all commands (almost): cleaner DMS closing at the end

python/obitools3/commands/align.pyx

@@ -266,9 +266,9 @@ 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()
+    i_dms.close(force=True)
     
     logger("info", "Done.")
   

python/obitools3/commands/alignpairedend.pyx

@@ -247,10 +247,10 @@ def run(config):
     #print("\n\nOutput view:\n````````````", file=sys.stderr)
     #print(repr(view), file=sys.stderr)
     
-    input[0].close()
+    input[0].close(force=True)
     if two_views:
-        rinput[0].close()
+        rinput[0].close(force=True)
-    output[0].close()
+    output[0].close(force=True)
 
     logger("info", "Done.")
     

python/obitools3/commands/annotate.pyx

@@ -379,7 +379,7 @@ def run(config):
     # If the input and the output DMS are different, delete the temporary imported view used to create the final view
     if i_dms != o_dms:
         View.delete_view(o_dms, imported_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
-    i_dms.close()
+    i_dms.close(force=True)
 
     logger("info", "Done.")

python/obitools3/commands/build_ref_db.pyx

@@ -97,9 +97,9 @@ 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()
+    i_dms.close(force=True)
 
     logger("info", "Done.")
     

python/obitools3/commands/cat.pyx

@@ -133,7 +133,7 @@ def run(config):
     #print(repr(view), file=sys.stderr)
 
     for d in idms_list:
-        d.close()
+        d.close(force=True)
-    o_dms.close()
+    o_dms.close(force=True)
     
     logger("info", "Done.")

python/obitools3/commands/clean.pyx

@@ -124,8 +124,8 @@ 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()
+    i_dms.close(force=True)
 
     logger("info", "Done.")

python/obitools3/commands/count.pyx

@@ -56,3 +56,5 @@ def run(config):
         print(count2)
     else:
         print(count1)
+    
+    input[0].close(force=True)

python/obitools3/commands/export.pyx

@@ -86,7 +86,7 @@ def run(config):
     if not BrokenPipeError and not IOError:
         output_object.close()
     iview.close()
-    input[0].close()
+    input[0].close(force=True)
 
     logger("info", "Done.")
 

python/obitools3/commands/grep.pyx

@@ -370,7 +370,7 @@ def run(config):
     # If the input and the output DMS are different, delete the temporary imported view used to create the final view
     if i_dms != o_dms:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
-    i_dms.close()
+    i_dms.close(force=True)
 
     logger("info", "Done.")

python/obitools3/commands/head.pyx

@@ -103,7 +103,7 @@ def run(config):
     # If the input and the output DMS are different, delete the temporary imported view used to create the final view
     if i_dms != o_dms:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
-    i_dms.close()
+    i_dms.close(force=True)
     
     logger("info", "Done.")

python/obitools3/commands/history.pyx

@@ -55,3 +55,4 @@ def run(config):
         else:
             raise Exception("ASCII history only available for views")
     
+    input[0].close(force=True)

python/obitools3/commands/less.pyx

@@ -46,5 +46,5 @@ def run(config):
     process.wait()
 
     iview.close()
-    input[0].close()
+    input[0].close(force=True)
 

python/obitools3/commands/ls.pyx

@@ -36,6 +36,7 @@ def run(config):
         l = []
         for view in input[0]:
             l.append(tostr(view) + "\t(Date created: " + str(bytes2str_object(dms[view].comments["Date created"]))+")")
+            dms[view].close()
         l.sort()
         for v in l:
             print(v)
@@ -52,3 +53,4 @@ def run(config):
         print("\n### Comments:")
         print(str(input[1].comments))
     
+    input[0].close(force=True)

python/obitools3/commands/sort.pyx

@@ -141,7 +141,7 @@ def run(config):
     # If the input and the output DMS are different, delete the temporary imported view used to create the final view
     if i_dms != o_dms:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
-    i_dms.close()
+    i_dms.close(force=True)
 
     logger("info", "Done.")

python/obitools3/commands/tail.pyx

@@ -106,7 +106,7 @@ def run(config):
     # If the input and the output DMS are different, delete the temporary imported view used to create the final view
     if i_dms != o_dms:
         View.delete_view(i_dms, o_view_name)
-        o_dms.close()
+        o_dms.close(force=True)
-    i_dms.close()
+    i_dms.close(force=True)
     
     logger("info", "Done.")

python/obitools3/commands/test.pyx

@@ -529,7 +529,7 @@ def run(config):
         test_taxo(config, infos)
     
     infos['view'].close()
-    infos['dms'].close()
+    infos['dms'].close(force=True)
     shutil.rmtree(config['obi']['defaultdms']+'.obidms', ignore_errors=True)
      
     print("Done.")