From df700863848c9ce381abfd9c0293dda1bf8607f6 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 17 Oct 2018 11:27:50 +0200
Subject: [PATCH] New command: obi export

---
 python/obitools3/commands/export.pyx | 170 ++++++++++-----------------
 1 file changed, 64 insertions(+), 106 deletions(-)

diff --git a/python/obitools3/commands/export.pyx b/python/obitools3/commands/export.pyx
index 24c670a..c4da6d4 100644
--- a/python/obitools3/commands/export.pyx
+++ b/python/obitools3/commands/export.pyx
@@ -1,107 +1,65 @@
-# from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
-# from obitools3.dms.dms import OBIDMS       # TODO cimport doesn't work
-# from obitools3.utils cimport bytes2str
-#  
-# import time
-# import re
-# 
-# 
-# __title__="Export a NUC_SEQS view to a fasta or fastq file"
-#  
-#  
-# default_config = {   'inputview'    : None,
-#                  }
-#  
-# def addOptions(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=parser.add_argument_group('obi export specific options')
-#  
-#     group.add_argument('--format','-f',
-#                        action="store", dest="export:format",
-#                        metavar='<FORMAT>',
-#                        default="fasta",
-#                        type=str,
-#                        help="Export in the format <FORMAT>, 'fasta' or 'fastq'. Default: 'fasta'.")         # TODO export in csv
-#  
+#cython: language_level=3
+
+from obitools3.apps.progress cimport ProgressBar  # @UnresolvedImport
+from obitools3.uri.decode import open_uri
+from obitools3.apps.config import logger
+from obitools3.dms import DMS
+from obitools3.dms.obiseq import Nuc_Seq
+
+from obitools3.apps.optiongroups import addMinimalInputOption, \
+                                        addExportOutputOption
+
+
+__title__="Export a view to a different file format"
+
+
+def addOptions(parser):
+    
+    addMinimalInputOption(parser)
+    addExportOutputOption(parser)
+
+
 def run(config):
-    pass
-#      
-#     # TODO import doesn't work
-#     NUC_SEQUENCE_COLUMN = "NUC_SEQ"
-#     ID_COLUMN = "ID"
-#     DEFINITION_COLUMN = "DEFINITION"
-#     QUALITY_COLUMN = "QUALITY"    
-#      
-#     special_columns = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
-#      
-#     # Open DMS
-#     d = OBIDMS(config['obi']['defaultdms'])
-#      
-#     # Open input view
-#     iview = d.open_view(config['obi']['inputview'])
-#      
-#     print(iview.type)
-#      
-#     # TODO check that the view has the type NUC_SEQS
-#     if ((config['export']['format'] == "fasta") or (config['export']['format'] == "fastq")) and (iview.type != "NUC_SEQS_VIEW") :   # TODO find a way to import those macros
-#         raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
-#      
-#     # Initialize the progress bar
-#     pb = ProgressBar(len(iview), config, seconde=5)
-#      
-#     i=0
-#     for seq in iview :
-#         pb(i)
-#          
-#         toprint = ">"+seq.id+" "
-#          
-#         for col_name in seq :
-#             if col_name not in special_columns :
-#                 toprint = toprint + col_name + "=" + str(seq[col_name]) + "; "
-#          
-#         if DEFINITION_COLUMN in seq :
-#             toprint = toprint + seq.definition
-#          
-#         nucseq = bytes2str(seq.nuc_seq)
-#          
-#         if config['export']['format'] == "fasta" :
-#             nucseq = re.sub("(.{60})", "\\1\n", nucseq, 0, re.DOTALL)
-#          
-#         toprint = toprint + "\n" + nucseq
-#          
-#         if config['export']['format'] == "fastq" :
-#             toprint = toprint + "\n" + "+" + "\n" + seq.get_str_quality()
-#              
-#         print(toprint)
-#         i+=1
-#          
-#     iview.close()
-#     d.close()
-#      
-#     print("Done.")
-#      
-#      
-#  
-#      
-#      
-#      
-#      
-#          
\ No newline at end of file
+        
+    DMS.obi_atexit()
+    
+    logger("info", "obi export : exports a view to a different file format")
+    
+    # Open the input
+    input = open_uri(config['obi']['inputURI'])
+    if input is None:
+        raise Exception("Could not read input")
+    iview = input[1]
+            
+    # Open the output
+    output = open_uri(config['obi']['outputURI'],
+                      input=False)
+    if output is None:
+        raise Exception("Could not open output URI")
+
+    output_object = output[0]
+    writer = output[1]
+        
+     # Check that the input view has the type NUC_SEQS if needed    # TODO discuss, maybe bool property
+    if (output[2] == Nuc_Seq) and (iview.type != b"NUC_SEQS_VIEW") :  # Nuc_Seq_Stored? TODO
+        raise Exception("Error: the view to export in fasta or fastq format is not a NUC_SEQS view")
+   
+    # Initialize the progress bar
+    pb = ProgressBar(len(iview), config, seconde=5)
+    
+    i=0
+    for seq in iview :
+        pb(i)
+        try:
+            writer(seq)
+        except StopIteration:
+            break
+        i+=1
+
+    # TODO save command in input dms?
+    
+    output_object.close()
+    iview.close()
+    input[0].close()
+
+    logger("info", "obi export: Done")