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Clinical-Genomics / genotype

Simple genotype comparison of VCF files
http://taboo.readthedocs.org/en/latest/
MIT License
8 stars 2 forks source link

Error handling #8

Closed robinandeer closed 8 years ago

robinandeer commented 9 years ago

Handle the error from attempting to upload the same sample id twice more gracefully

No handlers could be found for logger "taboo.input.vcf.core"
Traceback (most recent call last):
  File "/home/hiseq.clinical/miniconda/envs/prod/bin/taboo", line 9, in <module>
    load_entry_point('taboo==0.1.0', 'console_scripts', 'taboo')()
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python2.7/site-packages/click/core.py", line 664, in __call__
    return self.main(*args, **kwargs)
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python2.7/site-packages/click/core.py", line 644, in main
    rv = self.invoke(ctx)
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python2.7/site-packages/click/core.py", line 991, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python2.7/site-packages/click/core.py", line 837, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/hiseq.clinical/miniconda/envs/prod/lib/python2.7/site-packages/click/core.py", line 464, in invoke
    return callback(*args, **kwargs)
  File "/mnt/hds/proj/bioinfo/apps/taboo/taboo/subcommands/load/cli.py", line 20, in load
    load_vcf(context.parent.store, input_path, rsnumber_stream, origin=origin)
  File "/mnt/hds/proj/bioinfo/apps/taboo/taboo/input/vcf/core.py", line 38, in load_vcf
    raise exception
sqlalchemy.exc.IntegrityError: (sqlite3.IntegrityError) UNIQUE constraint failed: sample.sample_id, sample.origin [SQL: u'INSERT INTO sample (sample_id, origin) VALUES (?, ?)'] [parameters: (u'ADM978A15', 'sequencing')]