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Source code for galaxy.tools.actions.model_operations

import logging
from typing import TYPE_CHECKING

from galaxy.tools.actions import (

    from galaxy.managers.context import ProvidesUserContext

log = logging.getLogger(__name__)

[docs]class ModelOperationToolAction(DefaultToolAction): produces_real_jobs = False
[docs] def check_inputs_ready(self, tool, trans, incoming, history, execution_cache=None, collection_info=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, collection_info ) tool.check_inputs_ready(inp_data, inp_dataset_collections)
[docs] def execute( self, tool, trans, incoming=None, set_output_hid=False, overwrite=True, history=None, job_params=None, execution_cache=None, collection_info=None, job_callback=None, skip=False, **kwargs, ): incoming = incoming or {} trans.check_user_activation() if execution_cache is None: execution_cache = ToolExecutionCache(trans) current_user_roles = execution_cache.current_user_roles ( history, inp_data, inp_dataset_collections, preserved_tags, preserved_hdca_tags, all_permissions, ) = self._collect_inputs(tool, trans, incoming, history, current_user_roles, collection_info) # 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 = {} input_collections = {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, dataset_collection_elements=kwargs.get("dataset_collection_elements", None), on_text=on_text, incoming=incoming, params=wrapped_params.params, job_params=job_params, tags=preserved_tags, hdca_tags=preserved_hdca_tags, ) # # 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, tags=preserved_tags, hdca_tags=preserved_hdca_tags, skip=skip, ) self._record_inputs(trans, tool, job, incoming, inp_data, inp_dataset_collections) self._record_outputs(job, out_data, output_collections) if job_callback: job_callback(job) if skip: job.state = job.states.SKIPPED else: job.state = job.states.OK trans.sa_session.add(job) # Queue the job for execution # trans.app.job_manager.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(f"Calling produce_outputs, tool is {tool}") return job, out_data, history
def _produce_outputs( self, trans: "ProvidesUserContext", tool, out_data, output_collections, incoming, history, tags, hdca_tags, skip ): tag_handler = trans.tag_handler tool.produce_outputs( trans, out_data, output_collections, incoming, history=history, tags=tags, hdca_tags=hdca_tags, tag_handler=tag_handler, ) mapped_over_elements = output_collections.dataset_collection_elements if mapped_over_elements: for name, value in out_data.items(): if name in mapped_over_elements: value.visible = False mapped_over_elements[name].hda = value # We probably need to mark all outputs as skipped, not just the outputs of whatever the database op tools do ? # This is probably not exactly right, but it might also work in most cases if skip: for output_collection in output_collections.out_collections.values(): output_collection.mark_as_populated() for hdca in output_collections.out_collection_instances.values(): hdca.visible = False # Would we also need to replace the datasets with skipped datasets? trans.sa_session.add_all(out_data.values())