diff --git a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
index 1a4d0edd65ac9de3e66cf66c78d0bffc458ea854..fa9c13b0453d28bc0608c38aecb18d5c17fed5c5 100644
--- a/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Hive/DBSQL/AnalysisJobAdaptor.pm
@@ -42,6 +42,7 @@ package Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
use strict;
use Bio::EnsEMBL::Hive::Worker;
use Bio::EnsEMBL::Hive::AnalysisJob;
+use Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Sys::Hostname;
use Data::UUID;
@@ -62,22 +63,28 @@ sub CreateNewJob {
return undef unless(scalar @args);
- my ($input_id, $analysis, $input_analysis_job_id, $blocked) =
+ my ($input_id, $analysis, $prev_analysis_job_id, $blocked) =
rearrange([qw(INPUT_ID ANALYSIS input_job_id BLOCK )], @args);
- $input_analysis_job_id=0 unless($input_analysis_job_id);
+ $prev_analysis_job_id=0 unless($prev_analysis_job_id);
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 have adaptor connected to database")
+ unless($analysis->adaptor and $analysis->adaptor->db);
+ my $dbc = $analysis->adaptor->db->dbc;
+
+ my $dataDBA = new Bio::EnsEMBL::Hive::DBSQL::AnalysisDataAdaptor($dbc);
+ my $input_analysis_data_id = $dataDBA->store($input_id);
+
my $sql = "INSERT ignore into analysis_job ".
- " SET input_id=\"$input_id\" ".
- " ,input_analysis_job_id='$input_analysis_job_id' ".
+ " SET input_analysis_data_id=\"$input_analysis_data_id\" ".
+ " ,prev_analysis_job_id='$prev_analysis_job_id' ".
" ,analysis_id='".$analysis->dbID ."' ";
$sql .= " ,status='BLOCKED', job_claim='BLOCKED'" if($blocked);
- my $dbc = $analysis->adaptor->db->dbc;
my $sth = $dbc->prepare($sql);
$sth->execute();
my $dbID = $sth->{'mysql_insertid'};
@@ -239,9 +246,10 @@ sub _columns {
my $self = shift;
return qw (a.analysis_job_id
- a.input_analysis_job_id
+ a.prev_analysis_job_id
a.analysis_id
- a.input_id
+ a.input_analysis_data_id
+ a.output_analysis_data_id
a.job_claim
a.hive_id
a.status
@@ -265,7 +273,6 @@ sub _objs_from_sth {
$job->dbID($column{'analysis_job_id'});
$job->analysis_id($column{'analysis_id'});
- $job->input_id($column{'input_id'});
$job->job_claim($column{'job_claim'});
$job->hive_id($column{'hive_id'});
$job->status($column{'status'});
@@ -274,6 +281,10 @@ sub _objs_from_sth {
$job->branch_code($column{'branch_code'});
$job->adaptor($self);
+ my $input_id = $self->db->get_AnalysisDataAdaptor->
+ fetch_by_dbID($column{'input_analysis_data_id'});
+ $job->input_id($input_id);
+
push @jobs, $job;
}
$sth->finish;
diff --git a/sql/tables.sql b/sql/tables.sql
index 4dfc880955c45d5120aa3bb43c44a6270168e93a..42fe815cb8ad5bc14402cbb598866a6423cd94df 100644
--- a/sql/tables.sql
+++ b/sql/tables.sql
@@ -135,31 +135,35 @@ CREATE TABLE analysis_ctrl_rule (
-- by workers, are updated as the work is done, with a final update on completion.
--
-- semantics:
--- analysis_job_id - autoincrement id
--- input_analysis_job_id - previous analysis_job which created this one (and passed input_id)
--- analysis_id - the analysis_id needed to accomplish this job.
--- input_id - input data passed into Analysis:RunnableDB to control the work
--- job_claim - UUID set by workers as the fight over jobs
--- hive_id - link to hive table to define which worker claimed this job
--- status - state the job is in
--- retry_count - number times job had to be reset when worker failed to run it
--- completed - timestamp when job was completed
--- branch_code - switch-like branching control, default=1 (ie true)
+-- analysis_job_id - autoincrement id
+-- prev_analysis_job_id - previous analysis_job which created this one (and passed input_id)
+-- analysis_id - the analysis_id needed to accomplish this job.
+-- input_analysis_data_id - input data passed into Analysis:RunnableDB to control the work
+-- foreign key join to analysis_data table
+-- output_analysis_data_id - ouput data passed from Analysis:RunnableDB to be passed to next job
+-- foreign key join to analysis_data table
+-- job_claim - UUID set by workers as the fight over jobs
+-- hive_id - link to hive table to define which worker claimed this job
+-- status - state the job is in
+-- retry_count - number times job had to be reset when worker failed to run it
+-- completed - timestamp when job was completed
+-- branch_code - switch-like branching control, default=1 (ie true)
CREATE TABLE analysis_job (
- analysis_job_id int(10) NOT NULL auto_increment,
- input_analysis_job_id int(10) NOT NULL, #analysis_job which created this from rules
- analysis_id int(10) NOT NULL,
- input_id varchar(100) not null,
- job_claim varchar(40) NOT NULL default '', #UUID
- hive_id int(10) NOT NULL,
- status enum('READY','BLOCKED','CLAIMED','GET_INPUT','RUN','WRITE_OUTPUT','DONE','FAILED') DEFAULT 'READY' NOT NULL,
- retry_count int(10) default 0 not NULL,
- completed datetime NOT NULL,
- branch_code int(10) default 1 NOT NULL,
+ analysis_job_id int(10) NOT NULL auto_increment,
+ prev_analysis_job_id int(10) NOT NULL, #analysis_job which created this from rules
+ analysis_id int(10) NOT NULL,
+ input_analysis_data_id int(10) NOT NULL,
+ output_analysis_data_id int(10) default 0 NOT NULL,
+ job_claim varchar(40) NOT NULL default '', #UUID
+ hive_id int(10) NOT NULL,
+ status enum('READY','BLOCKED','CLAIMED','GET_INPUT','RUN','WRITE_OUTPUT','DONE','FAILED') DEFAULT 'READY' NOT NULL,
+ retry_count int(10) default 0 not NULL,
+ completed datetime NOT NULL,
+ branch_code int(10) default 1 NOT NULL,
PRIMARY KEY (analysis_job_id),
- UNIQUE KEY input_id_analysis (input_id, analysis_id),
+ UNIQUE KEY input_id_analysis (input_analysis_data_id, analysis_id),
INDEX claim_analysis_status (job_claim, analysis_id, status),
INDEX analysis_status (analysis_id, status),
INDEX hive_id (hive_id)