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Source code for galaxy.managers.jobs
import json
import logging
from boltons.iterutils import remap
from six import string_types
from sqlalchemy import and_, false, func, or_
from sqlalchemy.orm import aliased
from sqlalchemy.sql import select
from galaxy import model
from galaxy.exceptions import (
ItemAccessibilityException,
ObjectNotFound,
RequestParameterInvalidException,
)
from galaxy.managers.collections import DatasetCollectionManager
from galaxy.managers.datasets import DatasetManager
from galaxy.managers.hdas import HDAManager
from galaxy.managers.lddas import LDDAManager
from galaxy.util import (
defaultdict,
ExecutionTimer,
listify,
)
log = logging.getLogger(__name__)
[docs]def get_path_key(path_tuple):
path_key = ""
tuple_elements = len(path_tuple)
for i, p in enumerate(path_tuple):
if isinstance(p, int):
sep = '_'
else:
sep = '|'
if i == (tuple_elements - 2) and p == 'values':
# dataset inputs are always wrapped in lists. To avoid 'rep_factorName_0|rep_factorLevel_2|countsFile|values_0',
# we remove the last 2 items of the path tuple (values and list index)
return path_key
if path_key:
path_key = "%s%s%s" % (path_key, sep, p)
else:
path_key = p
return path_key
[docs]class JobManager(object):
[docs] def get_accessible_job(self, trans, decoded_job_id):
job = trans.sa_session.query(trans.app.model.Job).filter(trans.app.model.Job.id == decoded_job_id).first()
if job is None:
raise ObjectNotFound()
belongs_to_user = (job.user == trans.user) if job.user else (job.session_id == trans.get_galaxy_session().id)
if not trans.user_is_admin and not belongs_to_user:
# Check access granted via output datasets.
if not job.output_datasets:
raise ItemAccessibilityException("Job has no output datasets.")
for data_assoc in job.output_datasets:
if not self.dataset_manager.is_accessible(data_assoc.dataset.dataset, trans.user):
raise ItemAccessibilityException("You are not allowed to rerun this job.")
trans.sa_session.refresh(job)
return job
[docs] def stop(self, job, message=None):
if not job.finished:
job.mark_deleted(self.app.config.track_jobs_in_database)
self.app.model.context.current.flush()
self.app.job_manager.stop(job, message=message)
return True
else:
return False
[docs]class JobSearch(object):
"""Search for jobs using tool inputs or other jobs"""
[docs] def __init__(self, app):
self.app = app
self.sa_session = app.model.context
self.hda_manager = HDAManager(app)
self.dataset_collection_manager = DatasetCollectionManager(app)
self.ldda_manager = LDDAManager(app)
self.decode_id = self.app.security.decode_id
[docs] def by_tool_input(self, trans, tool_id, tool_version, param=None, param_dump=None, job_state='ok'):
"""Search for jobs producing same results using the 'inputs' part of a tool POST."""
user = trans.user
input_data = defaultdict(list)
def populate_input_data_input_id(path, key, value):
"""Traverses expanded incoming using remap and collects input_ids and input_data."""
if key == 'id':
path_key = get_path_key(path[:-2])
current_case = param_dump
for p in path:
current_case = current_case[p]
src = current_case['src']
current_case = param
for i, p in enumerate(path):
if p == 'values' and i == len(path) - 2:
continue
if isinstance(current_case, (list, dict)):
current_case = current_case[p]
identifier = getattr(current_case, "element_identifier", None)
input_data[path_key].append({'src': src,
'id': value,
'identifier': identifier,
})
return key, "__id_wildcard__"
return key, value
wildcard_param_dump = remap(param_dump, visit=populate_input_data_input_id)
return self.__search(tool_id=tool_id,
tool_version=tool_version,
user=user,
input_data=input_data,
job_state=job_state,
param_dump=param_dump,
wildcard_param_dump=wildcard_param_dump)
def __search(self, tool_id, tool_version, user, input_data, job_state=None, param_dump=None, wildcard_param_dump=None):
search_timer = ExecutionTimer()
def replace_dataset_ids(path, key, value):
"""Exchanges dataset_ids (HDA, LDA, HDCA, not Dataset) in param_dump with dataset ids used in job."""
if key == 'id':
current_case = param_dump
for p in path:
current_case = current_case[p]
src = current_case['src']
value = job_input_ids[src][value]
return key, value
return key, value
conditions = [and_(model.Job.tool_id == tool_id,
model.Job.user == user)]
if tool_version:
conditions.append(model.Job.tool_version == str(tool_version))
if job_state is None:
conditions.append(
model.Job.state.in_([model.Job.states.NEW,
model.Job.states.QUEUED,
model.Job.states.WAITING,
model.Job.states.RUNNING,
model.Job.states.OK])
)
else:
if isinstance(job_state, string_types):
conditions.append(model.Job.state == job_state)
elif isinstance(job_state, list):
o = []
for s in job_state:
o.append(model.Job.state == s)
conditions.append(
or_(*o)
)
# We now build the query filters that relate to the input datasets
# that this job uses. We keep track of the requested dataset id in `requested_ids`,
# the type (hda, hdca or lda) in `data_types`
# and the ids that have been used in the job that has already been run in `used_ids`.
requested_ids = []
data_types = []
used_ids = []
for k, input_list in input_data.items():
for type_values in input_list:
t = type_values['src']
v = type_values['id']
requested_ids.append(v)
data_types.append(t)
identifier = type_values['identifier']
if t == 'hda':
a = aliased(model.JobToInputDatasetAssociation)
b = aliased(model.HistoryDatasetAssociation)
c = aliased(model.HistoryDatasetAssociation)
d = aliased(model.JobParameter)
e = aliased(model.HistoryDatasetAssociationHistory)
conditions.append(and_(
model.Job.id == a.job_id,
a.name == k,
a.dataset_id == b.id, # b is the HDA use for the job
c.dataset_id == b.dataset_id,
c.id == v, # c is the requested job input HDA
# We need to make sure that the job we are looking for has been run with identical inputs.
# Here we deal with 3 requirements:
# - the jobs' input dataset (=b) version is 0, meaning the job's input dataset is not yet ready
# - b's update_time is older than the job create time, meaning no changes occurred
# - the job has a dataset_version recorded, and that versions' metadata matches c's metadata.
or_(
and_(or_(a.dataset_version.in_([0, b.version]),
b.update_time < model.Job.create_time),
b.name == c.name,
b.extension == c.extension,
b.metadata == c.metadata,
),
and_(b.id == e.history_dataset_association_id,
a.dataset_version == e.version,
e.name == c.name,
e.extension == c.extension,
e._metadata == c._metadata,
),
),
or_(b.deleted == false(), c.deleted == false())
))
if identifier:
conditions.append(and_(model.Job.id == d.job_id,
d.name == "%s|__identifier__" % k,
d.value == json.dumps(identifier)))
used_ids.append(a.dataset_id)
elif t == 'ldda':
a = aliased(model.JobToInputLibraryDatasetAssociation)
conditions.append(and_(
model.Job.id == a.job_id,
a.name == k,
a.ldda_id == v
))
used_ids.append(a.ldda_id)
elif t == 'hdca':
a = aliased(model.JobToInputDatasetCollectionAssociation)
b = aliased(model.HistoryDatasetCollectionAssociation)
c = aliased(model.HistoryDatasetCollectionAssociation)
conditions.append(and_(
model.Job.id == a.job_id,
a.name == k,
b.id == a.dataset_collection_id,
c.id == v,
b.name == c.name,
or_(and_(b.deleted == false(), b.id == v),
and_(or_(c.copied_from_history_dataset_collection_association_id == b.id,
b.copied_from_history_dataset_collection_association_id == c.id),
c.deleted == false(),
)
)
))
used_ids.append(a.dataset_collection_id)
else:
return []
for k, v in wildcard_param_dump.items():
wildcard_value = json.dumps(v, sort_keys=True).replace('"id": "__id_wildcard__"', '"id": %')
a = aliased(model.JobParameter)
conditions.append(and_(
model.Job.id == a.job_id,
a.name == k,
a.value.like(wildcard_value)
))
conditions.append(and_(
model.Job.any_output_dataset_collection_instances_deleted == false(),
model.Job.any_output_dataset_deleted == false()
))
query = self.sa_session.query(model.Job.id, *used_ids).filter(and_(*conditions))
for job in query.all():
# We found a job that is equal in terms of tool_id, user, state and input datasets,
# but to be able to verify that the parameters match we need to modify all instances of
# dataset_ids (HDA, LDDA, HDCA) in the incoming param_dump to point to those used by the
# possibly equivalent job, which may have been run on copies of the original input data.
job_input_ids = {}
if len(job) > 1:
# We do have datasets to check
job_id, current_jobs_data_ids = job[0], job[1:]
job_parameter_conditions = [model.Job.id == job_id]
for src, requested_id, used_id in zip(data_types, requested_ids, current_jobs_data_ids):
if src not in job_input_ids:
job_input_ids[src] = {requested_id: used_id}
else:
job_input_ids[src][requested_id] = used_id
new_param_dump = remap(param_dump, visit=replace_dataset_ids)
# new_param_dump has its dataset ids remapped to those used by the job.
# We now ask if the remapped job parameters match the current job.
for k, v in new_param_dump.items():
a = aliased(model.JobParameter)
job_parameter_conditions.append(and_(
a.name == k,
a.value == json.dumps(v, sort_keys=True)
))
else:
job_parameter_conditions = [model.Job.id == job]
query = self.sa_session.query(model.Job).filter(*job_parameter_conditions)
job = query.first()
if job is None:
continue
n_parameters = 0
# Verify that equivalent jobs had the same number of job parameters
# We skip chrominfo, dbkey, __workflow_invocation_uuid__ and identifer
# parameter as these are not passed along when expanding tool parameters
# and they can differ without affecting the resulting dataset.
for parameter in job.parameters:
if parameter.name.startswith("__"):
continue
if parameter.name in {'chromInfo', 'dbkey'} or parameter.name.endswith('|__identifier__'):
continue
n_parameters += 1
if not n_parameters == len(param_dump):
continue
log.info("Found equivalent job %s", search_timer)
return job
log.info("No equivalent jobs found %s", search_timer)
return None
[docs]def invocation_job_source_iter(sa_session, invocation_id):
# TODO: Handle subworkflows.
join = model.WorkflowInvocationStep.table.join(
model.WorkflowInvocation
)
statement = select(
[model.WorkflowInvocationStep.job_id, model.WorkflowInvocationStep.implicit_collection_jobs_id, model.WorkflowInvocationStep.state]
).select_from(
join
).where(
model.WorkflowInvocation.id == invocation_id
)
for row in sa_session.execute(statement):
if row[0]:
yield ('Job', row[0], row[2])
if row[1]:
yield ('ImplicitCollectionJobs', row[1], row[2])
[docs]def fetch_job_states(sa_session, job_source_ids, job_source_types):
assert len(job_source_ids) == len(job_source_types)
job_ids = set()
implicit_collection_job_ids = set()
workflow_invocations_job_sources = {}
workflow_invocation_states = {} # should be set before we walk step states to be conservative on whether things are done expanding yet
for job_source_id, job_source_type in zip(job_source_ids, job_source_types):
if job_source_type == "Job":
job_ids.add(job_source_id)
elif job_source_type == "ImplicitCollectionJobs":
implicit_collection_job_ids.add(job_source_id)
elif job_source_type == "WorkflowInvocation":
invocation_state = sa_session.query(model.WorkflowInvocation).get(job_source_id).state
workflow_invocation_states[job_source_id] = invocation_state
workflow_invocation_job_sources = []
for (invocation_step_source_type, invocation_step_source_id, invocation_step_state) in invocation_job_source_iter(sa_session, job_source_id):
workflow_invocation_job_sources.append((invocation_step_source_type, invocation_step_source_id, invocation_step_state))
if invocation_step_source_type == "Job":
job_ids.add(invocation_step_source_id)
elif invocation_step_source_type == "ImplicitCollectionJobs":
implicit_collection_job_ids.add(invocation_step_source_id)
workflow_invocations_job_sources[job_source_id] = workflow_invocation_job_sources
else:
raise RequestParameterInvalidException("Invalid job source type %s found." % job_source_type)
job_summaries = {}
implicit_collection_jobs_summaries = {}
for job_id in job_ids:
job_summaries[job_id] = summarize_jobs_to_dict(sa_session, sa_session.query(model.Job).get(job_id))
for implicit_collection_jobs_id in implicit_collection_job_ids:
implicit_collection_jobs_summaries[implicit_collection_jobs_id] = summarize_jobs_to_dict(sa_session, sa_session.query(model.ImplicitCollectionJobs).get(implicit_collection_jobs_id))
rval = []
for job_source_id, job_source_type in zip(job_source_ids, job_source_types):
if job_source_type == "Job":
rval.append(job_summaries[job_source_id])
elif job_source_type == "ImplicitCollectionJobs":
rval.append(implicit_collection_jobs_summaries[job_source_id])
else:
invocation_state = workflow_invocation_states[job_source_id]
invocation_job_summaries = []
invocation_implicit_collection_job_summaries = []
invocation_step_states = []
for (invocation_step_source_type, invocation_step_source_id, invocation_step_state) in workflow_invocations_job_sources[job_source_id]:
invocation_step_states.append(invocation_step_state)
if invocation_step_source_type == "Job":
invocation_job_summaries.append(job_summaries[invocation_step_source_id])
else:
invocation_implicit_collection_job_summaries.append(implicit_collection_jobs_summaries[invocation_step_source_id])
rval.append(summarize_invocation_jobs(job_source_id, invocation_job_summaries, invocation_implicit_collection_job_summaries, invocation_state, invocation_step_states))
return rval
[docs]def summarize_invocation_jobs(invocation_id, job_summaries, implicit_collection_job_summaries, invocation_state, invocation_step_states):
states = {}
if invocation_state == "scheduled":
all_scheduled = True
for invocation_step_state in invocation_step_states:
all_scheduled = all_scheduled and invocation_step_state == "scheduled"
if all_scheduled:
populated_state = "ok"
else:
populated_state = "new"
elif invocation_state in ["cancelled", "failed"]:
populated_state = "failed"
else:
# call new, ready => new
populated_state = "new"
def merge_states(component_states):
for key, value in component_states.items():
if key not in states:
states[key] = value
else:
states[key] += value
for job_summary in job_summaries:
merge_states(job_summary["states"])
for implicit_collection_job_summary in implicit_collection_job_summaries:
# 'new' (un-populated collections might not yet have a states entry)
if "states" in implicit_collection_job_summary:
merge_states(implicit_collection_job_summary["states"])
component_populated_state = implicit_collection_job_summary["populated_state"]
if component_populated_state == "failed":
populated_state = "failed"
elif component_populated_state == "new" and populated_state != "failed":
populated_state = "new"
rval = {
"id": invocation_id,
"model": "WorkflowInvocation",
"states": states,
"populated_state": populated_state,
}
return rval
[docs]def summarize_jobs_to_dict(sa_session, jobs_source):
"""Produce a summary of jobs for job summary endpoints.
:type jobs_source: a Job or ImplicitCollectionJobs or None
:param jobs_source: the object to summarize
:rtype: dict
:returns: dictionary containing job summary information
"""
rval = None
if jobs_source is None:
pass
elif isinstance(jobs_source, model.Job):
rval = {
"populated_state": "ok",
"states": {jobs_source.state: 1},
"model": "Job",
"id": jobs_source.id,
}
else:
populated_state = jobs_source.populated_state
rval = {
"id": jobs_source.id,
"populated_state": populated_state,
"model": "ImplicitCollectionJobs",
}
if populated_state == "ok":
# produce state summary...
states = {}
join = model.ImplicitCollectionJobs.table.join(
model.ImplicitCollectionJobsJobAssociation.table.join(model.Job)
)
statement = select(
[model.Job.state, func.count("*")]
).select_from(
join
).where(
model.ImplicitCollectionJobs.id == jobs_source.id
).group_by(
model.Job.state
)
for row in sa_session.execute(statement):
states[row[0]] = row[1]
rval["states"] = states
return rval
[docs]def summarize_job_metrics(trans, job):
"""Produce a dict-ified version of job metrics ready for tabular rendering.
Precondition: the caller has verified the job is accessible to the user
represented by the trans parameter.
"""
if not trans.user_is_admin and not trans.app.config.expose_potentially_sensitive_job_metrics:
return []
def metric_to_dict(metric):
metric_name = metric.metric_name
metric_value = metric.metric_value
metric_plugin = metric.plugin
title, value = trans.app.job_metrics.format(metric_plugin, metric_name, metric_value)
return dict(
title=title,
value=value,
plugin=metric_plugin,
name=metric_name,
raw_value=str(metric_value),
)
metrics = [m for m in job.metrics if m.plugin != 'env' or trans.user_is_admin]
return list(map(metric_to_dict, metrics))
[docs]def summarize_destination_params(trans, job):
"""Produce a dict-ified version of job destination parameters ready for tabular rendering.
Precondition: the caller has verified the job is accessible to the user
represented by the trans parameter.
"""
destination_params = {'Runner': job.job_runner_name,
'Runner Job ID': job.job_runner_external_id,
'Handler': job.handler}
destination_params.update(job.destination_params)
return destination_params
[docs]def summarize_job_parameters(trans, job):
"""Produce a dict-ified version of job parameters ready for tabular rendering.
Precondition: the caller has verified the job is accessible to the user
represented by the trans parameter.
"""
def inputs_recursive(input_params, param_values, depth=1, upgrade_messages=None):
if upgrade_messages is None:
upgrade_messages = {}
rval = []
for input_index, input in enumerate(input_params.values()):
if input.name in param_values:
if input.type == "repeat":
for i in range(len(param_values[input.name])):
rval.extend(inputs_recursive(input.inputs, param_values[input.name][i], depth=depth + 1))
elif input.type == "section":
# Get the value of the current Section parameter
rval.append(dict(text=input.name, depth=depth))
rval.extend(inputs_recursive(input.inputs, param_values[input.name], depth=depth + 1, upgrade_messages=upgrade_messages.get(input.name)))
elif input.type == "conditional":
try:
current_case = param_values[input.name]['__current_case__']
is_valid = True
except Exception:
current_case = None
is_valid = False
if is_valid:
rval.append(dict(text=input.test_param.label, depth=depth, value=input.cases[current_case].value))
rval.extend(inputs_recursive(input.cases[current_case].inputs, param_values[input.name], depth=depth + 1, upgrade_messages=upgrade_messages.get(input.name)))
else:
rval.append(dict(text=input.name, depth=depth, notes="The previously used value is no longer valid.", error=True))
elif input.type == "upload_dataset":
rval.append(dict(text=input.group_title(param_values), depth=depth, value="%s uploaded datasets" % len(param_values[input.name])))
elif input.type == "data":
value = []
for i, element in enumerate(listify(param_values[input.name])):
if element.history_content_type == "dataset":
hda = element
encoded_id = trans.security.encode_id(hda.id)
value.append({"src": "hda", "id": encoded_id, "hid": hda.hid, "name": hda.name})
else:
value.append({"hid": element.hid, "name": element.name})
rval.append(dict(text=input.label, depth=depth, value=value))
elif input.visible:
if hasattr(input, "label") and input.label:
label = input.label
else:
# value for label not required, fallback to input name (same as tool panel)
label = input.name
rval.append(dict(text=label, depth=depth, value=input.value_to_display_text(param_values[input.name]), notes=upgrade_messages.get(input.name, '')))
else:
# Parameter does not have a stored value.
# Get parameter label.
if input.type == "conditional":
label = input.test_param.label
elif input.type == "repeat":
label = input.label()
else:
label = input.label or input.name
rval.append(dict(text=label, depth=depth, notes="not used (parameter was added after this job was run)"))
return rval
# Load the tool
app = trans.app
toolbox = app.toolbox
tool = toolbox.get_tool(job.tool_id, job.tool_version)
assert tool is not None, 'Requested tool has not been loaded.'
params_objects = None
upgrade_messages = {}
has_parameter_errors = False
# Load parameter objects, if a parameter type has changed, it's possible for the value to no longer be valid
try:
params_objects = job.get_param_values(app, ignore_errors=False)
except Exception:
params_objects = job.get_param_values(app, ignore_errors=True)
# use different param_objects in the following line, since we want to display original values as much as possible
upgrade_messages = tool.check_and_update_param_values(job.get_param_values(app, ignore_errors=True),
trans,
update_values=False)
has_parameter_errors = True
parameters = inputs_recursive(tool.inputs, params_objects, depth=1, upgrade_messages=upgrade_messages)
return {"parameters": parameters, "has_parameter_errors": has_parameter_errors}