GitLab

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)

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

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

Allow skipping the port number; you no longer need to define your port if you are happy with driver's default (thanks to db_conn.pl and core's DBConnection)

Start using the new db_conn.pl script instead of building driver-specific commands and running them.

use SqlSchemaAdaptor to detect the current code's sql version and record it in 'hive_meta' (leave it out of tables.*sql* files)

move Core 'schema_version' out of tables.* files into HiveGeneric_conf (via ApiVersion), expose it for manipulation and make it available to PipeConfigs

new 'hive_meta' table to keep hive_sql_schema_version (=number of patches), hive_pipeline_name and hive_use_triggers

Changed an 'our' global variable to ENV{EHIVE_ROOT_DIR} to allow API-only users to set it and work as usual

PostgreSQL: connection parameters are now supplied on the command line (no need to set PG variables by hand)

Adding foreign keys to PostgreSQL schema by reusing the MySQL file (the syntax happens to be exactly the same!)

Has one known limitation (always INSERTs instead of INSERT_IGNORE and REPLACE) and may contain other bugs.

setting "-hive_force_init 1" will cause init_pipeline.pl to drop the database prior to creation (use with care!)

All Hive scripts now detect $::hive_root_dir and use it for setting the @INC so manual setting of PERL5LIB is only needed if using API directly

bugfix: check before storing rc (may be necessary in -analysis_topup mode) and warn about consequences of redefining it.

API extension: store() now also returns how many actual store operations (as opposed to fetching of already stored ones) it has performed