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Remove Unrelated Files (Again)

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Matthew Spelchak
2018-03-14 09:30:24 -05:00
parent 729714f940
commit 1319aa766d
7 changed files with 0 additions and 247 deletions
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.gitignore
-1
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@@ -144,4 +144,3 @@ doc/source/dev/schema.rst
*.rej
*~
.idea
*.bak
config/workflow_resource_mapper_conf.yml.sample
-14
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@@ -1,14 +0,0 @@
by_group:
default: default
groups:
default: [project, priority]
prio_basic: [{name: priority, options: ["low", "med"]}]
prio_advanced: [{name: priority, options: ["low", "med", "high"]}]
prio_super:
- time
- memory
- processors
- name: priority
options:
- ultra
- plus_ultra
config/workflow_resource_params_conf.xml.sample
-13
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@@ -1,13 +0,0 @@
<parameters>
<param label="Processors" name="processors" type="integer" size="2" min="1" max="64" value="" help="Number of processing cores, 'ppn' value (1-64). Leave blank to use default value." />
<param label="Memory" name="memory" type="integer" size="3" min="1" max="256" value="" help="Memory size in gigabytes, 'pmem' value (1-256). Leave blank to use default value." />
<param label="Time" name="time" type="integer" size="3" min="1" max="744" value="" help="Maximum job time in hours, 'walltime' value (1-744). Leave blank to use default value." />
<param label="Project" name="project" type="text" value="" help="Project to assign resource allocation to. Leave blank to use default value." />
<param label="Workflow Job Priority" name="priority" type="select" value="med" help="What priority should the jobs in this workflow run at? (Overrides any declared job priority)">
<option value="low" label="Low"/>
<option value="med" label="Medium"/>
<option value="high" label="High"/>
<option value="ultra" label="Ultra"/>
<option value="plus_ultra" label="Plus Ultra"/>
</param>
</parameters>
lib/galaxy/jobs/mapper.py
-5
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@@ -137,11 +137,6 @@ class JobRunnerMapper(object):
workflow_invocation_uuid = param_values.get("__workflow_invocation_uuid__", None)
actual_args["workflow_invocation_uuid"] = workflow_invocation_uuid
if "workflow_resource_params" in function_arg_names:
param_values = job.raw_param_dict()
workflow_resource_params = param_values.get("__workflow_resource_params__", None)
actual_args["workflow_resource_params"] = workflow_resource_params
return expand_function(**actual_args)
def __job_params(self, job):
lib/galaxy/util/__init__.py
-16
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@@ -817,22 +817,6 @@ def xml_text(root, name=None):
return ''
def parse_resource_parameters(resource_param_file):
"""Code shared between jobs and workflows for reading resource parameter configuration files.
TODO: Allow YAML in addition to XML.
"""
resource_parameters = {}
if os.path.exists(resource_param_file):
resource_definitions = parse_xml(resource_param_file)
resource_definitions_root = resource_definitions.getroot()
for parameter_elem in resource_definitions_root.findall("param"):
name = parameter_elem.get("name")
resource_parameters[name] = parameter_elem
return resource_parameters
# asbool implementation pulled from PasteDeploy
truthy = frozenset(['true', 'yes', 'on', 'y', 't', '1'])
falsy = frozenset(['false', 'no', 'off', 'n', 'f', '0'])
lib/galaxy/workflow/resources/__init__.py
-176
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@@ -1,176 +0,0 @@
"""This package is something a placeholder for workflow resource parameters.
This file defines the baked in resource mapper types, and this package contains an
example of a more open, pluggable approach with greater control.
"""
import functools
import logging
import os
import sys
from copy import deepcopy
import yaml
import galaxy.util
log = logging.getLogger(__name__)
def get_resource_mapper_function(app):
config = app.config
mapper = getattr(config, "workflow_resource_params_mapper", None)
if mapper is None:
return _null_mapper_function
elif ":" in mapper:
raw_function = _import_resource_mapping_function(mapper)
# Bind resource parameters here just to not re-parse over and over.
workflow_resource_params = _read_defined_parameter_definitions(config)
return functools.partial(raw_function, workflow_resource_params=workflow_resource_params)
else:
workflow_resource_params = _read_defined_parameter_definitions(config)
with open(mapper, "r") as f:
mapper_definition = yaml.load(f)
if "by_group" in mapper_definition:
by_group = mapper_definition["by_group"]
return functools.partial(_resource_parameters_by_group, by_group=by_group, workflow_resource_params=workflow_resource_params)
else:
raise Exception("Currently workflow parameter mapper definitions require a by_group definition.")
def _read_defined_parameter_definitions(config):
params_file = getattr(config, "workflow_resource_params_file", None)
if not params_file or not os.path.exists(params_file):
# Just re-use job resource parameters.
params_file = getattr(config, "job_resource_params_file", None)
if not params_file or not os.path.exists(params_file):
params_file = None
log.debug("Loading workflow resource parameter definitions from %s" % params_file)
if params_file:
return galaxy.util.parse_resource_parameters(params_file)
else:
return {}
def _resource_parameters_by_group(trans, **kwds):
user = trans.user
by_group = kwds["by_group"]
workflow_resource_params = kwds["workflow_resource_params"]
params = []
if validate_by_group_workflow_parameters_mapper(by_group, workflow_resource_params):
user_permissions = {}
user_groups = []
for g in user.groups:
user_groups.append(g.group.name)
default_group = by_group.get('default', None)
for group_name, group_def in by_group.get("groups", {}).items():
if group_name == default_group or group_name in user_groups:
for tag in group_def:
if type(tag) is dict:
if tag.get('name') not in user_permissions:
user_permissions[tag.get('name')] = {}
for option in tag.get('options'):
user_permissions[tag.get('name')][option] = {}
else:
if tag not in user_permissions:
user_permissions[tag] = {}
# user_permissions is now set.
params = get_workflow_parameter_list(workflow_resource_params, user_permissions)
return params
# returns an array of parameters that a users set of permissions can access.
def get_workflow_parameter_list(params, user_permissions):
param_list = []
for param_name, param_elem in params.items():
attr = deepcopy(param_elem.attrib)
if attr['name'] in user_permissions:
# Allow 'select' type parameters to be used
if attr['type'] == 'select':
option_data = []
reject_list = []
for option_elem in param_elem.findall("option"):
if option_elem.attrib['value'] in user_permissions[attr['name']]:
option_data.append({
'label': option_elem.attrib['label'],
'value': option_elem.attrib['value']
})
else:
reject_list.append(option_elem.attrib['label'])
attr['data'] = option_data
attr_help = ""
if 'help' in attr:
attr_help = attr['help']
if reject_list:
attr_help += "<br/><br/>The following options are available but disabled.<br/>" + \
str(reject_list) + \
"<br/>If you believe this is a mistake, please contact your Galaxy admin."
attr['help'] = attr_help
param_list.append(attr)
return param_list
def validate_by_group_workflow_parameters_mapper(by_group, workflow_resource_params):
valid = True
try:
if 'default' not in by_group:
raise Exception("'workflow_resource_params_mapper' YAML file is malformed, 'default' attribute not found!")
default_group = by_group['default']
if 'groups' not in by_group:
raise Exception("'workflow_resource_params_mapper' YAML file is malformed, 'groups' attribute not found!")
if default_group not in by_group['groups']:
raise Exception("'workflow_resource_params_mapper' YAML file is malformed, default group with title '" +
default_group + "' not found in 'groups'!")
for group in by_group['groups']:
for attrib in by_group['groups'][group]:
if type(attrib) is dict:
if 'name' not in attrib:
raise Exception("'workflow_resource_params_mapper' YAML file is malformed, "
"'name' attribute not found in attribute of group '" + group + "'!")
if attrib['name'] not in workflow_resource_params:
raise Exception("'workflow_resource_params_mapper' YAML file is malformed, group with name '" +
attrib['name'] + "' not found in 'workflow_resource_params'!")
if 'options' not in attrib:
raise Exception("'workflow_resource_params_mapper' YAML file is malformed, "
"'options' attribute not found in attribute of group '" + group + "'!")
valid_options = []
for param_option in workflow_resource_params[attrib['name']]:
valid_options.append(param_option.attrib['value'])
for option in attrib['options']:
if option not in valid_options:
raise Exception("'workflow_resource_params_mapper' YAML file is malformed, '" + option +
"' in 'options' of '" + attrib['name'] + "' not found in attribute of group '" + group + "'!")
else:
if attrib not in workflow_resource_params:
raise Exception("'workflow_resource_params_mapper' YAML file is malformed, attribute with name "
"'" + attrib + "' not found in 'workflow_resource_params'!")
except Exception as e:
log.exception(e)
valid = False
pass
return valid
def _import_resource_mapping_function(qualified_function_path):
full_module_name, function_name = qualified_function_path.split(":", 1)
try:
__import__(full_module_name)
except ImportError:
raise Exception("Failed to find workflow resource mapper module %s" % full_module_name)
module = sys.modules[full_module_name]
if hasattr(module, function_name):
return getattr(module, function_name)
else:
raise Exception("Failed to find workflow resource mapper function %s.%s" % (full_module_name, function_name))
def _null_mapper_function(*args, **kwds):
return None
lib/galaxy/workflow/resources/example.py.sample
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@@ -1,22 +0,0 @@
import logging
log = logging.getLogger( __name__ )
def admin_mapping(trans, stored_workflow, **kwds):
"""
This example workflow resource parameter mapping simply provides admins the ability to
specify priorities for workflows. To enable this setup ``workflow_resource_params_file``
in the Galaxy configuration with a priority definition input called "priority" (such
as in the example), copy this file without the .sample extension, and set
``workflow_resource_params_mapper`` to ``galaxy.workflow.resources.example:admin_mapping``.
"""
workflow_resource_params = kwds["workflow_resource_params"]
if trans.user_is_admin():
priority_attrib = workflow_resource_params.get("priority").attrib
priority_attrib['data'] = []
for child in workflow_resource_params.get('priority').getchildren():
priority_attrib['data'].append(child.attrib)
time_attrib = workflow_resource_params.get("time").attrib
return [priority_attrib, time_attrib]
return None