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 from arvfile import *
  26 import errors
  27 import util
  28
  29 # Set up Arvados logging based on the user's configuration.
  30 # All Arvados code should log under the arvados hierarchy.
  31 log_handler = logging.StreamHandler()
  32 log_handler.setFormatter(logging.Formatter(
  33         '%(asctime)s %(name)s[%(process)d] %(levelname)s: %(message)s',
  34         '%Y-%m-%d %H:%M:%S'))
  35 logger = logging.getLogger('arvados')
  36 logger.addHandler(log_handler)
  37 logger.setLevel(logging.DEBUG if config.get('ARVADOS_DEBUG')
  38                 else logging.WARNING)
  39
  40 def task_set_output(self,s):
  41     api('v1').job_tasks().update(uuid=self['uuid'],
  42                                  body={
  43             'output':s,
  44             'success':True,
  45             'progress':1.0
  46             }).execute()
  47
  48 _current_task = None
  49 def current_task():
  50     global _current_task
  51     if _current_task:
  52         return _current_task
  53     t = api('v1').job_tasks().get(uuid=os.environ['TASK_UUID']).execute()
  54     t = UserDict.UserDict(t)
  55     t.set_output = types.MethodType(task_set_output, t)
  56     t.tmpdir = os.environ['TASK_WORK']
  57     _current_task = t
  58     return t
  59
  60 _current_job = None
  61 def current_job():
  62     global _current_job
  63     if _current_job:
  64         return _current_job
  65     t = api('v1').jobs().get(uuid=os.environ['JOB_UUID']).execute()
  66     t = UserDict.UserDict(t)
  67     t.tmpdir = os.environ['JOB_WORK']
  68     _current_job = t
  69     return t
  70
  71 def getjobparam(*args):
  72     return current_job()['script_parameters'].get(*args)
  73
  74 def get_job_param_mount(*args):
  75     return os.path.join(os.environ['TASK_KEEPMOUNT'], current_job()['script_parameters'].get(*args))
  76
  77 def get_task_param_mount(*args):
  78     return os.path.join(os.environ['TASK_KEEPMOUNT'], current_task()['parameters'].get(*args))
  79
  80 class JobTask(object):
  81     def __init__(self, parameters=dict(), runtime_constraints=dict()):
  82         print "init jobtask %s %s" % (parameters, runtime_constraints)
  83
  84 class job_setup:
  85     @staticmethod
  86     def one_task_per_input_file(if_sequence=0, and_end_task=True, input_as_path=False):
  87         if if_sequence != current_task()['sequence']:
  88             return
  89         job_input = current_job()['script_parameters']['input']
  90         cr = CollectionReader(job_input)
  91         cr.normalize()
  92         for s in cr.all_streams():
  93             for f in s.all_files():
  94                 if input_as_path:
  95                     task_input = os.path.join(job_input, s.name(), f.name())
  96                 else:
  97                     task_input = f.as_manifest()
  98                 new_task_attrs = {
  99                     'job_uuid': current_job()['uuid'],
 100                     'created_by_job_task_uuid': current_task()['uuid'],
 101                     'sequence': if_sequence + 1,
 102                     'parameters': {
 103                         'input':task_input
 104                         }
 105                     }
 106                 api('v1').job_tasks().create(body=new_task_attrs).execute()
 107         if and_end_task:
 108             api('v1').job_tasks().update(uuid=current_task()['uuid'],
 109                                        body={'success':True}
 110                                        ).execute()
 111             exit(0)
 112
 113     @staticmethod
 114     def one_task_per_input_stream(if_sequence=0, and_end_task=True):
 115         if if_sequence != current_task()['sequence']:
 116             return
 117         job_input = current_job()['script_parameters']['input']
 118         cr = CollectionReader(job_input)
 119         for s in cr.all_streams():
 120             task_input = s.tokens()
 121             new_task_attrs = {
 122                 'job_uuid': current_job()['uuid'],
 123                 'created_by_job_task_uuid': current_task()['uuid'],
 124                 'sequence': if_sequence + 1,
 125                 'parameters': {
 126                     'input':task_input
 127                     }
 128                 }
 129             api('v1').job_tasks().create(body=new_task_attrs).execute()
 130         if and_end_task:
 131             api('v1').job_tasks().update(uuid=current_task()['uuid'],
 132                                        body={'success':True}
 133                                        ).execute()
 134             exit(0)