From da91ffc2c723bb7945b2d056f13a1ac8d8f31fcb Mon Sep 17 00:00:00 2001
From: mercierc <celine.mercier@scionresearch.com>
Date: Mon, 31 May 2021 16:57:20 +1200
Subject: [PATCH] URI decoding: fixed reading a taxonomy before any view

---
 python/obitools3/uri/decode.pyx | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/python/obitools3/uri/decode.pyx b/python/obitools3/uri/decode.pyx
index fc424eb..d88c187 100644
--- a/python/obitools3/uri/decode.pyx
+++ b/python/obitools3/uri/decode.pyx
@@ -192,7 +192,7 @@ def open_uri(uri,
     
     config = getConfiguration()
     urip = urlparse(urib)
-            
+        
     if 'obi' not in config:
         config['obi']={}
     
@@ -209,13 +209,14 @@ def open_uri(uri,
     scheme = urip.scheme
     
     error = None
-    
-    if urib != b"-" and \
+        
+    if b'/taxonomy/' in urib or \
+        (urib != b"-" and \
         (scheme==b"dms" or \
          (scheme==b"" and \
           (((not input) and "outputformat" not in config["obi"]) or \
-          (input and "inputformat" not in config["obi"])))):   # TODO maybe not best way
-        
+          (input and "inputformat" not in config["obi"]))))):   # TODO maybe not best way
+                
         if default_dms is not None and b"/" not in urip.path:   # assuming view to open in default DMS (TODO discuss)
             dms=(default_dms, urip.path)
         else:
@@ -223,7 +224,7 @@ def open_uri(uri,
         
         if dms is None and default_dms is not None:
             dms=(default_dms, urip.path)
-
+                
         if dms is not None:
             if dms_only:
                 return (dms[0],
@@ -248,7 +249,7 @@ def open_uri(uri,
                 
                 if default_dms is None:
                     config["obi"]["defaultdms"]=resource[0]
-                                
+                
                 return (resource[0],
                         resource[1],
                         type(resource[1]),
@@ -464,7 +465,7 @@ def open_uri(uri,
         if format is not None:
             if seqtype==b"nuc":
                 objclass = Nuc_Seq    # Nuc_Seq_Stored? TODO
-                if format==b"fasta" or format==b"silva":
+                if format==b"fasta" or format==b"silva" or format==b"rdp":
                     if input:
                         iseq = fastaNucIterator(file, 
                                                 skip=skip,