@@ -381,13 +381,17 @@ def get_study_hash(seqinfo):
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def fix_canceled_runs (seqinfo ):
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"""Function that adds cancelme_ to known bad runs which were forgotten
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"""
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- accession_number = get_unique (seqinfo , 'accession_number' )
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- if accession_number in fix_accession2run :
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- lgr .info ("Considering some runs possibly marked to be "
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- "canceled for accession %s" , accession_number )
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- badruns = fix_accession2run [accession_number ]
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- badruns_pattern = '|' .join (badruns )
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- for i , s in enumerate (seqinfo ):
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+ if not fix_accession2run :
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+ return seqinfo # nothing to do
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+ for i , s in enumerate (seqinfo ):
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+ accession_number = getattr (s , 'accession_number' )
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+ if accession_number and accession_number in fix_accession2run :
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+ lgr .info ("Considering some runs possibly marked to be "
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+ "canceled for accession %s" , accession_number )
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+ # This code is reminiscent of prior logic when operating on
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+ # a single accession, but left as is for now
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+ badruns = fix_accession2run [accession_number ]
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+ badruns_pattern = '|' .join (badruns )
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if re .match (badruns_pattern , s .series_id ):
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lgr .info ('Fixing bad run {0}' .format (s .series_id ))
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fixedkwargs = dict ()
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