Merge remote-tracking branch 'origin/master'

Author: akeshavan

.travis.yml

@@ -1,15 +1,25 @@
-# Config file for automatic testing at travis-ci.org
-
-language: python
-python:
-  - 3.6
-  - 3.5
-  - 3.4
-
-# Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
-install: pip install -U tox-travis
-
-# Command to run tests, e.g. python setup.py test
-script: tox
-
-
+sudo: false
+language: node_js
+node_js:
+- '6.0'
+cache:
+  directories:
+  - preafqViewer/node_modules
+branches:
+  only:
+  - master
+notifications:
+  email: false
+before_script:
+- cd preafqViewer
+- npm prune
+script:
+- npm run build
+- npm test
+after_success:
+- bash ./deploy.sh
+env:
+  global:
+  - GH_USER: akeshavan
+  - GH_REPO: preAFQ
+  - secure: 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

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']
+)