Source code for galaxy.tools.actions.metadata

import logging
import os
from collections import OrderedDict
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={}, 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
        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("Added set external metadata job to the job queue, id: %s" % 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={}, set_output_hid=False, overwrite=True,
                        history=None, job_params=None):
        """
        Execute using application.
        """

        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)
        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,
                                                                     validate_outputs=validate_outputs,
                                                                     max_metadata_value_size=app.config.max_metadata_value_size,
                                                                     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()

        # Queue the job for execution
        app.job_manager.enqueue(job, tool=tool)
        # FIXME: need to add event logging to app and log events there rather than trans.
        # trans.log_event( "Added set external metadata job to the job queue, id: %s" % str(job.id), tool_id=job.tool_id )

        # clear e.g. converted files
        dataset.datatype.before_setting_metadata(dataset)

        return job, OrderedDict()