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Source code for galaxy.tools.imp_exp

import datetime
import json
import logging
import os
import shutil
import tempfile
from json import dumps, load

from sqlalchemy.orm import eagerload, eagerload_all
from sqlalchemy.sql import expression

from galaxy import model
from galaxy.exceptions import MalformedContents
from galaxy.model.item_attrs import UsesAnnotations
from galaxy.web.framework.helpers import to_unicode

log = logging.getLogger(__name__)


[docs]class JobImportHistoryArchiveWrapper(object, UsesAnnotations): """ Class provides support for performing jobs that import a history from an archive. """
[docs] def __init__(self, app, job_id): self.app = app self.job_id = job_id self.sa_session = self.app.model.context
[docs] def cleanup_after_job(self): """ Set history, datasets, and jobs' attributes and clean up archive directory. """ # # Helper methods. # def file_in_dir(file_path, a_dir): """ Returns true if file is in directory. """ abs_file_path = os.path.abspath(file_path) return os.path.split(abs_file_path)[0] == a_dir def get_tag_str(tag, value): """ Builds a tag string for a tag, value pair. """ if not value: return tag else: return tag + ":" + value # # Import history. # jiha = self.sa_session.query(model.JobImportHistoryArchive).filter_by(job_id=self.job_id).first() if jiha: try: archive_dir = jiha.archive_dir archive_dir = os.path.realpath(archive_dir) user = jiha.job.user # Bioblend previous to 17.01 exported histories with an extra subdir. if not os.path.exists(os.path.join(archive_dir, 'history_attrs.txt')): 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 # # Create history. # history_attr_file_name = os.path.join(archive_dir, 'history_attrs.txt') history_attrs = load(open(history_attr_file_name)) # Create history. new_history = model.History(name='imported from archive: %s' % history_attrs['name'], user=user) new_history.importing = True new_history.hid_counter = history_attrs['hid_counter'] new_history.genome_build = history_attrs['genome_build'] self.sa_session.add(new_history) jiha.history = new_history self.sa_session.flush() # Add annotation, tags. if user: self.add_item_annotation(self.sa_session, user, new_history, history_attrs['annotation']) """ TODO: figure out to how add tags to item. for tag, value in history_attrs[ 'tags' ].items(): trans.app.tag_handler.apply_item_tags( trans, trans.user, new_history, get_tag_str( tag, value ) ) """ # # Create datasets. # datasets_attrs_file_name = os.path.join(archive_dir, 'datasets_attrs.txt') datasets_attrs = load(open(datasets_attrs_file_name)) provenance_file_name = datasets_attrs_file_name + ".provenance" if os.path.exists(provenance_file_name): provenance_attrs = load(open(provenance_file_name)) datasets_attrs += provenance_attrs # Get counts of how often each dataset file is used; a file can # be linked to multiple dataset objects (HDAs). datasets_usage_counts = {} for dataset_attrs in datasets_attrs: temp_dataset_file_name = \ os.path.realpath(os.path.join(archive_dir, dataset_attrs['file_name'])) if (temp_dataset_file_name not in datasets_usage_counts): datasets_usage_counts[temp_dataset_file_name] = 0 datasets_usage_counts[temp_dataset_file_name] += 1 # Create datasets. for dataset_attrs in datasets_attrs: metadata = dataset_attrs['metadata'] # Create dataset and HDA. hda = 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'], dbkey=metadata['dbkey'], metadata=metadata, history=new_history, create_dataset=True, sa_session=self.sa_session) if 'uuid' in dataset_attrs: hda.dataset.uuid = dataset_attrs["uuid"] if dataset_attrs.get('exported', True) is False: hda.state = hda.states.DISCARDED hda.deleted = True hda.purged = True else: hda.state = hda.states.OK self.sa_session.add(hda) self.sa_session.flush() new_history.add_dataset(hda, genome_build=None) hda.hid = dataset_attrs['hid'] # Overwrite default hid set when HDA added to history. # TODO: Is there a way to recover permissions? Is this needed? # permissions = trans.app.security_agent.history_get_default_permissions( new_history ) # trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) self.sa_session.flush() if dataset_attrs.get('exported', True) is True: # Do security check and move/copy dataset data. temp_dataset_file_name = \ os.path.realpath(os.path.abspath(os.path.join(archive_dir, dataset_attrs['file_name']))) if not file_in_dir(temp_dataset_file_name, os.path.join(archive_dir, "datasets")): raise MalformedContents("Invalid dataset path: %s" % temp_dataset_file_name) if datasets_usage_counts[temp_dataset_file_name] == 1: self.app.object_store.update_from_file(hda.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: try: file_list = os.listdir(os.path.join(archive_dir, dataset_extra_files_path)) except OSError: file_list = [] if file_list: for extra_file in file_list: self.app.object_store.update_from_file( hda.dataset, extra_dir='dataset_%s_files' % hda.dataset.id, alt_name=extra_file, file_name=os.path.join(archive_dir, dataset_extra_files_path, extra_file), create=True) else: datasets_usage_counts[temp_dataset_file_name] -= 1 shutil.copyfile(temp_dataset_file_name, hda.file_name) hda.dataset.set_total_size() # update the filesize record in the database # Set tags, annotations. if user: self.add_item_annotation(self.sa_session, user, hda, dataset_attrs['annotation']) # TODO: Set tags. """ for tag, value in dataset_attrs[ 'tags' ].items(): trans.app.tag_handler.apply_item_tags( trans, trans.user, hda, get_tag_str( tag, value ) ) self.sa_session.flush() """ # Although metadata is set above, need to set metadata to recover BAI for BAMs. if hda.extension == 'bam': self.app.datatypes_registry.set_external_metadata_tool.tool_action.execute_via_app( self.app.datatypes_registry.set_external_metadata_tool, self.app, jiha.job.session_id, new_history.id, jiha.job.user, incoming={'input1': hda}, overwrite=False ) # # Create jobs. # # Decode jobs attributes. def as_hda(obj_dct): """ Hook to 'decode' an HDA; method uses history and HID to get the HDA represented by the encoded object. This only works because HDAs are created above. """ if obj_dct.get('__HistoryDatasetAssociation__', False): return self.sa_session.query(model.HistoryDatasetAssociation) \ .filter_by(history=new_history, hid=obj_dct['hid']).first() return obj_dct jobs_attr_file_name = os.path.join(archive_dir, 'jobs_attrs.txt') jobs_attrs = load(open(jobs_attr_file_name), object_hook=as_hda) # Create each job. for job_attrs in jobs_attrs: imported_job = model.Job() imported_job.user = user # TODO: set session? # imported_job.session = trans.get_galaxy_session().id imported_job.history = new_history imported_job.imported = True imported_job.tool_id = job_attrs['tool_id'] imported_job.tool_version = job_attrs['tool_version'] imported_job.set_state(job_attrs['state']) imported_job.info = job_attrs.get('info', None) imported_job.exit_code = job_attrs.get('exit_code', None) imported_job.traceback = job_attrs.get('traceback', None) imported_job.stdout = job_attrs.get('stdout', None) imported_job.stderr = job_attrs.get('stderr', None) imported_job.command_line = job_attrs.get('command_line', None) try: imported_job.create_time = datetime.datetime.strptime(job_attrs["create_time"], "%Y-%m-%dT%H:%M:%S.%f") imported_job.update_time = datetime.datetime.strptime(job_attrs["update_time"], "%Y-%m-%dT%H:%M:%S.%f") except Exception: pass self.sa_session.add(imported_job) self.sa_session.flush() class HistoryDatasetAssociationIDEncoder(json.JSONEncoder): """ Custom JSONEncoder for a HistoryDatasetAssociation that encodes an HDA as its ID. """ def default(self, obj): """ Encode an HDA, default encoding for everything else. """ if isinstance(obj, model.HistoryDatasetAssociation): return obj.id return json.JSONEncoder.default(self, obj) # Set parameters. May be useful to look at metadata.py for creating parameters. # TODO: there may be a better way to set parameters, e.g.: # for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): # job.add_parameter( name, value ) # to make this work, we'd need to flesh out the HDA objects. The code below is # relatively similar. for name, value in job_attrs['params'].items(): # Transform parameter values when necessary. if isinstance(value, model.HistoryDatasetAssociation): # HDA input: use hid to find input. input_hda = self.sa_session.query(model.HistoryDatasetAssociation) \ .filter_by(history=new_history, hid=value.hid).first() value = input_hda.id # print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id ) imported_job.add_parameter(name, dumps(value, cls=HistoryDatasetAssociationIDEncoder)) # TODO: Connect jobs to input datasets. # Connect jobs to output datasets. for output_hid in job_attrs['output_datasets']: # print "%s job has output dataset %i" % (imported_job.id, output_hid) output_hda = self.sa_session.query(model.HistoryDatasetAssociation) \ .filter_by(history=new_history, hid=output_hid).first() if output_hda: imported_job.add_output_dataset(output_hda.name, output_hda) # Connect jobs to input datasets. if 'input_mapping' in job_attrs: for input_name, input_hid in job_attrs['input_mapping'].items(): input_hda = self.sa_session.query(model.HistoryDatasetAssociation) \ .filter_by(history=new_history, hid=input_hid).first() if input_hda: imported_job.add_input_dataset(input_name, input_hda) self.sa_session.flush() # Done importing. new_history.importing = False self.sa_session.flush() # Cleanup. if os.path.exists(archive_dir): shutil.rmtree(archive_dir) except Exception as e: jiha.job.stderr += "Error cleaning up history import job: %s" % e self.sa_session.flush() raise
[docs]class JobExportHistoryArchiveWrapper(object, UsesAnnotations): """ Class provides support for performing jobs that export a history to an archive. """
[docs] def __init__(self, job_id): self.job_id = job_id
[docs] def get_history_datasets(self, trans, history): """ Returns history's datasets. """ query = (trans.sa_session.query(trans.model.HistoryDatasetAssociation) .filter(trans.model.HistoryDatasetAssociation.history == history) .options(eagerload("children")) .join("dataset") .options(eagerload_all("dataset.actions")) .order_by(trans.model.HistoryDatasetAssociation.hid) .filter(trans.model.HistoryDatasetAssociation.deleted == expression.false()) .filter(trans.model.Dataset.purged == expression.false())) return query.all()
# TODO: should use db_session rather than trans in this method.
[docs] def setup_job(self, trans, jeha, include_hidden=False, include_deleted=False): """ Perform setup for job to export a history into an archive. Method generates attribute files for export, sets the corresponding attributes in the jeha object, and returns a command line for running the job. The command line includes the command, inputs, and options; it does not include the output file because it must be set at runtime. """ # # Helper methods/classes. # def get_item_tag_dict(item): """ Create dictionary of an item's tags. """ tags = {} for tag in item.tags: tag_user_tname = to_unicode(tag.user_tname) tag_user_value = to_unicode(tag.user_value) tags[tag_user_tname] = tag_user_value return tags def prepare_metadata(metadata): """ Prepare metatdata for exporting. """ for name, value in list(metadata.items()): # Metadata files are not needed for export because they can be # regenerated. if isinstance(value, trans.app.model.MetadataFile): del metadata[name] return metadata class HistoryDatasetAssociationEncoder(json.JSONEncoder): """ Custom JSONEncoder for a HistoryDatasetAssociation. """ def default(self, obj): """ Encode an HDA, default encoding for everything else. """ if isinstance(obj, trans.app.model.HistoryDatasetAssociation): rval = { "__HistoryDatasetAssociation__": True, "create_time": obj.create_time.__str__(), "update_time": obj.update_time.__str__(), "hid": obj.hid, "name": to_unicode(obj.name), "info": to_unicode(obj.info), "blurb": obj.blurb, "peek": obj.peek, "extension": obj.extension, "metadata": prepare_metadata(dict(obj.metadata.items())), "parent_id": obj.parent_id, "designation": obj.designation, "deleted": obj.deleted, "visible": obj.visible, "file_name": obj.file_name, "uuid": (lambda uuid: str(uuid) if uuid else None)(obj.dataset.uuid), "annotation": to_unicode(getattr(obj, 'annotation', '')), "tags": get_item_tag_dict(obj), "extra_files_path": obj.extra_files_path } if not obj.visible and not include_hidden: rval['exported'] = False elif obj.deleted and not include_deleted: rval['exported'] = False else: rval['exported'] = True return rval return json.JSONEncoder.default(self, obj) # # Create attributes/metadata files for export. # temp_output_dir = tempfile.mkdtemp() # Write history attributes to file. history = jeha.history history_attrs = { "create_time": history.create_time.__str__(), "update_time": history.update_time.__str__(), "name": to_unicode(history.name), "hid_counter": history.hid_counter, "genome_build": history.genome_build, "annotation": to_unicode(self.get_item_annotation_str(trans.sa_session, history.user, history)), "tags": get_item_tag_dict(history), "includes_hidden_datasets": include_hidden, "includes_deleted_datasets": include_deleted } history_attrs_filename = tempfile.NamedTemporaryFile(dir=temp_output_dir).name history_attrs_out = open(history_attrs_filename, 'w') history_attrs_out.write(dumps(history_attrs)) history_attrs_out.close() jeha.history_attrs_filename = history_attrs_filename # Write datasets' attributes to file. datasets = self.get_history_datasets(trans, history) included_datasets = [] datasets_attrs = [] provenance_attrs = [] for dataset in datasets: dataset.annotation = self.get_item_annotation_str(trans.sa_session, history.user, dataset) if (not dataset.visible and not include_hidden) or (dataset.deleted and not include_deleted): provenance_attrs.append(dataset) else: datasets_attrs.append(dataset) included_datasets.append(dataset) datasets_attrs_filename = tempfile.NamedTemporaryFile(dir=temp_output_dir).name datasets_attrs_out = open(datasets_attrs_filename, 'w') datasets_attrs_out.write(dumps(datasets_attrs, cls=HistoryDatasetAssociationEncoder)) datasets_attrs_out.close() jeha.datasets_attrs_filename = datasets_attrs_filename provenance_attrs_out = open(datasets_attrs_filename + ".provenance", 'w') provenance_attrs_out.write(dumps(provenance_attrs, cls=HistoryDatasetAssociationEncoder)) provenance_attrs_out.close() # # Write jobs attributes file. # # Get all jobs associated with included HDAs. jobs_dict = {} for hda in included_datasets: # Get the associated job, if any. If this hda was copied from another, # we need to find the job that created the origial 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 # Get the job object. job = None for assoc in job_hda.creating_job_associations: job = assoc.job break if not job: # No viable job. continue jobs_dict[job.id] = job # Get jobs' attributes. jobs_attrs = [] for id, job in jobs_dict.items(): job_attrs = {} job_attrs['tool_id'] = job.tool_id job_attrs['tool_version'] = job.tool_version job_attrs['state'] = job.state job_attrs['info'] = job.info job_attrs['traceback'] = job.traceback job_attrs['command_line'] = job.command_line job_attrs['stderr'] = job.stderr job_attrs['stdout'] = job.stdout job_attrs['exit_code'] = job.exit_code job_attrs['create_time'] = job.create_time.isoformat() job_attrs['update_time'] = job.update_time.isoformat() # Get the job's parameters try: params_objects = job.get_param_values(trans.app) except: # Could not get job params. continue params_dict = {} for name, value in params_objects.items(): params_dict[name] = value job_attrs['params'] = params_dict # -- Get input, output datasets. -- input_datasets = [] input_mapping = {} for assoc in job.input_datasets: # Optional data inputs will not have a dataset. if assoc.dataset: input_datasets.append(assoc.dataset.hid) input_mapping[assoc.name] = assoc.dataset.hid job_attrs['input_datasets'] = input_datasets job_attrs['input_mapping'] = input_mapping output_datasets = [assoc.dataset.hid for assoc in job.output_datasets] job_attrs['output_datasets'] = output_datasets jobs_attrs.append(job_attrs) jobs_attrs_filename = tempfile.NamedTemporaryFile(dir=temp_output_dir).name jobs_attrs_out = open(jobs_attrs_filename, 'w') jobs_attrs_out.write(dumps(jobs_attrs, cls=HistoryDatasetAssociationEncoder)) jobs_attrs_out.close() jeha.jobs_attrs_filename = jobs_attrs_filename # # Create and return command line for running tool. # options = "" if jeha.compressed: options = "-G" return "%s %s %s %s" % (options, history_attrs_filename, datasets_attrs_filename, jobs_attrs_filename)
[docs] def cleanup_after_job(self, db_session): """ Remove temporary directory and attribute files generated during setup for this job. """ # Get jeha for job. jeha = db_session.query(model.JobExportHistoryArchive).filter_by(job_id=self.job_id).first() if jeha: for filename in [jeha.history_attrs_filename, jeha.datasets_attrs_filename, jeha.jobs_attrs_filename]: try: os.remove(filename) except Exception as e: log.debug('Failed to cleanup attributes file (%s): %s' % (filename, e)) temp_dir = os.path.split(jeha.history_attrs_filename)[0] try: shutil.rmtree(temp_dir) except Exception as e: log.debug('Error deleting directory containing attribute files (%s): %s' % (temp_dir, e))