sdk/python/arvados/__init__.py

   1 import gflags
   2 import httplib
   3 import httplib2
   4 import logging
   5 import os
   6 import pprint
   7 import sys
   8 import types
   9 import subprocess
  10 import json
  11 import UserDict
  12 import re
  13 import hashlib
  14 import string
  15 import bz2
  16 import zlib
  17 import fcntl
  18 import time
  19 import threading
  20
  21 from api import *
  22 from collection import *
  23 from keep import *
  24 from stream import *
  25 import errors
  26 import util
  27
  28 def task_set_output(self,s):
  29     api('v1').job_tasks().update(uuid=self['uuid'],
  30                                  body={
  31             'output':s,
  32             'success':True,
  33             'progress':1.0
  34             }).execute()
  35
  36 _current_task = None
  37 def current_task():
  38     global _current_task
  39     if _current_task:
  40         return _current_task
  41     t = api('v1').job_tasks().get(uuid=os.environ['TASK_UUID']).execute()
  42     t = UserDict.UserDict(t)
  43     t.set_output = types.MethodType(task_set_output, t)
  44     t.tmpdir = os.environ['TASK_WORK']
  45     _current_task = t
  46     return t
  47
  48 _current_job = None
  49 def current_job():
  50     global _current_job
  51     if _current_job:
  52         return _current_job
  53     t = api('v1').jobs().get(uuid=os.environ['JOB_UUID']).execute()
  54     t = UserDict.UserDict(t)
  55     t.tmpdir = os.environ['JOB_WORK']
  56     _current_job = t
  57     return t
  58
  59 def getjobparam(*args):
  60     return current_job()['script_parameters'].get(*args)
  61
  62 def get_job_param_mount(*args):
  63     return os.path.join(os.environ['TASK_KEEPMOUNT'], current_job()['script_parameters'].get(*args))
  64
  65 def get_task_param_mount(*args):
  66     return os.path.join(os.environ['TASK_KEEPMOUNT'], current_task()['parameters'].get(*args))
  67
  68 class JobTask(object):
  69     def __init__(self, parameters=dict(), runtime_constraints=dict()):
  70         print "init jobtask %s %s" % (parameters, runtime_constraints)
  71
  72 class job_setup:
  73     @staticmethod
  74     def one_task_per_input_file(if_sequence=0, and_end_task=True, input_as_path=False):
  75         if if_sequence != current_task()['sequence']:
  76             return
  77         job_input = current_job()['script_parameters']['input']
  78         cr = CollectionReader(job_input)
  79         for s in cr.all_streams():
  80             for f in s.all_files():
  81                 if input_as_path:
  82                     task_input = os.path.join(job_input, s.name(), f.name())
  83                 else:
  84                     task_input = f.as_manifest()
  85                 new_task_attrs = {
  86                     'job_uuid': current_job()['uuid'],
  87                     'created_by_job_task_uuid': current_task()['uuid'],
  88                     'sequence': if_sequence + 1,
  89                     'parameters': {
  90                         'input':task_input
  91                         }
  92                     }
  93                 api('v1').job_tasks().create(body=new_task_attrs).execute()
  94         if and_end_task:
  95             api('v1').job_tasks().update(uuid=current_task()['uuid'],
  96                                        body={'success':True}
  97                                        ).execute()
  98             exit(0)
  99
 100     @staticmethod
 101     def one_task_per_input_stream(if_sequence=0, and_end_task=True):
 102         if if_sequence != current_task()['sequence']:
 103             return
 104         job_input = current_job()['script_parameters']['input']
 105         cr = CollectionReader(job_input)
 106         for s in cr.all_streams():
 107             task_input = s.tokens()
 108             new_task_attrs = {
 109                 'job_uuid': current_job()['uuid'],
 110                 'created_by_job_task_uuid': current_task()['uuid'],
 111                 'sequence': if_sequence + 1,
 112                 'parameters': {
 113                     'input':task_input
 114                     }
 115                 }
 116             api('v1').job_tasks().create(body=new_task_attrs).execute()
 117         if and_end_task:
 118             api('v1').job_tasks().update(uuid=current_task()['uuid'],
 119                                        body={'success':True}
 120                                        ).execute()
 121             exit(0)
 122
 123