Update SQL scripts, Changes and tidy up code

- Modify SQL commands to reflect changes in rna_seqc table.
- Update upgrade-schema-60.x SQL script as well as data/schema.txt.
- Change rna_seqc check POD 'DESCRIPTION' to be more accurate.
- Delete instances of the qc_report_dir attribute which is no longer used.
- Update Changes file with latest er... changes.

Changes

@@ -1,14 +1,15 @@
 LIST OF CHANGES FOR NPG-QC PACKAGE
 
+ - remove attribute qc_report_dir from check object: the output directory
+   is created by default using the sample's filename root
  - upgrade_schema-60.x to create rna_seqc table has been included.
- - npg_qc::autoqc::qc_store - load rna_seqc results into npg_qc db
-   (requires rna_seqc table exists in database).
- - Updated data/schema.txt including definition for rna_seqc table.
+ - npg_qc::autoqc::qc_store - load rna_seqc results into npg_qc db:
+   requires rna_seqc table exists in database.
+ - updated data/schema.txt including definition for rna_seqc table.
  - SeQC:
-   - Added template for rna_seqc check with selected metrics shown
+   - added template for rna_seqc check with selected metrics shown
      in summary
-   - Include a link to original RNA-SeQC report only visible 
-     when db_lookup=0.
+   - include a link to original RNA-SeQC report in check's template
  - translation from a database composition representation to the
      npg_tracking::glossary::composition type object
  - db query for compisition-based tables should include a condition

data/schema.txt

@@ -1140,7 +1140,6 @@ DROP TABLE IF EXISTS `rna_seqc`;
 CREATE TABLE `rna_seqc` (
   `id_rna_seqc` bigint(20) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Auto-generated primary key',
   `id_seq_composition` bigint(20) unsigned NOT NULL COMMENT 'A foreign key referencing the id_seq_composition column of the seq_composition table',
-  `path` varchar(256) DEFAULT NULL,
   `info` text,
   `rrna` float unsigned DEFAULT NULL,
   `rrna_rate` float unsigned DEFAULT NULL,
@@ -1159,9 +1158,10 @@ CREATE TABLE `rna_seqc` (
   `end_3_norm` float unsigned DEFAULT NULL,
   `other_metrics` text,
   PRIMARY KEY (`id_rna_seqc`),
+  UNIQUE KEY `rna_seqc_id_compos_unq` (`id_seq_composition`),
   KEY `rna_seqc_compos` (`id_seq_composition`),
   CONSTRAINT `rna_seqc_compos` FOREIGN KEY (`id_seq_composition`) REFERENCES `seq_composition` (`id_seq_composition`) ON DELETE NO ACTION ON UPDATE NO ACTION
-) ENGINE=InnoDB  DEFAULT CHARSET=utf8;
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 /*!40101 SET character_set_client = @saved_cs_client */;
 
 --

lib/npg_qc/autoqc/checks/rna_seqc.pm

@@ -339,10 +339,11 @@ npg_qc::autoqc::checks::rna_seqc
 
 =head1 DESCRIPTION
 
-QC check that runs Broad Institute's RNA-SeQC software over an RNA sample.
-Files generated by RNA-SeQC are overwriten everytime it is executed and except
-for the directory where the metrics are stored (named after Sample ID) all use
-the same names. The user must consider this when passing the value of qc_report_dir. 
+QC check that runs Broad Institute's RNA-SeQC; a java program which computes a
+series of quality control metrics for RNA-seq data. The output consists of
+HTML reports and tab delimited files of metrics data from which a selection of
+them are extracted to generate an autoqc result. The output directory is
+created by default using the sample's filename root.
 
 =head1 SUBROUTINES/METHODS
 

scripts/upgrade_schema/upgrade_schema-60.x

@@ -2,7 +2,7 @@
 -- Table structure for table `rna_seqc`
 --
 
-CREATE TABLE IF NOT EXISTS `rna_seqc` (
+CREATE TABLE `rna_seqc` (
   `id_rna_seqc` bigint(20) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Auto-generated primary key',
   `id_seq_composition` bigint(20) unsigned NOT NULL COMMENT 'A foreign key referencing the id_seq_composition column of the seq_composition table',
   `info` text,
@@ -23,9 +23,10 @@ CREATE TABLE IF NOT EXISTS `rna_seqc` (
   `end_3_norm` float unsigned DEFAULT NULL,
   `other_metrics` text,
   PRIMARY KEY (`id_rna_seqc`),
+  UNIQUE KEY `rna_seqc_id_compos_unq` (`id_seq_composition`),
   KEY `rna_seqc_compos` (`id_seq_composition`),
   CONSTRAINT `rna_seqc_compos` FOREIGN KEY (`id_seq_composition`) REFERENCES `seq_composition` (`id_seq_composition`) ON DELETE NO ACTION ON UPDATE NO ACTION
-) ENGINE=InnoDB  DEFAULT CHARSET=utf8;
+) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 --
 --
 --

t/60-autoqc-checks-rna_seqc.t

@@ -31,7 +31,7 @@ subtest 'Find CLASSPATH' => sub {
     isa_ok ($rnaseqc, 'npg_qc::autoqc::checks::rna_seqc');
     lives_ok { $rnaseqc->result; } 'result object created';
     local $ENV{CLASSPATH} = q[];
-    throws_ok {npg_qc::autoqc::checks::rna_seqc->new(id_run => 2, path => q[mypath], position => 1, qc_report_dir => q[t/data])}
+    throws_ok {npg_qc::autoqc::checks::rna_seqc->new(id_run => 2, path => q[mypath], position => 1,)}
         qr/Can\'t find \'RNA-SeQC\.jar\' because CLASSPATH is not set/,
         q[Fails to create object when RNA-SeQC.jar not found];
 };