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Table 'validator.transcript_info' doesn't exist #46

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phwhite-coh opened this issue Dec 17, 2020 · 0 comments
Open

Table 'validator.transcript_info' doesn't exist #46

phwhite-coh opened this issue Dec 17, 2020 · 0 comments

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@phwhite-coh
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After my latest 'git pull' I'm getting this error during requests:

restvv_1   | CRITICAL: <class 'mysql.connector.errors.ProgrammingError'> 1146 (42S02): Table 'validator.transcript_info' doesn't exist
restvv_1   | [2020-12-17 23:23:05,612] ERROR in app: Exception on /VariantValidator/variantvalidator/GRCh37/NM_000088.3:c.589G>T/all [GET]
restvv_1   | Traceback (most recent call last):
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/mysql/connector/connection_cext.py", line 506, in cmd_query
restvv_1   |     raw_as_string=raw_as_string)
restvv_1   | _mysql_connector.MySQLInterfaceError: Table 'validator.transcript_info' doesn't exist
restvv_1   | 
restvv_1   | During handling of the above exception, another exception occurred:
restvv_1   | 
restvv_1   | Traceback (most recent call last):
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/VariantValidator/modules/vvMixinCore.py", line 446, in validate
restvv_1   |     toskip = use_checking.structure_checks(my_variant, self)
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/VariantValidator/modules/use_checking.py", line 71, in structure_checks
restvv_1   |     variant.gene_symbol = validator.db.get_gene_symbol_from_transcript_id(variant.input_parses.ac)
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/VariantValidator/modules/vvDBGet.py", line 66, in get_gene_symbol_from_transcript_id
restvv_1   |     return str(self.execute(query)[0])
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/VariantValidator/modules/utils.py", line 18, in wrapper
restvv_1   |     out = func(self, *args, **kwargs)
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/VariantValidator/modules/vvDBGet.py", line 19, in execute
restvv_1   |     cursor.execute(query)
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/mysql/connector/cursor_cext.py", line 266, in execute
restvv_1   |     raw_as_string=self._raw_as_string)
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/mysql/connector/connection_cext.py", line 509, in cmd_query
restvv_1   |     sqlstate=exc.sqlstate)
restvv_1   | mysql.connector.errors.ProgrammingError: 1146 (42S02): Table 'validator.transcript_info' doesn't exist
restvv_1   | 
restvv_1   | During handling of the above exception, another exception occurred:
restvv_1   | 
restvv_1   | Traceback (most recent call last):
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/flask/app.py", line 1950, in full_dispatch_request
restvv_1   |     rv = self.dispatch_request()
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/flask/app.py", line 1936, in dispatch_request
restvv_1   |     return self.view_functions[rule.endpoint](**req.view_args)
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/flask_restplus/api.py", line 325, in wrapper
restvv_1   |     resp = resource(*args, **kwargs)
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/flask/views.py", line 89, in view
restvv_1   |     return self.dispatch_request(*args, **kwargs)
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/flask_restplus/resource.py", line 44, in dispatch_request
restvv_1   |     resp = meth(*args, **kwargs)
restvv_1   |   File "/app/rest_VariantValidator/endpoints/variantvalidator_endpoints.py", line 55, in get
restvv_1   |     validate = vval.validate(variant_description, genome_build, select_transcripts)
restvv_1   |   File "/usr/local/lib/python3.6/site-packages/VariantValidator/modules/vvMixinCore.py", line 1134, in validate
restvv_1   |     raise fn.VariantValidatorError('Validation error')
restvv_1   | VariantValidator.modules.utils.VariantValidatorError: Validation error
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