Fixed the ultimate bug with embl (and genbank) parsers: raising any
exception in a python generator makes it unable to resume. So now, exceptions are not raised but printed, then functions return None and that's handled at higher level.
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@ -5,6 +5,7 @@ import os
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from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.dms.view.view cimport View
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from obitools3.dms.view import RollbackException
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from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
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from obitools3.dms.column.column cimport Column
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from obitools3.dms.obiseq cimport Nuc_Seq
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@ -153,6 +154,13 @@ def run(config):
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i = 0
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for entry in entries :
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if entry is None: # error or exception handled at lower level, not raised because Python generators can't resume after any exception is raised
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if config['obi']['skiperror']:
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i-=1
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continue
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else:
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raise RollbackException("obi import error, rollbacking view", view)
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pb(i)
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if NUC_SEQS_view:
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