From 88451116e828a02469fb790eb0281a9752fde216 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Tue, 17 Sep 2019 12:28:10 +0200
Subject: [PATCH] URIs: added stdout output (empty URI)

---
 python/obitools3/uri/decode.pyx | 64 ++++++++++++++++++---------------
 1 file changed, 35 insertions(+), 29 deletions(-)

diff --git a/python/obitools3/uri/decode.pyx b/python/obitools3/uri/decode.pyx
index 1b0c93d..b246f3b 100755
--- a/python/obitools3/uri/decode.pyx
+++ b/python/obitools3/uri/decode.pyx
@@ -3,6 +3,8 @@
 from urllib.parse import urlparse, urlunparse, parse_qs, ParseResultBytes
 from os.path import isdir, isfile, basename, join
 
+import sys
+
 from obitools3.dms.dms import DMS
 
 from obitools3.parsers.fasta import fastaNucIterator
@@ -224,34 +226,35 @@ def open_uri(uri,
                         type(dms[1]),
                         urlunparse(urip),
                         len(dms[0]))
-            try:
-                resource=open_dms_element(dms[0],
-                                          dms[1],
-                                          create,
-                                          newviewtype)
-                                
-                scheme=b"dms"
-                urip = ParseResultBytes(scheme=b"dms", 
-                                        netloc=urip.netloc, 
-                                        path=urip.path,
-                                        params=urip.params, 
-                                        query=urip.query, 
-                                        fragment=urip.fragment)
-                
-                if default_dms is None:
-                    config["obi"]["defaultdms"]=resource[0]
-                                
-                return (resource[0],
-                        resource[1],
-                        type(resource[1]),
-                        urlunparse(urip),
-                        len(resource[1]))
-            except Exception as e:
-                global obi_errno
-                if obi_errno == OBIVIEW_ALREADY_EXISTS_ERROR:
-                    raise Exception("View name already exists in this DMS")
-                error=e
-           
+            if dms[1]:
+                try:
+                    resource=open_dms_element(dms[0],
+                                              dms[1],
+                                              create,
+                                              newviewtype)
+                                    
+                    scheme=b"dms"
+                    urip = ParseResultBytes(scheme=b"dms", 
+                                            netloc=urip.netloc, 
+                                            path=urip.path,
+                                            params=urip.params, 
+                                            query=urip.query, 
+                                            fragment=urip.fragment)
+                    
+                    if default_dms is None:
+                        config["obi"]["defaultdms"]=resource[0]
+                                    
+                    return (resource[0],
+                            resource[1],
+                            type(resource[1]),
+                            urlunparse(urip),
+                            len(resource[1]))
+                except Exception as e:
+                    global obi_errno
+                    if obi_errno == OBIVIEW_ALREADY_EXISTS_ERROR:
+                        raise Exception("View name already exists in this DMS")
+                    error=e
+         
     if scheme==b"dms" :
         logger('Error','Could not open DMS URI: %s', uri)
         raise FileNotFoundError()
@@ -268,7 +271,10 @@ def open_uri(uri,
             iseq = urib
             objclass = bytes
     else:  # TODO update uopen to be able to write? 
-        file = open(urip.path, 'wb')
+        if urip.path:
+            file = open(urip.path, 'wb')
+        else:
+            file = sys.stdout.buffer
         
     if file is not None:
         qualifiers=parse_qs(urip.query)