4389: Merge branch 'master' into 4389-breadcrumbs-infinite-loop

[arvados.git] / sdk / python / arvados / __init__.py

diff --git a/sdk/python/arvados/__init__.py b/sdk/python/arvados/__init__.py
index b165412d46588e7ef48f4b0ad8e12faf15a06cd5..060ed95d959531917749584176c5f42b8c453f66 100644 (file)
--- a/sdk/python/arvados/__init__.py
+++ b/sdk/python/arvados/__init__.py
@@ -25,6 +25,17 @@ from stream import *
 import errors
 import util
 
+# Set up Arvados logging based on the user's configuration.
+# All Arvados code should log under the arvados hierarchy.
+log_handler = logging.StreamHandler()
+log_handler.setFormatter(logging.Formatter(
+        '%(asctime)s %(name)s[%(process)d] %(levelname)s: %(message)s',
+        '%Y-%m-%d %H:%M:%S'))
+logger = logging.getLogger('arvados')
+logger.addHandler(log_handler)
+logger.setLevel(logging.DEBUG if config.get('ARVADOS_DEBUG')
+                else logging.WARNING)
+
 def task_set_output(self,s):
     api('v1').job_tasks().update(uuid=self['uuid'],
                                  body={
@@ -59,20 +70,29 @@ def current_job():
 def getjobparam(*args):
     return current_job()['script_parameters'].get(*args)
 
+def get_job_param_mount(*args):
+    return os.path.join(os.environ['TASK_KEEPMOUNT'], current_job()['script_parameters'].get(*args))
+
+def get_task_param_mount(*args):
+    return os.path.join(os.environ['TASK_KEEPMOUNT'], current_task()['parameters'].get(*args))
+
 class JobTask(object):
     def __init__(self, parameters=dict(), runtime_constraints=dict()):
         print "init jobtask %s %s" % (parameters, runtime_constraints)
 
 class job_setup:
     @staticmethod
-    def one_task_per_input_file(if_sequence=0, and_end_task=True):
+    def one_task_per_input_file(if_sequence=0, and_end_task=True, input_as_path=False):
         if if_sequence != current_task()['sequence']:
             return
         job_input = current_job()['script_parameters']['input']
         cr = CollectionReader(job_input)
         for s in cr.all_streams():
             for f in s.all_files():
-                task_input = f.as_manifest()
+                if input_as_path:
+                    task_input = os.path.join(job_input, s.name(), f.name())
+                else:
+                    task_input = f.as_manifest()
                 new_task_attrs = {
                     'job_uuid': current_job()['uuid'],
                     'created_by_job_task_uuid': current_task()['uuid'],