All commands now handle outputing to another DMS + small fixes

python/obitools3/commands/annotate.pyx

@@ -8,7 +8,7 @@ from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption
 from obitools3.dms.view import RollbackException
 from functools import reduce
 from obitools3.apps.config import logger
-from obitools3.utils cimport tobytes
+from obitools3.utils cimport tobytes, str2bytes
 from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
                                         ID_COLUMN, \
                                         DEFINITION_COLUMN, \
@@ -272,24 +272,39 @@ def run(config):
     input = open_uri(config['obi']['inputURI'])
     if input is None:
         raise Exception("Could not read input view")
+    i_dms = input[0]
     i_view = input[1]
+    i_view_name = input[1].name
 
-    # Read the name of the output view
+    # Open the output: only the DMS, as the output view is going to be created by cloning the input view
-    uri = config['obi']['outputURI'].split('/')
+    # (could eventually be done via an open_uri() argument)
-    if len(uri)==2:
+    output = open_uri(config['obi']['outputURI'],
-        # Check that input and output DMS are the same (predicate, to discuss)
+                      input=False,
-        if config['obi']['inputURI'].split('/')[0] != uri[0]:
+                      dms_only=True)
-            raise Exception("Input and output DMS must be the same")
+    if output is None:
-        output_view_name = uri[1]
+        raise Exception("Could not create output view")
-    else:
+    o_dms = output[0]
-        output_view_name = uri[0]
+    o_view_name = output[1]
     
+    # If the input and output DMS are not the same, import the input view in the output DMS before cloning it to modify it
+    # (could be the other way around: clone and modify in the input DMS then import the new view in the output DMS)
+    if i_dms != o_dms:
+        imported_view_name = i_view_name
+        i=0
+        while imported_view_name in o_dms:  # Making sure view name is unique in output DMS
+            imported_view_name = i_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], i_view_name, imported_view_name)
+        i_view = o_dms[imported_view_name]
+        
     # Clone output view from input view
-    o_view = i_view.clone(output_view_name, comments=i_view.comments)  # TODO comments
+    o_view = i_view.clone(o_view_name)
     if o_view is None:
         raise Exception("Couldn't create output view")
+    i_view.close()
 
-    if 'taxoURI' in config['obi'] :   # TODO default None problem
+    # 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:
             raise Exception("Couldn't open taxonomy")
@@ -345,16 +360,19 @@ def run(config):
     # Save command config in View and DMS comments
     command_line = " ".join(sys.argv[1:])
     input_dms_name=[input[0].name]
-    input_view_name=[input[1].name]
+    input_view_name=[i_view_name]
     if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
-        input_dms_name.append(config['obi']['taxoURI'].split("/", 1)[0])
+        input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
-        input_view_name.append(config['obi']['taxoURI'].split("/", 1)[1])
+        input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
     o_view.write_config(config, "annotate", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
-    input[0].record_command_line(command_line)   # TODO assuming same dms
+    output[0].record_command_line(command_line)
 
     print("\n")
     print(repr(o_view))
 
-    input[0].close()
+    # If the input and the output DMS are different, delete the temporary imported view used to create the final view
-   # output[0].close()
+    if i_dms != o_dms:
+        View.delete_view(o_dms, imported_view_name)
+        o_dms.close()
+    i_dms.close()
     

python/obitools3/commands/clean.pyx

@@ -8,7 +8,7 @@ from obitools3.dms.capi.obiclean cimport obi_clean
 from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
 from obitools3.uri.decode import open_uri
 from obitools3.apps.config import logger
-from obitools3.utils cimport tobytes
+from obitools3.utils cimport tobytes, str2bytes
 from obitools3.dms.view.view cimport View
 from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
 
@@ -66,38 +66,58 @@ def run(config):
     DMS.obi_atexit()
     
     logger("info", "obi clean")
-    
-    # Open DMS
-    dms_name = config['obi']['inputURI'].split('/')[0]
-    dms = open_uri(dms_name)[0]
-    
-    # Read the name of the input view
-    uri_i = config['obi']['inputURI'].split('/')
-    i_view_name = uri_i[1]
 
-    # Read the name of the output view
+    # Open the input: only the DMS
-    uri_o = config['obi']['outputURI'].split('/')
+    input = open_uri(config['obi']['inputURI'],
-    if len(uri_o)==2:
+                     dms_only=True)
-        # Check that input and output DMS are the same (predicate, to discuss)
+    if input is None:
-        if dms_name != uri_o[0]:
+        raise Exception("Could not read input")
-            raise Exception("Input and output DMS must be the same")
+    i_dms = input[0]
-        o_view_name = uri_o[1]
+    i_dms_name = input[0].name
+    i_view_name = input[1]
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output")
+    o_dms = output[0]
+    final_o_view_name = output[1]
+    
+    # If the input and output DMS are not the same, run obiclean creating a temporary view that will be exported to 
+    # the right DMS and deleted in the other afterwards.
+    if i_dms != o_dms:
+        temporary_view_name = final_o_view_name
+        i=0
+        while temporary_view_name in i_dms:  # Making sure view name is unique in input DMS
+            temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
+            i+=1
+        o_view_name = temporary_view_name
     else:
-        o_view_name = uri_o[0]
+        o_view_name = final_o_view_name
-
+        
     # Save command config in View comments
     command_line = " ".join(sys.argv[1:])
-    comments = View.print_config(config, "clean", command_line, input_dms_name=[dms_name], input_view_name=[i_view_name])
+    comments = View.print_config(config, "clean", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
 
-    if obi_clean(tobytes(dms_name), tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
+    if obi_clean(tobytes(i_dms_name), 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'], 1) < 0:
         raise Exception("Error running obiclean")
-
+    
+    # If the input and output DMS are not the same, export result view to output DMS
+    if i_dms != o_dms:
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
+    
     # Save command config in DMS comments
-    dms.record_command_line(command_line)
+    o_dms.record_command_line(command_line)
 
     print("\n")
-    print(repr(dms[o_view_name]))
+    print(repr(o_dms[final_o_view_name]))
-
-    dms.close()
 
+    # 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()
+    
+    i_dms.close()

python/obitools3/commands/ecopcr.pyx

@@ -144,34 +144,37 @@ def run(config):
     DMS.obi_atexit()
     
     logger("info", "obi ecopcr")
-    
-    # TODO Bad URI reading because current one is not adapted
-    
-    # Get input DMS path
-    i_dms_name = config['obi']['inputURI'].split('/')[0]
-    
-    # Read the name of the input view
-    i_uri = config['obi']['inputURI'].split('/')
-    i_view_name = i_uri[1]
-    
-    # Read the name of the output view
-    o_uri = config['obi']['outputURI'].split('/')
-    if len(o_uri)==2:
-        # Get output DMS path
-        o_dms_name = o_uri[0]
-        o_view_name = o_uri[1]
-    else:
-        o_dms_name = i_dms_name
-        o_view_name = o_uri[0]
 
-    o_dms = open_uri(o_dms_name, input=False)[0]
+    # Open the input: only the DMS
-    
+    input = open_uri(config['obi']['inputURI'],
+                     dms_only=True)
+    if input is None:
+        raise Exception("Could not read input")
+    i_dms = input[0]
+    i_dms_name = input[0].name
+    i_view_name = input[1]
+
+    # Open the output: only the DMS
+    output = open_uri(config['obi']['outputURI'],
+                      input=False,
+                      dms_only=True)
+    if output is None:
+        raise Exception("Could not create output")
+    o_dms = output[0]
+    o_dms_name = output[0].name
+    o_view_name = output[1]
+
     # Read taxonomy name    
-    taxonomy_name = config['obi']['taxoURI'].split('/')[2]
+    taxonomy_name = config['obi']['taxoURI'].split("/")[-1]   # Robust in theory
-
+    
     # Save command config in View comments
     command_line = " ".join(sys.argv[1:])
-    comments = View.print_config(config, "ecopcr", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name, config['obi']['taxoURI']])
+    input_dms_name=[i_dms_name]
+    input_view_name= [i_view_name]
+    input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
+    input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
+
+    comments = View.print_config(config, "ecopcr", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
 
     # TODO: primers in comments?
 

python/obitools3/commands/grep.pyx

@@ -7,7 +7,7 @@ from obitools3.uri.decode import open_uri
 from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
-from obitools3.utils cimport tobytes
+from obitools3.utils cimport tobytes, str2bytes
 
 from functools import reduce
 import time
@@ -267,19 +267,28 @@ def run(config):
     input = open_uri(config["obi"]["inputURI"])
     if input is None:
         raise Exception("Could not read input view")
+    i_dms = input[0]
     i_view = input[1]
 
-    # Read the name of the output view
+    # Open the output: only the DMS
-    uri = config["obi"]["outputURI"].split("/")
+    output = open_uri(config['obi']['outputURI'],
-    if len(uri)==2:
+                      input=False,
-        # Check that input and output DMS are the same (predicate, to discuss)
+                      dms_only=True)
-        if config["obi"]["inputURI"].split("/")[0] != uri[0]:
+    if output is None:
-            raise Exception("Input and output DMS must be the same")
+        raise Exception("Could not create output view")
-        output_view_name = uri[1]
+    o_dms = output[0]
-    else:
+    o_view_name_final = output[1]
-        output_view_name = uri[0]
+    o_view_name = o_view_name_final
+    
+    # If the input and output DMS are not the same, create output view in input DMS first, then export it
+    # to output DMS, making sure the temporary view name is unique in the input DMS 
+    if i_dms != o_dms:
+        i=0
+        while o_view_name in i_dms:
+            o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
+            i+=1        
 
-    if "taxoURI" in config["obi"] :   # TODO default None problem
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
         taxo_uri = open_uri(config["obi"]["taxoURI"])
         if taxo_uri is None:
             raise Exception("Couldn't open taxonomy")
@@ -307,25 +316,32 @@ def run(config):
 
     # Create output view with the line selection
     try:
-        o_view = selection.materialize(output_view_name)
+        o_view = selection.materialize(o_view_name)
     except Exception, e:
         raise RollbackException("obi grep error, rollbacking view: "+str(e), o_view)
-
+    
-    # TODO DISCUSS if output URI to different DMS, copy view?
-
     # Save command config in View and DMS comments
     command_line = " ".join(sys.argv[1:])
     input_dms_name=[input[0].name]
     input_view_name=[input[1].name]
     if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
-        input_dms_name.append(config['obi']['taxoURI'].split("/", 1)[0])
+        input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
-        input_view_name.append(config['obi']['taxoURI'].split("/", 1)[1])
+        input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
     o_view.write_config(config, "grep", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
-    input[0].record_command_line(command_line)  # TODO assuming input and output dms are the same
+    o_dms.record_command_line(command_line)
+
+    # If input and output DMS are not the same, export the temporary view to the output DMS
+    # and delete the temporary view in the input DMS
+    if i_dms != o_dms:
+        o_view.close()
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
+        o_view = o_dms[o_view_name_final]
 
     print("\n")
     print(repr(o_view))
 
-    input[0].close()
+    # If the input and the output DMS are different, delete the temporary imported view used to create the final view
-    #output[0].close()
+    if i_dms != o_dms:
-    
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close()
+    i_dms.close()

python/obitools3/commands/head.pyx

@@ -7,6 +7,7 @@ from obitools3.uri.decode import open_uri
 from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
+from obitools3.utils cimport str2bytes
 
 import time
 import sys
@@ -37,50 +38,65 @@ def run(config):
     logger("info", "obi head")
 
     # Open the input
-    input = open_uri(config['obi']['inputURI'])
+    input = open_uri(config["obi"]["inputURI"])
     if input is None:
         raise Exception("Could not read input view")
     i_dms = input[0]
     i_view = input[1]
 
-    # Read the name of the output view
+    # Open the output: only the DMS
-    uri = config['obi']['outputURI'].split('/')
+    output = open_uri(config['obi']['outputURI'],
-    if len(uri)==2:
+                      input=False,
-        # Check that input and output DMS are the same (predicate, to discuss)
+                      dms_only=True)
-        if config['obi']['inputURI'].split('/')[0] != uri[0]:
+    if output is None:
-            raise Exception("Input and output DMS must be the same")
+        raise Exception("Could not create output view")
-        output_view_name = uri[1]
+    o_dms = output[0]
-    else:
+    o_view_name_final = output[1]
-        output_view_name = uri[0]
+    o_view_name = o_view_name_final
-
+    
-    # Initialize the progress bar
+    # If the input and output DMS are not the same, create output view in input DMS first, then export it
-    pb = ProgressBar(len(i_view), config, seconde=5)
+    # to output DMS, making sure the temporary view name is unique in the input DMS 
+    if i_dms != o_dms:
+        i=0
+        while o_view_name in i_dms:
+            o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
+            i+=1        
     
     n = min(config['head']['count'], len(i_view))
+
+    # Initialize the progress bar
+    pb = ProgressBar(n, config, seconde=5)
         
     selection = Line_selection(i_view)
     
     for i in range(n):
+        pb(i)
         selection.append(i)
-
-    # Save command config in View comments
-    command_line = " ".join(sys.argv[1:])
-    comments = View.get_config_dict(config, "head", command_line, input_dms_name=[i_dms.name], input_view_name=[i_view.name])
     
     # Create output view with the line selection
     try:
-        o_view = selection.materialize(output_view_name, comments=comments)
+        o_view = selection.materialize(o_view_name)
     except Exception, e:
         raise RollbackException("obi head error, rollbacking view: "+str(e), o_view)
     
-    # TODO DISCUSS if output URI to different DMS, copy view?
-
     # Save command config in DMS comments
-    i_dms.record_command_line(command_line)
+    command_line = " ".join(sys.argv[1:])
+    o_view.write_config(config, "head", command_line, input_dms_name=[i_dms.name], input_view_name=[i_view.name])
+    o_dms.record_command_line(command_line)
+
+    # If input and output DMS are not the same, export the temporary view to the output DMS
+    # and delete the temporary view in the input DMS
+    if i_dms != o_dms:
+        o_view.close()
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
+        o_view = o_dms[o_view_name_final]
 
     print("\n")
     print(repr(o_view))
 
-    input[0].close()
+    # If the input and the output DMS are different, delete the temporary imported view used to create the final view
-    #output[0].close()
+    if i_dms != o_dms:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close()
+    i_dms.close()
     

python/obitools3/commands/ngsfilter.pyx

@@ -511,7 +511,7 @@ def run(config):
     o_view.write_config(config, "ngsfilter", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
     unidentified.write_config(config, "ngsfilter", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
     # TODO add comment about unidentified seqs
-    output[0].record_command_line(command_line)   # TODO if same dms...
+    output[0].record_command_line(command_line)
     
     print("\n")
     print(repr(o_view))

python/obitools3/commands/sort.pyx

@@ -7,6 +7,8 @@ from obitools3.uri.decode import open_uri
 from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
+from obitools3.utils cimport str2bytes
+
 from obitools3.dms.capi.obitypes cimport OBI_BOOL, \
                                          OBI_CHAR, \
                                          OBI_FLOAT, \
@@ -70,20 +72,29 @@ def run(config):
     logger("info", "obi sort")
 
     # Open the input
-    input = open_uri(config['obi']['inputURI'])
+    input = open_uri(config["obi"]["inputURI"])
     if input is None:
         raise Exception("Could not read input view")
+    i_dms = input[0]
     i_view = input[1]
 
-    # Read the name of the output view
+    # Open the output: only the DMS
-    uri = config['obi']['outputURI'].split('/')
+    output = open_uri(config['obi']['outputURI'],
-    if len(uri)==2:
+                      input=False,
-        # Check that input and output DMS are the same (predicate, to discuss)
+                      dms_only=True)
-        if config['obi']['inputURI'].split('/')[0] != uri[0]:
+    if output is None:
-            raise Exception("Input and output DMS must be the same")
+        raise Exception("Could not create output view")
-        output_view_name = uri[1]
+    o_dms = output[0]
-    else:
+    o_view_name_final = output[1]
-        output_view_name = uri[0]
+    o_view_name = o_view_name_final
+    
+    # If the input and output DMS are not the same, create output view in input DMS first, then export it
+    # to output DMS, making sure the temporary view name is unique in the input DMS 
+    if i_dms != o_dms:
+        i=0
+        while o_view_name in i_dms:
+            o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
+            i+=1        
 
     # Initialize the progress bar
     pb = ProgressBar(len(i_view), config, seconde=5)
@@ -100,20 +111,29 @@ def run(config):
 
     # Create output view with the sorted line selection
     try:
-        o_view = selection.materialize(output_view_name, comments="obi sort: "+str(config['sort']['keys'])+"\n")
+        o_view = selection.materialize(o_view_name)
     except Exception, e:
         raise RollbackException("obi sort error, rollbacking view: "+str(e), o_view)
 
-    # TODO DISCUSS if output URI to different DMS, copy view?
-
     # Save command config in View and DMS comments
     command_line = " ".join(sys.argv[1:])
-    o_view.write_config(config, "sort", command_line, input_dms_name=[input[0].name], input_view_name=[input[1].name])
+    input_dms_name=[input[0].name]
-    input[0].record_command_line(command_line)     # TODO assuming same dms...
+    input_view_name=[input[1].name]
+    o_view.write_config(config, "sort", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
+    o_dms.record_command_line(command_line)
+
+    # If input and output DMS are not the same, export the temporary view to the output DMS
+    # and delete the temporary view in the input DMS
+    if i_dms != o_dms:
+        o_view.close()
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
+        o_view = o_dms[o_view_name_final]
 
     print("\n")
     print(repr(o_view))
 
-    input[0].close()
+    # If the input and the output DMS are different, delete the temporary imported view used to create the final view
-    #output[0].close()
+    if i_dms != o_dms:
-    
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close()
+    i_dms.close()

python/obitools3/commands/stats.pyx

@@ -143,7 +143,7 @@ def run(config):
         raise Exception("Could not read input view")
     i_view = input[1]
 
-    if 'taxoURI' in config['obi'] :   # TODO default None problem
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
         taxo_uri = open_uri(config['obi']['taxoURI'])
         if taxo_uri is None:
             raise Exception("Couldn't open taxonomy")

python/obitools3/commands/tail.pyx

@@ -7,6 +7,7 @@ from obitools3.uri.decode import open_uri
 from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
 from obitools3.dms.view import RollbackException
 from obitools3.apps.config import logger
+from obitools3.utils cimport str2bytes
 
 import time
 import sys
@@ -37,30 +38,39 @@ def run(config):
     logger("info", "obi tail")
 
     # Open the input
-    input = open_uri(config['obi']['inputURI'])
+    input = open_uri(config["obi"]["inputURI"])
     if input is None:
         raise Exception("Could not read input view")
     i_dms = input[0]
     i_view = input[1]
 
-    # Read the name of the output view
+    # Open the output: only the DMS
-    uri = config['obi']['outputURI'].split('/')
+    output = open_uri(config['obi']['outputURI'],
-    if len(uri)==2:
+                      input=False,
-        # Check that input and output DMS are the same (predicate, to discuss)
+                      dms_only=True)
-        if config['obi']['inputURI'].split('/')[0] != uri[0]:
+    if output is None:
-            raise Exception("Input and output DMS must be the same")
+        raise Exception("Could not create output view")
-        output_view_name = uri[1]
+    o_dms = output[0]
-    else:
+    o_view_name_final = output[1]
-        output_view_name = uri[0]
+    o_view_name = o_view_name_final
-
+    
-    # Initialize the progress bar
+    # If the input and output DMS are not the same, create output view in input DMS first, then export it
-    pb = ProgressBar(len(i_view), config, seconde=5)
+    # to output DMS, making sure the temporary view name is unique in the input DMS 
+    if i_dms != o_dms:
+        i=0
+        while o_view_name in i_dms:
+            o_view_name = o_view_name_final+b"_"+str2bytes(str(i))
+            i+=1        
     
     start = max(len(i_view) - config['tail']['count'], 0)
+
+    # Initialize the progress bar
+    pb = ProgressBar(len(i_view) - start, config, seconde=5)
         
     selection = Line_selection(i_view)
     
     for i in range(start, len(i_view)):
+        pb(i)
         selection.append(i)
 
     # Save command config in View comments
@@ -69,18 +79,28 @@ def run(config):
 
     # Create output view with the line selection
     try:
-        o_view = selection.materialize(output_view_name, comments="obi tail: "+str(len(selection))+"\n")
+        o_view = selection.materialize(o_view_name)
     except Exception, e:
         raise RollbackException("obi tail error, rollbacking view: "+str(e), o_view)
 
-    # TODO DISCUSS if output URI to different DMS, copy view?
-
     # Save command config in DMS comments
-    i_dms.record_command_line(command_line)
+    command_line = " ".join(sys.argv[1:])
+    o_view.write_config(config, "tail", command_line, input_dms_name=[i_dms.name], input_view_name=[i_view.name])
+    o_dms.record_command_line(command_line)
+
+    # If input and output DMS are not the same, export the temporary view to the output DMS
+    # and delete the temporary view in the input DMS
+    if i_dms != o_dms:
+        o_view.close()
+        View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, o_view_name_final)
+        o_view = o_dms[o_view_name_final]
 
     print("\n")
     print(repr(o_view))
 
-    input[0].close()
+    # If the input and the output DMS are different, delete the temporary imported view used to create the final view
-    #output[0].close()
+    if i_dms != o_dms:
+        View.delete_view(i_dms, o_view_name)
+        o_dms.close()
+    i_dms.close()
     

python/obitools3/commands/uniq.pyx

@@ -508,7 +508,7 @@ def run(config):
     entries = input[1]
     o_view = output[1]
     
-    if 'taxoURI' in config['obi'] :   # TODO default None problem
+    if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
         taxo_uri = open_uri(config['obi']['taxoURI'])
         if taxo_uri is None:
             raise RollbackException("Couldn't open taxonomy, rollbacking view", o_view)
@@ -529,8 +529,8 @@ def run(config):
     input_dms_name=[input[0].name]
     input_view_name=[input[1].name]
     if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
-        input_dms_name.append(config['obi']['taxoURI'].split("/", 1)[0])
+        input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
-        input_view_name.append(config['obi']['taxoURI'].split("/", 1)[1])
+        input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
     o_view.write_config(config, "uniq", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
     output[0].record_command_line(command_line)