mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
Nicola Soranzo
50 lines
1.6 KiB
Python
50 lines
1.6 KiB
Python
"""
|
|
Reads a JSON file and uses it to call into a datatype class to extract
|
|
a subset of a dataset for processing.
|
|
|
|
Used by jobs that split large files into pieces to be processed concurrently
|
|
on a gid in a scatter-gather mode. This does part of the scatter.
|
|
|
|
"""
|
|
|
|
import json
|
|
import logging
|
|
import os
|
|
import sys
|
|
|
|
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
|
|
|
|
# This junk is here to prevent loading errors
|
|
import galaxy.model.mapping # need to load this before we unpickle, in order to setup properties assigned by the mappers
|
|
|
|
galaxy.model.Job() # this looks REAL stupid, but it is REQUIRED in order for SA to insert parameters into the classes defined by the mappers --> it appears that instantiating ANY mapper'ed class would suffice here
|
|
|
|
logging.basicConfig()
|
|
log = logging.getLogger(__name__)
|
|
|
|
|
|
def __main__():
|
|
"""
|
|
Argument: a JSON file
|
|
"""
|
|
file_path = sys.argv.pop(1)
|
|
if not os.path.isfile(file_path):
|
|
# Nothing to do - some splitters don't write a JSON file
|
|
sys.exit(0)
|
|
data = json.load(open(file_path))
|
|
try:
|
|
class_name_parts = data["class_name"].split(".")
|
|
module_name = ".".join(class_name_parts[:-1])
|
|
class_name = class_name_parts[-1]
|
|
mod = __import__(module_name, globals(), locals(), [class_name])
|
|
cls = getattr(mod, class_name)
|
|
if not cls.process_split_file(data):
|
|
sys.stderr.write("Writing split file failed\n")
|
|
sys.exit(1)
|
|
except Exception as e:
|
|
sys.stderr.write(str(e))
|
|
sys.exit(1)
|
|
|
|
|
|
__main__()
|