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Regenerating SQL Alchemy database files

Instructions for refreshing the SQL Alchemy database files.

Running sqlacodegen

  • Install sqlacodegen if it is not already installed.
    • pip install sqlacodegen
  • Run sqlacodegen against production or reporting, depending on the files you'd like to refresh. Replace <postgresql_pw> with your relevant password and update <reporting_database> with the name of the appropriate reporting database.
    • Production: sqlacodegen postgresql://ctabone:<postgresql_pw>@flysql19:5432/production_chado --outfile production.py
    • Reporting: sqlacodegen postgresql://ctabone:<postgresql_pw>@flysql20:5432/<reporting_database> --outfile reporting.py
  • Move the output file into harvdev_utils/production or harvdev_utils/reporting as appropriate. This will overwrite the existing file.
  • In the production or reporting directory, run the script production_gene_init.py or reporting_gen_init.py as appropriate (e.g. python production_gene_init.py). This will regenerate the __init__.py file with up-to-date classes.