From 82916933095374b552d33baa5a596113d3357904 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Tue, 8 Nov 2016 11:19:12 +0100
Subject: [PATCH] obi grep: updated to work with the new line selection class
 and within the local sequence environment, and progress bar functioning

---
 python/obitools3/commands/grep.pyx | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/python/obitools3/commands/grep.pyx b/python/obitools3/commands/grep.pyx
index e056dd1..2a75e86 100644
--- a/python/obitools3/commands/grep.pyx
+++ b/python/obitools3/commands/grep.pyx
@@ -1,7 +1,7 @@
 from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
-from obitools3.obidms._obidms import OBIDMS, OBIView, OBIView_NUC_SEQS    # TODO cimport doesn't work
-
+from obitools3.obidms._obidms import OBIDMS, OBIView, OBIView_line_selection    # TODO cimport doesn't work
 
+from functools import reduce
 import time
 
 __title__="Grep view lines that match the given predicates"
@@ -43,7 +43,7 @@ def addOptions(parser):
     group=parser.add_argument_group('obi grep specific options')
 
     group.add_argument('--predicate','-p',
-                       action="store", dest="grep:predicate",
+                       action="append", dest="grep:predicates",
                        metavar='<PREDICATE>',
                        default=None,
                        type=str,
@@ -59,29 +59,33 @@ def run(config):
     iview = d.open_view(config['obi']['inputview'])
     
     # Initialize the progress bar
-    #pb = ProgressBar(len(iview), config, seconde=5)
+    pb = ProgressBar(len(iview), config, seconde=5)
         
     # Apply filter
-    # TODO try both kinds of line selection functions to check efficiency
-    selection = []
+    selection = OBIView_line_selection(iview)
     for i in range(len(iview)) :
-        #pb(i)
+        pb(i)
         line = iview[i]
-        if isinstance(iview, OBIView_NUC_SEQS) :    # put this somewhere else for efficiency
-            sequence = line
-        if eval(config['grep']['predicate']) :
+                
+        loc_env = {'sequence': line, 'line': line}      # TODO add taxonomy
+        
+        good = (reduce(lambda bint x, bint y: x and y,
+                (bool(eval(p, loc_env, line))
+                for p in config['grep']['predicates']), True))
+        
+        if good :
             selection.append(i)
          
     # Create output view with the line selection
-    oview = d.new_view(config['obi']['outputview'], view_to_clone=iview, line_selection=selection, comments="obi grep: "+config['grep']['predicate']+"\n")
+    oview = d.new_view(config['obi']['outputview'], line_selection=selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
 
-    repr(oview)
+    #print("\n")
+    #print(repr(oview))
 
     iview.close()
     oview.close()
     d.close()
     
-    print("Done.")