Populate Database¶

Overview¶

The POPULATE_DB process executes SQL files against Ensembl core databases to populate them with statistics, metadata, or other computed information.

Process Details¶

• Label: default
• Tag: Uses database name (meta.dbname)
• Conditional Execution: Only runs when params.apply_ensembl_stats OR params.apply_ensembl_beta_metakeys is true

Inputs¶

Required Metadata Fields¶

• dbname: Target database name

Outputs¶

Parameters¶

Required¶

• params.mysql_ensadmin: Path to MySQL admin script/command
• params.host: Database host
• params.apply_ensembl_stats: Boolean flag to enable statistics population
• params.apply_ensembl_beta_metakeys: Boolean flag to enable beta metakeys population

Script Details¶

The process: 1. Executes the mysql_ensadmin script with host and database name 2. Redirects the SQL file as input to populate the database 3. Captures MySQL version information 4. Generates a versions file

Command Structure¶

${params.mysql_ensadmin}/${params.host} ${meta.dbname} < ${sql_file}

Dependencies¶

• MySQL client
• mysql_ensadmin script (Ensembl admin utility)
• Database write access with appropriate privileges

Use Cases¶

This process is used to: - Load gene and transcript statistics into core databases - Insert computed metadata keys - Apply database schema updates - Populate summary tables

Conditional Execution¶

The process only runs when at least one of these conditions is true: - params.apply_ensembl_stats == true: Apply statistical summaries - params.apply_ensembl_beta_metakeys == true: Apply beta metadata keys

Notes¶

• The versions file is marked as optional
• SQL execution is performed via the mysql_ensadmin utility for standardized database administration
• The process assumes SQL files are pre-validated and safe to execute
• No rollback mechanism is provided; ensure SQL files are tested before production use