Source code for bioblend.galaxy.workflows
"""
Contains possible interactions with the Galaxy Workflows
"""
from bioblend.galaxy.client import Client
import simplejson
import os
[docs]class WorkflowClient(Client):
def __init__(self, galaxy_instance):
self.module = 'workflows'
super(WorkflowClient, self).__init__(galaxy_instance)
[docs] def get_workflows(self):
"""
Get a list of all workflows
:rtype: list
:return: A list of workflow dicts.
For example::
[{u'id': u'92c56938c2f9b315',
u'name': u'Simple',
u'url': u'/api/workflows/92c56938c2f9b315'}]
"""
return Client._get(self)
[docs] def show_workflow(self, workflow_id):
"""
Display information needed to run a workflow
:type workflow_id: string
:param workflow_id: Encoded workflow ID
:rtype: list
:return: A description of the workflow and its inputs as a JSON object.
For example::
{u'id': u'92c56938c2f9b315',
u'inputs': {u'23': {u'label': u'Input Dataset', u'value': u''}},
u'name': u'Simple',
u'url': u'/api/workflows/92c56938c2f9b315'}
"""
return Client._get(self, id=workflow_id)
[docs] def import_workflow_json(self, workflow_json):
"""
Imports a new workflow given a json representation of a previously exported
workflow.
"""
payload = {}
payload['workflow'] = workflow_json
url = self.gi._make_url(self)
url = '/'.join([url, "upload"])
return Client._post(self, url=url, payload=payload)
[docs] def import_workflow_from_local_path(self, file_local_path):
"""
Imports a new workflow given the path to a file containing a previously
exported workflow.
"""
with open(file_local_path, 'rb') as fp:
workflow_json = simplejson.load(fp)
return self.import_workflow_json(workflow_json)
[docs] def export_workflow_json(self, workflow_id):
"""
Exports a workflow in json format
:type workflow_id: string
:param workflow_id: Encoded workflow ID
"""
url = self.gi._make_url(self)
url = '/'.join([url, "download"])
url = '/'.join([url, workflow_id])
return Client._get(self, url=url)
[docs] def export_workflow_to_local_path(self, workflow_id, file_local_path, use_default_filename=True):
"""
Exports a workflow in json format to a given local path.
:type workflow_id: string
:param workflow_id: Encoded workflow ID
:type file_local_path: string
:param file_local_path: Local path to which the exported file will be saved.
(Should not contain filename if use_default_name=True)
:type use_default_name: boolean
:param use_default_name: If the use_default_name parameter is True, the exported
file will be saved as file_local_path/Galaxy-Workflow-%s.ga,
where %s is the workflow name.
If use_default_name is False, file_local_path is assumed to
contain the full file path including filename.
"""
workflow_json = self.export_workflow_json(workflow_id)
if use_default_filename:
filename = 'Galaxy-Workflow-%s.ga' % workflow_json['name']
file_local_path = os.path.join(file_local_path, filename)
with open(file_local_path, 'wb') as fp:
workflow_json = simplejson.dump(workflow_json, fp)
return workflow_json
[docs] def run_workflow(self, workflow_id, dataset_map, history_id=None, history_name=None,
import_inputs_to_history=False):
"""
Run the workflow identified by ``workflow_id``
:type workflow_id: string
:param workflow_id: Encoded workflow ID
:type dataset_map: string or dict
:param dataset_map: A mapping of workflow inputs to datasets. The datasets
source can be a LibraryDatasetDatasetAssociation (``ldda``),
LibraryDataset (``ld``), or HistoryDatasetAssociation (``hda``).
The map must be in the following format:
``{'<input>': {'id': <encoded dataset ID>, 'src': '[ldda, ld, hda]'}}``
(eg, ``{'23': {'id': '29beef4fadeed09f', 'src': 'ld'}}``)
:type history_id: string
:param history_id: The encoded history ID where to store the workflow output.
``history_id`` OR ``history_name`` should be provided but not both!
:type history_name: string
:param history_name: Create a new history with the given name to store the
workflow output. ``history_id`` OR ``history_name``
should be provided but not both!
:type import_inputs_to_history: bool
:param import_inputs_to_history: If ``True``, used workflow inputs will be imported
into the history. If ``False``, only workflow outputs
will be visible in the given history.
:rtype: dict
:return: A dict containing the history ID where the outputs are placed as well as
output dataset IDs.
For example::
{u'history': u'64177123325c9cfd',
u'outputs': [u'aa4d3084af404259']}
"""
payload = {}
payload['workflow_id'] = workflow_id
payload['ds_map'] = dataset_map
if history_id:
payload['history'] = 'hist_id={0}'.format(history_id)
elif history_name:
payload['history'] = history_name
else:
print "Must provide history_id or history_name argument"
if import_inputs_to_history is False:
payload['no_add_to_history'] = True
return Client._post(self, payload)