Merge pull request #13 from cancerit/feature/prerelease_n_basic_tests

Feature/prerelease n basic tests

.gitignore

@@ -8,3 +8,5 @@
 /README.md
 /perl/MYMETA.json
 /perl/MYMETA.yml
+/perl/docs/
+/perl/perltidy.LOG

perl/MANIFEST

@@ -0,0 +1,70 @@
+bin/compare_CN_and_fusion.pl
+bin/compare_overlapping_fusions.pl
+bin/defuse.pl
+bin/filter_fusions.pl
+bin/process_qcstats.pl
+bin/star_fusion.pl
+bin/star_mapping.pl
+bin/tophat_add_strand.pl
+bin/tophat_fusion.pl
+config/defuse.ini
+config/star.ini
+config/tophat.ini
+docs.tar.gz
+docs/pod_html/_blkbluw.css
+docs/pod_html/_blkcynw.css
+docs/pod_html/_blkgrng.css
+docs/pod_html/_blkmagw.css
+docs/pod_html/_grygrnk.css
+docs/pod_html/_grygrnw.css
+docs/pod_html/_podly.js
+docs/pod_html/_whtgrng.css
+docs/pod_html/_whtnavk.css
+docs/pod_html/_whtprpk.css
+docs/pod_html/_whtpurk.css
+docs/pod_html/compare_overlapping_fusions.html
+docs/pod_html/defuse.html
+docs/pod_html/filter_fusions.html
+docs/pod_html/index.html
+docs/pod_html/star_fusion.html
+docs/pod_html/star_mapping.html
+docs/pod_html/tophat_add_strand.html
+docs/pod_html/tophat_fusion.html
+docs/reports_html/common.js
+docs/reports_html/cover.14
+docs/reports_html/cover.css
+docs/reports_html/coverage.html
+docs/reports_html/css.js
+docs/reports_html/index.html
+docs/reports_html/lib-Sanger-CGP-CgpRna-pm--subroutine.html
+docs/reports_html/lib-Sanger-CGP-CgpRna-pm.html
+docs/reports_html/lib-Sanger-CGP-CompareFusions-FusionAnnotation-pm--branch.html
+docs/reports_html/lib-Sanger-CGP-CompareFusions-FusionAnnotation-pm--subroutine.html
+docs/reports_html/lib-Sanger-CGP-CompareFusions-FusionAnnotation-pm.html
+docs/reports_html/lib-Sanger-CGP-CompareFusions-Implement-pm--branch.html
+docs/reports_html/lib-Sanger-CGP-CompareFusions-Implement-pm--subroutine.html
+docs/reports_html/lib-Sanger-CGP-CompareFusions-Implement-pm.html
+docs/reports_html/lib-Sanger-CGP-Defuse-Implement-pm--branch.html
+docs/reports_html/lib-Sanger-CGP-Defuse-Implement-pm--subroutine.html
+docs/reports_html/lib-Sanger-CGP-Defuse-Implement-pm.html
+docs/reports_html/lib-Sanger-CGP-RnaQC-Implement-pm--branch.html
+docs/reports_html/lib-Sanger-CGP-RnaQC-Implement-pm--subroutine.html
+docs/reports_html/lib-Sanger-CGP-RnaQC-Implement-pm.html
+docs/reports_html/lib-Sanger-CGP-Star-Implement-pm--branch.html
+docs/reports_html/lib-Sanger-CGP-Star-Implement-pm--subroutine.html
+docs/reports_html/lib-Sanger-CGP-Star-Implement-pm.html
+docs/reports_html/standardista-table-sorting.js
+docs/reports_text/coverage.txt
+lib/Sanger/CGP/CgpRna.pm
+lib/Sanger/CGP/CompareFusions/FusionAnnotation.pm
+lib/Sanger/CGP/CompareFusions/Implement.pm
+lib/Sanger/CGP/Defuse/Implement.pm
+lib/Sanger/CGP/RnaQC/Implement.pm
+lib/Sanger/CGP/Star/Implement.pm
+lib/Sanger/CGP/Tophat/Implement.pm
+Makefile.PL
+MANIFEST			This list of files
+perltidy.LOG
+t/1_pm_compile.t
+t/2_pl_compile.t
+t/data/tst.txt

perl/Makefile.PL

@@ -33,7 +33,6 @@
 
 
 use ExtUtils::MakeMaker;
-use File::ShareDir::Install;
 
 WriteMakefile(
   NAME          => 'cgpRna',
@@ -50,6 +49,3 @@ WriteMakefile(
                      'File::Which' => 1.09,
                    }
 );
-
-package MY;
-use File::ShareDir::Install qw( postamble );

perl/t/1_pm_compile.t

@@ -0,0 +1,56 @@
+# this is a catch all to ensure all modules do compile
+# added as lots of 'use' functionality is dynamic in pipeline
+# and need to be sure that all modules compile.
+# simple 'perl -c' is unlikely to work on head scripts any more.
+
+use strict;
+use Data::Dumper;
+use Test::More;
+use List::Util qw(first);
+use File::Find;
+use Cwd;
+use Try::Tiny qw(try finally);
+use File::Spec;
+
+use FindBin qw($Bin);
+my $lib_path = "$Bin/../lib";
+
+# Add modules here that cannot be instantiated (should be extended and have no 'new')
+# or need a set of inputs - these should be tested in own test script
+use constant MODULE_SKIP => qw();
+
+
+my $init_cwd = getcwd;
+
+my @modules;
+try {
+  chdir($lib_path);
+  find({ wanted => \&build_module_set, no_chdir => 1 }, './');
+} finally {
+  chdir $init_cwd;
+  die "The try block died with: @_\n" if(@_);
+};
+
+for my $mod(@modules) {
+  use_ok($mod) or BAIL_OUT("Unable to 'use' module $mod");
+}
+
+for my $mod(@modules) {
+  ok($mod->VERSION, "Check version inheritance exists ($mod)");
+  if($mod->can('new')) { # only try new on things that have new defined
+    new_ok($mod) unless( first {$mod eq $_} MODULE_SKIP );
+  }
+}
+
+done_testing();
+
+sub build_module_set {
+  if($_ =~ m/\.pm$/) {
+
+    my ($dir_str,$file) = (File::Spec->splitpath( $_ ))[1,2];
+    $file =~ s/\.pm$//;
+    my @dirs = File::Spec->splitdir( $dir_str );
+    shift @dirs;
+    push @modules, (join '::', @dirs).$file;
+  }
+}

perl/t/2_pl_compile.t

@@ -0,0 +1,48 @@
+# this is a catch all to ensure all modules do compile
+# added as lots of 'use' functionality is dynamic in pipeline
+# and need to be sure that all modules compile.
+# simple 'perl -c' is unlikely to work on head scripts any more.
+
+use strict;
+use Data::Dumper;
+use Test::More;
+use List::Util qw(first);
+use Try::Tiny qw(try catch);
+use autodie qw(:all);
+use File::Find;
+
+use FindBin qw($Bin);
+my $script_path = "$Bin/../bin";
+
+use constant COMPILE_SKIP => qw();
+
+my $perl = $^X;
+
+my @scripts;
+find({ wanted => \&build_path_set, no_chdir => 1 }, $script_path);
+
+for(@scripts) {
+  my $script = $_;
+  if( first {$script =~ m/$_$/} COMPILE_SKIP ) {
+    note("SKIPPING: Script with known issues: $script");
+    next;
+  }
+  my $message = "Compilation check: $script";
+  my $command = "$perl -c $script";
+  my ($pid, $process);
+  try {
+    $pid = open $process, $command.' 2>&1 |';
+    while(<$process>){};
+    close $process;
+    pass($message);
+  }
+  catch {
+    fail($message);
+  };
+}
+
+done_testing();
+
+sub build_path_set {
+  push @scripts, $_ if($_ =~ m/\.pl$/);
+}

prerelease.sh

@@ -0,0 +1,56 @@
+#!/bin/bash
+
+set -eu # exit on first error or undefined value in subtitution
+set -o pipefail
+
+# get current directory
+INIT_DIR=`pwd`
+
+# get location of this file
+MY_PATH="`dirname \"$0\"`"              # relative
+MY_PATH="`( cd \"$MY_PATH\" && pwd )`"  # absolutized and normalized
+if [ -z "$MY_PATH" ] ; then
+  # error; for some reason, the path is not accessible
+  # to the script (e.g. permissions re-evaled after suid)
+  echo Failed to determine location of script >2
+  exit 1  # fail
+fi
+# change into the location of the script
+cd $MY_PATH/perl
+rm -rf blib
+rm -rf docs
+
+echo '### Running perl tests ###'
+
+export HARNESS_PERL_SWITCHES=-MDevel::Cover=-db,reports,-ignore,'t/.*\.t'
+mkdir -p docs/reports_text
+prove -w -I lib
+echo
+echo '### Generating test/pod coverage reports ###'
+# removed 'condition' from coverage as '||' 'or' doesn't work properly
+cover -coverage branch,subroutine,pod -report_c0 50 -report_c1 85 -report_c2 100 -report html_basic reports -silent
+cover -coverage branch,subroutine,pod -report text reports -silent > docs/reports_text/coverage.txt
+rm -rf reports/structure reports/digests reports/cover.13 reports/runs
+cp reports/coverage.html reports/index.html
+mv reports docs/reports_html
+unset HARNESS_PERL_SWITCHES
+
+echo '### Generating POD ###'
+mkdir -p docs/pod_html
+perl -MPod::Simple::HTMLBatch -e 'Pod::Simple::HTMLBatch::go' lib:bin docs/pod_html > /dev/null
+
+echo '### Archiving docs folder ###'
+tar cz -f docs.tar.gz docs
+
+# generate manifest, and cleanup
+echo '### Generating MANIFEST ###'
+# delete incase any files are moved, the make target just adds stuff
+rm -f MANIFEST
+# cleanup things which could break the manifest
+rm -rf install_tmp
+perl Makefile.PL > /dev/null
+make manifest &> /dev/null
+rm -f Makefile MANIFEST.bak pm_to_blib MYMETA.*
+
+# change back to original dir
+cd $INIT_DIR

setup.sh

@@ -124,10 +124,8 @@ cd $INIT_DIR
 
 # make sure that build is self contained
 unset PERL5LIB
-ARCHNAME=`perl -e 'use Config; print $Config{archname};'`
 PERLROOT=$INST_PATH/lib/perl5
-PERLARCH=$PERLROOT/$ARCHNAME
-export PERL5LIB="$PERLROOT:$PERLARCH"
+export PERL5LIB="$PERLROOT"
 
 # Set PYTHONPATH as well so that RSeQC can be installed
 unset PYTHONPATH
@@ -171,15 +169,12 @@ if [ -e $SETUP_DIR/star.success ]; then
 else
 (
   cd $SETUP_DIR
-  set -x
-  if [ ! -e star ]; then
-    get_distro "star" $SOURCE_STAR
-    mkdir -p star
-    tar --strip-components 1 -C star -zxf star.tar.gz
-  fi
-  cp star/bin/Linux_x86_64/STAR $INST_PATH/bin/.
-  cp star/STAR-Fusion-*/STAR-Fusion $INST_PATH/bin/.
-  cp star/STAR-Fusion-*/lib/* $PERLROOT/.
+  get_distro "star" $SOURCE_STAR &&
+  mkdir -p star && 
+  tar --strip-components 1 -C star -zxf star.tar.gz &&
+  cp star/bin/Linux_x86_64/STAR $INST_PATH/bin/. &&
+  cp star/STAR-Fusion-*/STAR-Fusion $INST_PATH/bin/. &&
+  cp star/STAR-Fusion-*/lib/* $PERLROOT/. &&
   touch $SETUP_DIR/star.success
   )>>$INIT_DIR/setup.log 2>&1
 fi
@@ -193,14 +188,11 @@ if [ -e $SETUP_DIR/rseqc.success ]; then
 else
 (
   cd $SETUP_DIR
-  set -x
-  if [ ! -e rseqc ]; then
-    get_distro "rseqc" $SOURCE_RSEQC
-    mkdir -p rseqc
-    tar --strip-components 1 -C rseqc -zxf rseqc.tar.gz
-  fi
-  cd $SETUP_DIR/rseqc
-  python ./setup.py install --prefix=$INST_PATH
+  get_distro "rseqc" $SOURCE_RSEQC &&
+  mkdir -p rseqc &&
+  tar --strip-components 1 -C rseqc -zxf rseqc.tar.gz &&
+  cd $SETUP_DIR/rseqc &&
+  python ./setup.py install --prefix=$INST_PATH &&
   touch $SETUP_DIR/rseqc.success
   )>>$INIT_DIR/setup.log 2>&1
 fi
@@ -227,11 +219,11 @@ done_message "" "Failed during installation of core dependencies."
 # Install cgpRna code
 echo -n "Installing cgpRna..."
 (
-  cd $INIT_DIR/perl
-  perl Makefile.PL INSTALL_BASE=$INST_PATH
-  make
-  make test
-  make install
+  cd $INIT_DIR/perl &&
+  perl Makefile.PL INSTALL_BASE=$INST_PATH &&
+  make &&
+  make test &&
+  make install &&
   cp $INIT_DIR/perl/config/star.ini $INST_PATH/config/
 ) >>$INIT_DIR/setup.log 2>&1
 done_message "" "cgpRna install failed."
@@ -249,4 +241,4 @@ echo "Please add the following to beginning of PYTHONPATH:"
 echo "  $PYTHONROOT"
 echo
 
-exit 0
+exit 0