RF: Make Context sub-class from Config, and a few associated changes

bip/__init__.py

 import os.path as op
 
-basedir     = op.dirname(__file__)
-__version__ = open(op.join(basedir, 'VERSION')).read()
+BIPDIR      = op.dirname(__file__)
+__version__ = open(op.join(BIPDIR, 'VERSION')).read()

bip/main.py

@@ -25,6 +25,8 @@ import json
 from file_tree import FileTree
 from pipe_tree import Pipeline, Ref
 import bip
+from bip.utils import get_data
+from bip.utils.config import Config
 from bip.utils.log_utils import setup_logging
 from bip.pipelines import struct_T1, struct_T2_FLAIR, struct_FS
 from bip.pipelines import struct_swMRI, struct_asl, IDPs_gen
@@ -44,14 +46,17 @@ class Usage(Exception):
     def __init__(self, msg):
         self.msg = msg
 
-class Context:
 
-    def __init__(self, subject=""):
 
-        self.subject    = subject
-        self.BIPDIR     = bip.__path__[0]
-        self.FSLDIR     = os.environ['FSLDIR']
-        self.gdc        = self.get_data('GDC/UKB.txt')
+class Context(Config):
+
+    def __init__(self, subject, *args, **kwargs):
+
+        Config.__init__(self, *args, **kwargs)
+
+        self.subject = subject
+        self.BIPDIR  = bip.BIPDIR
+        self.FSLDIR  = os.environ['FSLDIR']
 
         with open(self.get_data('dMRI/autoptx/struct_list.json'), 'r',
                                 encoding="utf-8") as f:
@@ -76,16 +81,10 @@ class Context:
         return basedir + fileName
 
     def get_data(self, fileName):
-        fileName.replace('/', os.sep)
-        basedir = self.BIPDIR + os.sep + 'data' + os.sep
-        return basedir + fileName
-
-    #def save_context(self, file_name):
-    #    with open(file_name, "wt") as config_file:
-    #        config_file.write(self.to_json())
+        return bip.utils.get_data(fileName)
 
 
-def parseArguments(ctx):
+def parseArguments():
 
     #########################
     # ARGUMENT PARSING CODE #
@@ -103,7 +102,7 @@ def parseArguments(ctx):
                         help='Number of echo times for SWI data (default: 2)',
                         dest="echoes_SWI")
     parser.add_argument("-Q", "--basic_QC_file", action="store", nargs="?",
-                        default=ctx.get_data("config/ideal_config_sizes_UKBB.json"),
+                        default=utils.get_data("config/ideal_config_sizes_UKBB.json"),
                         help='File with the ideal configuration of the files +'\
                              '(default: UKB)',
                         dest="basic_QC_file")
@@ -161,9 +160,6 @@ def parseArguments(ctx):
     if subject[-1] =='/':
         subject = subject[0:len(subject)-1]
 
-    ctx.subject = subject
-    ctx.argsa = argsa
-
     # Parsing number of SWI coils argument
     if not argsa.coils_SWI:
         coils_SWI = 32
@@ -285,10 +281,9 @@ def parseArguments(ctx):
 
 def main():
 
-    #ctx = Context(gdc=)
-    ctx = Context()
-
-    parseArguments(ctx)
+    args      = parseArguments()
+    ctx       = Context(args.subject)
+    ctx.argsa = args
 
     setup_logging(op.join(ctx.subject, 'logs', 'main.log'))
 

bip/utils/__init__.py

@@ -14,6 +14,8 @@ import            os
 import            time
 import            errno
 
+import            bip
+
 
 log = logging.getLogger(__name__)
 
@@ -49,3 +51,9 @@ def lockdir(dirname, delay=5):
         log.debug('Relinquishing lock on %s', dirname)
         os.close( fd)
         os.unlink(lockfile)
+
+
+def get_data(filename):
+    """Return the filename, prefixed with the bip/data/ directory path. """
+    filename.replace('/', os.sep)
+    return op.join(bipdir, 'data', filename)