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obi import: importing a view to a DMS now uses the C API (more efficient

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and imports all metadata)
This commit is contained in:
Celine Mercier
2019-09-21 12:49:29 +02:00
parent f0f7edf152
commit 06f9d6da60
2 changed files with 26 additions and 12 deletions
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28
python/obitools3/commands/import.pyx
View File

@ -14,6 +14,7 @@ from obitools3.dms.taxo.taxo cimport Taxonomy
from obitools3.utils cimport tobytes, \
tostr, \
get_obitype, \
update_obitype
@ -25,6 +26,8 @@ from obitools3.dms.capi.obiview cimport VIEW_TYPE_NUC_SEQS, \
COUNT_COLUMN, \
TAXID_COLUMN
from obitools3.dms.capi.obidms cimport obi_import_view
from obitools3.dms.capi.obitypes cimport obitype_t, \
OBI_VOID, \
OBI_QUAL
@ -124,7 +127,7 @@ def run(config):
else:
v = None
if config['obi']['taxdump']:
if config['obi']['taxdump'] or isinstance(input[1], View):
dms_only=True
else:
dms_only=False
@ -134,20 +137,31 @@ def run(config):
newviewtype=v,
dms_only=dms_only)
if output is None:
raise Exception("Could not create output view")
raise Exception("Could not open output")
o_dms = output[0]
# If importing a view between two DMS, use C API
if isinstance(input[1], View):
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 :
raise Exception("Error importing a view in a DMS")
o_dms.record_command_line(" ".join(sys.argv[1:]))
o_dms.close()
logger("info", "Done.")
return
# Read taxdump
if config['obi']['taxdump']: # The input is a taxdump to import in a DMS
# Check if taxonomy name isn't already taken
dms = output[0]
taxo_name = output[1]
if Taxonomy.exists(dms, taxo_name.split(b'/')[1]):
if Taxonomy.exists(o_dms, taxo_name.split(b'/')[1]):
raise Exception("Taxonomy name already exists in this DMS")
taxo = Taxonomy.open_taxdump(dms, config['obi']['inputURI'])
taxo = Taxonomy.open_taxdump(o_dms, config['obi']['inputURI'])
taxo.write(taxo_name)
taxo.close()
dms.record_command_line(" ".join(sys.argv[1:]))
dms.close()
o_dms.record_command_line(" ".join(sys.argv[1:]))
o_dms.close()
logger("info", "Done.")
return

4
python/obitools3/commands/ls.pyx
View File

@ -5,7 +5,7 @@ from obitools3.apps.config import logger
from obitools3.dms import DMS
from obitools3.dms.taxo.taxo cimport Taxonomy
from obitools3.apps.optiongroups import addMinimalInputOption
from obitools3.utils cimport tostr
from obitools3.utils cimport tostr, bytes2str_object
__title__="Print a preview of a DMS, view, column...."
@ -35,7 +35,7 @@ def run(config):
dms = input[0]
l = []
for view in input[0]:
l.append(tostr(view) + "\t(Date created: " + tostr(dms[view].comments["Date created"])+")")
l.append(tostr(view) + "\t(Date created: " + str(bytes2str_object(dms[view].comments["Date created"]))+")")
l.sort()
for v in l:
print(v)