Basic obi less

python/obitools3/commands/less.pyx

@@ -1,35 +1,15 @@
 #cython: language_level=3
 
-from obitools3.dms.dms cimport DMS       # TODO cimport doesn't work
+from obitools3.apps.optiongroups import addSequenceInputOption
-from obitools3.dms.view.view cimport View    # TODO cimport doesn't work
+from obitools3.uri.decode import open_uri
 
-
-# TODO with URIs
  
 __title__="Less equivalent"
  
-default_config = {   'inputview'    : None,
+
-                 }
- 
 def addOptions(parser):
- 
+
-    # TODO put this common group somewhere else but I don't know where
+    addSequenceInputOption(parser)
-    group=parser.add_argument_group('DMS and view options')
- 
-    group.add_argument('--default-dms','-d', 
-                       action="store", dest="obi:defaultdms",
-                       metavar='<DMS NAME>',
-                       default=None,
-                       type=str,
-                       help="Name of the default DMS for reading and writing data.")
- 
-    group.add_argument('--view','-v',
-                       action="store", dest="obi:view",
-                       metavar='<VIEW NAME>',
-                       default=None,
-                       type=str,
-                       help="Name of the view to print.")
-  
  
     group=parser.add_argument_group('obi less specific options')
  
@@ -38,29 +18,24 @@ def addOptions(parser):
                      metavar='<N>',
                      default=10,
                      type=int,
-                     help="Print N sequences (default: 10)")
+                     help="Print N entries (default: 10)")
  
 
 def run(config):
     
-    cdef DMS    d
+    cdef object entries
-    cdef View   view
     cdef int    n
-     
+
-    # Open DMS
+    input = open_uri(config['obi']['inputURI'])
-    d = DMS.open(config['obi']['defaultdms'])
+       
-     
+    entries = input[1]
-    # Open input view
-    view = View.open(d, config['obi']['view'])
     
-    if config['less']['print'] > len(view) :
+    if config['less']['print'] > len(entries) :
-        n = len(view)
+        n = len(entries)
     else :
         n = config['less']['print']
         
     # Print
     for i in range(n) :
-        print(repr(view[i]))
+        print(repr(entries[i]))
-     
-    d.close()