substituted the overloaded legacy 'analysis' table by a slimmer 'analysis_base'

modules/Bio/EnsEMBL/Hive.pm

@@ -65,14 +65,13 @@ use Sys::Hostname;
 use Bio::EnsEMBL::Utils::Argument;
 use Bio::EnsEMBL::Utils::Exception;
 
-use Bio::EnsEMBL::Analysis;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-
+use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
 use Bio::EnsEMBL::Hive::DBSQL::AnalysisStatsAdaptor;
 use Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
 use Bio::EnsEMBL::Hive::DBSQL::AnalysisCtrlRuleAdaptor;
 use Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
+use Bio::EnsEMBL::Hive::Analysis;
 use Bio::EnsEMBL::Hive::Extensions;
 use Bio::EnsEMBL::Hive::Queen;
 use Bio::EnsEMBL::Hive::URLFactory;

modules/Bio/EnsEMBL/Hive/Analysis.pm

+=pod 
+
+=head1 NAME
+
+  Bio::EnsEMBL::Hive::Analysis
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+    An Analysis object represents a "stage" of the Hive pipeline that groups together
+    all jobs that share the same module and the same common parameters.
+
+    Individual Jobs are said to "belong" to an Analysis.
+
+    Control rules unblock when their condition Analyses are done.
+
+=head1 CONTACT
+
+  Please contact ehive-users@ebi.ac.uk mailing list with questions/suggestions.
+
+=cut
+
+package Bio::EnsEMBL::Hive::Analysis;
+
+use strict;
+use Bio::EnsEMBL::Utils::Argument;  # import 'rearrange()'
+
+use base (  'Bio::EnsEMBL::Storable',       # inherit dbID(), adaptor() and new() methods
+         );
+ 
+
+sub new {
+    my $class = shift @_;
+
+    my $self = $class->SUPER::new( @_ );    # deal with Storable stuff
+
+    my ($logic_name, $module, $parameters) =
+         rearrange([qw(logic_name module parameters) ], @_);
+
+    $self->logic_name($logic_name)  if($logic_name);
+    $self->module($module)          if($module);
+    $self->parameters($parameters)  if($parameters);
+
+    return $self;
+}
+
+
+sub logic_name {
+    my $self = shift @_;
+
+    if(@_) {
+        $self->{'_logic_name'} = shift @_;
+    }
+    return $self->{'_logic_name'};
+}
+
+
+sub module {
+    my $self = shift @_;
+
+    if(@_) {
+        $self->{'_module'} = shift @_;
+    }
+    return $self->{'_module'};
+}
+
+
+sub parameters {
+    my $self = shift @_;
+
+    if(@_) {
+        $self->{'_parameters'} = shift @_;
+    }
+    return $self->{'_parameters'};
+}
+
+
+=head2 process
+
+  Arg [1]    : none
+  Example    : $process = $analysis->process;
+  Description: construct a Process object from the $analysis->module name
+  Returntype : Bio::EnsEMBL::Hive::Process subclass 
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub process {
+    my $self = shift;
+
+    my $process_class = $self->module
+                     or die "Analysis '".$self->logic_name."' does not have its 'module' defined";
+
+    if($process_class!~/::/) {
+        $process_class = 'Bio::EnsEMBL::Hive::Runnable::'.$process_class;
+    }
+
+    my $file = $process_class;
+    $file =~ s/::/\//g;
+    require "${file}.pm";
+
+    my $process_object = $process_class->new(
+                                -db       => $self->adaptor->db,
+                                -input_id => '1',
+                                -analysis => $self,
+                                );
+
+    return $process_object;
+}
+
+
+=head2 url
+
+  Arg [1]    : none
+  Example    : $url = $analysis->url;
+  Description: Constructs a URL string for this database connection
+               Follows the general URL rules.
+  Returntype : string of format
+               mysql://<user>:<pass>@<host>:<port>/<dbname>/analysis?logic_name=<name>
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub url {
+    my $self = shift;
+
+    return undef unless($self->adaptor);
+
+    return $self->adaptor->db->dbc->url . '/analysis?logic_name=' . $self->logic_name;
+}
+
+
+=head2 stats
+
+  Arg [1]    : none
+  Example    : $stats = $analysis->stats;
+  Description: returns the AnalysisStats object associated with this Analysis
+               object.  Does not cache, but pull from database by using the
+               Analysis objects adaptor->db.
+  Returntype : Bio::EnsEMBL::Hive::AnalysisStats object
+  Exceptions : none
+  Caller     : general
+
+=cut
+
+sub stats {
+    my $self = shift;
+
+    # Not cached internally since we want it to always be in sync with the database.
+    # Otherwise the user application would need to be aware of the sync state and send explicit 'sync' calls.
+
+    my $stats = $self->adaptor->db->get_AnalysisStatsAdaptor->fetch_by_analysis_id($self->dbID);
+    return $stats;
+}
+
+
+sub toString {
+    my $self = shift @_;
+
+    return (ref($self).': '.join(', ', map { $_.'="'.$self->$_().'"' } qw(dbID logic_name module parameters) ));
+}
+
+1;
+

modules/Bio/EnsEMBL/Hive/AnalysisCtrlRule.pm

@@ -131,11 +131,11 @@ sub condition_analysis_url {
 
 =head2 ctrled_analysis
 
-  Arg[1]  : (optional) Bio::EnsEMBL::Analysis object
+  Arg[1]  : (optional) Bio::EnsEMBL::Hive::Analysis object
   Usage   : $self->ctrled_analysis($anal);
   Function: Get/set method for the analysis which will be BLOCKED until all
             of its condition analyses are 'DONE'
-  Returns : Bio::EnsEMBL::Analysis
+  Returns : Bio::EnsEMBL::Hive::Analysis
   
 =cut
 
@@ -144,9 +144,9 @@ sub ctrled_analysis {
 
   # setter mode
   if( defined $analysis ) {
-    unless ($analysis->isa('Bio::EnsEMBL::Analysis')) {
+    unless ($analysis->isa('Bio::EnsEMBL::Hive::Analysis')) {
       throw(
-        "ctrled_analysis arg must be a [Bio::EnsEMBL::Analysis]".
+        "ctrled_analysis arg must be a [Bio::EnsEMBL::Hive::Analysis]".
         "not a [$analysis]");
     }
     $self->{'_ctrled_analysis'} = $analysis;
@@ -158,8 +158,7 @@ sub ctrled_analysis {
      and defined($self->ctrled_analysis_id)
      and defined($self->adaptor))
   {
-    $self->{'_ctrled_analysis'} =
-      $self->adaptor->db->get_AnalysisAdaptor->fetch_by_dbID($self->ctrled_analysis_id);
+    $self->{'_ctrled_analysis'} = $self->adaptor->db->get_AnalysisAdaptor->fetch_by_dbID($self->ctrled_analysis_id);
   }
   return $self->{'_ctrled_analysis'};
 }
@@ -167,11 +166,11 @@ sub ctrled_analysis {
 
 =head2 condition_analysis
 
-  Arg[1]  : (optional) Bio::EnsEMBL::Analysis object
+  Arg[1]  : (optional) Bio::EnsEMBL::Hive::Analysis object
   Usage   : $self->condition_analysis($anal);
   Function: Get/set method for the analysis which must be 'DONE' in order for
             the controlled analysis to be un-BLOCKED
-  Returns : Bio::EnsEMBL::Analysis
+  Returns : Bio::EnsEMBL::Hive::Analysis
   
 =cut
 
@@ -179,9 +178,9 @@ sub condition_analysis {
   my ($self,$analysis) = @_;
 
   if( defined $analysis ) {
-    unless ($analysis->isa('Bio::EnsEMBL::Analysis')) {
+    unless ($analysis->isa('Bio::EnsEMBL::Hive::Analysis')) {
       throw(
-        "condition_analysis arg must be a [Bio::EnsEMBL::Analysis]".
+        "condition_analysis arg must be a [Bio::EnsEMBL::Hive::Analysis]".
         "not a [$analysis]");
     }
     $self->{'_condition_analysis'} = $analysis;

modules/Bio/EnsEMBL/Hive/AnalysisStats.pm

@@ -28,9 +28,9 @@ package Bio::EnsEMBL::Hive::AnalysisStats;
 use strict;
 use Scalar::Util ('weaken');
 
-use Bio::EnsEMBL::Analysis;
-use Bio::EnsEMBL::DBSQL::DBAdaptor;
-use Bio::EnsEMBL::Hive::Worker;
+#use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::Hive::Analysis;
+#use Bio::EnsEMBL::Hive::Worker;
 
     ## Minimum amount of time in msec that a worker should run before reporting
     ## back to the hive. This is used when setting the batch_size automatically.

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

@@ -8,9 +8,12 @@
 
   $analysis_adaptor = $db_adaptor->get_AnalysisAdaptor;
 
+  $analysis_adaptor = $analysis_object->adaptor;
+
 =head1 DESCRIPTION
 
-  This module extends EnsEMBL Core's AnalysisAdaptor, adding some Hive-specific stuff.
+  Module to encapsulate all db access for persistent class Analysis.
+  There should be just one such adaptor per application and database connection.
 
 =head1 CONTACT
 
@@ -22,10 +25,25 @@
 package Bio::EnsEMBL::Hive::DBSQL::AnalysisAdaptor;
 
 use strict;
+use Bio::EnsEMBL::Hive::Analysis;
+use Bio::EnsEMBL::Hive::URLFactory;
 
-use base ('Bio::EnsEMBL::DBSQL::AnalysisAdaptor');
+use base ('Bio::EnsEMBL::Hive::DBSQL::ObjectAdaptor');
 
-use Bio::EnsEMBL::Hive::URLFactory;
+
+sub default_table_name {
+    return 'analysis_base';
+}
+
+
+sub default_insertion_method {
+    return 'INSERT';
+}
+
+
+sub object_class {
+    return 'Bio::EnsEMBL::Hive::Analysis';
+}
 
 
 =head2 fetch_by_logic_name_or_url

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

@@ -57,7 +57,7 @@ use base ('Bio::EnsEMBL::DBSQL::BaseAdaptor');
 =head2 CreateNewJob
 
   Args       : -input_id => string of input_id which will be passed to run the job (or a Perl hash that will be automagically stringified)
-               -analysis => Bio::EnsEMBL::Analysis object from a database
+               -analysis => Bio::EnsEMBL::Hive::Analysis object from a database
                -block        => int(0,1) set blocking state of job (default = 0)
                -input_job_id => (optional) job_id of job that is creating this
                                 job.  Used purely for book keeping.
@@ -86,8 +86,8 @@ sub CreateNewJob {
 
   throw("must define input_id") unless($input_id);
   throw("must define analysis") unless($analysis);
-  throw("analysis must be [Bio::EnsEMBL::Analysis] not a [$analysis]")
-    unless($analysis->isa('Bio::EnsEMBL::Analysis'));
+  throw("analysis must be [Bio::EnsEMBL::Hive::Analysis] not a [$analysis]")
+    unless($analysis->isa('Bio::EnsEMBL::Hive::Analysis'));
   throw("analysis must have adaptor connected to database")
     unless($analysis->adaptor and $analysis->adaptor->db);
   throw("Please specify prev_job object instead of input_job_id if available") if ($prev_job_id);   # 'obsolete' message

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

@@ -209,7 +209,7 @@ sub primary_key_constraint {
 sub fetch_by_dbID {
     my $self = shift @_;    # the rest in @_ should be primary_key column values
 
-    return $self->fetch_all( $self->primary_key_constraint( @_ ) );
+    return $self->fetch_all( $self->primary_key_constraint( @_ ), 1 );
 }
 
 

modules/Bio/EnsEMBL/Hive/DataflowRule.pm

@@ -183,8 +183,8 @@ sub to_analysis_url {
 
   Usage   : $self->from_analysis($analysis);
   Function: Get/set method for the condition analysis object of this rule.
-  Returns : Bio::EnsEMBL::Analysis
-  Args    : Bio::EnsEMBL::Analysis
+  Returns : Bio::EnsEMBL::Hive::Analysis
+  Args    : Bio::EnsEMBL::Hive::Analysis
   
 =cut
 
@@ -193,9 +193,9 @@ sub from_analysis {
 
   # setter mode
   if( defined $analysis ) {
-    unless ($analysis->isa('Bio::EnsEMBL::Analysis')) {
+    unless ($analysis->isa('Bio::EnsEMBL::Hive::Analysis')) {
       throw(
-        "from_analysis arg must be a [Bio::EnsEMBL::Analysis]".
+        "from_analysis arg must be a [Bio::EnsEMBL::Hive::Analysis]".
         "not a [$analysis]");
     }
     $self->{'_from_analysis'} = $analysis;
@@ -218,8 +218,8 @@ sub from_analysis {
 
   Usage   : $self->to_analysis($analysis);
   Function: Get/set method for the goal analysis object of this rule.
-  Returns : Bio::EnsEMBL::Analysis
-  Args    : Bio::EnsEMBL::Analysis
+  Returns : Bio::EnsEMBL::Hive::Analysis
+  Args    : Bio::EnsEMBL::Hive::Analysis
   
 =cut
 

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

@@ -47,10 +47,12 @@ package Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
 
 use strict;
 use warnings;
+
 use Bio::EnsEMBL::Utils::Argument;          # import 'rearrange()'
 use Bio::EnsEMBL::Hive::Utils 'stringify';  # import 'stringify()'
 use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
+use Bio::EnsEMBL::Hive::Analysis;
 use Bio::EnsEMBL::Hive::Extensions;
 
 use base ('Bio::EnsEMBL::Hive::DependentOptions');
@@ -377,8 +379,8 @@ sub run {
     my %seen_logic_name = ();
 
     foreach my $aha (@{$self->pipeline_analyses}) {
-        my ($logic_name, $module, $parameters_hash, $program_file, $input_ids, $blocked, $batch_size, $hive_capacity, $failed_job_tolerance, $max_retry_count, $can_be_empty, $rc_id, $rc_name, $priority) =
-             rearrange([qw(logic_name module parameters program_file input_ids blocked batch_size hive_capacity failed_job_tolerance max_retry_count can_be_empty rc_id rc_name priority)], %$aha);
+        my ($logic_name, $module, $parameters_hash, $input_ids, $blocked, $batch_size, $hive_capacity, $failed_job_tolerance, $max_retry_count, $can_be_empty, $rc_id, $rc_name, $priority) =
+             rearrange([qw(logic_name module parameters input_ids blocked batch_size hive_capacity failed_job_tolerance max_retry_count can_be_empty rc_id rc_name priority)], %$aha);
 
         unless($logic_name) {
             die "logic_name' must be defined in every analysis";
@@ -412,11 +414,10 @@ sub run {
                 $rc_id = $rc->dbID();
             }
 
-            $analysis = Bio::EnsEMBL::Analysis->new(
+            $analysis = Bio::EnsEMBL::Hive::Analysis->new(
                 -logic_name      => $logic_name,
                 -module          => $module,
                 -parameters      => stringify($parameters_hash || {}),    # have to stringify it here, because Analysis code is external wrt Hive code
-                -program_file    => $program_file,
             );
             $analysis_adaptor->store($analysis);
 

modules/Bio/EnsEMBL/Hive/Process.pm

@@ -428,7 +428,7 @@ sub go_figure_dbc {
     Usage   :  $self->analysis;
     Function:  Returns the Analysis object associated with this
                instance of the Process.
-    Returns :  Bio::EnsEMBL::Analysis object
+    Returns :  Bio::EnsEMBL::Hive::Analysis object
 
 =cut
 
@@ -436,8 +436,8 @@ sub analysis {
   my ($self, $analysis) = @_;
 
   if($analysis) {
-    throw("Not a Bio::EnsEMBL::Analysis object")
-      unless ($analysis->isa("Bio::EnsEMBL::Analysis"));
+    throw("Not a Bio::EnsEMBL::Hive::Analysis object")
+      unless ($analysis->isa("Bio::EnsEMBL::Hive::Analysis"));
     $self->{'_analysis'} = $analysis;
   }
   return $self->{'_analysis'};

modules/Bio/EnsEMBL/Hive/Queen.pm

@@ -695,7 +695,7 @@ sub count_running_workers {
 
 =head2 schedule_workers
 
-  Arg[1]     : Bio::EnsEMBL::Analysis object (optional)
+  Arg[1]     : Bio::EnsEMBL::Hive::Analysis object (optional)
   Example    : $count = $queen->schedule_workers();
   Description: Runs through the analyses in the system which are waiting
                for workers to be created for them.  Calculates the maximum
@@ -842,9 +842,12 @@ sub print_running_worker_counts {
   my $self = shift;
 
   print "\n===== Stats of live Workers according to the Queen: ======\n";
-  my $sql = "SELECT logic_name, count(*) FROM worker, analysis ".
-            "WHERE worker.analysis_id=analysis.analysis_id AND worker.cause_of_death='' ".
-            "GROUP BY worker.analysis_id";
+  my $sql = qq{ SELECT logic_name, count(*)
+                FROM worker
+                JOIN analysis_base USING(analysis_id)
+                WHERE worker.cause_of_death=''
+                GROUP BY worker.analysis_id
+  };
 
   my $total_workers = 0;
   my $sth = $self->prepare($sql);
@@ -882,7 +885,7 @@ sub monitor {
               sum(work_done/(UNIX_TIMESTAMP()-UNIX_TIMESTAMP(born)))/count(*), }
   ). qq{
           group_concat(DISTINCT logic_name)
-      FROM worker left join analysis USING (analysis_id)
+      FROM worker left join analysis_base USING (analysis_id)
       WHERE cause_of_death = ''
   };
       

modules/Bio/EnsEMBL/Hive/Utils/Graph.pm

@@ -24,11 +24,11 @@ See inline
 
 =head1 AUTHOR
 
-$Author: mm14 $
+$Author: lg4 $
 
 =head1 VERSION
 
-$Revision: 1.21 $
+$Revision: 1.22 $
 
 =cut
 
@@ -346,7 +346,7 @@ sub _dataflow_rules {
         my ($from_node, $to_id, $to_node) = ( _analysis_node_name($from_analysis_id)      );
     
             # Different treatment for analyses and tables:
-        if(check_ref($to, 'Bio::EnsEMBL::Analysis')) {
+        if(check_ref($to, 'Bio::EnsEMBL::Hive::Analysis')) {
             $to_id   = $to->dbID();
             $to_node = _analysis_node_name($to_id);
         } elsif(check_ref($to, 'Bio::EnsEMBL::Hive::NakedTable')) {

modules/Bio/EnsEMBL/Hive/Worker.pm

@@ -65,7 +65,7 @@ package Bio::EnsEMBL::Hive::Worker;
 
 use strict;
 use POSIX;
-use Bio::EnsEMBL::Analysis;
+use Bio::EnsEMBL::Hive::Analysis;
 use Bio::EnsEMBL::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Utils::Argument;
 use Bio::EnsEMBL::Utils::Exception;
@@ -143,13 +143,13 @@ sub execute_writes {
 
 =head2 analysis
 
-  Arg [1] : (optional) Bio::EnsEMBL::Analysis $value
+  Arg [1] : (optional) Bio::EnsEMBL::Hive::Analysis $value
   Title   :   analysis
   Usage   :   $value = $self->analysis;
               $self->analysis($$analysis);
   Description: Get/Set analysis object of this Worker
   DefaultValue : undef
-  Returntype : Bio::EnsEMBL::Analysis object
+  Returntype : Bio::EnsEMBL::Hive::Analysis object
 
 =cut
 
@@ -158,8 +158,8 @@ sub analysis {
   my $analysis = shift;
 
   if(defined($analysis)) {
-    throw("analysis arg must be a [Bio::EnsEMBL::Analysis] not a [$analysis]")
-       unless($analysis->isa('Bio::EnsEMBL::Analysis'));
+    throw("analysis arg must be a [Bio::EnsEMBL::Hive::Analysis] not a [$analysis]")
+       unless($analysis->isa('Bio::EnsEMBL::Hive::Analysis'));
     $self->{'_analysis'} = $analysis;
   }
 

scripts/cmd_hive.pl

@@ -171,13 +171,10 @@ sub create_analysis {
     # No existing analysis with this logic_name. Create a new one.
     print("creating analysis '$logic_name' to be computed using module '$module' with parameters '$parameters'\n");
 
-    $self->{_analysis} = Bio::EnsEMBL::Analysis->new (
-        -db              => '',
-        -db_file         => '',
-        -db_version      => '1',
-        -parameters      => $parameters,
+    $self->{_analysis} = Bio::EnsEMBL::Hive::Analysis->new (
         -logic_name      => $logic_name,
         -module          => $module,
+        -parameters      => $parameters,
       );
     $DBA->get_AnalysisAdaptor()->store($self->{_analysis});
 

scripts/lsf_report.pl

@@ -58,7 +58,7 @@ sub main {
                    count(*) workers,
                    min(mem), avg(mem), max(mem),
                    min(swap), avg(swap), max(swap)
-            FROM analysis
+            FROM analysis_base
             JOIN analysis_stats USING(analysis_id)
             JOIN resource_class rc USING(resource_class_id)
             LEFT JOIN worker USING(analysis_id)

sql/foreign_keys.mysql

 # introducing the FOREIGN KEY constraints as a separate file (so that they could be optionally switched on or off):
 
-ALTER TABLE analysis_description    ADD FOREIGN KEY (analysis_id)           REFERENCES analysis(analysis_id);
-ALTER TABLE worker                  ADD FOREIGN KEY (analysis_id)           REFERENCES analysis(analysis_id);
-ALTER TABLE dataflow_rule           ADD FOREIGN KEY (from_analysis_id)      REFERENCES analysis(analysis_id);
-ALTER TABLE analysis_ctrl_rule      ADD FOREIGN KEY (ctrled_analysis_id)    REFERENCES analysis(analysis_id);
-ALTER TABLE job                     ADD FOREIGN KEY (analysis_id)           REFERENCES analysis(analysis_id);
-ALTER TABLE analysis_stats          ADD FOREIGN KEY (analysis_id)           REFERENCES analysis(analysis_id);
-ALTER TABLE analysis_stats_monitor  ADD FOREIGN KEY (analysis_id)           REFERENCES analysis(analysis_id);
+ALTER TABLE worker                  ADD FOREIGN KEY (analysis_id)           REFERENCES analysis_base(analysis_id);
+ALTER TABLE dataflow_rule           ADD FOREIGN KEY (from_analysis_id)      REFERENCES analysis_base(analysis_id);
+ALTER TABLE analysis_ctrl_rule      ADD FOREIGN KEY (ctrled_analysis_id)    REFERENCES analysis_base(analysis_id);
+ALTER TABLE job                     ADD FOREIGN KEY (analysis_id)           REFERENCES analysis_base(analysis_id);
+ALTER TABLE analysis_stats          ADD FOREIGN KEY (analysis_id)           REFERENCES analysis_base(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);

sql/patch_2012-09-04.sql

+
+# Substitute the legacy 'analysis' table with the slimmer version 'analysis_base',
+# but do not bother deleting the original table in the patch
+# because of the many already established foreign key relationships.
+
+CREATE TABLE analysis_base (
+  analysis_id                 int(10) unsigned NOT NULL AUTO_INCREMENT,
+  logic_name                  VARCHAR(40) NOT NULL,
+  module                      VARCHAR(255),
+  parameters                  TEXT,
+
+  PRIMARY KEY (analysis_id),
+  UNIQUE KEY logic_name_idx (logic_name)
+
+) COLLATE=latin1_swedish_ci ENGINE=InnoDB;
+
+INSERT INTO analysis_base (analysis_id, logic_name, module, parameters) SELECT analysis_id, logic_name, module, parameters FROM analysis;
+

sql/procedures.mysql

@@ -19,7 +19,7 @@ CREATE OR REPLACE VIEW progress AS
             j.retry_count,
             CASE WHEN j.status IS NULL THEN 0 ELSE count(*) END cnt,
             job_id example_job_id
-    FROM analysis a LEFT JOIN job j USING (analysis_id)
+    FROM analysis_base a LEFT JOIN job j USING (analysis_id)
     GROUP BY a.analysis_id, j.status, j.retry_count
     ORDER BY a.analysis_id, j.status;
 
@@ -35,7 +35,7 @@ CREATE OR REPLACE VIEW msg AS
     SELECT a.analysis_id, a.logic_name, m.*
     FROM job_message m
     JOIN job j USING (job_id)
-    JOIN analysis a USING (analysis_id);
+    JOIN analysis_base a USING (analysis_id);
 
 
 #### time an analysis or group of analyses (given by a name pattern) ######################################
@@ -53,7 +53,7 @@ READS SQL DATA
         (UNIX_TIMESTAMP(max(last_check_in))-UNIX_TIMESTAMP(min(born)))/60 AS measured_in_minutes,
         (UNIX_TIMESTAMP(max(last_check_in))-UNIX_TIMESTAMP(min(born)))/3600 AS measured_in_hours,
         (UNIX_TIMESTAMP(max(last_check_in))-UNIX_TIMESTAMP(min(born)))/3600/24 AS measured_in_days
-        FROM worker JOIN analysis USING (analysis_id)
+        FROM worker JOIN analysis_base USING (analysis_id)
         WHERE logic_name like param_logic_name_pattern;