Skip to content

Commit

Permalink
Allowing for configurable priorities.
Browse files Browse the repository at this point in the history 
Any priority listed in the global 'default desinations' section in the tool destinations config is considered a valid priority. All other priorities are invalid.
This allows for the configuration and usage of an arbitrary number of priorities
  • Loading branch information
Matthew Spelchak committed Feb 1, 2018
1 parent e9f05cb commit 71460a6
Showing 1 changed file with 93 additions and 87 deletions.
180 changes: 93 additions & 87 deletions lib/galaxy/jobs/dynamic_tool_destination.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,13 +13,17 @@
import re
from functools import reduce


# log to galaxy's logger
log = logging.getLogger(__name__)

# does a lot more logging when set to true
verbose = True

"""
list of all valid priorities, inferred from the global
default_desinations section of the config
"""
priority_list = []

class MalformedYMLException(Exception):
pass
Expand Down Expand Up @@ -393,34 +397,29 @@ def __validate_destination(cls, valid_rule, return_bool, rule, tool, counter):
valid_rule = False
elif isinstance(rule["destination"], dict):
if ("priority" in rule["destination"] and isinstance(rule["destination"]["priority"], dict)):
if "med" not in rule["destination"]["priority"]:
error = "No 'med' priority destination for rule " + str(counter)
error += " in '" + str(tool) + "'."
if not return_bool:
error += " Ignoring..."
if verbose:
log.debug(error)
valid_rule = False
else:
for priority in rule["destination"]["priority"]:
if priority not in ["low", "med", "high"]:
error = "Invalid priority destination '" + str(priority)
error += "' for rule " + str(counter)
error += " in '" + str(tool) + "'."
if not return_bool:
error += " Ignoring..."
if verbose:
log.debug(error)
valid_rule = False
elif not isinstance(rule["destination"]["priority"][priority], str):
error = "No '" + str(priority)
error += "'priority destination for rule " + str(counter)
error += " in '" + str(tool) + "'."
if not return_bool:
error += " Ignoring..."
if verbose:
log.debug(error)
valid_rule = False

#### new code
for priority in rule["destination"]["priority"]:
if priority not in priority_list:
error = "Invalid priority classification: "
error += str(priority)
if not return_bool:
error += " Ignoring..."
if verbose:
log.debug(error)
valid_rule = False

elif not isinstance(rule["destination"]["priority"][priority], str):
error = "No '" + str(priority)
error += "'priority classification for rule " + str(counter)
error += " in '" + str(tool) + "'."
if not return_bool:
error += " Ignoring..."
if verbose:
log.debug(error)
valid_rule = False

#### new code ends here
else:
error = "No destination specified for rule " + str(counter)
error += " in '" + str(tool) + "'."
Expand Down Expand Up @@ -755,32 +754,26 @@ def infinite_defaultdict():
elif isinstance(obj['default_destination'], dict):
if ('priority' in obj['default_destination'] and
isinstance(obj['default_destination']['priority'], dict)):
if 'med' not in obj['default_destination']['priority']:
error = "No default 'med' priority destination!"
if verbose:
log.debug(error)
valid_config = False
else:
for priority in obj['default_destination']['priority']:
if priority in ['low', 'med', 'high']:
if isinstance(
obj['default_destination']['priority'][priority],
str):
new_config['default_destination']['priority'][
priority] = obj[
'default_destination']['priority'][priority]
else:
error = ("No default '" + str(priority) +
"' priority destination in config!")
if verbose:
log.debug(error)
valid_config = False
else:
error = ("Invalid default priority destination '" +
str(priority) + "' found in config!")
if verbose:
log.debug(error)
valid_config = False

####My new code

for priority in obj['default_destination']['priority']:

if isinstance(obj['default_destination']['priority'][priority],
str):
if priority not in priority_list:
priority_list.append(priority)

new_config['default']['priority'][priority] = obj[
'default_destination']['priority'][priority]

else:
error = ("Invalid default priority classification '" +
str(priority_classification) + "' found in config!")
if verbose:
log.debug(error)
valid_config = False

else:
error = "No default priority destinations specified in config!"
if verbose:
Expand All @@ -804,11 +797,18 @@ def infinite_defaultdict():

if isinstance(curr, dict):
if 'priority' in curr and isinstance(curr['priority'], str):
if curr['priority'] in ['low', 'med', 'high']:
"""
#### my new code
if curr['priority'] in priority_list:
new_config['users'][user]['priority'] = curr['priority']
"""
if curr['priority'] in ['low', 'med', 'high']: ### DO THINGS HERE (maybe)
new_config['users'][user]['priority'] = curr['priority']
else:
error = ("User '" + user + "', priority is not valid!" +
" Must be either low, med, or high.")
error = ("User '" + user + "', priority classification "
+ "is not valid: Must be one of the values "
+ "specified in the config.")
if verbose:
log.debug(error)
valid_config = False
Expand Down Expand Up @@ -846,37 +846,43 @@ def infinite_defaultdict():
new_config['tools'][tool]['default_destination'] = (curr['default_destination'])
tool_has_default = True
elif isinstance(curr['default_destination'], dict):

if ('priority' in curr['default_destination'] and isinstance(curr['default_destination']['priority'], dict)):
if ('med' not in curr['default_destination']['priority']):
error = "No default 'med' priority destination "
error += "for " + str(tool) + "!"
if verbose:
log.debug(error)
valid_config = False
else:
for priority in curr['default_destination']['priority']:
destination = curr['default_destination']['priority'][priority]
if priority in ['low', 'med', 'high']:
if isinstance(destination, str):
new_config['tools'][tool]['default_destination']['priority'][priority] = destination
tool_has_default = True
else:
error = ("No default '" +
str(priority) +
"' priority destination " +
"for " + str(tool) +
" in config!")
if verbose:
log.debug(error)
valid_config = False
####new code
####May not be necessary check
all_mandatory_classes_defined = True
for priority in priority_list:
if priority not in curr['default_destination']['priority']:
error = ("No default for priority classification "
+ str(priority) + " in tool " + str(tool))
if verbose:
log.debug(error)
valid_config = False
all_mandatory_classes_defined = False

## if all_mandatory_classes_defined == True:
for priority in curr['default_destination']['priority']:
destination = curr['default_destination']['priority'][priority]
if priority in priority_list:
if isinstance(destination, str):
new_config['tools'][tool]['default_destination'][
'priority'][priority] = destination
tool_has_default = True
else:
error = ("Invalid default priority " +
"destination '" + str(priority) +
"' for " + str(tool) +
"found in config!")
error = ("No default '" + str(priority) +
"' priority classification for tool "
+ str(tool) + " in config!")
if verbose:
log.debug(error)
valid_config = False

else:
error = ("Invalid default priority classification '" +
str(priority) + "' for " + str(tool)
+ " found in config!")
if verbose:
log.debug(error)
valid_config = False
else:
error = "No default priority destinations specified"
error += " for " + str(tool) + " in config!"
Expand Down Expand Up @@ -1104,7 +1110,7 @@ def importer(test):
global JobDestination
global JobMappingException
if test:
class JobDestionation(object):
class JobDestination(object):
def __init__(self, *kwd):
self.id = kwd.get('id')
self.nativeSpec = kwd.get('params')['nativeSpecification']
Expand Down Expand Up @@ -1177,7 +1183,7 @@ def map_tool_to_destination(
records += 1
except NameError:
pass
# Loop through each input file and adds the size to the total
# Loops through each input file and adds the size to the total
# or looks through db for records
for da in inp_data:
try:
Expand Down Expand Up @@ -1227,7 +1233,7 @@ def map_tool_to_destination(
fail_message = None

# set default priority to med
default_priority = 'med'
default_priority = 'med' ###May need to find a better default
priority = default_priority

if config is not None:
Expand Down

0 comments on commit 71460a6

Please sign in to comment.