From e096b929dc848b4cd86d353eabb4faaf31392e74 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Fri, 10 Aug 2018 10:39:26 +0200
Subject: [PATCH] New command: obi tail

---
 python/obitools3/commands/tail.pyx | 77 ++++++++++++++++++++++++++++++
 1 file changed, 77 insertions(+)
 create mode 100644 python/obitools3/commands/tail.pyx

diff --git a/python/obitools3/commands/tail.pyx b/python/obitools3/commands/tail.pyx
new file mode 100644
index 0000000..c5b0d4e
--- /dev/null
+++ b/python/obitools3/commands/tail.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 last lines of a view."
+
+ 
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addMinimalOutputOption(parser)
+
+    group=parser.add_argument_group('obi tail specific options')
+
+    group.add_argument('-n', '--sequence-count',
+                       action="store", dest="tail:count",
+                       metavar='<N>',
+                       default=10,
+                       type=int,
+                       help="Number of last records to keep.")
+
+     
+def run(config):
+     
+    DMS.obi_atexit()
+    
+    logger("info", "obi tail")
+
+    # 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)
+    
+    start = max(len(i_view) - config['tail']['count'], 0)
+        
+    selection = Line_selection(i_view)
+    
+    for i in range(start, len(i_view)):
+        selection.append(i)
+    
+    # Create output view with the line selection
+    try:
+        o_view = selection.materialize(output_view_name, comments="obi tail: "+str(len(selection))+"\n")
+    except Exception, e:
+        raise RollbackException("obi tail 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()
+