diff --git a/MANIFEST b/MANIFEST
index 80a8f6b7..e5027ee9 100644
--- a/MANIFEST
+++ b/MANIFEST
@@ -9,7 +9,6 @@ bin/npg_pipeline_post_qc_review
bin/npg_pipeline_preexec_references
bin/npg_pipeline_script_must_be_unique_runner
bin/npg_pipeline_seqchksum_comparator
-bin/npg_receipt4run_is_deletable
bin/npg_run_is_deletable
Build.PL
Changes
diff --git a/bin/npg_receipt4run_is_deletable b/bin/npg_receipt4run_is_deletable
deleted file mode 100755
index d0ff8c4a..00000000
--- a/bin/npg_receipt4run_is_deletable
+++ /dev/null
@@ -1,201 +0,0 @@
-#!/usr/bin/env perl
-
-use strict;
-use warnings;
-use FindBin qw($Bin $Script);
-use lib ( -d "$Bin/../lib/perl5" ? "$Bin/../lib/perl5" : "$Bin/../lib" );
-use Log::Log4perl qw{:levels};
-use Getopt::Long;
-use Readonly;
-use File::Temp qw(tempdir);
-use DateTime;
-use Pod::Usage;
-use File::Slurp;
-use Carp;
-use File::Copy;
-
-use WTSI::DNAP::Warehouse::Schema;
-
-our $VERSION = '0';
-
-Readonly::Scalar my $STATUS_SUCCESS => 'SUCCESS';
-Readonly::Scalar my $STATUS_PASS => 'PASS';
-Readonly::Scalar my $RECEIPT_DELIM => qq[\t];
-
-my $help;
-my $file_path;
-
-GetOptions (
- 'help' => \$help,
- 'receipt_path=s' => \$file_path,
- );
-if ($help) { pod2usage(0); }
-
-
-my $layout = '%d %-5p %c - %m%n';
-Log::Log4perl->easy_init({layout => $layout,
- level => $INFO,
- utf8 => 1});
-my $logger = Log::Log4perl->get_logger();
-
-$file_path or
- ($logger->error('--receipt_path argument is required') and exit 1);
-$logger->info("Receipt file to use $file_path");
-
-my $schema = WTSI::DNAP::Warehouse::Schema->connect();
-
-my $rs = $schema->resultset('IseqExternalProductMetric')->search(
- {manifest_upload_status => $STATUS_SUCCESS,
- format_validation => $STATUS_PASS},
- {column => qw(supplier_sample_name file_name md5_staging)}
-);
-
-my $count = $rs->count;
-if ($count == 0) {
- $logger->info('No receipts available, exiting');
- exit 0;
-} else {
- $logger->info("Receipts for $count products are available");
-}
-
-my @lines = ();
-push @lines, join $RECEIPT_DELIM, ('Bucket key', 'WSI_MD5', 'SBG_MD5', 'Match?');
-while (my $row = $rs->next()) {
- push @lines, join $RECEIPT_DELIM,
- (join q[/], $row->supplier_sample_name, $row->file_name),
- $row->md5_staging,
- $row->md5_staging,
- 'correct';
-}
-@lines = map { $_ . qq[\n] } @lines;
-
-my $tdir = tempdir( CLEANUP => 1 );
-my $filename = "$tdir/receipt";
-$logger->info("Writing to temp file $filename");
-write_file($filename, @lines);
-0 == system "bzip2 $filename" or croak "Failed to compress $filename";
-$filename .= '.bz2';
-
-my $new_path;
-my $compressed_file_path = $file_path . '.bz2';
-if (-e $compressed_file_path) {
- if (not -f $compressed_file_path) {
- croak "$compressed_file_path exists and is not a file";
- }
- $new_path = join q[.],
- $file_path, DateTime->now()->strftime(q[%Y%m%d-%T]), 'bz2';
- move($compressed_file_path, $new_path) or croak
- "Failed to move $compressed_file_path to $new_path";
-}
-move($filename, $compressed_file_path) or croak
- "Failed to move $filename to $compressed_file_path";
-$new_path && $logger->info("Moved existing $compressed_file_path to $new_path");
-$logger->info("Created new $compressed_file_path");
-
-exit 0;
-
-__END__
-
-=head1 NAME
-
-npg_receipt4run_is_deletable
-
-=head1 USAGE
-
-npg_receipt4run_is_deletable --help
-
-npg_receipt4run_is_deletable --receipt_path
-
-=head1 REQUIRED ARGUMENTS
-
---receipt_path file path of the receipt
-
-=head1 OPTIONS
-
---help
---receipt_path
-
-=head1 EXIT STATUS
-
-0
-
-=head1 CONFIGURATION
-
-=head1 SYNOPSIS
-
-Uses data from ml warehouse to generate a list of externally
-acknowledged products. The list is written to a compressed file. The path
-of the new file is as given by the --receipt_path plus the .bz2 extension.
-
-This file will be used by the npg_run_is_deletable
-script, see npg_pipeline::validation::s3.
-
-=head1 DESCRIPTION
-
-npg_receipt4run_is_deletable --help
-npg_receipt4run_is_deletable --file_path
-
-=head1 SUBROUTINES/METHODS
-
-=head1 DIAGNOSTICS
-
-=head1 CONFIGURATION AND ENVIRONMENT
-
-=head1 DEPENDENCIES
-
-=over
-
-=item strict
-
-=item warnings
-
-=item lib
-
-=item FindBin
-
-=item Log::Log4perl
-
-=item Getopt::Long
-
-=item Readonly
-
-=item File::Temp
-
-=item DateTime
-
-=item Pod::Usage
-
-=item File::Slurp
-
-=item Carp
-
-=item File::Copy
-
-=item WTSI::DNAP::Warehouse::Schema
-
-=back
-
-=head1 INCOMPATIBILITIES
-
-=head1 BUGS AND LIMITATIONS
-
-=head1 AUTHOR
-
-Marina Gourtovaia
-
-=head1 LICENSE AND COPYRIGHT
-
-Copyright (C) 2019 Genome Research Limited
-
-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
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see .
diff --git a/bin/npg_run_is_deletable b/bin/npg_run_is_deletable
index 6ed1450a..396990e5 100755
--- a/bin/npg_run_is_deletable
+++ b/bin/npg_run_is_deletable
@@ -19,7 +19,6 @@ my $their_log_level = $verbose ? 'DEBUG' : 'WARN';
##no critic (ValuesAndExpressions::ProhibitImplicitNewlines)
my $log4perl_config = qq(
log4perl.logger = $my_log_level, A1
- log4perl.category.npg_pipeline.validation.s3 = $their_log_level, A1
log4perl.category.npg_pipeline.validation.irods = $their_log_level, A1
log4perl.category.npg_pipeline.validation.autoqc = $their_log_level, A1
log4perl.logger.WTSI.NPG.iRODS = OFF, A1
diff --git a/lib/npg_pipeline/product/release.pm b/lib/npg_pipeline/product/release.pm
index 56f3f6ce..e240921b 100644
--- a/lib/npg_pipeline/product/release.pm
+++ b/lib/npg_pipeline/product/release.pm
@@ -106,7 +106,6 @@ sub is_release_data {
Arg [2] : Str, type of release
Example : $obj->is_for_release($product, 'irods');
- $obj->is_for_release($product, 's3');
Description: Return true if the product is to be released via the
mechanism defined by the second argument.
@@ -376,10 +375,6 @@ product release.
The configuration file gives per-study settings and a default to be
used for any study without a specific configuration.
- S3:
- enable: S3 release enabled if true.
- url: The S3 bucket URL to send to.
-
irods:
enable: iRODS release enabled if true.
@@ -387,24 +382,15 @@ e.g.
---
default:
- s3:
- enable: false
- url: null
irods:
enable: true
study:
- study_id: "5290"
- s3:
- enable: true
- url: "s3://product_bucket"
irods:
enable: false
- study_id: "1000"
- s3:
- enable: false
- url: null
irods:
enable: true