From 187053026f4a5c40edefbc2344df7ea859c4b612 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Thu, 29 Aug 2019 16:10:09 +0200
Subject: [PATCH] Better detection of missing taxonomy

---
 python/obitools3/commands/annotate.pyx | 2 +-
 python/obitools3/commands/grep.pyx     | 2 +-
 python/obitools3/commands/stats.pyx    | 2 +-
 python/obitools3/commands/uniq.pyx     | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)
 mode change 100755 => 100644 python/obitools3/commands/grep.pyx

diff --git a/python/obitools3/commands/annotate.pyx b/python/obitools3/commands/annotate.pyx
index f93960a..2f76449 100755
--- a/python/obitools3/commands/annotate.pyx
+++ b/python/obitools3/commands/annotate.pyx
@@ -306,7 +306,7 @@ def run(config):
     # Open taxonomy if there is one
     if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
         taxo_uri = open_uri(config['obi']['taxoURI'])
-        if taxo_uri is None:
+        if taxo_uri is None or taxo_uri[2] == bytes:
             raise Exception("Couldn't open taxonomy")
         taxo = taxo_uri[1]
     else :
diff --git a/python/obitools3/commands/grep.pyx b/python/obitools3/commands/grep.pyx
old mode 100755
new mode 100644
index e41867a..a32995d
--- a/python/obitools3/commands/grep.pyx
+++ b/python/obitools3/commands/grep.pyx
@@ -290,7 +290,7 @@ def run(config):
 
     if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
         taxo_uri = open_uri(config["obi"]["taxoURI"])
-        if taxo_uri is None:
+        if taxo_uri is None or taxo_uri[2] == bytes:
             raise Exception("Couldn't open taxonomy")
         taxo = taxo_uri[1]
     else :
diff --git a/python/obitools3/commands/stats.pyx b/python/obitools3/commands/stats.pyx
index 98341f5..f9a181d 100755
--- a/python/obitools3/commands/stats.pyx
+++ b/python/obitools3/commands/stats.pyx
@@ -146,7 +146,7 @@ def run(config):
 
     if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
         taxo_uri = open_uri(config['obi']['taxoURI'])
-        if taxo_uri is None:
+        if taxo_uri is None or taxo_uri[2] == bytes:
             raise Exception("Couldn't open taxonomy")
         taxo = taxo_uri[1]
     else :
diff --git a/python/obitools3/commands/uniq.pyx b/python/obitools3/commands/uniq.pyx
index d733492..d093cb7 100644
--- a/python/obitools3/commands/uniq.pyx
+++ b/python/obitools3/commands/uniq.pyx
@@ -526,7 +526,7 @@ def run(config):
     
     if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
         taxo_uri = open_uri(config['obi']['taxoURI'])
-        if taxo_uri is None:
+        if taxo_uri is None or taxo_uri[2] == bytes:
             raise RollbackException("Couldn't open taxonomy, rollbacking view", o_view)
         taxo = taxo_uri[1]
     else :