start using procedures.pgsql with two main views ("progress" and "msg")

modules/Bio/EnsEMBL/Hive/PipeConfig/HiveGeneric_conf.pm

@@ -135,9 +135,10 @@ sub pipeline_create_commands {
             $self->o('hive_force_init') ? ( $self->db_execute_command($db_conn, 'DROP DATABASE IF EXISTS '.$self->o($db_conn, '-dbname'), 0 ) ) : (),
             $self->db_execute_command($db_conn, 'CREATE DATABASE '.$self->o($db_conn, '-dbname'), 0 ),
 
-                # standard eHive tables, triggers, foreign_keys and procedures:
+                # standard eHive tables, foreign_keys and procedures:
             $self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/tables.pgsql',
             $self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/foreign_keys.sql',
+            $self->db_connect_command($db_conn).' <'.$self->o('hive_root_dir').'/sql/procedures.pgsql',
         ],
     }->{ $self->o($db_conn, '-driver') };
 

sql/procedures.pgsql

+-- ------------------------------------------------------------------------
+--
+-- Some stored functions, views and procedures used in hive:
+--
+
+
+-- show hive progress for analyses (turned into a view to give extra flexibility) ----------------
+--
+-- Thanks to Greg Jordan for the idea and the original version
+--
+-- Usage:
+--       select * from progress;                                         # the whole table (may take ages to generate, depending on the size of your pipeline)
+--       select * from progress where logic_name like 'family_blast%';   # only show family_blast-related analyses
+--       select * from progress where retry_count>1;                     # only show jobs that have been tried more than once
+
+CREATE OR REPLACE VIEW progress AS
+    SELECT a.logic_name || '(' || a.analysis_id || ')' analysis_name_and_id,
+        MIN(rc.name) resource_class,
+        j.status,
+        j.retry_count,
+        CASE WHEN j.status IS NULL THEN 0 ELSE count(*) END cnt,
+        MIN(job_id) example_job_id
+    FROM        analysis_base a
+    LEFT JOIN   job j USING (analysis_id)
+    LEFT JOIN   resource_class rc ON (a.resource_class_id=rc.resource_class_id)
+    GROUP BY a.analysis_id, j.status, j.retry_count
+    ORDER BY a.analysis_id, j.status;
+
+
+-- a convenient view that also incorporates (otherwise redundant) analysis_id and logic_name ------------
+--
+-- Usage:
+--       select * from msg;
+--       select * from msg where analysis_id=18;
+--       select * from msg where logic_name like 'family_blast%';
+
+CREATE OR REPLACE VIEW msg AS
+    SELECT a.analysis_id, a.logic_name, m.*
+    FROM log_message m
+    JOIN worker w USING (worker_id)
+    LEFT JOIN job j ON (j.job_id=m.job_id)
+    LEFT JOIN analysis_base a ON (a.analysis_id=j.analysis_id);
+