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Source code for galaxy.jobs.actions.post
"""
Actions to be run at job completion (or output hda creation, as in the case of
immediate_actions listed below. Currently only used in workflows.
"""
import datetime
import socket
from markupsafe import escape
from galaxy.util import send_mail
from galaxy.util.logging import get_logger
log = get_logger(__name__)
[docs]class DefaultJobAction(object):
"""
Base job action.
"""
name = "DefaultJobAction"
verbose_name = "Default Job"
[docs] @classmethod
def get_short_str(cls, pja):
if pja.action_arguments:
return "%s -> %s" % (pja.action_type, escape(pja.action_arguments))
else:
return "%s" % pja.action_type
[docs]class EmailAction(DefaultJobAction):
"""
This action sends an email to the galaxy user responsible for a job.
"""
name = "EmailAction"
verbose_name = "Email Notification"
[docs] @classmethod
def execute(cls, app, sa_session, action, job, replacement_dict):
frm = app.config.email_from
if frm is None:
if action.action_arguments and 'host' in action.action_arguments:
host = action.action_arguments['host']
else:
host = socket.getfqdn()
frm = 'galaxy-no-reply@%s' % host
to = job.user.email
subject = "Galaxy workflow step notification '%s'" % (job.history.name)
outdata = ', '.join(ds.dataset.display_name() for ds in job.output_datasets)
body = "Your Galaxy job generating dataset '%s' is complete as of %s." % (outdata, datetime.datetime.now().strftime("%I:%M"))
try:
send_mail(frm, to, subject, body, app.config)
except Exception as e:
log.error("EmailAction PJA Failed, exception: %s" % e)
[docs] @classmethod
def get_short_str(cls, pja):
if pja.action_arguments and 'host' in pja.action_arguments:
return "Email the current user from server %s when this job is complete." % escape(pja.action_arguments['host'])
else:
return "Email the current user when this job is complete."
[docs]class ChangeDatatypeAction(DefaultJobAction):
name = "ChangeDatatypeAction"
verbose_name = "Change Datatype"
[docs] @classmethod
def execute(cls, app, sa_session, action, job, replacement_dict):
for dataset_assoc in job.output_datasets:
if action.output_name == '' or dataset_assoc.name == action.output_name:
app.datatypes_registry.change_datatype(dataset_assoc.dataset, action.action_arguments['newtype'])
[docs] @classmethod
def get_short_str(cls, pja):
return "Set the datatype of output '%s' to '%s'" % (escape(pja.output_name),
escape(pja.action_arguments['newtype']))
[docs]class RenameDatasetAction(DefaultJobAction):
name = "RenameDatasetAction"
verbose_name = "Rename Dataset"
[docs] @classmethod
def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict):
# Prevent renaming a dataset to the empty string.
input_names = {}
# Lookp through inputs find one with "to_be_replaced" input
# variable name, and get the replacement name
for input_key, step_input in step_inputs.items():
if step_input and hasattr(step_input, "name"):
input_names[input_key] = step_input.name
new_name = cls._gen_new_name(action, input_names, replacement_dict)
if new_name:
for name, step_output in step_outputs.items():
if action.output_name == '' or name == action.output_name:
step_output.name = new_name
@classmethod
def _gen_new_name(self, action, input_names, replacement_dict):
new_name = None
if action.action_arguments and action.action_arguments.get('newname', ''):
new_name = action.action_arguments['newname']
# TODO: Unify and simplify replacement options.
# Add interface through workflow editor UI
# The following if statement will process a request to rename
# using an input file name.
# TODO: Replace all matching code with regex
# Proper syntax is #{input_file_variable | option 1 | option n}
# where
# input_file_variable = is the name of an module input variable
# | = the delimiter for added options. Optional if no options.
# options = basename, upper, lower
# basename = keep all of the file name except the extension
# (everything before the final ".")
# upper = force the file name to upper case
# lower = force the file name to lower case
# suggested additions:
# "replace" option so you can replace a portion of the name,
# support multiple #{name} in one rename action...
start_pos = 0
while new_name.find("#{", start_pos) > -1:
to_be_replaced = ""
# This assumes a single instance of #{variable} will exist
start_pos = new_name.find("#{", start_pos) + 2
end_pos = new_name.find("}", start_pos)
to_be_replaced = new_name[start_pos:end_pos]
input_file_var = to_be_replaced
# Pull out the piped controls and store them for later
# parsing.
tokens = to_be_replaced.split("|")
operations = []
if len(tokens) > 1:
input_file_var = tokens[0].strip()
for i in range(1, len(tokens)):
operations.append(tokens[i].strip())
# Treat . as special symbol (breaks parameter names anyway)
# to allow access to repeat elements, for instance first
# repeat in cat1 would be something like queries_0.input2.
input_file_var = input_file_var.replace(".", "|")
replacement = input_names.get(input_file_var, "")
# In case name was None.
replacement = replacement or ''
# Do operations on replacement
# Any control that is not defined will be ignored.
# This should be moved out to a class or module function
for operation in operations:
# Basename returns everything prior to the final '.'
if operation == "basename":
fields = replacement.split(".")
replacement = fields[0]
if len(fields) > 1:
temp = ""
for i in range(1, len(fields) - 1):
temp += "." + fields[i]
replacement += temp
elif operation == "upper":
replacement = replacement.upper()
elif operation == "lower":
replacement = replacement.lower()
new_name = new_name.replace("#{%s}" % to_be_replaced, replacement)
if replacement_dict:
for k, v in replacement_dict.items():
new_name = new_name.replace("${%s}" % k, v)
return new_name
[docs] @classmethod
def execute(cls, app, sa_session, action, job, replacement_dict):
input_names = {}
# Lookp through inputs find one with "to_be_replaced" input
# variable name, and get the replacement name
for input_assoc in job.input_datasets:
if input_assoc.dataset:
input_names[input_assoc.name] = input_assoc.dataset.name
# Ditto for collections...
for input_assoc in job.input_dataset_collections:
# Either a HDCA or a DCE - only HDCA has a name.
has_collection = input_assoc.dataset_collection
if has_collection and hasattr(has_collection, "name"):
input_names[input_assoc.name] = has_collection.name
new_name = cls._gen_new_name(action, input_names, replacement_dict)
if new_name:
for dataset_assoc in job.output_datasets:
if action.output_name == '' or dataset_assoc.name == action.output_name:
dataset_assoc.dataset.name = new_name
for dataset_collection_assoc in job.output_dataset_collection_instances:
if action.output_name == '' or dataset_collection_assoc.name == action.output_name:
dataset_collection_assoc.dataset_collection_instance.name = new_name
[docs] @classmethod
def get_short_str(cls, pja):
# Prevent renaming a dataset to the empty string.
if pja.action_arguments and pja.action_arguments.get('newname', ''):
return "Rename output '%s' to '%s'." % (escape(pja.output_name),
escape(pja.action_arguments['newname']))
else:
return "Rename action used without a new name specified. Output name will be unchanged."
[docs]class HideDatasetAction(DefaultJobAction):
name = "HideDatasetAction"
verbose_name = "Hide Dataset"
[docs] @classmethod
def execute(cls, app, sa_session, action, job, replacement_dict):
for dataset_assoc in job.output_datasets:
if dataset_assoc.dataset.state != dataset_assoc.dataset.states.ERROR and (action.output_name == '' or dataset_assoc.name == action.output_name):
dataset_assoc.dataset.visible = False
for dataset_collection_assoc in job.output_dataset_collection_instances:
if action.output_name == '' or dataset_collection_assoc.name == action.output_name:
dataset_collection_assoc.dataset_collection_instance.visible = False
[docs] @classmethod
def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict):
for name, step_output in step_outputs.items():
if action.output_name == '' or name == action.output_name:
step_output.visible = False
[docs] @classmethod
def get_short_str(cls, pja):
return "Hide output '%s'." % escape(pja.output_name)
[docs]class DeleteDatasetAction(DefaultJobAction):
# This is disabled for right now. Deleting a dataset in the middle of a workflow causes errors (obviously) for the subsequent steps using the data.
name = "DeleteDatasetAction"
verbose_name = "Delete Dataset"
[docs] @classmethod
def execute(cls, app, sa_session, action, job, replacement_dict):
for dataset_assoc in job.output_datasets:
if action.output_name == '' or dataset_assoc.name == action.output_name:
dataset_assoc.dataset.deleted = True
for dataset_collection_assoc in job.output_dataset_collection_instances:
if action.output_name == '' or dataset_collection_assoc.name == action.output_name:
dataset_collection_assoc.dataset_collection_instance.deleted = True
[docs] @classmethod
def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict):
for name, step_output in step_outputs.items():
if action.output_name == '' or name == action.output_name:
step_output.deleted = True
[docs]class ColumnSetAction(DefaultJobAction):
name = "ColumnSetAction"
verbose_name = "Assign Columns"
[docs] @classmethod
def execute(cls, app, sa_session, action, job, replacement_dict):
for dataset_assoc in job.output_datasets:
if action.output_name == '' or dataset_assoc.name == action.output_name:
for k, v in action.action_arguments.items():
if v:
# Try to use both pure integer and 'cX' format.
if not isinstance(v, int):
if v[0] == 'c':
v = v[1:]
v = int(v)
if v != 0:
setattr(dataset_assoc.dataset.metadata, k, v)
[docs] @classmethod
def get_short_str(cls, pja):
return "Set the following metadata values:<br/>" + "<br/>".join('%s : %s' % (escape(k), escape(v)) for k, v in pja.action_arguments.items())
[docs]class SetMetadataAction(DefaultJobAction):
name = "SetMetadataAction"
# DBTODO Setting of Metadata is currently broken and disabled. It should not be used (yet).
[docs] @classmethod
def execute(cls, app, sa_session, action, job, replacement_dict):
for data in job.output_datasets:
data.set_metadata(action.action_arguments['newtype'])
[docs]class DeleteIntermediatesAction(DefaultJobAction):
name = "DeleteIntermediatesAction"
verbose_name = "Delete Non-Output Completed Intermediate Steps"
[docs] @classmethod
def execute(cls, app, sa_session, action, job, replacement_dict):
# TODO Optimize this later. Just making it work for now.
# TODO Support purging as well as deletion if user_purge is enabled.
# Dataset candidates for deletion must be
# 1) Created by the workflow.
# 2) Not have any job_to_input_dataset associations with states other
# than OK or DELETED. If a step errors, we don't want to delete/purge it
# automatically.
# 3) Not marked as a workflow output.
# POTENTIAL ISSUES: When many outputs are being finish()ed
# concurrently, sometimes non-terminal steps won't be cleaned up
# because of the lag in job state updates.
sa_session.flush()
if not job.workflow_invocation_step:
log.debug("This job is not part of a workflow invocation, delete intermediates aborted.")
return
wfi = job.workflow_invocation_step.workflow_invocation
sa_session.refresh(wfi)
if wfi.active:
log.debug("Workflow still scheduling so new jobs may appear, skipping deletion of intermediate files.")
# Still evaluating workflow so we don't yet have all workflow invocation
# steps to start looking at.
return
outputs_defined = wfi.workflow.has_outputs_defined()
if outputs_defined:
wfi_steps = [wfistep for wfistep in wfi.steps if not wfistep.workflow_step.workflow_outputs and wfistep.workflow_step.type == "tool"]
jobs_to_check = []
for wfi_step in wfi_steps:
sa_session.refresh(wfi_step)
wfi_step_job = wfi_step.job
if wfi_step_job:
jobs_to_check.append(wfi_step_job)
else:
log.debug("No job found yet for wfi_step %s, (step %s)" % (wfi_step, wfi_step.workflow_step))
for j2c in jobs_to_check:
creating_jobs = []
for input_dataset in j2c.input_datasets:
if not input_dataset.dataset:
log.debug("PJA Async Issue: No dataset attached to input_dataset %s during handling of workflow invocation %s" % (input_dataset.id, wfi))
elif not input_dataset.dataset.creating_job:
log.debug("PJA Async Issue: No creating job attached to dataset %s during handling of workflow invocation %s" % (input_dataset.dataset.id, wfi))
else:
creating_jobs.append((input_dataset, input_dataset.dataset.creating_job))
for (input_dataset, creating_job) in creating_jobs:
sa_session.refresh(creating_job)
sa_session.refresh(input_dataset)
for input_dataset in [x.dataset for (x, creating_job) in creating_jobs if creating_job.workflow_invocation_step and creating_job.workflow_invocation_step.workflow_invocation == wfi]:
# note that the above input_dataset is a reference to a
# job.input_dataset.dataset at this point
safe_to_delete = True
for job_to_check in [d_j.job for d_j in input_dataset.dependent_jobs]:
if job_to_check != job and job_to_check.state not in [job.states.OK, job.states.DELETED]:
log.trace("Workflow Intermediates cleanup attempted, but non-terminal state '%s' detected for job %s" % (job_to_check.state, job_to_check.id))
safe_to_delete = False
if safe_to_delete:
# Support purging here too.
input_dataset.mark_deleted()
else:
# No workflow outputs defined, so we can't know what to delete.
# We could make this work differently in the future
pass
[docs] @classmethod
def get_short_str(cls, pja):
return "Delete parent datasets of this step created in this workflow that aren't flagged as outputs."
[docs]class TagDatasetAction(DefaultJobAction):
name = "TagDatasetAction"
verbose_name = "Add tag to dataset"
action = "Add"
direction = "to"
[docs] @classmethod
def execute_on_mapped_over(cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict):
if action.action_arguments:
tags = [t.replace('#', 'name:') if t.startswith('#') else t for t in [t.strip() for t in action.action_arguments.get('tags', '').split(',') if t.strip()]]
if tags:
for name, step_output in step_outputs.items():
if action.output_name == '' or name == action.output_name:
cls._execute(trans.app, trans.user, step_output, tags)
[docs] @classmethod
def execute(cls, app, sa_session, action, job, replacement_dict):
if action.action_arguments:
tags = [t.replace('#', 'name:') if t.startswith('#') else t for t in [t.strip() for t in action.action_arguments.get('tags', '').split(',') if t.strip()]]
if tags:
for dataset_assoc in job.output_datasets:
if action.output_name == '' or dataset_assoc.name == action.output_name:
cls._execute(app, job.user, dataset_assoc.dataset, tags)
for dataset_collection_assoc in job.output_dataset_collection_instances:
if action.output_name == '' or dataset_collection_assoc.name == action.output_name:
cls._execute(app, job.user, dataset_collection_assoc.dataset_collection_instance, tags)
sa_session.flush()
@classmethod
def _execute(cls, app, user, output, tags):
app.tag_handler.add_tags_from_list(user, output, tags)
[docs] @classmethod
def get_short_str(cls, pja):
if pja.action_arguments and pja.action_arguments.get('tags', ''):
return "%s tag(s) '%s' %s '%s'." % (cls.action,
escape(pja.action_arguments['tags']),
cls.direction,
escape(pja.output_name))
else:
return "%s Tag action used without a tag specified. No tag will be added." % cls.action
[docs]class RemoveTagDatasetAction(TagDatasetAction):
name = "RemoveTagDatasetAction"
verbose_name = "Remove tag from dataset"
action = "Remove"
direction = "from"
@classmethod
def _execute(cls, app, user, output, tags):
app.tag_handler.remove_tags_from_list(user, output, tags)
[docs]class ActionBox(object):
actions = {"RenameDatasetAction": RenameDatasetAction,
"HideDatasetAction": HideDatasetAction,
"ChangeDatatypeAction": ChangeDatatypeAction,
"ColumnSetAction": ColumnSetAction,
"EmailAction": EmailAction,
"DeleteIntermediatesAction": DeleteIntermediatesAction,
"TagDatasetAction": TagDatasetAction,
"RemoveTagDatasetAction": RemoveTagDatasetAction}
public_actions = ['RenameDatasetAction', 'ChangeDatatypeAction',
'ColumnSetAction', 'EmailAction',
'DeleteIntermediatesAction', 'TagDatasetAction',
'RemoveTagDatasetAction']
# Actions that can be applied ahead of the job execution while workflow is still
# being scheduled and jobs created.
immediate_actions = ['ChangeDatatypeAction', 'RenameDatasetAction',
'TagDatasetAction', 'RemoveTagDatasetAction']
# Actions that will be applied to implicit mapped over collection outputs and not
# just individual outputs when steps include mapped over tools and implicit collection outputs.
mapped_over_output_actions = ['RenameDatasetAction', 'HideDatasetAction',
'TagDatasetAction', 'RemoveTagDatasetAction']
[docs] @classmethod
def get_short_str(cls, action):
if action.action_type in ActionBox.actions:
return ActionBox.actions[action.action_type].get_short_str(action)
else:
return "Unknown Action"
[docs] @classmethod
def handle_incoming(cls, incoming):
npd = {}
for key, val in incoming.items():
if key.startswith('pja'):
sp = key.split('__')
ao_key = sp[2] + sp[1]
# flag / output_name / pjatype / desc
if ao_key not in npd:
npd[ao_key] = {'action_type': sp[2],
'output_name': sp[1],
'action_arguments': {}}
if len(sp) > 3:
if sp[3] == 'output_name':
npd[ao_key]['output_name'] = val
else:
npd[ao_key]['action_arguments'][sp[3]] = val
else:
# Not pja stuff.
pass
return npd
[docs] @classmethod
def execute_on_mapped_over(cls, trans, sa_session, pja, step_inputs, step_outputs, replacement_dict=None):
if pja.action_type in ActionBox.actions:
ActionBox.actions[pja.action_type].execute_on_mapped_over(trans, sa_session, pja, step_inputs, step_outputs, replacement_dict)
[docs] @classmethod
def execute(cls, app, sa_session, pja, job, replacement_dict=None):
if pja.action_type in ActionBox.actions:
ActionBox.actions[pja.action_type].execute(app, sa_session, pja, job, replacement_dict)