Merge pull request #563 from wtsi-npg/devel

merge from devel to master to create release 91.0.0

Author: mgcam

.travis.yml

@@ -2,7 +2,7 @@ sudo: required
 addons:
   apt:
     packages:
-    - libgd2-xpm-dev
+    - libgd-dev
 language: perl
 dist:
   - bionic

Build.PL

@@ -167,7 +167,6 @@ my $builder = $class->new(
                 'HTTP::Request::Common'           => '5.822',
                 'HTTP::Response'                  => 0,
                 'IO::All'                         => '0.39',
-                'IO::All::FTP'                    => 0,
                 'IO::Scalar'                      => '2.110',
                 'IPC::System::Simple'             => 0,
                 'JSON'                            => '2.12',

Changes

@@ -1,11 +1,51 @@
 LIST OF CHANGES
 
+release 91.0.0
+ - modified is_i5opposite when there is no reverse read
+ - removed scripts for monitoring instruments via ftp; related
+   modules and methods, their tests and test data are removed
+ - code for staging monitor reorganised so that the Monitor::Runfolder
+   class has methods for updating run, run_lane records and run tags
+   and the Monitor::Runfolder::Staging class mainly deals with staging
+   folder inspection and changes; some methods renamed to remove
+   ambiguity about their functionality
+ - some of the functionality of the instrument monitor is incorporated
+   into the staging monitor script code, namely, (1) setting 'multiplex',
+   'paired_read' and 'single_read' tags and (2) deletion of superfluous
+   lanes; this functionality is now available for NovaSeq instruments,
+   while previously it was missing for this instrument type
+ - redundant 'rta' run tag is not longer set
+ - redundant Mirror.completed file is no longer created in the run
+   folder
+ - functionality for checking instruments' wash status and setting
+   'was required' instrument tag is lost; this shoud be done outside
+   of staging monitor
+ - npg_tracking::util::pipeline_config:
+     move bqsr and haplotype caller to a tertiary section which can be
+     set specifically by reference or by using a default study config;
+     restrict access to attributes which should not be set by the caller
+     (local_bin, product_config);
+     enable setting product release configuration file path via the
+     new product_conf_file_path attribute
+ - genome reference hierarchy in the current samplesheet is not compatible with
+   the latest version of MiSeq Illumina software; setting Workflow value to
+   GenerateFastQ prevents the instrument's software from using this value,
+   hence we can stop setting genome reference path altogether
+ - make impossible to download cbcl file via tracking web pages
+ - runs_on_batch method of npg::run::model is refactored not to cache
+   the return value; proper input checking is added
+ - error on run creation if the batch id associated with the run is already
+   associated with one of active runs, i.e. a run that has no current status
+   or its current status is not either 'run cancelled' or 'run stopped early
+
 release 90.3.0
-- npg_tracking::glossary::moniker - added a method for file name
-  parsing to retrieve id_run, position, tag_index, suffix and
-  extension
-- tracking server instrument visualization - remove visual cue
-  for connection delay since ftp-ing to instruments is discontinued
+ - npg_tracking::glossary::moniker -
+     added a method for file name parsing to retrieve id_run,
+     position, tag_index, suffix and extension;
+     private attributes are prevented from being serialized under
+     MooseX::Storage framework
+ - tracking server instrument visualization - remove visual cue
+   for connection delay since ftp-ing to instruments is discontinued
 
 release 90.2.1
  - staging area daemon to save the flowcell barcode to the

MANIFEST

@@ -1,12 +1,9 @@
-bin/cbot_checker
 bin/event_notifications
 bin/illumina_instruments_uptime
-bin/InstrumentPoller
 bin/npg_daemon_control
 bin/npg_move_runfolder
 bin/npg_status2file
 bin/npg_status_watcher
-bin/seq_instr_checker
 bin/staging_area_monitor
 bin/npg_deletable_dr_runs
 Build.PL
@@ -150,18 +147,11 @@ htdocs/js/wtsi/prototype-1.6.0.3.js
 htdocs/js/wtsi/sorttable.js
 htdocs/js/wtsi/zebra.js
 INSTALL
-lib/Monitor/Cbot.pm
-lib/Monitor/Cbot/InstrumentStatus.pm
-lib/Monitor/Cbot/RunInfo.pm
-lib/Monitor/Cbot/RunList.pm
-lib/Monitor/Instrument.pm
 lib/Monitor/Roles/Cycle.pm
 lib/Monitor/Roles/Schema.pm
 lib/Monitor/Roles/Username.pm
 lib/Monitor/RunFolder.pm
 lib/Monitor/RunFolder/Staging.pm
-lib/Monitor/SRS/FTP.pm
-lib/Monitor/SRS/Local.pm
 lib/Monitor/Staging.pm
 lib/npg/api/annotation.pm
 lib/npg/api/base.pm
@@ -472,15 +462,8 @@ t/30-api-run.t
 t/30-api-run_lane.t
 t/30-api-run_status_dict.t
 t/30-api-util.t
-t/34-monitor-cbot-instrument_status.t
-t/34-monitor-cbot-run_info.t
-t/34-monitor-cbot-run_list.t
-t/34-monitor-cbot.t
-t/34-monitor-instrument.t
 t/34-monitor-runfolder-staging.t
 t/34-monitor-runfolder.t
-t/34-monitor-srs-ftp.t
-t/34-monitor-srs-local.t
 t/34-monitor-staging.t
 t/36-npg_tracking-monitor-status.t
 t/40-st-base.t
@@ -513,10 +496,6 @@ t/80-npg_tracking-report-event2followers.t
 t/80-npg_tracking-report-event2subscribers.t
 t/90-reference.t
 t/data/090414_IL24_2726.tar.bz2
-t/data/cbot/cBot1/GetRunList.xml
-t/data/cbot/cBot1/InstrumentStatus.xml
-t/data/cbot/cBot1/RunInfo/091111_OEM-0B6VO7E14KH_0001.xml
-t/data/cbot/cBot2/InstrumentStatus.xml
 t/data/dbic_fixtures/000-Designation.yml
 t/data/dbic_fixtures/000-EntityType.yml
 t/data/dbic_fixtures/000-InstrumentStatusDict.yml
@@ -573,15 +552,6 @@ t/data/fixtures_lims_wh/100-IseqRunLaneMetric.yml
 t/data/fixtures_lims_wh/100-IseqRunStatus.yml
 t/data/fixtures_lims_wh/100-StudyUser.yml
 t/data/fixtures_lims_wh/200-IseqProductMetric.yml
-t/data/gaii/Events.log
-t/data/gaii/Events.Update
-t/data/gaii/ftp/Find_Me
-t/data/gaii/ftp/Runs/100611_IL2_0022/Recipe_GA2-PEM_2x76Cycle_v7.7.xml
-t/data/gaii/ftp/Runs/100628_IL2_04929/Run.completed
-t/data/gaii/ftp/Runs/100914_HS3_05281_A_205MBABXX/Basecalling_Netcopy_complete_READ2.txt
-t/data/gaii/ftp/Runs/100914_HS3_05281_A_205MBABXX/Data/reports/StatusUpdate.xml
-t/data/gaii/ftp/Runs/100914_HS3_05281_A_205MBABXX/ImageAnalysis_Netcopy_complete_READ2.txt
-t/data/gaii/ftp/Runs/100914_HS3_05281_A_205MBABXX/RunInfo.xml
 t/data/gaii/staging/IL3/incoming/100622_IL3_01234/this_run_is_not_complete_yet
 t/data/gaii/staging/IL5/incoming/100621_IL5_01204/Data/Intensities/L001/C1.1/s_1_1.cif
 t/data/gaii/staging/IL5/incoming/100621_IL5_01204/Data/Intensities/L001/C1.1/s_1_2.cif
@@ -711,8 +681,6 @@ t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Recipe_GA2-PEM_2x76Cycle_v7.
 t/data/gaii/staging/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/Data/reports/StatusUpdate.xml
 t/data/gaii/staging/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/RTAComplete.txt
 t/data/gaii/staging/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/RunInfo.xml
-t/data/hiseq/ftp/Runs_E/100914_HS3_05281_A_205MBABXX/Data/reports/StatusUpdate.xml
-t/data/hiseq/ftp/Runs_E/100914_HS3_05281_A_205MBABXX/RunInfo.xml
 t/data/long_info/nfs/sf20/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/RunInfo.xml
 t/data/long_info/nfs/sf20/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/runParameters.xml
 t/data/long_info/nfs/sf20/ILorHSany_sf20/incoming/100914_HS3_05281_A_205MBABXX/Data/Intensities/BaseCalls/config.xml
@@ -798,6 +766,7 @@ t/data/npg_api_run/npg/run/604.xml
 t/data/npg_api_run/npg/run/636.xml
 t/data/pipeline_config/study_config_present/product_release.yml
 t/data/pipeline_config/study_config_absent/product_release.yml
+t/data/pipeline_config/study_config_tertiary_present/product_release.yml
 t/data/rendered/20-view-administration_create_instrument_mod.html
 t/data/rendered/20-view-administration_create_instrument_status.html
 t/data/rendered/20-view-administration_create_run_status.html
@@ -978,6 +947,20 @@ t/data/request/npg/run/1234.xml
 t/data/request/npg/run_status.xml
 t/data/request/npg/run_status_dict.xml
 t/data/request/st/assets/50801.xml
+t/data/run_info/runInfo.hiseq4000.single.twoind.xml
+t/data/run_info/runInfo.hiseq4000.xml
+t/data/run_info/runInfo.hiseq.rr.single.xml
+t/data/run_info/runInfo.hiseq.rr.truseq.xml
+t/data/run_info/runInfo.hiseq.rr.twoind.xml
+t/data/run_info/runInfo.hiseq.rr.xml
+t/data/run_info/runInfo.hiseq.xml
+t/data/run_info/runInfo.hiseqx.upgraded.xml
+t/data/run_info/runInfo.hiseqx.xml
+t/data/run_info/runInfo.miniseq.xml
+t/data/run_info/runInfo.miseq.xml
+t/data/run_info/runInfo.nextseq.xml
+t/data/run_info/runInfo.novaseq.xml
+t/data/run_info/runInfo.novaseq.xp.xml
 t/data/run_params/RunParameters.miniseq.xml
 t/data/run_params/RunParameters.nextseq.xml
 t/data/run_params/RunParameters.novaseq.xml
@@ -1603,10 +1586,6 @@ t/data/test45/st/studies/297.xml
 t/data/test45/st/studies/333.xml
 t/data/test45/st/studies/365.xml
 t/data/test45/st/studies/700.xml
-t/data/gaii/ftp/Runs/100611_IL2_0022/Data/Intensities/.gitignore
-t/data/gaii/ftp/Runs/100611_IL2_mb110610/.gitignore
-t/data/gaii/ftp/Runs/100628_IL2_04929/Data/.gitignore
-t/data/gaii/ftp/Runs/this_is_not_a_run/.gitignore
 t/data/gaii/staging/IL12/incoming/100721_IL12_05222/Data/Intensities/L001/.gitignore
 t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C1.1/.gitignore
 t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L001/C10.1/.gitignore
@@ -1654,7 +1633,6 @@ t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L006/.gitigno
 t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L007/.gitignore
 t/data/gaii/staging/IL3/incoming/100622_IL3_01234/Data/Intensities/L008/.gitignore
 t/data/gaii/staging/IL3/skip_this_one/090810_IL12_3289/.gitignore
-t/data/gaii/staging/IL4/incoming/101026_IL4_0095/.gitignore
 t/data/gaii/staging/IL5/incoming/100708_IL3_04998/.gitignore
 t/data/gaii/staging/IL5/incoming/100708_IL3_04999/Images/L001/.gitignore
 t/data/gaii/staging/IL5/incoming/not_a_valid_run_folder/.gitignore
@@ -1712,9 +1690,6 @@ t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C6.1/.
 t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C7.1/.gitignore
 t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C8.1/.gitignore
 t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Data/Intensities/L001/C9.1/.gitignore
-t/data/hiseq/ftp/Runs_D/.gitignore
-t/data/hiseq/ftp/Runs_E/100914_HS3_05281_A_205MBABXX/Images/L001/.gitignore
-t/data/hiseq/ftp/Runs_E/100914_HS3_05281_A_205MBABXX/Processed/L001/.gitignore
 t/data/repos2/references2/Homo_sapiens/GRCh37_53/.gitignore
 t/data/repos2/references2/Homo_sapiens/NCBI36/.gitignore
 t/data/repos2/references2/Human_herpesvirus_4/EB1/.gitignore
@@ -1724,7 +1699,6 @@ t/data/repos2/references2/PhiX/Illumina/.gitignore
 t/data/repos2/references2/PhiX/Sanger/.gitignore
 t/dbh.pm
 t/dbic_util.pm
-t/ftp_util.pm
 t/perlcriticrc
 t/request.pm
 t/useragent.pm