Merge pull request #821 from wtsi-npg/devel

pull from devel to master to create release 101.1.0

Changes

@@ -1,5 +1,22 @@
 LIST OF CHANGES
 
+release 101.1.0
+ - Deleted npg_tracking::illumina::run::short_info and
+   npg_tracking::illumina::run::locations, their functionality is moved to
+   npg_tracking::illumina::run::folder.
+ - Moved a build method for the run_folder attribute from
+   npg_tracking::illumina::run_folder to npg_tracking::illumina::run::folder.
+ - Preparation for the deletion of unused instrument_utilisation table from
+   the tracking db schema:
+   - dropped instrument_utilisation table from the db schema, which is used
+     for testing the tracking web application,
+   - suppressed generation of the DBIx ORM class for this table and deleted
+     the class.
+ - Added an option to exclude lanes from a merge (see st::api::lims
+   aggregate_libraries method).
+ - Extended the basic search functionality of the tracking web application by
+   enabling a search for lane annotations.
+
 release 101.0.0
  - npg_tracking::illumina::run::short_info
      - Stopped parsing out run details from the run folder name. Deleted

MANIFEST

@@ -225,9 +225,7 @@ lib/npg_tracking/glossary/tag.pm
 lib/npg_tracking/illumina/run.pm
 lib/npg_tracking/illumina/runfolder.pm
 lib/npg_tracking/illumina/run/folder.pm
-lib/npg_tracking/illumina/run/folder/location.pm
 lib/npg_tracking/illumina/run/long_info.pm
-lib/npg_tracking/illumina/run/short_info.pm
 lib/npg_tracking/Schema.pm
 lib/npg_tracking/Schema/Result/Annotation.pm
 lib/npg_tracking/Schema/Result/Designation.pm
@@ -243,7 +241,6 @@ lib/npg_tracking/Schema/Result/InstrumentModDict.pm
 lib/npg_tracking/Schema/Result/InstrumentStatus.pm
 lib/npg_tracking/Schema/Result/InstrumentStatusAnnotation.pm
 lib/npg_tracking/Schema/Result/InstrumentStatusDict.pm
-lib/npg_tracking/Schema/Result/InstrumentUtilisation.pm
 lib/npg_tracking/Schema/Result/Manufacturer.pm
 lib/npg_tracking/Schema/Result/Run.pm
 lib/npg_tracking/Schema/Result/RunAnnotation.pm
@@ -410,7 +407,6 @@ t/50-decorator.t
 t/60-illumina-runfolder.t
 t/60-illumina-run-folder.t
 t/60-illumina-run-long_info.t
-t/60-illumina-run-short_info.t
 t/60-illumina-run.t
 t/60-util-mailer.t
 t/70-bin-npg_status2file.t

lib/npg/model/search.pm

@@ -1,7 +1,3 @@
-#########
-# Author:        rmp
-# Created:       2008-01
-#
 package npg::model::search;
 use strict;
 use warnings;
@@ -77,7 +73,7 @@ sub results {
                        AND    content LIKE ?), "%$term%"];
 
   #########
-  # search run annotations
+  # search annotations
   #
   push @{$queries}, [q(SELECT 'run'        AS type,
                               ra.id_run    AS primary_key,
@@ -89,6 +85,16 @@ sub results {
                        AND    a.comment LIKE   ?
                        ORDER BY date DESC
                        LIMIT 100), "%$term%"];
+  push @{$queries}, [q(SELECT 'run_lane'        AS type,
+                              rla.id_run_lane   AS primary_key,
+                              'annotation' AS location,
+                              a.comment    AS context
+                       FROM   annotation     a,
+                              run_lane_annotation rla
+                       WHERE  rla.id_annotation = a.id_annotation
+                       AND    a.comment LIKE   ?
+                       ORDER BY date DESC
+                       LIMIT 100), "%$term%"];
 
   #########
   # search instrument annotations & statuses
@@ -492,7 +498,7 @@ Roger Pettett, E<lt>[email protected]<gt>
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2007 GRL, by Roger Pettett
+Copyright (C) 2007, 2013, 2014, 2017, 2024 Genome Research Ltd.
 
 This library is free software; you can redistribute it and/or modify
 it under the same terms as Perl itself, either Perl version 5.8.4 or,

lib/npg_tracking/Schema/Result/InstrumentFormat.pm

@@ -147,21 +147,6 @@ __PACKAGE__->set_primary_key("id_instrument_format");
 
 =head1 RELATIONS
 
-=head2 instrument_utilisations
-
-Type: has_many
-
-Related object: L<npg_tracking::Schema::Result::InstrumentUtilisation>
-
-=cut
-
-__PACKAGE__->has_many(
-  "instrument_utilisations",
-  "npg_tracking::Schema::Result::InstrumentUtilisation",
-  { "foreign.id_instrument_format" => "self.id_instrument_format" },
-  { cascade_copy => 0, cascade_delete => 0 },
-);
-
 =head2 instruments
 
 Type: has_many
@@ -208,8 +193,8 @@ __PACKAGE__->has_many(
 );
 
 
-# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30
-# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:esNDL3mLvW19/fKjWfsX/g
+# Created by DBIx::Class::Schema::Loader v0.07052 @ 2024-04-09 10:35:17
+# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:elkjaVkCGUOAo8WzkpdV/A
 
 # Author:        [email protected]
 # Created:       2010-04-08