renamed 'job_message' table to 'log_message' and JobMessageAdaptor to LogMessageAdaptor everywhere

modules/Bio/EnsEMBL/Hive/AnalysisJob.pm

@@ -212,7 +212,7 @@ sub incomplete {            # Job should set this to 0 prior to throwing if the
 
 =head2 warning
 
-    Description:    records a non-error message in 'job_message' table linked to the current job
+    Description:    records a non-error message in 'log_message' table linked to the current job
 
 =cut
 
@@ -220,7 +220,7 @@ sub warning {
     my ($self, $msg) = @_;
 
     if( my $job_adaptor = $self->adaptor ) {
-        $job_adaptor->db->get_JobMessageAdaptor()->store_job_message($self->dbID, $msg, 0);
+        $job_adaptor->db->get_LogMessageAdaptor()->store_job_message($self->dbID, $msg, 0);
     } else {
         print STDERR "Warning: $msg\n";
     }

modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm

@@ -622,7 +622,7 @@ sub release_undone_jobs_from_worker {
             }
         }
 
-        $self->db()->get_JobMessageAdaptor()->store_job_message($job_id, $msg, not $passed_on );
+        $self->db()->get_LogMessageAdaptor()->store_job_message($job_id, $msg, not $passed_on );
 
         unless($passed_on) {
             $self->release_and_age_job( $job_id, $max_retry_count, not $resource_overusage );

modules/Bio/EnsEMBL/Hive/DBSQL/DBAdaptor.pm

@@ -63,7 +63,7 @@ sub get_available_adaptors {
         'DataflowRule'        => 'Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor',
         'ResourceDescription' => 'Bio::EnsEMBL::Hive::DBSQL::ResourceDescriptionAdaptor',
         'ResourceClass'       => 'Bio::EnsEMBL::Hive::DBSQL::ResourceClassAdaptor',
-        'JobMessage'          => 'Bio::EnsEMBL::Hive::DBSQL::JobMessageAdaptor',
+        'LogMessage'          => 'Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor',
         'NakedTable'          => 'Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor',
 
             # "old" Hive adaptors (having their own fetching/storing code) :

modules/Bio/EnsEMBL/Hive/DBSQL/JobMessageAdaptor.pm → modules/Bio/EnsEMBL/Hive/DBSQL/LogMessageAdaptor.pm

@@ -2,13 +2,13 @@
 
 =head1 NAME
 
-    Bio::EnsEMBL::Hive::DBSQL::JobMessageAdaptor
+    Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor
 
 =head1 SYNOPSIS
 
-    $dba->get_JobMessageAdaptor->store_job_message($job_id, $msg, $is_error);
+    $dba->get_LogMessageAdaptor->store_job_message($job_id, $msg, $is_error);
 
-    $dba->get_JobMessageAdaptor->store_worker_message($worker_id, $msg, $is_error);
+    $dba->get_LogMessageAdaptor->store_worker_message($worker_id, $msg, $is_error);
 
 =head1 DESCRIPTION
 
@@ -21,7 +21,7 @@
 =cut
 
 
-package Bio::EnsEMBL::Hive::DBSQL::JobMessageAdaptor;
+package Bio::EnsEMBL::Hive::DBSQL::LogMessageAdaptor;
 
 use strict;
 
@@ -29,7 +29,7 @@ use base ('Bio::EnsEMBL::Hive::DBSQL::NakedTableAdaptor');
 
 
 sub default_table_name {
-    return 'job_message';
+    return 'log_message';
 }
 
 

modules/Bio/EnsEMBL/Hive/RunnableDB/DatabaseDumper.pm

@@ -63,7 +63,7 @@ sub fetch_input {
     $self->param('ignores', \@ignores);
 
     # Would be good to have this from eHive
-    my @ehive_tables = qw(worker dataflow_rule analysis_base analysis_ctrl_rule job job_message job_file analysis_data resource_description analysis_stats analysis_stats_monitor monitor msg progress resource_class);
+    my @ehive_tables = qw(worker dataflow_rule analysis_base analysis_ctrl_rule job log_message job_file analysis_data resource_description analysis_stats analysis_stats_monitor monitor msg progress resource_class);
     $self->param('nb_ehive_tables', scalar(@ehive_tables));
 
     # Connection parameters

modules/Bio/EnsEMBL/Hive/RunnableDB/LongMult/Start.pm

@@ -91,7 +91,7 @@ sub write_output {  # nothing to write out, but some dataflow to perform:
         # "fan out" into branch#2 first
     $self->dataflow_output_id($output_ids, 2);
 
-    $self->warning(scalar(@$output_ids).' multiplication jobs have been created');     # warning messages get recorded into 'job_message' table
+    $self->warning(scalar(@$output_ids).' multiplication jobs have been created');     # warning messages get recorded into 'log_message' table
 
         # then flow into the branch#1 funnel; input_id would flow into branch#1 by default anyway, but we request it here explicitly:
     $self->dataflow_output_id($self->input_id, 1);

modules/Bio/EnsEMBL/Hive/Worker.pm

@@ -510,7 +510,7 @@ sub run {
     } or do {
         my $msg = $@;
         warn "Could not specialize worker:\n\t$msg\n";
-        $self->adaptor->db->get_JobMessageAdaptor()->store_worker_message($self->dbID, $msg, 1 );
+        $self->adaptor->db->get_LogMessageAdaptor()->store_worker_message($self->dbID, $msg, 1 );
 
         $self->cause_of_death('SEE_MSG') unless($self->cause_of_death());   # some specific causes could have been set prior to die "...";
     };
@@ -532,7 +532,7 @@ sub run {
         } or do {
             my $msg = "Could not compile Runnable '".$self->analysis->module."' :\n\t".$@;
             warn "$msg\n";
-            $self->adaptor->db->get_JobMessageAdaptor()->store_worker_message($self->dbID, $msg, 1 );
+            $self->adaptor->db->get_LogMessageAdaptor()->store_worker_message($self->dbID, $msg, 1 );
 
             $self->cause_of_death('SEE_MSG');
         };
@@ -677,7 +677,7 @@ sub run_one_batch {
             my $job_status_at_the_moment = $job->status();
             my $action = $job->incomplete ? 'died' : 'exited';
             $job_completion_line = "\njob $job_id : $action in status '$job_status_at_the_moment' for the following reason: $msg_thrown\n";
-            $self->adaptor->db->get_JobMessageAdaptor()->store_job_message($job_id, $msg_thrown, $job->incomplete );
+            $self->adaptor->db->get_LogMessageAdaptor()->store_job_message($job_id, $msg_thrown, $job->incomplete );
         }
 
         print STDERR $job_completion_line if($self->log_dir and ($self->debug or $job->incomplete));            # one copy goes to the job's STDERR

sql/foreign_keys.mysql

@@ -8,12 +8,12 @@ ALTER TABLE analysis_stats          ADD FOREIGN KEY (analysis_id)
 ALTER TABLE analysis_stats_monitor  ADD FOREIGN KEY (analysis_id)               REFERENCES analysis_base(analysis_id);
 
 ALTER TABLE job                     ADD FOREIGN KEY (worker_id)                 REFERENCES worker(worker_id);
-ALTER TABLE job_message             ADD FOREIGN KEY (worker_id)                 REFERENCES worker(worker_id);
+ALTER TABLE log_message             ADD FOREIGN KEY (worker_id)                 REFERENCES worker(worker_id);
 ALTER TABLE job_file                ADD FOREIGN KEY (worker_id)                 REFERENCES worker(worker_id);
 
 ALTER TABLE job                     ADD FOREIGN KEY (prev_job_id)               REFERENCES job(job_id);
 ALTER TABLE job                     ADD FOREIGN KEY (semaphored_job_id)         REFERENCES job(job_id);
-ALTER TABLE job_message             ADD FOREIGN KEY (job_id)                    REFERENCES job(job_id);
+ALTER TABLE log_message             ADD FOREIGN KEY (job_id)                    REFERENCES job(job_id);
 ALTER TABLE job_file                ADD FOREIGN KEY (job_id)                    REFERENCES job(job_id);
 
 ALTER TABLE resource_description    ADD FOREIGN KEY (resource_class_id)         REFERENCES resource_class(resource_class_id);

sql/patch_2012-11-29.sql

+    # renaming job_message into a more generic log_message:
+
+CREATE TABLE log_message (
+  log_message_id            int(10) NOT NULL AUTO_INCREMENT,
+  job_id                    int(10) DEFAULT NULL,
+  worker_id                 int(10) unsigned NOT NULL,
+  time                      timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
+  retry                     int(10) DEFAULT NULL,
+  status                    enum('UNKNOWN','SPECIALIZATION','COMPILATION','READY','PRE_CLEANUP','FETCH_INPUT','RUN','WRITE_OUTPUT','POST_CLEANUP','PASSED_ON') DEFAULT 'UNKNOWN',
+  msg                       text,
+  is_error                  TINYINT,
+
+  PRIMARY KEY               (log_message_id),
+  INDEX worker_id           (worker_id),
+  INDEX job_id              (job_id)
+
+) COLLATE=latin1_swedish_ci ENGINE=InnoDB;
+
+INSERT INTO log_message (log_message_id, job_id, worker_id, time, retry, status, msg, is_error) SELECT * from job_message;
+
+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 analysis_base a ON (a.analysis_id=w.analysis_id)
+    LEFT JOIN job j ON (j.job_id=m.job_id);
+

sql/procedures.mysql

@@ -33,7 +33,7 @@ CREATE OR REPLACE VIEW progress AS
 
 CREATE OR REPLACE VIEW msg AS
     SELECT a.analysis_id, a.logic_name, m.*
-    FROM job_message m
+    FROM log_message m
     JOIN worker w USING (worker_id)
     LEFT JOIN analysis_base a ON (a.analysis_id=w.analysis_id)
     LEFT JOIN job j ON (j.job_id=m.job_id);
@@ -105,7 +105,7 @@ CREATE PROCEDURE drop_hive_tables()
 MODIFIES SQL DATA
 BEGIN
     DROP VIEW IF EXISTS msg, progress;
-    DROP TABLE IF EXISTS monitor, analysis_stats_monitor, resource_description, resource_class, analysis_data, job_file, dataflow_rule, analysis_ctrl_rule, analysis_stats, job_message, job, worker;
+    DROP TABLE IF EXISTS monitor, analysis_stats_monitor, resource_description, resource_class, analysis_data, job_file, dataflow_rule, analysis_ctrl_rule, analysis_stats, log_message, job, worker;
 END; //
 DELIMITER ;
 

sql/procedures.sqlite

@@ -33,7 +33,7 @@ CREATE VIEW IF NOT EXISTS progress AS
 
 CREATE VIEW IF NOT EXISTS msg AS
     SELECT a.analysis_id, a.logic_name, m.*
-    FROM job_message m
+    FROM log_message m
     JOIN worker w USING (worker_id)
     LEFT JOIN analysis_base a ON (a.analysis_id=w.analysis_id)
     LEFT JOIN job j ON (j.job_id=m.job_id);

sql/tables.sql

@@ -215,14 +215,14 @@ CREATE TABLE job (
 
 -- ---------------------------------------------------------------------------------
 --
--- Table structure for table 'job_message'
+-- Table structure for table 'log_message'
 --
 -- overview:
 --      In case a job throws a message (via die/throw), this message is registered in this table.
 --      It may or may not indicate that the job was unsuccessful via is_error flag.
 --
 -- semantics:
---       job_message_id     - an autoincremented primary id of the message
+--       log_message_id     - an autoincremented primary id of the message
 --               job_id     - the id of the job that threw the message (or NULL if it was outside of a message)
 --            worker_id     - the 'current' worker
 --                 time     - when the message was thrown
@@ -231,8 +231,8 @@ CREATE TABLE job (
 --                  msg     - string that contains the message
 --             is_error     - binary flag
 
-CREATE TABLE job_message (
-  job_message_id            int(10) NOT NULL AUTO_INCREMENT,
+CREATE TABLE log_message (
+  log_message_id            int(10) NOT NULL AUTO_INCREMENT,
   job_id                    int(10) DEFAULT NULL,
   worker_id                 int(10) unsigned NOT NULL,
   time                      timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
@@ -241,7 +241,7 @@ CREATE TABLE job_message (
   msg                       text,
   is_error                  TINYINT,
 
-  PRIMARY KEY               (job_message_id),
+  PRIMARY KEY               (log_message_id),
   INDEX worker_id           (worker_id),
   INDEX job_id              (job_id)
 

sql/tables.sqlite

@@ -199,14 +199,14 @@ CREATE        INDEX IF NOT EXISTS worker_idx ON job (worker_id);
 
 -- ---------------------------------------------------------------------------------
 --
--- Table structure for table 'job_message'
+-- Table structure for table 'log_message'
 --
 -- overview:
 --      In case a job throws a message (via die/throw), this message is registered in this table.
 --      It may or may not indicate that the job was unsuccessful via is_error flag.
 --
 -- semantics:
---       job_message_id     - an autoincremented primary id of the message
+--       log_message_id     - an autoincremented primary id of the message
 --               job_id     - the id of the job that threw the message (or NULL if it was outside of a message)
 --            worker_id     - the 'current' worker
 --                 time     - when the message was thrown
@@ -215,8 +215,8 @@ CREATE        INDEX IF NOT EXISTS worker_idx ON job (worker_id);
 --                  msg     - string that contains the message
 --             is_error     - binary flag
 
-CREATE TABLE job_message (
-  job_message_id            INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT,
+CREATE TABLE log_message (
+  log_message_id            INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT,
   job_id                    INTEGER DEFAULT NULL,
   worker_id                 INTEGER NOT NULL,
   time                      timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP,
@@ -225,8 +225,8 @@ CREATE TABLE job_message (
   msg                       TEXT,
   is_error                  BOOLEAN
 );
-CREATE        INDEX IF NOT EXISTS worker_idx ON job_message (worker_id);
-CREATE        INDEX IF NOT EXISTS job_idx ON job_message (job_id);
+CREATE        INDEX IF NOT EXISTS worker_idx ON log_message (worker_id);
+CREATE        INDEX IF NOT EXISTS job_idx ON log_message (job_id);
 
 
 -- ---------------------------------------------------------------------------------