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 # Set up Arvados logging based on the user's configuration.
  29 # All Arvados code should log under the arvados hierarchy.
  30 log_handler = logging.StreamHandler()
  31 log_handler.setFormatter(logging.Formatter(
  32         '%(asctime)s %(name)s[%(process)d] %(levelname)s: %(message)s',
  33         '%Y-%m-%d %H:%M:%S'))
  34 logger = logging.getLogger('arvados')
  35 logger.addHandler(log_handler)
  36 logger.setLevel(logging.DEBUG if config.get('ARVADOS_DEBUG')
  37                 else logging.WARNING)
  38
  39 def task_set_output(self,s):
  40     api('v1').job_tasks().update(uuid=self['uuid'],
  41                                  body={
  42             'output':s,
  43             'success':True,
  44             'progress':1.0
  45             }).execute()
  46
  47 _current_task = None
  48 def current_task():
  49     global _current_task
  50     if _current_task:
  51         return _current_task
  52     t = api('v1').job_tasks().get(uuid=os.environ['TASK_UUID']).execute()
  53     t = UserDict.UserDict(t)
  54     t.set_output = types.MethodType(task_set_output, t)
  55     t.tmpdir = os.environ['TASK_WORK']
  56     _current_task = t
  57     return t
  58
  59 _current_job = None
  60 def current_job():
  61     global _current_job
  62     if _current_job:
  63         return _current_job
  64     t = api('v1').jobs().get(uuid=os.environ['JOB_UUID']).execute()
  65     t = UserDict.UserDict(t)
  66     t.tmpdir = os.environ['JOB_WORK']
  67     _current_job = t
  68     return t
  69
  70 def getjobparam(*args):
  71     return current_job()['script_parameters'].get(*args)
  72
  73 def get_job_param_mount(*args):
  74     return os.path.join(os.environ['TASK_KEEPMOUNT'], current_job()['script_parameters'].get(*args))
  75
  76 def get_task_param_mount(*args):
  77     return os.path.join(os.environ['TASK_KEEPMOUNT'], current_task()['parameters'].get(*args))
  78
  79 class JobTask(object):
  80     def __init__(self, parameters=dict(), runtime_constraints=dict()):
  81         print "init jobtask %s %s" % (parameters, runtime_constraints)
  82
  83 class job_setup:
  84     @staticmethod
  85     def one_task_per_input_file(if_sequence=0, and_end_task=True, input_as_path=False):
  86         if if_sequence != current_task()['sequence']:
  87             return
  88         job_input = current_job()['script_parameters']['input']
  89         cr = CollectionReader(job_input)
  90         for s in cr.all_streams():
  91             for f in s.all_files():
  92                 if input_as_path:
  93                     task_input = os.path.join(job_input, s.name(), f.name())
  94                 else:
  95                     task_input = f.as_manifest()
  96                 new_task_attrs = {
  97                     'job_uuid': current_job()['uuid'],
  98                     'created_by_job_task_uuid': current_task()['uuid'],
  99                     'sequence': if_sequence + 1,
 100                     'parameters': {
 101                         'input':task_input
 102                         }
 103                     }
 104                 api('v1').job_tasks().create(body=new_task_attrs).execute()
 105         if and_end_task:
 106             api('v1').job_tasks().update(uuid=current_task()['uuid'],
 107                                        body={'success':True}
 108                                        ).execute()
 109             exit(0)
 110
 111     @staticmethod
 112     def one_task_per_input_stream(if_sequence=0, and_end_task=True):
 113         if if_sequence != current_task()['sequence']:
 114             return
 115         job_input = current_job()['script_parameters']['input']
 116         cr = CollectionReader(job_input)
 117         for s in cr.all_streams():
 118             task_input = s.tokens()
 119             new_task_attrs = {
 120                 'job_uuid': current_job()['uuid'],
 121                 'created_by_job_task_uuid': current_task()['uuid'],
 122                 'sequence': if_sequence + 1,
 123                 'parameters': {
 124                     'input':task_input
 125                     }
 126                 }
 127             api('v1').job_tasks().create(body=new_task_attrs).execute()
 128         if and_end_task:
 129             api('v1').job_tasks().update(uuid=current_task()['uuid'],
 130                                        body={'success':True}
 131                                        ).execute()
 132             exit(0)
 133
 134