Merge pull request #451 from iainrb/fluidigm_qc_publish

Add option to publish Fluidigm QC results to iRODS

doc/CHANGELOG.md

@@ -4,6 +4,12 @@ Change log for WTSI genotyping pipeline
 
 Latest version is hosted at: https://github.com/wtsi-npg/genotyping
 
+Release 1.14.2: 2017-03-31
+--------------------------
+
+Added:
+- Fluidigm QC script has option to publish results to iRODS
+
 Release 1.14.1: 2017-03-28
 --------------------------
 

src/perl/bin/qc_fluidigm.pl

@@ -5,6 +5,7 @@ package main;
 use strict;
 use warnings;
 use Cwd qw(abs_path);
+use DateTime;
 use File::Copy qw(cp);
 use File::Temp qw(tempfile);
 use File::Spec::Functions qw(tmpdir);
@@ -16,6 +17,7 @@ package main;
 use WTSI::NPG::Genotyping::Fluidigm::AssayDataObject;
 use WTSI::NPG::Genotyping::Fluidigm::QC;
 use WTSI::NPG::iRODS;
+use WTSI::NPG::SimplePublisher;
 use WTSI::NPG::Utilities qw(user_session_log);
 
 my $uid = `whoami`;
@@ -32,6 +34,7 @@ sub run {
     my $log4perl_config;
     my $new_csv;
     my $old_csv;
+    my $publish_dest;
     my $query_path;
     my $verbose;
     my @filter_key;
@@ -47,6 +50,7 @@ sub run {
                'logconf=s'      => \$log4perl_config,
                'new-csv=s'      => \$new_csv,
                'old-csv=s'      => \$old_csv,
+               'publish-dest=s' => \$publish_dest,
                'query-path=s'   => \$query_path,
                'verbose'        => \$verbose,
                ''               => \$stdio); # Permits trailing '-' for STDIN
@@ -87,6 +91,11 @@ sub run {
             $new_csv = $old_csv;
         }
     }
+    if ($publish_dest && ! $new_csv) {
+        pod2usage(-msg => "Must specify --new-csv or --in-place for ".
+                      "publication of output to iRODS",
+                  -exitval => 2);
+    }
     # set up logging
     my @log_levels;
     if ($debug) { push @log_levels, $DEBUG; }
@@ -143,6 +152,14 @@ sub run {
     $qc->write_csv($fh);
     if (defined $new_csv) {
         close $fh || $log->logcroak("Cannot close CSV output");
+        if (defined $publish_dest) {
+            my $publisher = WTSI::NPG::SimplePublisher->new(irods => $irods);
+            my $published = $publisher->publish_file($new_csv,
+                                                     [],
+                                                     $publish_dest,
+                                                     DateTime->now);
+            $log->info('Published Fluidigm QC output to iRODS: ', $published);
+        }
     }
     if (defined $temp) {
         my $cp_ok = cp($temp, $new_csv);
@@ -177,6 +194,9 @@ =head1 SYNOPSIS
                  to STDOUT.
   --old-csv      Path of a CSV file from which to read existing QC records.
                  Optional.
+  --publish-dest An iRODS collection for publication of the CSV output file.
+                 Optional; if not given, output is not published to iRODS.
+                 Not valid if output is being written to STDOUT.
   --query-path   An iRODS path to query for Fluidigm DataObjects. Required,
                  unless iRODS paths are supplied on STDIN using the '-'
                  option.

src/perl/t/WTSI/NPG/Genotyping/Fluidigm/QCTest.pm

@@ -10,7 +10,7 @@ use File::Copy qw/copy/;
 use File::Slurp qw/read_file/;
 use File::Temp qw/tempdir/;
 use Set::Scalar;
-use Test::More tests => 17;
+use Test::More tests => 19;
 use Test::Exception;
 use Text::CSV;
 
@@ -131,6 +131,18 @@ sub script_metaquery : Test(2) {
     _validate_csv_output("$tmp/$csv_name", $msg);
 }
 
+sub script_publish : Test(2) {
+    my $irods = WTSI::NPG::iRODS->new;
+    my $publish_dest = $irods_tmp_coll.'/qc_output';
+    my $cmd = "$script --query-path $irods_tmp_coll ".
+        "--publish-dest $publish_dest ".
+        "--old-csv $tmp/$csv_name --in-place --logconf $logconf --debug";
+    $log->info("Running command '$cmd'");
+    ok(system($cmd)==0, "Script with --publish-dest exits OK");
+    my $obj_path = $publish_dest.'/'.$csv_name;
+    ok($irods->is_object($obj_path), 'QC output published to '.$obj_path);
+}
+
 sub script_update : Test(2) {
     # ensure an entry with outdated md5 checksum is replaced
     my $cmd = "$script --query-path $irods_tmp_coll ".