/usr/lib/python2.7/dist-packages/bioblend/galaxy/workflows/__init__.py is in python-bioblend 0.7.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 | """
Contains possible interactions with the Galaxy Workflows
"""
from bioblend.galaxy.client import Client
import json
import os
class WorkflowClient(Client):
def __init__(self, galaxy_instance):
self.module = 'workflows'
super(WorkflowClient, self).__init__(galaxy_instance)
# the 'deleted' option is not available for workflows
def get_workflows(self, workflow_id=None, name=None, published=False):
"""
Get all workflows or filter the specific one(s) via the provided ``name``
or ``workflow_id``. Provide only one argument, ``name`` or ``workflow_id``,
but not both.
:type workflow_id: str
:param workflow_id: Encoded workflow ID (incompatible with ``name``)
:type name: str
:param name: Filter by name of workflow (incompatible with
``workflow_id``). If multiple names match the given name, all the
workflows matching the argument will be returned.
:type published: bool
:param published: if ``True``, return also published 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'}]
"""
if workflow_id is not None and name is not None:
raise ValueError('Provide only one argument between name or workflow_id, but not both')
kwargs = {}
if published:
kwargs['params'] = {'show_published': 'True'}
workflows = Client._get(self, **kwargs)
if workflow_id is not None:
workflow = next((_ for _ in workflows if _['id'] == workflow_id), None)
workflows = [workflow] if workflow is not None else []
elif name is not None:
workflows = [_ for _ in workflows if _['name'] == name]
return workflows
def show_workflow(self, workflow_id):
"""
Display information needed to run a workflow
:type workflow_id: str
:param workflow_id: Encoded workflow ID
:rtype: dict
: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)
def get_workflow_inputs(self, workflow_id, label):
"""
Get a list of workflow input IDs that match the given label.
If no input matches the given label, an empty list is returned.
:type workflow_id: str
:param workflow_id: Encoded workflow ID
:type label: str
:param label: label to filter workflow inputs on
:rtype: list
:return: list of workflow inputs matching the label query
"""
wf = Client._get(self, id=workflow_id)
inputs = wf['inputs']
return [id for id in inputs if inputs[id]['label'] == label]
def import_workflow_json(self, workflow_json):
"""
Imports a new workflow given a json representation of a previously exported
workflow.
:type workflow_json: str
:param workflow_json: JSON string representing the workflow to be imported
"""
payload = {}
payload['workflow'] = workflow_json
url = self.gi._make_url(self)
url = _join(url, "upload")
return Client._post(self, url=url, payload=payload)
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.
:type file_local_path: str
:param file_local_path: File to upload to the server for new workflow
"""
with open(file_local_path, 'r') as fp:
workflow_json = json.load(fp)
return self.import_workflow_json(workflow_json)
def import_shared_workflow(self, workflow_id):
"""
Imports a new workflow from the shared published workflows.
:type workflow_id: str
:param workflow_id: Encoded workflow ID
:rtype: dict
:return: A description of the workflow.
For example::
{u'id': u'ee0e2b4b696d9092',
u'model_class': u'StoredWorkflow',
u'name': u'Super workflow that solves everything!',
u'published': False,
u'tags': [],
u'url': u'/api/workflows/ee0e2b4b696d9092'}
"""
payload = {}
payload['workflow_id'] = workflow_id
url = self.gi._make_url(self)
url = _join(url, 'import')
return Client._post(self, url=url, payload=payload)
def export_workflow_json(self, workflow_id):
"""
Exports a workflow
:type workflow_id: str
:param workflow_id: Encoded workflow ID
:rtype: dict
:return: Dict representing the workflow requested
"""
url = self.gi._make_url(self)
url = _join(url, "download", workflow_id)
return Client._get(self, url=url)
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: str
:param workflow_id: Encoded workflow ID
:type file_local_path: str
: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_filename: bool
:param use_default_filename: 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, 'w') as fp:
json.dump(workflow_json, fp)
def run_workflow(self, workflow_id, dataset_map=None, params=None,
history_id=None, history_name=None,
import_inputs_to_history=False, replacement_params=None):
"""
Run the workflow identified by ``workflow_id``. This method is deprecated
please use ``invoke_workflow`` instead.
:type workflow_id: str
:param workflow_id: Encoded workflow ID
:type dataset_map: str 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]'}}``
(e.g. ``{'23': {'id': '29beef4fadeed09f', 'src': 'ld'}}``)
:type params: str or dict
:param params: A mapping of tool parameters that are non-datasets parameters. The map must be in the
following format:
``{'blastn': {'param': 'evalue', 'value': '1e-06'}}``
:type history_id: str
:param history_id: The encoded history ID where to store the workflow
output. Alternatively, ``history_name`` may be specified to create a
new history.
:type history_name: str
:param history_name: Create a new history with the given name to store
the workflow output. If both ``history_id`` and ``history_name`` are
provided, ``history_name`` is ignored. If neither is specified, a new
'Unnamed history' is created.
: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.
:type replacement_params: dict
:param replacement_params: pattern-based replacements for post-job actions (see below)
: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']}
The ``replacement_params`` dict should map parameter names in
post-job actions (PJAs) to their runtime values. For
instance, if the final step has a PJA like the following::
{u'RenameDatasetActionout_file1': {
u'action_arguments': {u'newname': u'${output}'},
u'action_type': u'RenameDatasetAction',
u'output_name': u'out_file1'}}
then the following renames the output dataset to 'foo'::
replacement_params = {'output': 'foo'}
see also `this email thread
<http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-September/006875.html>`_.
.. warning::
This method is deprecated, please use ``invoke_workflow`` instead.
``run_workflow`` will wait for the whole workflow to be scheduled
before returning and will not scale to large workflows as a result.
``invoke_workflow`` also features improved default behavior for
dataset input handling.
"""
payload = {}
payload['workflow_id'] = workflow_id
if dataset_map:
payload['ds_map'] = dataset_map
if params:
payload['parameters'] = params
if replacement_params:
payload['replacement_params'] = replacement_params
if history_id:
payload['history'] = 'hist_id={0}'.format(history_id)
elif history_name:
payload['history'] = history_name
if import_inputs_to_history is False:
payload['no_add_to_history'] = True
return Client._post(self, payload)
def invoke_workflow(self, workflow_id, inputs=None, params=None,
history_id=None, history_name=None,
import_inputs_to_history=False, replacement_params=None,
allow_tool_state_corrections=None):
"""
Invoke the workflow identified by ``workflow_id``. This will
cause a workflow to be scheduled and return an object describing
the workflow invocation.
:type workflow_id: str
:param workflow_id: Encoded workflow ID
:type inputs: dict
:param inputs: A mapping of workflow inputs to datasets and dataset collections.
The datasets source can be a LibraryDatasetDatasetAssociation (``ldda``),
LibraryDataset (``ld``), HistoryDatasetAssociation (``hda``), or
HistoryDatasetCollectionAssociation (``hdca``).
The map must be in the following format:
``{'<input_index>': {'id': <encoded dataset ID>, 'src': '[ldda, ld, hda, hdca]'}}``
(e.g. ``{'2': {'id': '29beef4fadeed09f', 'src': 'hda'}}``)
This map may also be indexed by the UUIDs of the workflow steps,
as indicated by the ``uuid`` property of steps returned from the
Galaxy API.
:type params: str or dict
:param params: A mapping of tool parameters that are non-datasets parameters. The map must be in the
following format:
``{'blastn': {'param': 'evalue', 'value': '1e-06'}}``
:type history_id: str
:param history_id: The encoded history ID where to store the workflow
output. Alternatively, ``history_name`` may be specified to create a
new history.
:type history_name: str
:param history_name: Create a new history with the given name to store
the workflow output. If both ``history_id`` and ``history_name`` are
provided, ``history_name`` is ignored. If neither is specified, a new
'Unnamed history' is created.
: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.
:type allow_tool_state_corrections: bool
:param allow_tool_state_corrections: If True, allow Galaxy to fill in missing tool state
when running workflows. This may be useful
for workflows using tools that have changed
over time or for workflows built outside of
Galaxy with only a subset of inputs defined.
:type replacement_params: dict
:param replacement_params: pattern-based replacements for post-job actions (see below)
:rtype: dict
:return: A dict containing the workflow invocation describing the scheduling
of the workflow. For example::
{u'inputs': {u'0': {u'src': u'hda', u'id': u'a7db2fac67043c7e', u'uuid': u'7932ffe0-2340-4952-8857-dbaa50f1f46a'}},
u'update_time': u'2015-10-31T22:00:26',
u'uuid': u'c8aa2b1c-801a-11e5-a9e5-8ca98228593c',
u'history_id': u'2f94e8ae9edff68a',
u'workflow_id': u'03501d7626bd192f',
u'state': u'ready',
u'steps': [{u'workflow_step_uuid': u'b81250fd-3278-4e6a-b269-56a1f01ef485',
u'update_time': u'2015-10-31T22:00:26',
u'job_id': None,
u'state': None,
u'workflow_step_label': None,
u'order_index': 0,
u'action': None,
u'model_class': u'WorkflowInvocationStep',
u'workflow_step_id': u'cbbbf59e8f08c98c',
u'id': u'd413a19dec13d11e'},
{u'workflow_step_uuid': u'e62440b8-e911-408b-b124-e05435d3125e',
u'update_time': u'2015-10-31T22:00:26',
u'job_id': u'e89067bb68bee7a0',
u'state': u'new',
u'workflow_step_label':None,
u'order_index': 1,
u'action': None,
u'model_class': u'WorkflowInvocationStep',
u'workflow_step_id': u'964b37715ec9bd22',
u'id': u'2f94e8ae9edff68a'},
],
u'model_class': u'WorkflowInvocation',
u'id': u'df7a1f0c02a5b08e'
}
The ``replacement_params`` dict should map parameter names in
post-job actions (PJAs) to their runtime values. For
instance, if the final step has a PJA like the following::
{u'RenameDatasetActionout_file1': {
u'action_arguments': {u'newname': u'${output}'},
u'action_type': u'RenameDatasetAction',
u'output_name': u'out_file1'}}
then the following renames the output dataset to 'foo'::
replacement_params = {'output': 'foo'}
see also `this email thread
<http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-September/006875.html>`_.
.. warning::
Historically, the ``run_workflow`` method consumed a ``dataset_map``
data structure that was indexed by unencoded workflow step IDs. These
IDs would not be stable across Galaxy instances. The new ``inputs``
property is instead indexed by either the ``order_index`` property which
is stable across workflow imports or the step UUID which is also stable.
"""
payload = {}
payload['workflow_id'] = workflow_id
if inputs:
payload['inputs'] = inputs
if params:
payload['parameters'] = params
if replacement_params:
payload['replacement_params'] = replacement_params
if history_id:
payload['history'] = 'hist_id={0}'.format(history_id)
elif history_name:
payload['history'] = history_name
if import_inputs_to_history is False:
payload['no_add_to_history'] = True
if allow_tool_state_corrections is not None:
payload['allow_tool_state_corrections'] = allow_tool_state_corrections
url = self.gi._make_url(self)
url = _join(url, workflow_id, "invocations")
return Client._post(self, payload, url=url)
def show_invocation(self, workflow_id, invocation_id):
""" Get a workflow invocation object representing the scheduling of
a workflow. This object may be sparse at first (missing inputs and
invocation steps) and will become more populated as the workflow
is actually scheduled.
:type workflow_id: str
:param workflow_id: Encoded workflow ID
:type invocation_id: str
:param invocation_id: Encoded workflow invocation ID
:rtype: dict
:return: The workflow invocation.
For example::
{u'inputs': {u'0': {u'src': u'hda', u'id': u'a7db2fac67043c7e', u'uuid': u'7932ffe0-2340-4952-8857-dbaa50f1f46a'}},
u'update_time': u'2015-10-31T22:00:26',
u'uuid': u'c8aa2b1c-801a-11e5-a9e5-8ca98228593c',
u'history_id': u'2f94e8ae9edff68a',
u'workflow_id': u'03501d7626bd192f',
u'state': u'ready',
u'steps': [{u'workflow_step_uuid': u'b81250fd-3278-4e6a-b269-56a1f01ef485',
u'update_time': u'2015-10-31T22:00:26',
u'job_id': None,
u'state': None,
u'workflow_step_label': None,
u'order_index': 0,
u'action': None,
u'model_class': u'WorkflowInvocationStep',
u'workflow_step_id': u'cbbbf59e8f08c98c',
u'id': u'd413a19dec13d11e'},
{u'workflow_step_uuid': u'e62440b8-e911-408b-b124-e05435d3125e',
u'update_time': u'2015-10-31T22:00:26',
u'job_id': u'e89067bb68bee7a0',
u'state': u'new',
u'workflow_step_label':None,
u'order_index': 1,
u'action': None,
u'model_class': u'WorkflowInvocationStep',
u'workflow_step_id': u'964b37715ec9bd22',
u'id': u'2f94e8ae9edff68a'},
],
u'model_class': u'WorkflowInvocation',
u'id': u'df7a1f0c02a5b08e'
}
"""
url = self._invocation_url(workflow_id, invocation_id)
return Client._get(self, url=url)
def get_invocations(self, workflow_id):
""" Get a list containing all the workflow invocations corresponding
to the specified workflow.
:type workflow_id: str
:param workflow_id: Encoded workflow ID
:rtype: list
:return: A list of workflow invocations.
For example::
[{u'update_time': u'2015-10-31T22:00:22',
u'uuid': u'c8aa2b1c-801a-11e5-a9e5-8ca98228593c',
u'history_id': u'2f94e8ae9edff68a',
u'workflow_id': u'03501d7626bd192f',
u'state': u'new',
u'model_class': u'WorkflowInvocation',
u'id': u'df7a1f0c02a5b08e'}
]
"""
url = self._invocations_url(workflow_id)
return Client._get(self, url=url)
def cancel_invocation(self, workflow_id, invocation_id):
""" Cancel the scheduling of a workflow.
:type workflow_id: str
:param workflow_id: Encoded workflow ID
:type invocation_id: str
:param invocation_id: Encoded workflow invocation ID
"""
url = self._invocation_url(workflow_id, invocation_id)
return Client._delete(self, url=url)
def show_invocation_step(self, workflow_id, invocation_id, step_id):
""" See the details of a particular workflow invocation step.
:type workflow_id: str
:param workflow_id: Encoded workflow ID
:type invocation_id: str
:param invocation_id: Encoded workflow invocation ID
:type step_id: str
:param step_id: Encoded workflow invocation step ID
:rtype: dict
:return: The workflow invocation step.
For example::
{u'workflow_step_uuid': u'4060554c-1dd5-4287-9040-8b4f281cf9dc',
u'update_time': u'2015-10-31T22:11:14',
u'job_id': None,
u'state': None,
u'workflow_step_label': None,
u'order_index': 2,
u'action': None,
u'model_class': u'WorkflowInvocationStep',
u'workflow_step_id': u'52e496b945151ee8',
u'id': u'63cd3858d057a6d1'}
"""
url = self._invocation_step_url(workflow_id, invocation_id, step_id)
return Client._get(self, url=url)
def run_invocation_step_action(self, workflow_id, invocation_id, step_id, action):
""" Execute an action for an active workflow invocation step. The
nature of this action and what is expected will vary based on the
the type of workflow step (the only currently valid action is True/False
for pause steps).
:type workflow_id: str
:param workflow_id: Encoded workflow ID
:type invocation_id: str
:param invocation_id: Encoded workflow invocation ID
:type step_id: str
:param step_id: Encoded workflow invocation step ID
:type action: object
:param action: Action to use when updating state, semantics depends on
step type.
"""
url = self._invocation_step_url(workflow_id, invocation_id, step_id)
payload = {"action": action}
return Client._put(self, payload, url=url)
def delete_workflow(self, workflow_id):
"""
Delete a workflow identified by `workflow_id`.
:type workflow_id: str
:param workflow_id: Encoded workflow ID
.. warning::
Deleting a workflow is irreversible - all workflow data
will be permanently deleted.
"""
payload = {}
return Client._delete(self, payload, id=workflow_id)
def _invocation_step_url(self, workflow_id, invocation_id, step_id):
return _join(self._invocation_url(workflow_id, invocation_id), "steps", step_id)
def _invocation_url(self, workflow_id, invocation_id):
return _join(self._invocations_url(workflow_id), invocation_id)
def _invocations_url(self, workflow_id):
return _join(self._workflow_url(workflow_id), "invocations")
def _workflow_url(self, workflow_id):
url = self.gi._make_url(self)
url = _join(url, workflow_id)
return url
def _join(*args):
return "/".join(args)
__all__ = ['WorkflowClient']
|