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Source code for galaxy.tools.actions.model_operations

import logging

from galaxy.tools.actions import (
    DefaultToolAction,
    OutputCollections,
    ToolExecutionCache,
)
from galaxy.util.odict import odict

log = logging.getLogger(__name__)


[docs]class ModelOperationToolAction(DefaultToolAction):
[docs] def check_inputs_ready(self, tool, trans, incoming, history, execution_cache=None): if execution_cache is None: execution_cache = ToolExecutionCache(trans) current_user_roles = execution_cache.current_user_roles history, inp_data, inp_dataset_collections = self._collect_inputs(tool, trans, incoming, history, current_user_roles) tool.check_inputs_ready(inp_data, inp_dataset_collections)
[docs] def execute(self, tool, trans, incoming={}, set_output_hid=False, overwrite=True, history=None, job_params=None, mapping_over_collection=False, execution_cache=None, **kwargs): if execution_cache is None: execution_cache = ToolExecutionCache(trans) current_user_roles = execution_cache.current_user_roles history, inp_data, inp_dataset_collections = self._collect_inputs(tool, trans, incoming, history, current_user_roles) # Build name for output datasets based on tool name and input names on_text = self._get_on_text(inp_data) # wrapped params are used by change_format action and by output.label; only perform this wrapping once, as needed wrapped_params = self._wrapped_params(trans, tool, incoming) out_data = odict() input_collections = dict((k, v[0][0]) for k, v in inp_dataset_collections.items()) output_collections = OutputCollections( trans, history, tool=tool, tool_action=self, input_collections=input_collections, mapping_over_collection=mapping_over_collection, on_text=on_text, incoming=incoming, params=wrapped_params.params, job_params=job_params, ) # # Create job. # job, galaxy_session = self._new_job_for_session(trans, tool, history) self._produce_outputs(trans, tool, out_data, output_collections, incoming=incoming, history=history) self._record_inputs(trans, tool, job, incoming, inp_data, inp_dataset_collections, current_user_roles) self._record_outputs(job, out_data, output_collections) job.state = job.states.OK trans.sa_session.add(job) trans.sa_session.flush() # ensure job.id are available # Queue the job for execution # trans.app.job_queue.put( job.id, tool.id ) # trans.log_event( "Added database job action to the job queue, id: %s" % str(job.id), tool_id=job.tool_id ) log.info("Calling produce_outputs, tool is %s" % tool) return job, out_data
def _produce_outputs(self, trans, tool, out_data, output_collections, incoming, history, **kwargs): tool.produce_outputs(trans, out_data, output_collections, incoming, history=history) trans.sa_session.add_all(out_data.values()) trans.sa_session.flush()