From adf5cbef9715af67d8b805103770745c8de68cff Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Fri, 28 Jul 2017 09:55:43 +0200
Subject: [PATCH] Added DMS method to create a DMS if it doesn't already
 exists, otherwise opens it

---
 python/obitools3/commands/import.pyx |  7 ++---
 python/obitools3/dms/capi/obidms.pxd |  1 +
 python/obitools3/dms/dms.pyx         | 38 ++++++++++++++++++----------
 3 files changed, 27 insertions(+), 19 deletions(-)

diff --git a/python/obitools3/commands/import.pyx b/python/obitools3/commands/import.pyx
index 7badd0e..de684eb 100644
--- a/python/obitools3/commands/import.pyx
+++ b/python/obitools3/commands/import.pyx
@@ -147,11 +147,8 @@ def run(config):
     inputs = uopen(config['import']['filename'])
 
     # Create or open DMS
-    try:
-        d = DMS.test_open(config['obi']['defaultdms'])
-    except :
-        d = DMS.new(config['obi']['defaultdms'])
-
+    d = DMS.open_or_new(config['obi']['defaultdms'])
+    
     get_quality = False
     NUC_SEQS_view = False
     if config['import']['seqinformat']=='fasta':
diff --git a/python/obitools3/dms/capi/obidms.pxd b/python/obitools3/dms/capi/obidms.pxd
index be3fb00..0671223 100644
--- a/python/obitools3/dms/capi/obidms.pxd
+++ b/python/obitools3/dms/capi/obidms.pxd
@@ -12,6 +12,7 @@ cdef extern from "obidms.h" nogil:
     OBIDMS_p obi_open_dms(const_char_p dms_path)
     OBIDMS_p obi_test_open_dms(const_char_p dms_path)
     OBIDMS_p obi_create_dms(const_char_p dms_path)
+    int obi_dms_exists(const char* dms_path)
     int obi_close_dms(OBIDMS_p dms)
     char* obi_dms_get_dms_path(OBIDMS_p dms)
     char* obi_dms_get_full_path(OBIDMS_p dms, const_char_p path_name)
diff --git a/python/obitools3/dms/dms.pyx b/python/obitools3/dms/dms.pyx
index 2392c66..48e8213 100644
--- a/python/obitools3/dms/dms.pyx
+++ b/python/obitools3/dms/dms.pyx
@@ -5,9 +5,9 @@ from libc.stdlib  cimport free
 from cpython.list cimport PyList_Size
 
 from .capi.obidms cimport obi_open_dms, \
-                          obi_test_open_dms, \
                           obi_create_dms, \
                           obi_close_dms, \
+                          obi_dms_exists, \
                           obi_dms_get_full_path
                                                       
 from .capi.obitypes cimport const_char_p
@@ -29,6 +29,29 @@ cdef class DMS(OBIWrapper):
     cdef inline OBIDMS_p pointer(self):
         return <OBIDMS_p>(self._pointer)
     
+    @staticmethod
+    def open_or_new(object dms_name) :
+        cdef OBIDMS_p pointer
+        cdef DMS dms
+        cdef bytes dms_name_b = tobytes(dms_name)
+        if DMS.exists(dms_name_b) :
+            pointer = obi_open_dms(<const_char_p> dms_name_b)      
+        else :
+            pointer = obi_create_dms(<const_char_p> dms_name_b)  
+        if pointer == NULL :
+            raise Exception("Failed opening or creating an OBIDMS")
+        dms = OBIWrapper.new_wrapper(DMS, pointer)
+        return dms
+    
+    @staticmethod
+    def exists(object dms_name):
+        cdef bytes dms_name_b = tobytes(dms_name)
+        cdef int rep
+        rep = obi_dms_exists(dms_name_b)
+        if rep < 0 :
+            raise RuntimeError("Error checking if a DMS exists")
+        else :
+            return bool(rep)
     
     @staticmethod
     def new(object dms_name) :
@@ -52,19 +75,6 @@ cdef class DMS(OBIWrapper):
             raise Exception("Failed opening an OBIDMS")
         dms = OBIWrapper.new_wrapper(DMS, pointer)
         return dms
-   
-
-    @staticmethod
-    def test_open(object dms_name) :
-        cdef OBIDMS_p pointer
-        cdef DMS dms
-        cdef bytes dms_name_b = tobytes(dms_name)
-        pointer = obi_test_open_dms(<const_char_p> dms_name_b)      
-        if pointer != NULL :
-            dms = OBIWrapper.new_wrapper(DMS, pointer)
-        else :
-            dms = None
-        return dms
     
     
     def close(self) :