From 13952358b38be4b9e3274bcd40ee2ff59a85d6e4 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Thu, 25 Jul 2019 11:59:19 +0200
Subject: [PATCH] Fixed a bug where some commands wouldn't work if the input
 DMS was not in the current directory

---
 python/obitools3/commands/align.pyx        | 2 +-
 python/obitools3/commands/build_ref_db.pyx | 2 +-
 python/obitools3/commands/clean.pyx        | 2 +-
 python/obitools3/commands/ecopcr.pyx       | 4 ++--
 python/obitools3/commands/ecotag.pyx       | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/python/obitools3/commands/align.pyx b/python/obitools3/commands/align.pyx
index 8f2396d..fa6e640 100644
--- a/python/obitools3/commands/align.pyx
+++ b/python/obitools3/commands/align.pyx
@@ -229,7 +229,7 @@ def run(config):
     
     # Call cython alignment function
       # Using default ID columns of the view. TODO discuss adding option
-    align_columns(i_dms_name,  \
+    align_columns(i_dms.full_path,  \
                   i_view_name,  \
                   o_view_name,  \
                   input_view_2_n   = i_view_name_2,  \
diff --git a/python/obitools3/commands/build_ref_db.pyx b/python/obitools3/commands/build_ref_db.pyx
index 6e541a2..f171bb5 100755
--- a/python/obitools3/commands/build_ref_db.pyx
+++ b/python/obitools3/commands/build_ref_db.pyx
@@ -81,7 +81,7 @@ def run(config):
     input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
     comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
 
-    if build_reference_db(tobytes(i_dms_name), tobytes(i_view_name), tobytes(taxonomy_name), tobytes(o_view_name), comments, config['build_ref_db']['threshold']) < 0:
+    if build_reference_db(i_dms.full_path, tobytes(i_view_name), tobytes(taxonomy_name), tobytes(o_view_name), comments, config['build_ref_db']['threshold']) < 0:
         raise Exception("Error building a reference database")
     
     # If the input and output DMS are not the same, export result view to output DMS
diff --git a/python/obitools3/commands/clean.pyx b/python/obitools3/commands/clean.pyx
index f908294..00ed4bc 100755
--- a/python/obitools3/commands/clean.pyx
+++ b/python/obitools3/commands/clean.pyx
@@ -107,7 +107,7 @@ def run(config):
     command_line = " ".join(sys.argv[1:])
     comments = View.print_config(config, "clean", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
 
-    if obi_clean(tobytes(i_dms_name), tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
+    if obi_clean(i_dms.full_path, tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
               config['clean']['distance'], config['clean']['ratio'], config['clean']['heads-only'], config['clean']['thread-count']) < 0:
         raise Exception("Error running obiclean")
     
diff --git a/python/obitools3/commands/ecopcr.pyx b/python/obitools3/commands/ecopcr.pyx
index 0e93562..65f8a8b 100755
--- a/python/obitools3/commands/ecopcr.pyx
+++ b/python/obitools3/commands/ecopcr.pyx
@@ -178,8 +178,8 @@ def run(config):
 
     # TODO: primers in comments?
 
-    if obi_ecopcr(tobytes(i_dms_name), tobytes(i_view_name), tobytes(taxonomy_name), \
-                  tobytes(o_dms_name), tobytes(o_view_name), comments, \
+    if obi_ecopcr(i_dms.full_path, tobytes(i_view_name), tobytes(taxonomy_name), \
+                  o_dms.full_path, tobytes(o_view_name), comments, \
                   tobytes(config['ecopcr']['primer1']), tobytes(config['ecopcr']['primer2']), \
                   config['ecopcr']['error'], \
                   config['ecopcr']['min-length'], config['ecopcr']['max-length'], \
diff --git a/python/obitools3/commands/ecotag.pyx b/python/obitools3/commands/ecotag.pyx
index 3417bd9..d6326d2 100755
--- a/python/obitools3/commands/ecotag.pyx
+++ b/python/obitools3/commands/ecotag.pyx
@@ -101,7 +101,7 @@ def run(config):
     input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
     comments = View.print_config(config, "ecotag", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
 
-    if obi_ecotag(tobytes(i_dms_name), tobytes(i_view_name), \
+    if obi_ecotag(i_dms.full_path, tobytes(i_view_name), \
                   tobytes(ref_dms_name), tobytes(ref_view_name), \
                   tobytes(taxo_dms_name), tobytes(taxonomy_name), \
                   tobytes(o_view_name), comments,