Merge pull request #610 from wtsi-npg/devel

pull from devel to master to create release 91.12.0

Changes

@@ -1,5 +1,14 @@
 LIST OF CHANGES
 
+release 91.12.0
+ - Change instrument and instrument format pages to only show current
+   instruments and instrument formats
+ - Remove superfluous columns in display tables for lists of instruments
+   and instrument formats
+ - Remove unused views (templates) for an instrument manufacturer
+ - Remove manufacturer model and view classes, create manufacturer_name
+   method in the instrument and instrument_format model classes
+
 release 91.11.0
  - a partial reimplementation of the serialization framework for components
    and compositions in order to speed-up frequently used methods 

MANIFEST

@@ -64,10 +64,6 @@ data/templates/instrument_status_menu.tt2
 data/templates/instrument_status_read_xml.tt2
 data/templates/instrument_top.tt2
 data/templates/instrument_update_statuses.tt2
-data/templates/manufacturer_add.tt2
-data/templates/manufacturer_create.tt2
-data/templates/manufacturer_list.tt2
-data/templates/manufacturer_read.tt2
 data/templates/run_add.tt2
 data/templates/run_annotation_add_ajax.tt2
 data/templates/run_annotation_add_input_form.tt2
@@ -182,7 +178,6 @@ lib/npg/model/instrument_mod_dict.pm
 lib/npg/model/instrument_status.pm
 lib/npg/model/instrument_status_annotation.pm
 lib/npg/model/instrument_status_dict.pm
-lib/npg/model/manufacturer.pm
 lib/npg/model/run.pm
 lib/npg/model/run_annotation.pm
 lib/npg/model/run_lane.pm
@@ -215,7 +210,6 @@ lib/npg/view/instrument_format.pm
 lib/npg/view/instrument_mod.pm
 lib/npg/view/instrument_status.pm
 lib/npg/view/instrument_status_annotation.pm
-lib/npg/view/manufacturer.pm
 lib/npg/view/run.pm
 lib/npg/view/run_annotation.pm
 lib/npg/view/run_lane.pm
@@ -360,7 +354,6 @@ t/10-model-instrument_mod_dict.t
 t/10-model-instrument_status.t
 t/10-model-instrument_status_annotation.t
 t/10-model-instrument_status_dict.t
-t/10-model-manufacturer.t
 t/10-model-run.t
 t/10-model-run_annotation.t
 t/10-model-run_lane.t

data/templates/instrument_format_list.tt2

@@ -1,27 +1,23 @@
-<!-- begin $Id: instrument_format_list.tt2 6141 2009-08-13 09:19:17Z dj3 $ -->
-
 [% PROCESS instrument_formats_menu.tt2
 %]
 
-
 <table id="instrument_formats" class="sortable zebra">
   <thead>
     <tr>
       <th>Instrument Manufacturer</th>
       <th>Instrument Model</th>
-      <th>Is Current</th>
-      <th>Instrument Count</th>
+      <th>Current Instrument Count</th>
     </tr>
   </thead>
   <tbody>
 [% FOREACH instrument_format = model.instrument_formats %]
-  <tr>
-    <td><a href="[% SCRIPT_NAME %]/manufacturer/[% instrument_format.id_manufacturer %]">[% instrument_format.manufacturer.name %]</a></td>
-    <td><a href="[% SCRIPT_NAME %]/instrument_format/[% instrument_format.id_instrument_format %]">[% instrument_format.model %]</a></td>
-    <td>[% IF instrument_format.iscurrent %]<img src="/icons/silk/tick.png" alt="tick.png" title="yes" />[% ELSE %]<img src="/icons/silk/cross.png" alt="cross.png" title="no" />[% END %]</td>
-    <td>[% instrument_format.instrument_count %]</td>
-  </tr>
+  [% IF instrument_format.iscurrent %]
+    <tr>
+      <td>[% instrument_format.manufacturer_name %]</td>
+      <td><a href="[% SCRIPT_NAME %]/instrument_format/[% instrument_format.id_instrument_format %]">[% instrument_format.model %]</a></td>
+      <td>[% instrument_format.current_instruments_count %]</td>
+    </tr>
+  [% END %]
 [% END %]
   </tbody>
 </table>
-<!-- end $Id: instrument_format_list.tt2 6141 2009-08-13 09:19:17Z dj3 $ -->

data/templates/instrument_format_read.tt2

@@ -1,23 +1,17 @@
-<!-- begin $Id: instrument_format_read.tt2 2662 2008-08-06 12:23:37Z rmp $ -->
 <table id="instruments" class="sortable zebra">
- <caption>Instruments for format [% model.manufacturer.name %] [% model.model %]</caption>
+ <caption>Instruments for format [% model.manufacturer_name %] [% model.model %]</caption>
  <thead>
   <tr>
    <th>Name</th>
    <th>Model</th>
    <th>External Name</th>
-   <th>Serial #</th>
-   <th>Is Current</th>
   </tr>
  </thead>
- <tbody>[% FOREACH instrument = model.instruments %]
+ <tbody>[% FOREACH instrument = model.instruments; IF instrument.iscurrent %]
   <tr>
    <td><a href="[% SCRIPT_NAME %]/instrument/[% instrument.id_instrument %]">[% instrument.name %]</a></td>
    <td>[% instrument.model %]</td>
    <td>[% instrument.external_name %]</td>
-   <td>[% instrument.serial %]</td>
-   <td>[% IF instrument.iscurrent %]<img src="/icons/silk/tick.png" alt="tick.png" title="yes" />[% ELSE %]<img src="/icons/silk/cross.png" alt="cross.png" title="no" />[% END %]</td>
-  </tr>[% END %]
+  </tr>[% END; END %]
  </tbody>
 </table>
-<!-- end $Id: instrument_format_read.tt2 2662 2008-08-06 12:23:37Z rmp $ -->

data/templates/instrument_list_textual.tt2

@@ -9,8 +9,6 @@
    <th>Model</th>
    <th>External Name</th>
    <th>Designation</th>
-   <th>Serial #</th>
-   <th>Is Current</th>
    <th>Current Run</th>
    <th>Current Status</th>
    <th>Status Comment</th>
@@ -23,8 +21,6 @@
    <td>[% instrument.model %]</td>
    <td>[% instrument.external_name %]</td>
    <td>[% IF instrument.designations %][% FOREACH designation = instrument.designations %][% designation.description | html %]&nbsp;[% END %][% ELSE %]&nbsp;[% END %]</td>
-   <td>[% instrument.serial %]</td>
-   <td>[% IF instrument.iscurrent %]<img src="/icons/silk/tick.png" alt="tick.png" title="yes" />[% ELSE %]<img src="/icons/silk/cross.png" alt="cross.png" title="no" />[% END %]</td>
    <td>[% PROCESS current_runs_info %]</td>
    <td>[% instrument.current_instrument_status.instrument_status_dict.description %]</td>
    <td>[% instrument.current_instrument_status.comment %]</td>
@@ -65,4 +61,4 @@
 [%- BLOCK run_info -%]
 [%- status = current_run.current_run_status.description -%]
 [%- IF status %]<a href="[% SCRIPT_NAME %]/run/[% current_run.id_run %]">[% current_run.name %]</a> [% status %][% ELSE; idle; END -%]
-[%- END -%]
+[%- END -%]

data/templates/instrument_read.tt2

@@ -9,7 +9,7 @@
 <div class="page_title">[% title %]</div>
 <table id="instrument_info_table">
  <tr><th>Model</th><td><a href="[% SCRIPT_NAME %]/instrument_format/[% model.id_instrument_format %]">[% model.instrument_format.model %]</a>&nbsp;</td></tr>
- <tr><th>Manufacturer</th><td>[% mname = model.manufacturer.name; mname = mname ? mname : '&nbsp;'; mname; %]</td></tr>
+ <tr><th>Manufacturer</th><td>[% mname = model.manufacturer_name; mname = mname ? mname : '&nbsp;'; mname; %]</td></tr>
  [% IF model.serial %]<tr><th>Serial Number</th><td>[% model.serial %]&nbsp;</td></tr>[% END %]
  [% IF model.designations %]<tr><th>Designations</th><td>[% FOREACH designation = model.designations %][% designation.description | html %]&nbsp;[% END %]</td></tr>[% END %]
 

data/templates/instrument_top.tt2

@@ -1,4 +1,4 @@
-[% labels    = ['current status', 'formats'] -%]
+[% labels    = ['current status', 'current formats'] -%]
 [% addresses = ['instrument/graphical', 'instrument_format'] -%]
 [% counts    = [0, 2] -%]
 <p class="npgmenu1">

lib/npg/controller.pm

@@ -7,7 +7,6 @@ use base qw(ClearPress::controller);
 use npg::decorator;
 
 use npg::model::instrument_format;
-use npg::model::manufacturer;
 use npg::model::instrument;
 use npg::model::instrument_annotation;
 use npg::model::instrument_status;
@@ -24,7 +23,6 @@ use npg::model::run_lane_annotation;
 use npg::model::instrument_status_annotation;
 
 use npg::view::annotation;
-use npg::view::manufacturer;
 use npg::view::instrument_format;
 use npg::view::instrument_status;
 use npg::view::instrument_annotation;
@@ -111,11 +109,17 @@ npg::controller - NPG tracking controller
 
 =head1 AUTHOR
 
-Roger M Pettett
+=over
+
+=item Roger M Pettett
+
+=item Marina Gourtovaia
+
+=back
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2016 GRL
+Copyright (C) 2006,2014,2016,2020,2021 Genome Research Ltd.
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by

lib/npg/model/instrument.pm

@@ -1,8 +1,5 @@
-#########
-# Author:        rmp
-# Created:       2006-10-31
-#
 package npg::model::instrument;
+
 use strict;
 use warnings;
 use base qw(npg::model);
@@ -178,14 +175,9 @@ sub model {
   return $self->instrument_format->model();
 }
 
-sub id_manufacturer {
-  my $self = shift;
-  return $self->instrument_format->id_manufacturer();
-}
-
-sub manufacturer {
+sub manufacturer_name {
   my $self = shift;
-  return $self->instrument_format->manufacturer();
+  return $self->instrument_format->manufacturer_name();
 }
 
 sub runs {
@@ -666,13 +658,9 @@ Has a side-effect of updating an instrument's current instrument_status to 'wash
 
   my $sModel = $oInstrument->model();
 
-=head2 id_manufacturer - id_manufacturer of this machine, via its instrument_format
-
-  my $iIdManufacturer = $oInstrument->id_manufacturer();
-
-=head2 manufacturer - npg::model::manufacturer of this machine, via its instrument_format
+=head2 manufacturer_name - the name of the manufacturer of this instrument
 
-  my $oManufacturer = $oInstrument->manufacturer();
+  my $oManufacturer = $oInstrument->manufacturer_name();
 
 =head2 instrument_statuses - arrayref of npg::model::instrument_statuses for this instrument
 
@@ -776,11 +764,17 @@ returns true if the instrument is a MiSeq, false otherwise
 
 =head1 AUTHOR
 
-Roger Pettett, E<lt>[email protected]E<gt>
+=over
+
+=item Roger Pettett, E<lt>[email protected]E<gt>
+
+=item Marina Gourtovaia
+
+=back
 
 =head1 LICENSE AND COPYRIGHT
 
-Copyright (C) 2008 GRL, by Roger Pettett
+Copyright (C) 2006,2008,2013,2014,2016,2018,2021 Genome Research Ltd.
 
 This file is part of NPG.