ecotag: now closing all DMS properly

python/obitools3/commands/ecotag.pyx

@@ -64,10 +64,10 @@ def run(config):
     ref_view_name = ref[1]
 
     # Check that the threshold demanded is greater than or equal to the threshold used to build the reference database
-    if config['ecotag']['threshold'] < eval(i_dms[ref_view_name].comments["ref_db_threshold"]) :
+    if config['ecotag']['threshold'] < eval(ref_dms[ref_view_name].comments["ref_db_threshold"]) :
         print("Error: The threshold demanded (%f) is lower than the threshold used to build the reference database (%f).", 
-              config['ecotag']['threshold'], i_dms[ref_view_name].comments["ref_db_threshold"])
-
+              config['ecotag']['threshold'], ref_dms[ref_view_name].comments["ref_db_threshold"])
+    
     # Open the output: only the DMS
     output = open_uri(config['obi']['outputURI'],
                       input=False,
@@ -126,9 +126,11 @@ def run(config):
     # If the input and the output DMS are different, delete the temporary result view in the input DMS
     if i_dms != o_dms:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
     
-    i_dms.close()
+    taxo_dms.close(force=True)
+    ref_dms.close(force=True)
+    i_dms.close(force=True)
     
     logger("info", "Done.")
 

python/obitools3/dms/dms.pyx

@@ -94,16 +94,16 @@ cdef class DMS(OBIWrapper):
         return dms
     
     
-    def close(self) :
+    def close(self, force=False) :
         '''
-        Closes the DMS instance and free the associated memory
+        Closes the DMS instance and free the associated memory (no counter, closing is final)
         
         The `close` method is automatically called by the object destructor.
         '''
         cdef OBIDMS_p pointer = self.pointer()
         if self.active() :
             OBIWrapper.close(self)
-            if (obi_close_dms(pointer, False)) < 0 :
+            if (obi_close_dms(pointer, force=force)) < 0 :
                 raise Exception("Problem closing an OBIDMS")
 
 
@@ -254,7 +254,8 @@ cdef class DMS(OBIWrapper):
     # bash command history property getter
     @property
     def bash_history(self):
-        s = b"#!/bin/bash\n\n"
+        #s = b"#!${bash}/bin/bash\n\n"
+        s = b""
         first = True
         for command in self.command_line_history:
             s+=b"#"

python/obitools3/version.py

@@ -1,5 +1,5 @@
 major = 3
 minor = 0
-serial= '0-beta11'
+serial= '0-beta12a'
 
 version ="%d.%02d.%s" % (major,minor,serial)