From d4f7e02c85fd5af5f54b20ece0c117edad82693a Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Fri, 16 Mar 2018 19:04:54 +0100
Subject: [PATCH] New obi grep working with URI API

---
 python/obitools3/commands/grep.pyx | 120 +++++++++++++++--------------
 1 file changed, 61 insertions(+), 59 deletions(-)

diff --git a/python/obitools3/commands/grep.pyx b/python/obitools3/commands/grep.pyx
index 1e01710..733a530 100644
--- a/python/obitools3/commands/grep.pyx
+++ b/python/obitools3/commands/grep.pyx
@@ -1,52 +1,25 @@
 #cython: language_level=3
 
 from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
-from obitools3.dms.dms import DMS       # TODO cimport doesn't work
-from obitools3.dms.view.view import View, Line_selection    # TODO cimport doesn't work
- 
- 
-from obitools3.apps.optiongroups import addSequenceInputOption
+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, addTaxonomyInputOption, addMinimalOutputOption
+from obitools3.dms.view import RollbackException
 from functools import reduce
+from obitools3.apps.config import logger
 import time
  
-__title__="Grep view lines that match the given predicates"
  
-default_config = {   'inputview'    : None,
-                     'outputview'   : None,
-                     'predicates'   : []
-                 }
+__title__="Grep view lines that match the given predicates"
+
  
 def addOptions(parser):
     
-    addSequenceInputOption(parser)
- 
-    # TODO put this common group somewhere else but I don't know where
-    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('--input-view','-i',
-                       action="store", dest="obi:inputview",
-                       metavar='<INPUT VIEW NAME>',
-                       default=None,
-                       type=str,
-                       help="Name of the input view, either raw if the view is in the default DMS,"
-                            " or in the form 'dms:view' if it is in another DMS.")
- 
-    group.add_argument('--output-view','-o',
-                       action="store", dest="obi:outputview",
-                       metavar='<OUTPUT VIEW NAME>',
-                       default=None,
-                       type=str,
-                       help="Name of the output view, either raw if the view is in the default DMS,"
-                            " or in the form 'dms:view' if it is in another DMS.")
- 
- 
+    addMinimalInputOption(parser)
+    addTaxonomyInputOption(parser)
+    addMinimalOutputOption(parser)
+
     group=parser.add_argument_group('obi grep specific options')
  
     group.add_argument('--predicate','-p',
@@ -59,34 +32,63 @@ def addOptions(parser):
      
 def run(config):
      
-    # Open DMS
-    d = DMS.open(config['obi']['defaultdms'])
-     
-    # Open input view 1
-    iview = View.open(d, config['obi']['inputview'])
-     
+    DMS.obi_atexit()
+    
+    logger("info", "obi grep")
+
+    # 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(b'/')[0] != uri[0]:
+            raise Exception("Input and output DMS must be the same")
+        output_view_name = uri[1]
+    else:
+        output_view_name = uri[0]
+
+    if 'taxoURI' in config['obi'] :   # TODO default None problem
+        taxo_uri = open_uri(config['obi']['taxoURI'])
+        if taxo_uri is None:
+            raise Exception("Couldn't open taxonomy")
+        taxo = taxo_uri[1]
+    else :
+        taxo = None
+
     # Initialize the progress bar
-    pb = ProgressBar(len(iview), config, seconde=5)
-         
+    pb = ProgressBar(len(i_view), config, seconde=5)
+ 
     # Apply filter
-    selection = Line_selection(iview)
-    for i in range(len(iview)) :
+    selection = Line_selection(i_view)
+    for i in range(len(i_view)):
         pb(i)
-        line = iview[i]
+        line = i_view[i]
                  
-        loc_env = {'sequence': line, 'line': line}      # TODO add taxonomy
-         
+        loc_env = {'sequence': line, 'line': line, 'taxonomy': taxo}
+        
         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 = selection.materialize(config['obi']['outputview'], comments="obi grep: "+str(config['grep']['predicates'])+"\n")
- 
+    try:
+        o_view = selection.materialize(output_view_name, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
+    except Exception, e:
+        raise RollbackException("obi grep error, rollbacking view: "+str(e), o_view)
+
+    # TODO DISCUSS if output URI to different DMS, copy view?
+
     print("\n")
-    print(repr(oview))
- 
-    d.close()
+    print(repr(o_view))
+
+    input[0].close()
+    #output[0].close()
+