New command: obi head

python/obitools3/commands/head.pyx

@@ -0,0 +1,77 @@
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.dms import DMS
+from obitools3.dms.view.view cimport View, Line_selection
+from obitools3.uri.decode import open_uri
+from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
+from obitools3.dms.view import RollbackException
+from obitools3.apps.config import logger
+
+import time
+ 
+
+__title__="Keep the N first lines of a view."
+
+ 
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addMinimalOutputOption(parser)
+
+    group=parser.add_argument_group('obi head specific options')
+
+    group.add_argument('-n', '--sequence-count',
+                       action="store", dest="head:count",
+                       metavar='<N>',
+                       default=10,
+                       type=int,
+                       help="Number of first records to keep.")
+
+     
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi head")
+
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input view")
+    i_view = input[1]
+
+    # Read the name of the output view
+    uri = config['obi']['outputURI'].split('/')
+    if len(uri)==2:
+        # Check that input and output DMS are the same (predicate, to discuss)
+        if config['obi']['inputURI'].split('/')[0] != uri[0]:
+            raise Exception("Input and output DMS must be the same")
+        output_view_name = uri[1]
+    else:
+        output_view_name = uri[0]
+
+    # Initialize the progress bar
+    pb = ProgressBar(len(i_view), config, seconde=5)
+    
+    n = min(config['head']['count'], len(i_view))
+        
+    selection = Line_selection(i_view)
+    
+    for i in range(n):
+        selection.append(i)
+    
+    # Create output view with the line selection
+    try:
+        o_view = selection.materialize(output_view_name, comments="obi head: "+str(config['head']['count'])+"\n")
+    except Exception, e:
+        raise RollbackException("obi head error, rollbacking view: "+str(e), o_view)
+
+    # TODO DISCUSS if output URI to different DMS, copy view?
+
+    print("\n")
+    print(repr(o_view))
+
+    input[0].close()
+    #output[0].close()
+