database errors

[cbaakman]

Some calls to 'create_prebuilt_visualization' return the following output:

INFO:ENST00000537860.1: {'error': "No gene region could be build for transcript ENST00000537860.1, reason: GeneRepository.retrieve_gene(transcription_id): Unexpected exception for transcription_id 'ENST00000537860.1'. (psycopg2.DatabaseError) error with status PGRES_TUPLES_OK and no message from the libpq [SQL: 'SELECT genes.id AS genes_id, genes.strand AS genes_strand, genes.gene_name AS genes_gene_name, genes.gencode_transcription_id AS genes_gencode_transcription_id, genes.gencode_translation_name AS genes_gencode_translation_name, genes.gencode_gene_id AS genes_gencode_gene_id, genes.havana_gene_id AS genes_havana_gene_id, genes.havana_translation_id AS genes_havana_translation_id, genes.sequence_length AS genes_sequence_length, genes.protein_id AS genes_protein_id \\nFROM genes \\nWHERE genes.gencode_transcription_id = %(gencode_transcription_id_1)s'] [parameters: {'gencode_transcription_id_1': 'ENST00000537860.1'}]"}

INFO:ENST00000371410.3: {'error': "No gene region could be build for transcript ENST00000371410.3, reason: GeneRepository.retrieve_gene(transcription_id): Unexpected exception for transcription_id 'ENST00000371410.3'. (psycopg2.DatabaseError) error with status PGRES_TUPLES_OK and no message from the libpq [SQL: 'SELECT genes.id AS genes_id, genes.strand AS genes_strand, genes.gene_name AS genes_gene_name, genes.gencode_transcription_id AS genes_gencode_transcription_id, genes.gencode_translation_name AS genes_gencode_translation_name, genes.gencode_gene_id AS genes_gencode_gene_id, genes.havana_gene_id AS genes_havana_gene_id, genes.havana_translation_id AS genes_havana_translation_id, genes.sequence_length AS genes_sequence_length, genes.protein_id AS genes_protein_id \\nFROM genes \\nWHERE genes.gencode_transcription_id = %(gencode_transcription_id_1)s'] [parameters: {'gencode_transcription_id_1': 'ENST00000371410.3'}]"}

@laurensvdwiel could you find out what is wrong with these database calls?

[Laurens van de Wiel]

Hey Coos,

Also this error is not reproducible on my local branch (identical to master with the exception of credentials) and it just works.

Again googling the error provides a list of things to do with concurrency and I found this one useful: https://groups.google.com/forum/#!topic/sqlalchemy/YRh_NPwWXfo

Here there is stated that ad-hoc sessions are not reccommended (so the try-finally), but instead use a single global session for all threads.

[Laurens van de Wiel]

@cbaakman can you check if this error is gone due to previous pull requests? And if so close it ? Thanks :)

[cbaakman]

This error doesn't show up in the logs anymore. Let's consider it fixed.