Create single subject pipeline

Author: Adam Richie-Halford

preafq/__init__.py

@@ -6,6 +6,51 @@
 __email__ = '[email protected]'
 __version__ = '0.1.0'
 
+import errno
+import logging
+import os
 
-from .preafq import download_prereqs, upload_to_s3  # noqa
-from . import fetch_hbn  # noqa
+from .preafq import upload_to_s3  # noqa
+from . import fetch_bids_s3  # noqa
+
+
+module_logger = logging.getLogger(__name__)
+
+# get the log level from environment variable
+if "AFQ_LOGLEVEL" in os.environ:
+    loglevel = os.environ['AFQ_LOGLEVEL']
+    module_logger.setLevel(getattr(logging, loglevel.upper()))
+else:
+    module_logger.setLevel(logging.WARNING)
+
+# create a file handler
+logpath = os.path.join(os.path.expanduser('~'), '.afq', 'afq.log')
+
+# Create the config directory if it doesn't exist
+logdir = os.path.dirname(logpath)
+try:
+    os.makedirs(logdir)
+except OSError as e:
+    pre_existing = (e.errno == errno.EEXIST and os.path.isdir(logdir))
+    if pre_existing:
+        pass
+    else:
+        raise e
+
+handler = logging.FileHandler(logpath, mode='w')
+handler.setLevel(logging.DEBUG)
+
+# create a logging format
+formatter = logging.Formatter(
+    '%(asctime)s - %(name)s - %(levelname)s - %(message)s'
+)
+handler.setFormatter(formatter)
+
+# add the handlers to the logger
+module_logger.addHandler(handler)
+module_logger.info('Started new preAFQ session')
+
+# Reduce verbosity of the boto logs
+logging.getLogger('boto').setLevel(logging.WARNING)
+logging.getLogger('boto3').setLevel(logging.WARNING)
+logging.getLogger('botocore').setLevel(logging.WARNING)

preafq/base.py

@@ -5,10 +5,13 @@
 from collections import namedtuple
 
 # Define the different namedtuple return types
-InputS3Keys = namedtuple(
-    'InputS3Keys',
-    ['subject', 'site', 'valid', 's3_keys']
+InputFiles = namedtuple(
+    'InputFiles',
+    ['subject', 'site', 'valid', 'files', 'file_type']
 )
 
-# Input files namedtuple
-InputFiles = namedtuple('InputFiles', ['subject', 'site', 'files'])
+# Input files (one type with session info and one without)
+InputFilesWithSession = namedtuple(
+    'InputFilesWithSession',
+    ['subject', 'site', 'session', 'files', 'file_type']
+)