C4-352 Patch error info to FileProcessed #243
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willronchetti
commented
Oct 21, 2020
willronchetti
commented
- When an error occurs in ingestion, patch the error string to the associated FileProcessed
netsettler
approved these changes
Oct 21, 2020
src/encoded/ingestion_listener.py
Outdated
| @@ -669,6 +682,8 @@ def post_variants_and_variant_samples(self, parser, file_meta): | |||
| success += 1 | |||
| except Exception as e: # ANNOTATION spec validation error, recoverable | |||
| log.error('Encountered exception posting variant at row %s: %s ' % (idx, e)) | |||
| if self.first_error is None: | |||
| self.first_error = str(e) | |||
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I would call this self.first_error_message if it's only going to have the string.
src/encoded/ingestion_listener.py
Outdated
| @@ -669,6 +682,8 @@ def post_variants_and_variant_samples(self, parser, file_meta): | |||
| success += 1 | |||
| except Exception as e: # ANNOTATION spec validation error, recoverable | |||
| log.error('Encountered exception posting variant at row %s: %s ' % (idx, e)) | |||
| if self.first_error is None: | |||
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Wouldn't not self.first_error be both simpler and more robust in case someone puts "" there. I only go for is None when the other falsey values would be possibly meaningful to mean something other than "missing".
KorayKirli
approved these changes
Oct 21, 2020
netsettler
approved these changes
Oct 21, 2020
| variant_props = get_item_or_none(request, variant, 'Variant') | ||
| variant_props = get_item_or_none(request, variant, 'Variant', frame='raw') | ||
| if variant_props is None: | ||
| raise RuntimeError('Got none for something that definitely exists') | ||
| file_path = '%s/bamsnap/chr%s:%s.png' % ( # file = accession of associated VCF file |
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Hmm. Is .png always the format? And the file seems to be accession file path, a kind of base filename, is that right? A doc string here would help, I guess. :)
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