Source code for galaxy.tools.actions.metadata

import logging
import os
from json import dumps

from galaxy.job_execution.datasets import DatasetPath
from galaxy.metadata import get_metadata_compute_strategy
from galaxy.util import asbool
from . import ToolAction

log = logging.getLogger(__name__)


[docs]class SetMetadataToolAction(ToolAction): """Tool action used for setting external metadata on an existing dataset""" produces_real_jobs = False
[docs] def execute( self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, job_params=None, **kwargs ): """ Execute using a web transaction. """ trans.check_user_activation() session = trans.get_galaxy_session() session_id = session and session.id history_id = trans.history and trans.history.id incoming = incoming or {} job, odict = self.execute_via_app( tool, trans.app, session_id, history_id, trans.user, incoming, set_output_hid, overwrite, history, job_params, ) # FIXME: can remove this when logging in execute_via_app method. trans.log_event(f"Added set external metadata job to the job queue, id: {str(job.id)}", tool_id=job.tool_id) return job, odict
[docs] def execute_via_app( self, tool, app, session_id, history_id, user=None, incoming=None, set_output_hid=False, overwrite=True, history=None, job_params=None, ): """ Execute using application. """ incoming = incoming or {} for name, value in incoming.items(): # Why are we looping here and not just using a fixed input name? Needed? if not name.startswith("input"): continue if isinstance(value, app.model.HistoryDatasetAssociation): dataset = value dataset_name = name type = "hda" break elif isinstance(value, app.model.LibraryDatasetDatasetAssociation): dataset = value dataset_name = name type = "ldda" break else: raise Exception("The dataset to set metadata on could not be determined.") sa_session = app.model.context # Create the job object job = app.model.Job() job.galaxy_version = app.config.version_major job.session_id = session_id job.history_id = history_id job.tool_id = tool.id if user: job.user_id = user.id if job_params: job.params = dumps(job_params) start_job_state = job.state # should be job.states.NEW try: # For backward compatibility, some tools may not have versions yet. job.tool_version = tool.version except AttributeError: job.tool_version = "1.0.1" job.dynamic_tool = tool.dynamic_tool job.state = ( job.states.WAITING ) # we need to set job state to something other than NEW, or else when tracking jobs in db it will be picked up before we have added input / output parameters sa_session.add(job) sa_session.flush() # ensure job.id is available # add parameters to job_parameter table # Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)? incoming["__ORIGINAL_DATASET_STATE__"] = dataset.state input_paths = [DatasetPath(dataset.id, real_path=dataset.file_name, mutable=False)] app.object_store.create(job, base_dir="job_work", dir_only=True, extra_dir=str(job.id)) job_working_dir = app.object_store.get_filename(job, base_dir="job_work", dir_only=True, extra_dir=str(job.id)) datatypes_config = os.path.join(job_working_dir, "registry.xml") app.datatypes_registry.to_xml_file(path=datatypes_config) external_metadata_wrapper = get_metadata_compute_strategy(app.config, job.id, tool_id=tool.id) output_datatasets_dict = { dataset_name: dataset, } validate_outputs = asbool(incoming.get("validate", False)) cmd_line = external_metadata_wrapper.setup_external_metadata( output_datatasets_dict, {}, sa_session, exec_dir=None, tmp_dir=job_working_dir, dataset_files_path=app.model.Dataset.file_path, output_fnames=input_paths, config_root=app.config.root, config_file=app.config.config_file, datatypes_config=datatypes_config, job_metadata=os.path.join(job_working_dir, "working", tool.provided_metadata_file), include_command=False, max_metadata_value_size=app.config.max_metadata_value_size, max_discovered_files=app.config.max_discovered_files, validate_outputs=validate_outputs, job=job, kwds={"overwrite": overwrite}, ) incoming["__SET_EXTERNAL_METADATA_COMMAND_LINE__"] = cmd_line for name, value in tool.params_to_strings(incoming, app).items(): job.add_parameter(name, value) # add the dataset to job_to_input_dataset table if type == "hda": job.add_input_dataset(dataset_name, dataset) elif type == "ldda": job.add_input_library_dataset(dataset_name, dataset) # Need a special state here to show that metadata is being set and also allow the job to run # i.e. if state was set to 'running' the set metadata job would never run, as it would wait for input (the dataset to set metadata on) to be in a ready state dataset._state = dataset.states.SETTING_METADATA job.state = start_job_state # job inputs have been configured, restore initial job state sa_session.flush() # clear e.g. converted files dataset.datatype.before_setting_metadata(dataset) return job, {}