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obi import: skip on error more robust

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Celine Mercier
2020-05-28 20:40:36 +02:00
parent a7dcf16c06
commit 6094ce2bbc
1 changed files with 122 additions and 113 deletions
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9
python/obitools3/commands/import.pyx
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@ -270,6 +270,8 @@ def run(config):
elif not i%50000: elif not i%50000:
logger("info", "Imported %d entries", i) logger("info", "Imported %d entries", i)
try:
if NUC_SEQS_view: if NUC_SEQS_view:
id_col[i] = entry.id id_col[i] = entry.id
def_col[i] = entry.definition def_col[i] = entry.definition
@ -388,6 +390,13 @@ def run(config):
# Fill value # Fill value
dcols[tag][0][i] = value dcols[tag][0][i] = value
except Exception as e:
print("\nCould not import sequence id:", entry.id, "(error raised:", e, ")")
if 'skiperror' in config['obi'] and not config['obi']['skiperror']:
raise e
else:
pass
i+=1 i+=1
if pb is not None: if pb is not None: