Merge branch 'version/2.4' into version/2.5

* version/2.4:
  Check that LSF detection works as expected
  bugfix: keep the modified $PATH local to the test, otherwise it will bleed into the other tests
  Make sure this is a real LSF (or openlava) and exclude Slurm clusters that ship "lsid"
  Don't use the enhanced mode as it messes up most analysis names

modules/Bio/EnsEMBL/Hive/Meadow/LSF.pm

@@ -77,12 +77,16 @@ our $VERSION = '5.2';       # Semantic version of the Meadow interface:
 =cut
 
 sub name {
-    my $mcni = 'My cluster name is';
+    my $re_lsf_names = qr/(IBM Spectrum LSF|Platform LSF|openlava project)/;
+    my $re_cluster_name = qr/^My cluster name is\s+(\S+)/;
     my @lsid_out = `lsid 2>/dev/null`;
 
+    my $is_lsf = 0;
     foreach my $lsid_line (@lsid_out) {
-        if ($lsid_line =~ /^$mcni\s+(\S+)/) {
-            return $1;
+        if ($lsid_line =~ $re_lsf_names) {
+            $is_lsf = 1;
+        } elsif ($lsid_line =~ $re_cluster_name) {
+            return $1 if $is_lsf;
         }
     }
 }

scripts/generate_timeline.pl

@@ -128,13 +128,13 @@ sub main {
     my @palette = qw(#E41A1C #377EB8 #4DAF4A #984EA3 #FF7F00 #FFFF33 #A65628 #F781BF #999999     #8DD3C7 #BEBADA #FB8072 #80B1D3 #FDB462 #B3DE69 #FCCDE5 #D9D9D9 #BC80BD #CCEBC5 #FFED6F    #2F4F4F);
 
     my %terminal_mapping = (
-        'emf' => 'emf',
-        'png' => 'png',
-        'svg' => 'svg',
-        'jpg' => 'jpeg',
-        'gif' => 'gif',
-        'ps'  => 'postscript eps enhanced colour',
-        'pdf' => 'pdf colour enhanced',
+        'emf' => 'emf noenhanced',
+        'png' => 'png noenhanced',
+        'svg' => 'svg noenhanced',
+        'jpg' => 'jpeg noenhanced',
+        'gif' => 'gif noenhanced',
+        'ps'  => 'postscript eps noenhanced colour',
+        'pdf' => 'pdf colour noenhanced',
     );
     my $gnuplot_terminal = undef;
     if ($output and $output =~ /\.(\w+)$/) {

t/04.meadow/fake_bin/lsid

@@ -15,5 +15,6 @@
 # limitations under the License.
 
 
+echo "Platform LSF"
 echo 'My cluster name is test_clUster'
 

t/04.meadow/lsf.t

@@ -21,13 +21,14 @@ use warnings;
 use Cwd;
 use File::Basename;
 
-use Test::More tests => 23;
+use Test::More tests => 25;
 use Test::Exception;
 
 use Bio::EnsEMBL::Hive::Utils::Config;
 
 BEGIN {
     use_ok( 'Bio::EnsEMBL::Hive::Valley' );
+    use_ok( 'Bio::EnsEMBL::Hive::Meadow::LSF' );
 }
 
 # Need EHIVE_ROOT_DIR to access the default config file
@@ -39,9 +40,12 @@ throws_ok {
     my $valley = Bio::EnsEMBL::Hive::Valley->new($config, 'LSF');
 } qr/Meadow 'LSF' does not seem to be available on this machine, please investigate at/, 'No LSF meadow if "lsid" is not present (or does not behave well';
 
+my $ini_path = $ENV{'PATH'};
+
 # WARNING: the data in this script must be in sync with what the fake
 # binaries output
-local $ENV{'PATH'} = $ENV{'EHIVE_ROOT_DIR'}.'/t/04.meadow/fake_bin:'.$ENV{'PATH'};
+{ # begin local $ENV{'PATH'}
+$ENV{'PATH'} = $ENV{'EHIVE_ROOT_DIR'}.'/t/04.meadow/fake_bin:'.$ini_path;
 
 my $test_pipeline_name = 'tracking_homo_sapiens_funcgen_81_38_hive';
 my $test_meadow_name = 'test_clUster';
@@ -229,5 +233,25 @@ lives_and( sub {
     is_deeply($h, {}, 'No bacct output when accounting disabled');
 }, 'Suppressed bacct when AccountingDisabled when checking a date range');
 
+} # end local $ENV{'PATH'}
+
+subtest "Cluster detection", sub {
+    my $lsf_detection_root_dir = $ENV{'EHIVE_ROOT_DIR'}.'/t/04.meadow/lsf_detection';
+    opendir( my $dir_fh, $lsf_detection_root_dir) || die "Can't opendir $lsf_detection_root_dir: $!";
+    foreach my $subdir ( readdir($dir_fh) ) {
+        next unless -d "$lsf_detection_root_dir/$subdir";
+        local $ENV{'PATH'} = "$lsf_detection_root_dir/$subdir:$ini_path";
+        if ($subdir =~ /^ok_(.*)$/) {
+            my $detected_name = Bio::EnsEMBL::Hive::Meadow::LSF::name();
+            ok($detected_name, "Detects $subdir");
+            is($detected_name, $1, "Correct cluster name");
+        } elsif ($subdir =~ /^no/) {
+            my $detected_name = Bio::EnsEMBL::Hive::Meadow::LSF::name();
+            ok(!$detected_name, "Does not detect $subdir");
+        }
+    }
+    closedir($dir_fh);
+};
+
 done_testing();
 

t/04.meadow/lsf_detection/no_slurm_gcloud/lsid

+#!/bin/sh
+
+exec cat <<EOF
+Slurm 20.02.3, Feb 1 2020
+Copyright SchedMD LLC, 2010-2017.
+
+My cluster name is g2
+My master name is g2-controller
+EOF
+

t/04.meadow/lsf_detection/ok_EBI/lsid

+#!/bin/sh
+
+# LSF EBI "noah" farm
+exec cat <<EOF
+IBM Spectrum LSF Standard 10.1.0.6, May 25 2018
+Copyright International Business Machines Corp. 1992, 2016.
+US Government Users Restricted Rights - Use, duplication or disclosure restricted by GSA ADP Schedule Contract with IBM Corp.
+
+My cluster name is EBI
+My master name is ebi-master-001
+EOF
+

t/04.meadow/lsf_detection/ok_YODA/lsid

+#!/bin/sh
+
+# LSF EBI "yoda" farm
+exec cat <<EOF
+IBM Spectrum LSF Standard 10.1.0.0, Jul 08 2016
+Copyright International Business Machines Corp. 1992, 2016.
+US Government Users Restricted Rights - Use, duplication or disclosure restricted by GSA ADP Schedule Contract with IBM Corp.
+
+My cluster name is YODA
+My master name is hh-yoda-02-02.ebi.ac.uk
+EOF
+

t/04.meadow/lsf_detection/ok_cluster1/lsid

+#!/bin/sh
+
+# Old LSF version (7.*)
+# http://sunray2.mit.edu/kits/platform-lsf/7.0.6/1/guides/kit_lsf_guide_source/admin/cluster_ops.html
+exec cat <<EOF
+Platform LSF 7 Update 6 May 6 2009
+Copyright 1992-2009 Platform Computing Corporation
+
+My cluster name is cluster1
+My master name is hostA 
+EOF
+

t/04.meadow/lsf_detection/ok_lsf91_bw3/lsid

+#!/bin/sh
+
+# Old LSF version (9.*)
+# https://www.bsc.es/support/LSF/9.1.2/lsf_admin/index.htm?cluster_info_viewing_lsf.html~main
+exec cat <<EOF
+IBM Platform LSF Standard 9.1.2, May 5 2013 
+© Copyright IBM Corporation 1992, 2013. 
+US Governmant Users Restricted Rights - Use, duplication or disclosure restricted
+  by GSA ADP Schedule Contract with IBM Corp.
+My cluster name is lsf91_bw3 
+My master name is delpe04.lsf.ibm.com
+EOF
+

t/04.meadow/lsf_detection/ok_openlava/lsid

+#!/bin/sh
+
+# openlava
+# https://jensd.be/404/linux/install-and-use-the-openlava-job-scheduler-and-openlava-web-gui-on-centos
+exec cat <<EOF
+openlava project 2.2, Nov  6 2014
+
+My cluster name is openlava
+My master name is node01
+EOF
+