GitLab

store_jobs_and_adjust_counters() now also deals with semaphore_count corrections. It is now the preferred job-creation interface.

bugfix: no hope for other DBD drivers to support detection of auto-incrementing fields => use our inernal fixed rule

bugfix: substituting --password for --pass to pacify mysql 5.5.34+ that no longer recognizes options by their prefix

ResourceDescription expanded to include both submission_cmd_args and worker_cmd_args. Both args can be specified in a PipeConfig file.

pipeline_name is now automatically computed from ClassName; simplified workshop's example files and slides

methods dbconn_2_mysql(), dbconn_2_pgsql(), db_connect_command(), db_execute_command() are DEPRECATED - use db_cmd.pl instead

added support for -pipeline_url as an input parameter (no need to supply hive_driver or password in this case)

now performing deep-stack substitution for whatever is dataflown into tables (rather than just dataflowing the output_id)

bugfix: substituting the accu signature on demand from the very depths of emitting job's param_stack

Simplified interface: now db_cmd.pl understands 'CREATE DATABASE' and 'DROP DATABASE' without parameters, given a full URL.

"parameter stack" implementation using two extra fields in job table. Accu content intended for any job_id has preference over Input_id content for the same job.

Dataflowing minimal information out of Runnables, relying on templates in PipeConfig file to extend it if needed

An important comment about UNIX sockets (without a port number) vs TCPIP sockets (with a port number).

Expose parts of pipeline_db, make them less EnsEMBL-specific, allow multiple failover initializers and use self-reference if none of them worked. Phasing out $self->o('ENV', …) expressions