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obi import: added --space-priority option to import a view line by line

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Celine Mercier
2020-07-26 17:36:52 +02:00
parent 24a737aa55
commit 50b292b489
1 changed files with 12 additions and 4 deletions
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16
python/obitools3/commands/import.pyx
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@ -77,6 +77,11 @@ def addOptions(parser):
help="Do a first readthrough of the dataset if it contains huge dictionaries (more than 100 keys) for " help="Do a first readthrough of the dataset if it contains huge dictionaries (more than 100 keys) for "
"a much faster import. This option is not recommended and will slow down the import in any other case.") "a much faster import. This option is not recommended and will slow down the import in any other case.")
group.add_argument('--space-priority',
action="store_true", dest="import:space_priority",
default=False,
help="If importing a view into another DMS, do it by importing each line, saving disk space if the original view "
"has a line selection associated.")
def run(config): def run(config):
@ -142,7 +147,7 @@ def run(config):
else: else:
v = None v = None
if config['obi']['taxdump'] or isinstance(input[1], View): if config['obi']['taxdump'] or (isinstance(input[1], View) and not config['import']['space_priority']):
dms_only=True dms_only=True
else: else:
dms_only=False dms_only=False
@ -170,12 +175,15 @@ def run(config):
logger("info", "Done.") logger("info", "Done.")
return return
# If importing a view between two DMS, use C API # If importing a view between two DMS and not wanting to save space if line selection in original view, use C API
if isinstance(input[1], View): if isinstance(input[1], View) and not config['import']['space_priority']:
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 : 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 :
input[0].close(force=True)
output[0].close(force=True)
raise Exception("Error importing a view in a DMS") raise Exception("Error importing a view in a DMS")
o_dms.record_command_line(" ".join(sys.argv[1:])) o_dms.record_command_line(" ".join(sys.argv[1:]))
o_dms.close() input[0].close(force=True)
output[0].close(force=True)
logger("info", "Done.") logger("info", "Done.")
return return