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obi import: fixed bug when importing a taxdump

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This commit is contained in:
Celine Mercier
2019-09-22 16:45:30 +02:00
parent ba9ba7aa60
commit 71276537a6
1 changed files with 14 additions and 15 deletions
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27
python/obitools3/commands/import.pyx
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@ -144,25 +144,24 @@ def run(config):
o_dms = output[0] o_dms = output[0]
# If importing a view between two DMS, use C API # Read taxdump
if isinstance(input[1], View): if config['obi']['taxdump']: # The input is a taxdump to import in a DMS
if obi_import_view(input[0].name_with_full_path, o_dms.name_with_full_path, input[1].name, tobytes((config['obi']['outputURI'].split('/'))[-1])) < 0 : # Check if taxonomy name isn't already taken
raise Exception("Error importing a view in a DMS") taxo_name = output[1].split(b'/')[1]
if Taxonomy.exists(o_dms, taxo_name):
raise Exception("Taxonomy name already exists in this DMS")
taxo = Taxonomy.open_taxdump(o_dms, config['obi']['inputURI'])
taxo.write(taxo_name)
taxo.close()
o_dms.record_command_line(" ".join(sys.argv[1:])) o_dms.record_command_line(" ".join(sys.argv[1:]))
o_dms.close() o_dms.close()
logger("info", "Done.") logger("info", "Done.")
return return
# If importing a view between two DMS, use C API
# Read taxdump if isinstance(input[1], View):
if config['obi']['taxdump']: # The input is a taxdump to import in a DMS if obi_import_view(input[0].name_with_full_path, o_dms.name_with_full_path, input[1].name, tobytes((config['obi']['outputURI'].split('/'))[-1])) < 0 :
# Check if taxonomy name isn't already taken raise Exception("Error importing a view in a DMS")
taxo_name = output[1]
if Taxonomy.exists(o_dms, taxo_name.split(b'/')[1]):
raise Exception("Taxonomy name already exists in this DMS")
taxo = Taxonomy.open_taxdump(o_dms, config['obi']['inputURI'])
taxo.write(taxo_name)
taxo.close()
o_dms.record_command_line(" ".join(sys.argv[1:])) o_dms.record_command_line(" ".join(sys.argv[1:]))
o_dms.close() o_dms.close()
logger("info", "Done.") logger("info", "Done.")