[dataset.dataset.id]
if file_name is not None:
as_dict["file_name"] = file_name
if extra_files_path is not None:
as_dict["extra_files_path"] = extra_files_path
return
if file_name:
if not os.path.exists(dir_path):
os.makedirs(dir_path)
conversion = self.dataset_implicit_conversions.get(dataset)
conversion_key = (
self.serialization_options.get_identifier(self.security, conversion) if conversion else None
)
target_filename = get_export_dataset_filename(
as_dict["name"], as_dict["extension"], dataset_hid, conversion_key=conversion_key
)
arcname = os.path.join(dir_name, target_filename)
src = file_name
dest = os.path.join(export_directory, arcname)
add(src, dest)
as_dict["file_name"] = arcname
if extra_files_path:
try:
file_list = os.listdir(extra_files_path)
except OSError:
file_list = []
if len(file_list):
extra_files_target_filename = get_export_dataset_extra_files_dir_name(
as_dict["name"], as_dict["extension"], dataset_hid, conversion_key=conversion_key
)
arcname = os.path.join(dir_name, extra_files_target_filename)
add(extra_files_path, os.path.join(export_directory, arcname))
as_dict["extra_files_path"] = arcname
else:
as_dict["extra_files_path"] = ""
self.dataset_id_to_path[dataset.dataset.id] = (as_dict.get("file_name"), as_dict.get("extra_files_path"))
[docs] def exported_key(
self,
obj: model.RepresentById,
) -> Union[str, int]:
return self.serialization_options.get_identifier(self.security, obj)
def __enter__(self) -> "DirectoryModelExportStore":
return self
[docs] def push_metadata_files(self):
for dataset in self.included_datasets:
for metadata_element in dataset.metadata.values():
if isinstance(metadata_element, model.MetadataFile):
metadata_element.update_from_file(metadata_element.get_file_name())
[docs] def export_job(self, job: model.Job, tool=None, include_job_data=True):
self.export_jobs([job], include_job_data=include_job_data)
if tool_source := getattr(tool, "tool_source", None):
with open(os.path.join(self.export_directory, "tool.xml"), "w") as out:
out.write(tool_source.to_string())
[docs] def export_jobs(
self,
jobs: Iterable[model.Job],
jobs_attrs: Optional[List[Dict[str, Any]]] = None,
include_job_data: bool = True,
) -> List[Dict[str, Any]]:
"""
Export jobs.
``include_job_data`` determines whether datasets associated with jobs should be exported as well.
This should generally be ``True``, except when re-exporting a job (to store the generated command line)
when running the set_meta script.
"""
jobs_attrs = jobs_attrs or []
for job in jobs:
job_attrs = job.serialize(self.security, self.serialization_options)
if include_job_data:
# -- Get input, output datasets. --
input_dataset_mapping: Dict[str, List[Union[str, int]]] = {}
output_dataset_mapping: Dict[str, List[Union[str, int]]] = {}
input_dataset_collection_mapping: Dict[str, List[Union[str, int]]] = {}
input_dataset_collection_element_mapping: Dict[str, List[Union[str, int]]] = {}
output_dataset_collection_mapping: Dict[str, List[Union[str, int]]] = {}
implicit_output_dataset_collection_mapping: Dict[str, List[Union[str, int]]] = {}
for id_assoc in job.input_datasets:
# Optional data inputs will not have a dataset.
if id_assoc.dataset:
name = id_assoc.name
if name not in input_dataset_mapping:
input_dataset_mapping[name] = []
input_dataset_mapping[name].append(self.exported_key(id_assoc.dataset))
if include_job_data:
self.add_dataset(id_assoc.dataset)
for od_assoc in job.output_datasets:
# Optional data inputs will not have a dataset.
if od_assoc.dataset:
name = od_assoc.name
if name not in output_dataset_mapping:
output_dataset_mapping[name] = []
output_dataset_mapping[name].append(self.exported_key(od_assoc.dataset))
if include_job_data:
self.add_dataset(od_assoc.dataset)
for idc_assoc in job.input_dataset_collections:
# Optional data inputs will not have a dataset.
if idc_assoc.dataset_collection:
name = idc_assoc.name
if name not in input_dataset_collection_mapping:
input_dataset_collection_mapping[name] = []
input_dataset_collection_mapping[name].append(self.exported_key(idc_assoc.dataset_collection))
if include_job_data:
self.export_collection(idc_assoc.dataset_collection)
for idce_assoc in job.input_dataset_collection_elements:
if idce_assoc.dataset_collection_element:
name = idce_assoc.name
if name not in input_dataset_collection_element_mapping:
input_dataset_collection_element_mapping[name] = []
input_dataset_collection_element_mapping[name].append(
self.exported_key(idce_assoc.dataset_collection_element)
)
if include_job_data:
if idce_assoc.dataset_collection_element.is_collection:
assert isinstance(
idce_assoc.dataset_collection_element.element_object, model.DatasetCollection
)
self.export_collection(idce_assoc.dataset_collection_element.element_object)
else:
assert isinstance(
idce_assoc.dataset_collection_element.element_object, model.DatasetInstance
)
self.add_dataset(idce_assoc.dataset_collection_element.element_object)
for odci_assoc in job.output_dataset_collection_instances:
# Optional data outputs will not have a dataset.
# These are implicit outputs, we don't need to export them
if odci_assoc.dataset_collection_instance:
name = odci_assoc.name
if name not in output_dataset_collection_mapping:
output_dataset_collection_mapping[name] = []
output_dataset_collection_mapping[name].append(
self.exported_key(odci_assoc.dataset_collection_instance)
)
for odc_assoc in job.output_dataset_collections:
if odc_assoc.dataset_collection:
name = odc_assoc.name
if name not in implicit_output_dataset_collection_mapping:
implicit_output_dataset_collection_mapping[name] = []
implicit_output_dataset_collection_mapping[name].append(
self.exported_key(odc_assoc.dataset_collection)
)
if include_job_data:
self.export_collection(odc_assoc.dataset_collection)
job_attrs["input_dataset_mapping"] = input_dataset_mapping
job_attrs["input_dataset_collection_mapping"] = input_dataset_collection_mapping
job_attrs["input_dataset_collection_element_mapping"] = input_dataset_collection_element_mapping
job_attrs["output_dataset_mapping"] = output_dataset_mapping
job_attrs["output_dataset_collection_mapping"] = output_dataset_collection_mapping
job_attrs["implicit_output_dataset_collection_mapping"] = implicit_output_dataset_collection_mapping
jobs_attrs.append(job_attrs)
jobs_attrs_filename = os.path.join(self.export_directory, ATTRS_FILENAME_JOBS)
with open(jobs_attrs_filename, "w") as jobs_attrs_out:
jobs_attrs_out.write(json_encoder.encode(jobs_attrs))
return jobs_attrs
[docs] def export_history(
self, history: model.History, include_hidden: bool = False, include_deleted: bool = False
) -> None:
app = self.app
assert app, "exporting histories requires being bound to a session and Galaxy app object"
export_directory = self.export_directory
history_attrs = history.serialize(app.security, self.serialization_options)
history_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_HISTORY)
with open(history_attrs_filename, "w") as history_attrs_out:
dump(history_attrs, history_attrs_out)
sa_session = app.model.session
# Write collections' attributes (including datasets list) to file.
stmt_hdca = (
select(model.HistoryDatasetCollectionAssociation)
.where(model.HistoryDatasetCollectionAssociation.history == history)
.where(model.HistoryDatasetCollectionAssociation.deleted == expression.false())
)
collections = sa_session.scalars(stmt_hdca)
for collection in collections:
# filter this ?
if not collection.populated:
break
if collection.state != "ok":
break
self.export_collection(collection, include_deleted=include_deleted)
# Write datasets' attributes to file.
actions_backref = model.Dataset.actions
stmt_hda = (
select(model.HistoryDatasetAssociation)
.where(model.HistoryDatasetAssociation.history == history)
.join(model.Dataset)
.options(joinedload(model.HistoryDatasetAssociation.dataset).joinedload(actions_backref))
.order_by(model.HistoryDatasetAssociation.hid)
.where(model.Dataset.purged == expression.false())
)
datasets = sa_session.scalars(stmt_hda).unique()
for dataset in datasets:
dataset.annotation = get_item_annotation_str(sa_session, history.user, dataset)
should_include_file = (dataset.visible or include_hidden) and (not dataset.deleted or include_deleted)
if not dataset.deleted and dataset.id in self.collection_datasets:
should_include_file = True
if dataset not in self.included_datasets:
if should_include_file:
self._ensure_dataset_file_exists(dataset)
if dataset.implicitly_converted_parent_datasets:
# fetching 0th of list but I think this is just a mapping quirk - I can't imagine how there
# would be more than one of these -John
conversion = dataset.implicitly_converted_parent_datasets[0]
self.add_implicit_conversion_dataset(dataset, should_include_file, conversion)
else:
self.add_dataset(dataset, include_files=should_include_file)
[docs] def export_library(
self, library: model.Library, include_hidden: bool = False, include_deleted: bool = False
) -> None:
self.included_libraries.append(library)
root_folder = library.root_folder
self.export_library_folder_contents(root_folder, include_hidden=include_hidden, include_deleted=include_deleted)
[docs] def export_library_folder(self, library_folder: model.LibraryFolder, include_hidden=False, include_deleted=False):
self.included_library_folders.append(library_folder)
self.export_library_folder_contents(
library_folder, include_hidden=include_hidden, include_deleted=include_deleted
)
[docs] def export_library_folder_contents(
self, library_folder: model.LibraryFolder, include_hidden: bool = False, include_deleted: bool = False
) -> None:
for library_dataset in library_folder.datasets:
ldda = library_dataset.library_dataset_dataset_association
should_include_file = (not ldda.visible or not include_hidden) and (not ldda.deleted or include_deleted)
self.add_dataset(ldda, should_include_file)
for folder in library_folder.folders:
self.export_library_folder_contents(folder, include_hidden=include_hidden, include_deleted=include_deleted)
[docs] def export_workflow_invocation(
self, workflow_invocation: model.WorkflowInvocation, include_hidden: bool = False, include_deleted: bool = False
) -> None:
self.included_invocations.append(workflow_invocation)
for input_dataset in workflow_invocation.input_datasets:
self.add_dataset(input_dataset.dataset)
for output_dataset in workflow_invocation.output_datasets:
self.add_dataset(output_dataset.dataset)
for input_dataset_collection in workflow_invocation.input_dataset_collections:
self.export_collection(input_dataset_collection.dataset_collection)
for output_dataset_collection in workflow_invocation.output_dataset_collections:
self.export_collection(output_dataset_collection.dataset_collection)
for workflow_invocation_step in workflow_invocation.steps:
for assoc in workflow_invocation_step.output_datasets:
self.add_dataset(assoc.dataset)
for assoc in workflow_invocation_step.output_dataset_collections:
self.export_collection(assoc.dataset_collection)
[docs] def add_job_output_dataset_associations(
self, job_id: int, name: str, dataset_instance: model.DatasetInstance
) -> None:
job_output_dataset_associations = self.job_output_dataset_associations
if job_id not in job_output_dataset_associations:
job_output_dataset_associations[job_id] = {}
job_output_dataset_associations[job_id][name] = dataset_instance
[docs] def export_collection(
self,
collection: Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation],
include_deleted: bool = False,
include_hidden: bool = False,
) -> None:
self.add_dataset_collection(collection)
# export datasets for this collection
has_collection = (
collection.collection if isinstance(collection, model.HistoryDatasetCollectionAssociation) else collection
)
for collection_dataset in has_collection.dataset_instances:
# ignoring include_hidden since the datasets will default to hidden for this collection.
if collection_dataset.deleted and not include_deleted:
include_files = False
else:
include_files = True
self.add_dataset(collection_dataset, include_files=include_files)
self.collection_datasets.add(collection_dataset.id)
[docs] def add_dataset_collection(
self, collection: Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]
) -> None:
self.collections_attrs.append(collection)
self.included_collections.append(collection)
[docs] def add_implicit_conversion_dataset(
self,
dataset: model.DatasetInstance,
include_files: bool,
conversion: model.ImplicitlyConvertedDatasetAssociation,
) -> None:
self.included_datasets[dataset] = (dataset, include_files)
self.dataset_implicit_conversions[dataset] = conversion
[docs] def add_dataset(self, dataset: model.DatasetInstance, include_files: bool = True) -> None:
self.included_datasets[dataset] = (dataset, include_files)
def _ensure_dataset_file_exists(self, dataset: model.DatasetInstance) -> None:
state = dataset.dataset.state
if state in [model.Dataset.states.OK] and not dataset.get_file_name():
log.error(
f"Dataset [{dataset.id}] does not exists on on object store [{dataset.dataset.object_store_id or 'None'}], while trying to export."
)
raise Exception(
f"Cannot export history dataset [{getattr(dataset, 'hid', '')}: {dataset.name}] with id {self.exported_key(dataset)}"
)
def _finalize(self) -> None:
export_directory = self.export_directory
datasets_attrs = []
provenance_attrs = []
for dataset, include_files in self.included_datasets.values():
if include_files:
datasets_attrs.append(dataset)
else:
provenance_attrs.append(dataset)
def to_json(attributes):
return json_encoder.encode([a.serialize(self.security, self.serialization_options) for a in attributes])
datasets_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_DATASETS)
with open(datasets_attrs_filename, "w") as datasets_attrs_out:
datasets_attrs_out.write(to_json(datasets_attrs))
with open(f"{datasets_attrs_filename}.provenance", "w") as provenance_attrs_out:
provenance_attrs_out.write(to_json(provenance_attrs))
libraries_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_LIBRARIES)
with open(libraries_attrs_filename, "w") as libraries_attrs_out:
libraries_attrs_out.write(to_json(self.included_libraries))
library_folders_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_LIBRARY_FOLDERS)
with open(library_folders_attrs_filename, "w") as library_folder_attrs_out:
library_folder_attrs_out.write(to_json(self.included_library_folders))
collections_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_COLLECTIONS)
with open(collections_attrs_filename, "w") as collections_attrs_out:
collections_attrs_out.write(to_json(self.collections_attrs))
conversions_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_CONVERSIONS)
with open(conversions_attrs_filename, "w") as conversions_attrs_out:
conversions_attrs_out.write(to_json(self.dataset_implicit_conversions.values()))
jobs_attrs = []
for job_id, job_output_dataset_associations in self.job_output_dataset_associations.items():
output_dataset_mapping: Dict[str, List[Union[str, int]]] = {}
for name, dataset in job_output_dataset_associations.items():
if name not in output_dataset_mapping:
output_dataset_mapping[name] = []
output_dataset_mapping[name].append(self.exported_key(dataset))
jobs_attrs.append({"id": job_id, "output_dataset_mapping": output_dataset_mapping})
if self.serialize_jobs:
#
# Write jobs attributes file.
#
# Get all jobs associated with included HDAs.
jobs_dict: Dict[str, model.Job] = {}
implicit_collection_jobs_dict = {}
def record_job(job):
if not job:
# No viable job.
return
jobs_dict[job.id] = job
if icja := job.implicit_collection_jobs_association:
implicit_collection_jobs = icja.implicit_collection_jobs
implicit_collection_jobs_dict[implicit_collection_jobs.id] = implicit_collection_jobs
def record_associated_jobs(obj):
# Get the job object.
job = None
for assoc in getattr(obj, "creating_job_associations", []):
# For mapped over jobs obj could be DatasetCollection, which has no creating_job_association
job = assoc.job
break
record_job(job)
for hda, _include_files in self.included_datasets.values():
# Get the associated job, if any. If this hda was copied from another,
# we need to find the job that created the original hda
if not isinstance(hda, (model.HistoryDatasetAssociation, model.LibraryDatasetDatasetAssociation)):
raise Exception(
f"Expected a HistoryDatasetAssociation or LibraryDatasetDatasetAssociation, but got a {type(hda)}: {hda}"
)
job_hda = hda
while job_hda.copied_from_history_dataset_association: # should this check library datasets as well?
job_hda = job_hda.copied_from_history_dataset_association
if not job_hda.creating_job_associations:
# No viable HDA found.
continue
record_associated_jobs(job_hda)
for hdca in self.included_collections:
record_associated_jobs(hdca)
self.export_jobs(jobs_dict.values(), jobs_attrs=jobs_attrs)
for invocation in self.included_invocations:
for step in invocation.steps:
for job in step.jobs:
record_job(job)
if step.implicit_collection_jobs:
implicit_collection_jobs = step.implicit_collection_jobs
implicit_collection_jobs_dict[implicit_collection_jobs.id] = implicit_collection_jobs
# Get jobs' attributes.
icjs_attrs = []
for icj in implicit_collection_jobs_dict.values():
icj_attrs = icj.serialize(self.security, self.serialization_options)
icjs_attrs.append(icj_attrs)
icjs_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_IMPLICIT_COLLECTION_JOBS)
with open(icjs_attrs_filename, "w") as icjs_attrs_out:
icjs_attrs_out.write(json_encoder.encode(icjs_attrs))
invocations_attrs = []
for invocation in self.included_invocations:
invocation_attrs = invocation.serialize(self.security, self.serialization_options)
workflows_directory = self.workflows_directory
safe_makedirs(workflows_directory)
workflow = invocation.workflow
workflow_key = self.serialization_options.get_identifier(self.security, workflow)
history = invocation.history
assert invocation_attrs
invocation_attrs["workflow"] = workflow_key
if not self.app:
raise Exception(f"Missing self.app in {self}.")
self.app.workflow_contents_manager.store_workflow_artifacts(
workflows_directory, workflow_key, workflow, user=history.user, history=history
)
invocations_attrs.append(invocation_attrs)
invocations_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_INVOCATIONS)
with open(invocations_attrs_filename, "w") as invocations_attrs_out:
dump(invocations_attrs, invocations_attrs_out)
export_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_EXPORT)
with open(export_attrs_filename, "w") as export_attrs_out:
dump({"galaxy_export_version": GALAXY_EXPORT_VERSION}, export_attrs_out)
def __exit__(
self, exc_type: Optional[Type[BaseException]], exc_val: Optional[BaseException], exc_tb: Optional[TracebackType]
) -> bool:
if exc_type is None:
self._finalize()
# http://effbot.org/zone/python-with-statement.htm
# Ignores TypeError exceptions
return isinstance(exc_val, TypeError)
[docs]class WriteCrates:
included_invocations: List[model.WorkflowInvocation]
export_directory: StrPath
included_datasets: Dict[model.DatasetInstance, Tuple[model.DatasetInstance, bool]]
dataset_implicit_conversions: Dict[model.DatasetInstance, model.ImplicitlyConvertedDatasetAssociation]
dataset_id_to_path: Dict[int, Tuple[Optional[str], Optional[str]]]
@property
@abc.abstractmethod
def workflows_directory(self) -> str: ...
def _generate_markdown_readme(self) -> str:
markdown_parts: List[str] = []
if self._is_single_invocation_export():
invocation = self.included_invocations[0]
name = invocation.workflow.name
create_time = invocation.create_time
markdown_parts.append("# Galaxy Workflow Invocation Export")
markdown_parts.append("")
markdown_parts.append(f"This crate describes the invocation of workflow {name} executed at {create_time}.")
else:
markdown_parts.append("# Galaxy Dataset Export")
return "\n".join(markdown_parts)
def _is_single_invocation_export(self) -> bool:
return len(self.included_invocations) == 1
def _init_crate(self) -> ROCrate:
is_invocation_export = self._is_single_invocation_export()
if is_invocation_export:
invocation_crate_builder = WorkflowRunCrateProfileBuilder(self)
return invocation_crate_builder.build_crate()
ro_crate = ROCrate()
markdown_path = os.path.join(self.export_directory, "README.md")
with open(markdown_path, "w") as f:
f.write(self._generate_markdown_readme())
properties = {
"name": "README.md",
"encodingFormat": "text/markdown",
"about": {"@id": "./"},
}
ro_crate.add_file(
markdown_path,
dest_path="README.md",
properties=properties,
)
for dataset, _ in self.included_datasets.values():
if dataset.dataset.id in self.dataset_id_to_path:
file_name, _ = self.dataset_id_to_path[dataset.dataset.id]
if file_name is None:
# The dataset was discarded or no longer exists. No file to export.
# TODO: should this be registered in the crate as a special case?
log.warning(
"RO-Crate export: skipping dataset [%s] with state [%s] because file does not exist.",
dataset.id,
dataset.state,
)
continue
name = dataset.name
encoding_format = dataset.datatype.get_mime()
properties = {
"name": name,
"encodingFormat": encoding_format,
}
ro_crate.add_file(
os.path.join(self.export_directory, file_name),
dest_path=file_name,
properties=properties,
)
workflows_directory = self.workflows_directory
if os.path.exists(workflows_directory):
for filename in os.listdir(workflows_directory):
is_computational_wf = not filename.endswith(".cwl")
workflow_cls = ComputationalWorkflow if is_computational_wf else WorkflowDescription
lang = "galaxy" if not filename.endswith(".cwl") else "cwl"
dest_path = os.path.join("workflows", filename)
is_main_entity = is_invocation_export and is_computational_wf
ro_crate.add_workflow(
source=os.path.join(workflows_directory, filename),
dest_path=dest_path,
main=is_main_entity,
cls=workflow_cls,
lang=lang,
)
found_workflow_licenses = set()
for workflow_invocation in self.included_invocations:
workflow = workflow_invocation.workflow
license = workflow.license
if license:
found_workflow_licenses.add(license)
if len(found_workflow_licenses) == 1:
ro_crate.license = next(iter(found_workflow_licenses))
# TODO: license per workflow
# TODO: API options to license workflow outputs seprately
# TODO: Export report as PDF and stick it in here
return ro_crate
[docs]class WorkflowInvocationOnlyExportStore(DirectoryModelExportStore):
[docs] def export_history(self, history: model.History, include_hidden: bool = False, include_deleted: bool = False):
"""Export history to store."""
raise NotImplementedError()
[docs] def export_library(self, history, include_hidden=False, include_deleted=False):
"""Export library to store."""
raise NotImplementedError()
@property
def only_invocation(self) -> model.WorkflowInvocation:
assert len(self.included_invocations) == 1
return self.included_invocations[0]
[docs]@dataclass
class BcoExportOptions:
galaxy_url: str
galaxy_version: str
merge_history_metadata: bool = False
override_environment_variables: Optional[Dict[str, str]] = None
override_empirical_error: Optional[Dict[str, str]] = None
override_algorithmic_error: Optional[Dict[str, str]] = None
override_xref: Optional[List[XrefItem]] = None
[docs]class BcoModelExportStore(WorkflowInvocationOnlyExportStore):
[docs] def __init__(self, uri, export_options: BcoExportOptions, **kwds):
temp_output_dir = tempfile.mkdtemp()
self.temp_output_dir = temp_output_dir
if "://" in str(uri):
self.out_file = os.path.join(temp_output_dir, "out")
self.file_source_uri = uri
export_directory = os.path.join(temp_output_dir, "export")
else:
self.out_file = uri
self.file_source_uri = None
export_directory = temp_output_dir
self.export_options = export_options
super().__init__(export_directory, **kwds)
def _finalize(self):
super()._finalize()
core_biocompute_object, object_id = self._core_biocompute_object_and_object_id()
write_to_file(object_id, core_biocompute_object, self.out_file)
if self.file_source_uri:
file_source_path = self.file_sources.get_file_source_path(self.file_source_uri)
file_source = file_source_path.file_source
assert os.path.exists(self.out_file)
file_source.write_from(file_source_path.path, self.out_file, user_context=self.user_context)
def _core_biocompute_object_and_object_id(self) -> Tuple[BioComputeObjectCore, str]:
assert self.app # need app.security to do anything...
export_options = self.export_options
workflow_invocation = self.only_invocation
history = workflow_invocation.history
workflow = workflow_invocation.workflow
stored_workflow = workflow.stored_workflow
def get_dataset_url(encoded_dataset_id: str):
return f"{export_options.galaxy_url}api/datasets/{encoded_dataset_id}/display"
# pull in the creator_metadata info from workflow if it exists
contributors = get_contributors(workflow.creator_metadata)
provenance_domain = ProvenanceDomain(
name=workflow.name,
version=bco_workflow_version(workflow),
review=[],
contributors=contributors,
license=workflow.license or "",
created=workflow_invocation.create_time.isoformat(),
modified=workflow_invocation.update_time.isoformat(),
)
keywords = []
for tag in stored_workflow.tags:
keywords.append(tag.user_tname)
if export_options.merge_history_metadata:
for tag in history.tags:
if tag.user_tname not in keywords:
keywords.append(tag.user_tname)
# metrics = {} ... TODO
pipeline_steps: List[PipelineStep] = []
software_prerequisite_tracker = SoftwarePrerequisiteTracker()
input_subdomain_items: List[InputSubdomainItem] = []
output_subdomain_items: List[OutputSubdomainItem] = []
for step in workflow_invocation.steps:
workflow_step = step.workflow_step
software_prerequisite_tracker.register_step(workflow_step)
if workflow_step.type == "tool":
workflow_outputs_list = set()
output_list: List[DescriptionDomainUri] = []
input_list: List[DescriptionDomainUri] = []
for wo in workflow_step.workflow_outputs:
workflow_outputs_list.add(wo.output_name)
for job in step.jobs:
for job_input in job.input_datasets:
if hasattr(job_input.dataset, "dataset_id"):
encoded_dataset_id = self.app.security.encode_id(job_input.dataset.dataset_id)
url = get_dataset_url(encoded_dataset_id)
input_uri_obj = DescriptionDomainUri(
# TODO: that should maybe be a step prefix + element identifier where appropriate.
filename=job_input.dataset.name,
uri=url,
access_time=job_input.dataset.create_time.isoformat(),
)
input_list.append(input_uri_obj)
for job_output in job.output_datasets:
if hasattr(job_output.dataset, "dataset_id"):
encoded_dataset_id = self.app.security.encode_id(job_output.dataset.dataset_id)
url = get_dataset_url(encoded_dataset_id)
output_obj = DescriptionDomainUri(
filename=job_output.dataset.name,
uri=url,
access_time=job_output.dataset.create_time.isoformat(),
)
output_list.append(output_obj)
if job_output.name in workflow_outputs_list:
output = OutputSubdomainItem(
mediatype=job_output.dataset.extension,
uri=InputAndOutputDomainUri(
filename=job_output.dataset.name,
uri=url,
access_time=job_output.dataset.create_time.isoformat(),
),
)
output_subdomain_items.append(output)
step_index = workflow_step.order_index
step_name = workflow_step.label or workflow_step.tool_id
pipeline_step = PipelineStep(
step_number=step_index,
name=step_name,
description=workflow_step.annotations[0].annotation if workflow_step.annotations else "",
version=workflow_step.tool_version,
prerequisite=[],
input_list=input_list,
output_list=output_list,
)
pipeline_steps.append(pipeline_step)
if workflow_step.type == "data_input" and step.output_datasets:
for output_assoc in step.output_datasets:
encoded_dataset_id = self.app.security.encode_id(output_assoc.dataset_id)
url = get_dataset_url(encoded_dataset_id)
input_obj = InputSubdomainItem(
uri=Uri(
uri=url,
filename=workflow_step.label,
access_time=workflow_step.update_time.isoformat(),
),
)
input_subdomain_items.append(input_obj)
if workflow_step.type == "data_collection_input" and step.output_dataset_collections:
for output_dataset_collection_association in step.output_dataset_collections:
encoded_dataset_id = self.app.security.encode_id(
output_dataset_collection_association.dataset_collection_id
)
url = f"{export_options.galaxy_url}api/dataset_collections/{encoded_dataset_id}/download"
input_obj = InputSubdomainItem(
uri=Uri(
uri=url,
filename=workflow_step.label,
access_time=workflow_step.update_time.isoformat(),
),
)
input_subdomain_items.append(input_obj)
usability_domain_str: List[str] = []
for a in stored_workflow.annotations:
usability_domain_str.append(a.annotation)
if export_options.merge_history_metadata:
for h in history.annotations:
usability_domain_str.append(h.annotation)
parametric_domain_items: List[ParametricDomainItem] = []
for inv_step in workflow_invocation.steps:
try:
for k, v in inv_step.workflow_step.tool_inputs.items():
param, value, step = k, v, inv_step.workflow_step.order_index
parametric_domain_items.append(
ParametricDomainItem(param=str(param), value=str(value), step=str(step))
)
except Exception:
continue
encoded_workflow_id = self.app.security.encode_id(workflow.id)
execution_domain = galaxy_execution_domain(
export_options.galaxy_url,
f"{export_options.galaxy_url}api/workflows?encoded_workflow_id={encoded_workflow_id}",
software_prerequisite_tracker.software_prerequisites,
export_options.override_environment_variables,
)
extension_domain = extension_domains(export_options.galaxy_url, export_options.galaxy_version)
error_domain = ErrorDomain(
empirical_error=export_options.override_empirical_error or {},
algorithmic_error=export_options.override_algorithmic_error or {},
)
usability_domain = UsabilityDomain(root=usability_domain_str)
description_domain = DescriptionDomain(
keywords=keywords,
xref=export_options.override_xref or [],
platform=["Galaxy"],
pipeline_steps=pipeline_steps,
)
parametric_domain = ParametricDomain(root=parametric_domain_items)
io_domain = InputAndOutputDomain(
input_subdomain=input_subdomain_items,
output_subdomain=output_subdomain_items,
)
core = BioComputeObjectCore(
description_domain=description_domain,
error_domain=error_domain,
execution_domain=execution_domain,
extension_domain=extension_domain,
io_domain=io_domain,
parametric_domain=parametric_domain,
provenance_domain=provenance_domain,
usability_domain=usability_domain,
)
encoded_invocation_id = self.app.security.encode_id(workflow_invocation.id)
url = f"{export_options.galaxy_url}api/invocations/{encoded_invocation_id}"
return core, url
[docs]class ROCrateModelExportStore(DirectoryModelExportStore, WriteCrates):
[docs] def __init__(self, crate_directory: StrPath, **kwds) -> None:
self.crate_directory = crate_directory
super().__init__(crate_directory, export_files="symlink", **kwds)
def _finalize(self) -> None:
super()._finalize()
ro_crate = self._init_crate()
ro_crate.write(self.crate_directory)
[docs]class ROCrateArchiveModelExportStore(DirectoryModelExportStore, WriteCrates):
file_source_uri: Optional[StrPath]
out_file: StrPath
[docs] def __init__(self, uri: StrPath, **kwds) -> None:
temp_output_dir = tempfile.mkdtemp()
self.temp_output_dir = temp_output_dir
if "://" in str(uri):
self.out_file = os.path.join(temp_output_dir, "out")
self.file_source_uri = uri
export_directory = os.path.join(temp_output_dir, "export")
else:
self.out_file = uri
self.file_source_uri = None
export_directory = temp_output_dir
super().__init__(export_directory, **kwds)
def _finalize(self) -> None:
super()._finalize()
ro_crate = self._init_crate()
ro_crate.write(self.export_directory)
out_file_name = str(self.out_file)
if out_file_name.endswith(".zip"):
out_file = out_file_name[: -len(".zip")]
else:
out_file = out_file_name
rval = shutil.make_archive(out_file, "fastzip", self.export_directory)
if not self.file_source_uri:
shutil.move(rval, self.out_file)
else:
if not self.file_sources:
raise Exception(f"Need self.file_sources but {type(self)} is missing it: {self.file_sources}.")
file_source_path = self.file_sources.get_file_source_path(self.file_source_uri)
file_source = file_source_path.file_source
assert os.path.exists(rval), rval
file_source.write_from(file_source_path.path, rval, user_context=self.user_context)
shutil.rmtree(self.temp_output_dir)
[docs]class TarModelExportStore(DirectoryModelExportStore):
file_source_uri: Optional[StrPath]
out_file: StrPath
[docs] def __init__(self, uri: StrPath, gzip: bool = True, **kwds) -> None:
self.gzip = gzip
temp_output_dir = tempfile.mkdtemp()
self.temp_output_dir = temp_output_dir
if "://" in str(uri):
self.out_file = os.path.join(temp_output_dir, "out")
self.file_source_uri = uri
export_directory = os.path.join(temp_output_dir, "export")
else:
self.out_file = uri
self.file_source_uri = None
export_directory = temp_output_dir
super().__init__(export_directory, **kwds)
def _finalize(self) -> None:
super()._finalize()
tar_export_directory(self.export_directory, self.out_file, self.gzip)
if self.file_source_uri:
if not self.file_sources:
raise Exception(f"Need self.file_sources but {type(self)} is missing it: {self.file_sources}.")
file_source_path = self.file_sources.get_file_source_path(self.file_source_uri)
file_source = file_source_path.file_source
assert os.path.exists(self.out_file)
file_source.write_from(file_source_path.path, self.out_file, user_context=self.user_context)
shutil.rmtree(self.temp_output_dir)
[docs]class BagDirectoryModelExportStore(DirectoryModelExportStore):
[docs] def __init__(self, out_directory: str, **kwds) -> None:
self.out_directory = out_directory
super().__init__(out_directory, **kwds)
def _finalize(self) -> None:
super()._finalize()
bdb.make_bag(self.out_directory)
[docs]class BagArchiveModelExportStore(BagDirectoryModelExportStore):
file_source_uri: Optional[StrPath]
[docs] def __init__(self, uri: StrPath, bag_archiver: str = "tgz", **kwds) -> None:
# bag_archiver in tgz, zip, tar
self.bag_archiver = bag_archiver
temp_output_dir = tempfile.mkdtemp()
self.temp_output_dir = temp_output_dir
if "://" in str(uri):
# self.out_file = os.path.join(temp_output_dir, "out")
self.file_source_uri = uri
export_directory = os.path.join(temp_output_dir, "export")
else:
self.out_file = uri
self.file_source_uri = None
export_directory = temp_output_dir
super().__init__(export_directory, **kwds)
def _finalize(self) -> None:
super()._finalize()
rval = bdb.archive_bag(self.export_directory, self.bag_archiver)
if not self.file_source_uri:
shutil.move(rval, self.out_file)
else:
if not self.file_sources:
raise Exception(f"Need self.file_sources but {type(self)} is missing it: {self.file_sources}.")
file_source_path = self.file_sources.get_file_source_path(self.file_source_uri)
file_source = file_source_path.file_source
assert os.path.exists(rval)
file_source.write_from(file_source_path.path, rval, user_context=self.user_context)
shutil.rmtree(self.temp_output_dir)
[docs]def get_export_store_factory(
app,
download_format: str,
export_files=None,
bco_export_options: Optional[BcoExportOptions] = None,
user_context=None,
) -> Callable[[StrPath], ModelExportStore]:
export_store_class: Union[
Type[TarModelExportStore],
Type[BagArchiveModelExportStore],
Type[ROCrateArchiveModelExportStore],
Type[BcoModelExportStore],
]
export_store_class_kwds = {
"app": app,
"export_files": export_files,
"serialize_dataset_objects": False,
"user_context": user_context,
}
if download_format in ["tar.gz", "tgz"]:
export_store_class = TarModelExportStore
export_store_class_kwds["gzip"] = True
elif download_format in ["tar"]:
export_store_class = TarModelExportStore
export_store_class_kwds["gzip"] = False
elif download_format == "rocrate.zip":
export_store_class = ROCrateArchiveModelExportStore
elif download_format == "bco.json":
export_store_class = BcoModelExportStore
export_store_class_kwds["export_options"] = bco_export_options
elif download_format.startswith("bag."):
bag_archiver = download_format[len("bag.") :]
if bag_archiver not in ["zip", "tar", "tgz"]:
raise RequestParameterInvalidException(f"Unknown download format [{download_format}]")
export_store_class = BagArchiveModelExportStore
export_store_class_kwds["bag_archiver"] = bag_archiver
else:
raise RequestParameterInvalidException(f"Unknown download format [{download_format}]")
return lambda path: export_store_class(path, **export_store_class_kwds)
[docs]def tar_export_directory(export_directory: StrPath, out_file: StrPath, gzip: bool) -> None:
tarfile_mode = "w"
if gzip:
tarfile_mode += ":gz"
with tarfile.open(out_file, tarfile_mode, dereference=True) as store_archive:
for export_path in os.listdir(export_directory):
store_archive.add(os.path.join(export_directory, export_path), arcname=export_path)
[docs]def get_export_dataset_filename(name: str, ext: str, hid: int, conversion_key: Optional[str]) -> str:
"""
Builds a filename for a dataset using its name an extension.
"""
base = "".join(c in FILENAME_VALID_CHARS and c or "_" for c in name)
if not conversion_key:
return f"{base}_{hid}.{ext}"
else:
return f"{base}_{hid}_conversion_{conversion_key}.{ext}"
[docs]def get_export_dataset_extra_files_dir_name(name: str, ext: str, hid: int, conversion_key: Optional[str]) -> str:
if not conversion_key:
return f"extra_files_path_{hid}"
else:
return f"extra_files_path_{hid}_conversion_{conversion_key}"
[docs]def imported_store_for_metadata(
directory: str, object_store: Optional[ObjectStore] = None
) -> BaseDirectoryImportModelStore:
import_options = ImportOptions(allow_dataset_object_edit=True, allow_edit=True)
import_model_store = get_import_model_store_for_directory(
directory, import_options=import_options, object_store=object_store
)
import_model_store.perform_import()
return import_model_store
[docs]def source_to_import_store(
source: Union[str, dict],
app: StoreAppProtocol,
import_options: Optional[ImportOptions],
model_store_format: Optional[ModelStoreFormat] = None,
user_context=None,
) -> ModelImportStore:
galaxy_user = user_context.user if user_context else None
if isinstance(source, dict):
if model_store_format is not None:
raise Exception(
"Can only specify a model_store_format as an argument to source_to_import_store in conjuction with URIs"
)
model_import_store: ModelImportStore = get_import_model_store_for_dict(
source,
import_options=import_options,
app=app,
user=galaxy_user,
)
else:
source_uri: str = str(source)
delete = False
tag_handler = app.tag_handler.create_tag_handler_session(galaxy_session=None)
if source_uri.startswith("file://"):
source_uri = source_uri[len("file://") :]
if "://" in source_uri:
user_context = ProvidesUserFileSourcesUserContext(user_context)
source_uri = stream_url_to_file(
source_uri, app.file_sources, prefix="gx_import_model_store", user_context=user_context
)
delete = True
target_path = source_uri
if target_path.endswith(".json"):
with open(target_path) as f:
store_dict = load(f)
assert isinstance(store_dict, dict)
model_import_store = get_import_model_store_for_dict(
store_dict,
import_options=import_options,
app=app,
user=galaxy_user,
)
elif os.path.isdir(target_path):
model_import_store = get_import_model_store_for_directory(
target_path, import_options=import_options, app=app, user=galaxy_user, tag_handler=tag_handler
)
else:
model_store_format = model_store_format or ModelStoreFormat.TGZ
if ModelStoreFormat.is_compressed(model_store_format):
try:
temp_dir = mkdtemp()
target_dir = CompressedFile(target_path).extract(temp_dir)
finally:
if delete:
os.remove(target_path)
model_import_store = get_import_model_store_for_directory(
target_dir, import_options=import_options, app=app, user=galaxy_user, tag_handler=tag_handler
)
elif ModelStoreFormat.is_bag(model_store_format):
model_import_store = BagArchiveImportModelStore(
target_path, import_options=import_options, app=app, user=galaxy_user
)
else:
raise Exception(f"Unknown model_store_format type encountered {model_store_format}")
return model_import_store
[docs]def payload_to_source_uri(payload) -> str:
if payload.store_content_uri:
source_uri = payload.store_content_uri
else:
store_dict = payload.store_dict
assert isinstance(store_dict, dict)
temp_dir = mkdtemp()
import_json = os.path.join(temp_dir, "import_store.json")
with open(import_json, "w") as f:
dump(store_dict, f)
source_uri = f"file://{import_json}"
return source_uri
[docs]def copy_dataset_instance_metadata_attributes(source: model.DatasetInstance, target: model.DatasetInstance) -> None:
target.metadata = source.metadata
target.blurb = source.blurb
target.peek = source.peek
target.info = source.info
target.tool_version = source.tool_version
target.extension = source.extension