Patch decoding of URL

python/obitools3/apps/config.pxd

@@ -7,4 +7,4 @@ cdef dict buildDefaultConfiguration(str root_config_name,
                                     dict  config)
 
 cpdef dict getConfiguration(str root_config_name=?,
-                                    dict  config=?)
+                                    dict  config=?)

python/obitools3/apps/config.pyx

@@ -101,3 +101,14 @@ cpdef dict getConfiguration(str root_config_name="__default__",
     config['__done__']=True
             
     return config
+
+def logger(level, *messages):
+    try:
+        config=getConfiguration()
+        root = config["__root_config__"]
+        l = config[root]['logger']
+        if config[root]['verbose']:
+            getattr(l, level)(*messages)
+    except:
+        print(*messages,file=sys.stderr)
+

python/obitools3/apps/logging.pyx

@@ -42,5 +42,7 @@ cpdef getLogger(dict config):
     rootlogger.setLevel(loglevel)
     
     config[root]['logger']=rootlogger
-    
+    config[root]['verbose']=True
+        
     return rootlogger
+

python/obitools3/apps/optiongroups/__init__.py

@@ -2,8 +2,8 @@ def __addInputOption(optionManager):
     
     optionManager.add_argument(
                     dest='obi:inputURI',  
-                    metavar='index', 
-                    help='index root filename (produced by the oa index command)')
+                    metavar='INPUT', 
+                    help='Data source URI')
     
 
     group = optionManager.add_argument_group("Restriction to a sub-part options",
@@ -23,7 +23,12 @@ def __addInputOption(optionManager):
                      type=int,
                      help="treat only N sequences")
 
-
+    group.add_argument('--na-string',
+                     action="store", dest="obi:nastring",
+                     default=b"NA",
+                     type=bytes,
+                     help="String associated to Non Available (NA) values")
+    
 
 def __addSequenceInputOption(optionManager):
     group = optionManager.add_argument_group("Input format options for sequence files")
@@ -124,12 +129,6 @@ def __addTabularInputOption(optionManager):
                      type=bytes,
                      help="Decimal separator")
     
-    group.add_argument('--na-string',
-                     action="store", dest="obi:nastring",
-                     default=b"NA",
-                     type=bytes,
-                     help="String associated to Non Available (NA) values")
-    
     group.add_argument('--strip-white',
                      action="store_false", dest="obi:stripwhite",
                      default=True,
@@ -161,3 +160,14 @@ def addAllInputOption(optionManager):
     __addInputOption(optionManager)
     __addSequenceInputOption(optionManager)
     __addTabularInputOption(optionManager)
+    
+    
+def __addOutputOption(optionManager):
+    
+    optionManager.add_argument(
+                    dest='obi:outputURI',  
+                    metavar='OUTPUT', 
+                    help='Data destination URI')
+
+def addMinimalOutputOption(optionManager):
+    __addOutputOption(optionManager)