def __init__(self, app):
super(HistoryContentsController, self).__init__(app)
self.hda_manager = hdas.HDAManager(app)
self.history_manager = histories.HistoryManager(app)
self.folder_manager = folders.FolderManager()
self.hda_serializer = hdas.HDASerializer(app)
self.hda_deserializer = hdas.HDADeserializer(app)
def __init__(self, app, **kwargs):
super(HistorySerializer, self).__init__(app, **kwargs)
self.history_manager = self.manager
self.hda_manager = hdas.HDAManager(app)
self.hda_serializer = hdas.HDASerializer(app)
self.history_contents_serializer = history_contents.HistoryContentsSerializer(app)
self.default_view = 'summary'
self.add_view('summary', [
'id',
'model_class',
'name',
'deleted',
'purged',
# 'count'
'url',
# TODO: why these?
'published',
'annotation',
'tags',
])
self.add_view('detailed', [
'contents_url',
'empty',
'size',
'user_id',
'create_time',
'update_time',
'importable',
'slug',
'username_and_slug',
'genome_build',
# TODO: remove the next three - instead getting the same info from the 'hdas' list
'state',
'state_details',
'state_ids',
# 'community_rating',
# 'user_rating',
], include_keys_from='summary')
# in the Historys' case, each of these views includes the keys from the previous
#: ..note: this is a custom view for newer (2016/3) UI and should be considered volatile
self.add_view('dev-detailed', [
'contents_url',
'size',
'user_id',
'create_time',
'update_time',
'importable',
'slug',
'username_and_slug',
'genome_build',
# 'contents_states',
'contents_active',
'hid_counter',
], include_keys_from='summary')
def __init__(self, app):
super(DCESerializer, self).__init__(app)
self.hda_serializer = hdas.HDASerializer(app)
self.dc_serializer = DCSerializer(app, dce_serializer=self)
self.default_view = 'summary'
self.add_view('summary', [
'id', 'model_class', 'element_index', 'element_identifier',
'element_type', 'object'
])
def set_up_managers(self):
super(HDASerializerTestCase, self).set_up_managers()
self.hda_serializer = hdas.HDASerializer(self.app)
def display_structured(self, trans, id=None):
"""
Display a history as a nested structure showing the jobs and workflow
invocations that created each dataset (if any).
"""
# Get history
if id is None:
id = trans.history.id
else:
id = self.decode_id(id)
# Expunge history from the session to allow us to force a reload
# with a bunch of eager loaded joins
trans.sa_session.expunge(trans.history)
history = trans.sa_session.query(model.History).options(
joinedload('active_datasets').joinedload('creating_job_associations').joinedload('job').joinedload('workflow_invocation_step').joinedload('workflow_invocation').joinedload('workflow'),
).get(id)
if not (history and ((history.user and trans.user and history.user.id == trans.user.id)
or (trans.history and history.id == trans.history.id)
or trans.user_is_admin)):
return trans.show_error_message("Cannot display history structure.")
# Resolve jobs and workflow invocations for the datasets in the history
# items is filled with items (hdas, jobs, or workflows) that go at the
# top level
items = []
# First go through and group hdas by job, if there is no job they get
# added directly to items
jobs = {}
for hda in history.active_datasets:
if hda.visible is False:
continue
# Follow "copied from ..." association until we get to the original
# instance of the dataset
original_hda = hda
# while original_hda.copied_from_history_dataset_association:
# original_hda = original_hda.copied_from_history_dataset_association
# Check if the job has a creating job, most should, datasets from
# before jobs were tracked, or from the upload tool before it
# created a job, may not
if not original_hda.creating_job_associations:
items.append((hda, None))
# Attach hda to correct job
# -- there should only be one creating_job_association, so this
# loop body should only be hit once
for assoc in original_hda.creating_job_associations:
job = assoc.job
if job in jobs:
jobs[job].append((hda, None))
else:
jobs[job] = [(hda, None)]
# Second, go through the jobs and connect to workflows
wf_invocations = {}
for job, hdas in jobs.items():
# Job is attached to a workflow step, follow it to the
# workflow_invocation and group
if job.workflow_invocation_step:
wf_invocation = job.workflow_invocation_step.workflow_invocation
if wf_invocation in wf_invocations:
wf_invocations[wf_invocation].append((job, hdas))
else:
wf_invocations[wf_invocation] = [(job, hdas)]
# Not attached to a workflow, add to items
else:
items.append((job, hdas))
# Finally, add workflow invocations to items, which should now
# contain all hdas with some level of grouping
items.extend(wf_invocations.items())
# Sort items by age
items.sort(key=(lambda x: x[0].create_time), reverse=True)
# logic taken from mako files
from galaxy.managers import hdas
hda_serializer = hdas.HDASerializer(trans.app)
hda_dicts = []
id_hda_dict_map = {}
for hda in history.active_datasets:
hda_dict = hda_serializer.serialize_to_view(hda, user=trans.user, trans=trans, view='detailed')
id_hda_dict_map[hda_dict['id']] = hda_dict
hda_dicts.append(hda_dict)
html_template = ''
for entity, children in items:
html_template += render_item(trans, entity, children)
return {
'name': history.name,
'history_json': hda_dicts,
'template': html_template
}