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All commands now handle outputing to another DMS + small fixes

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This commit is contained in:
Celine Mercier
2018-11-02 19:03:09 +01:00
parent 8a8e9e50b2
commit 35f3e7c30b
10 changed files with 266 additions and 153 deletions
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6
python/obitools3/commands/uniq.pyx
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@ -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_view_name.append(config['obi']['taxoURI'].split("/", 1)[1])
input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
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)