From 6618a1f16b8cebe20babe84b34340416efc25a22 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Thu, 17 Nov 2016 15:09:02 +0000 Subject: [PATCH 1/5] back to mysql 5.7.13 --- .travis.yml | 1 + .travis/before_install_mysql57.sh | 22 ++++++++++++++++------ 2 files changed, 17 insertions(+), 6 deletions(-) diff --git a/.travis.yml b/.travis.yml index e7e3541db..62fc7f47d 100644 --- a/.travis.yml +++ b/.travis.yml @@ -18,6 +18,7 @@ env: - TRAVIS_NODE_VERSION="4.5.0" before_install: + - ./.travis/before_install_mysql57.sh - ./.travis/before_install.sh install: - ./.travis/install.sh diff --git a/.travis/before_install_mysql57.sh b/.travis/before_install_mysql57.sh index 382938db7..684ea0815 100755 --- a/.travis/before_install_mysql57.sh +++ b/.travis/before_install_mysql57.sh @@ -11,20 +11,30 @@ sudo apt-get autoclean sudo rm -rf /var/lib/mysql sudo rm -rf /var/log/mysql -# Specify which version we want -echo "deb http://repo.mysql.com/apt/ubuntu/ precise mysql-5.7" | sudo tee /etc/apt/sources.list.d/mysql.list -sudo -E apt-get update -q -sudo -E apt-get -q -y install mysql-server libmysqlclient-dev libdbd-mysql-perl +# Get packages from oracle +sudo -E apt-get install libaio1 apparmor +wget http://downloads.mysql.com/archives/get/file/mysql-common_5.7.13-1ubuntu12.04_amd64.deb +wget http://downloads.mysql.com/archives/get/file/libmysqlclient20_5.7.13-1ubuntu12.04_amd64.deb +wget http://downloads.mysql.com/archives/get/file/mysql-community-client_5.7.13-1ubuntu12.04_amd64.deb +wget http://downloads.mysql.com/archives/get/file/mysql-client_5.7.13-1ubuntu12.04_amd64.deb +wget http://downloads.mysql.com/archives/get/file/mysql-community-server_5.7.13-1ubuntu12.04_amd64.deb +wget http://downloads.mysql.com/archives/get/file/mysql-server_5.7.13-1ubuntu12.04_amd64.deb +sudo debconf-set-selections <<< "mysql-server mysql-server/root_password password \"''\"" +sudo debconf-set-selections <<< "mysql-server mysql-server/root_password_again password \"''\"" +sudo dpkg-preconfigure mysql-community-server_5.7.13-1ubuntu12.04_amd64.deb +sudo dpkg -i mysql-{common,community-client,client,community-server,server}_*.deb +sudo dpkg -i libmysqlclient20_5.7.13-1ubuntu12.04_amd64.deb +sudo -E apt-get -q -y install libmysqlclient-dev libdbd-mysql-perl sudo /etc/init.d/mysql stop sleep 5 # Start the server without password -sudo mysqld --skip-grant-tables --explicit_defaults_for_timestamp=false --sql-mode="STRICT_TRANS_TABLES" & +sudo mysqld --user=root --skip-grant-tables --explicit_defaults_for_timestamp=false --sql-mode="STRICT_TRANS_TABLES" & #Give some time for server to start sleep 10 # print versions mysql --version -mysql -e "SELECT @@GLOBAL.sql_mode; SELECT @@SESSION.sql_mode; SHOW GLOBAL VARIABLES LIKE '%version%'; show variables like '%time%';" -uroot +mysql -h localhost -e "SELECT @@GLOBAL.sql_mode; SELECT @@SESSION.sql_mode; SHOW GLOBAL VARIABLES LIKE '%version%'; show variables like '%time%';" -uroot From c8576de39dd34b4fd50c0b7bbbfb69f9ed6b0718 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 18 Nov 2016 16:15:28 +0000 Subject: [PATCH 2/5] no templates rna_seqc results - we should not try rendering --- Changes | 2 ++ lib/npg_qc/autoqc/results/collection.pm | 1 + npg_qc_viewer/root/src/ui_checks/checks_in_full.tt2 | 2 +- 3 files changed, 4 insertions(+), 1 deletion(-) diff --git a/Changes b/Changes index e37b3041d..9c3cc9eb2 100644 --- a/Changes +++ b/Changes @@ -1,6 +1,8 @@ LIST OF CHANGES FOR NPG-QC PACKAGE +release 63.5 - a very concise replacement for NPG_QC pages + - no templates rna_seqc results - we should not try rendering release 62.4 - autoqc loader does not try loading a result for which there is diff --git a/lib/npg_qc/autoqc/results/collection.pm b/lib/npg_qc/autoqc/results/collection.pm index cec2a3dc9..62d4a107f 100644 --- a/lib/npg_qc/autoqc/results/collection.pm +++ b/lib/npg_qc/autoqc/results/collection.pm @@ -556,6 +556,7 @@ sub check_names { my @check_names = (); my $map = {}; foreach my $check (@{$self->checks_list}) { + if ($check eq 'rna_seqc') { next; } push @check_names, @{$classes->{$check}}; foreach my $name (@{$classes->{$check}}) { $map->{$name} = $check; diff --git a/npg_qc_viewer/root/src/ui_checks/checks_in_full.tt2 b/npg_qc_viewer/root/src/ui_checks/checks_in_full.tt2 index 37111efae..cd82a3d83 100644 --- a/npg_qc_viewer/root/src/ui_checks/checks_in_full.tt2 +++ b/npg_qc_viewer/root/src/ui_checks/checks_in_full.tt2 @@ -3,7 +3,7 @@ lane_collection = rl_map.${lane_key}; NEXT IF (!lane_collection || lane_collection.size == 0); temp = lane_collection.sort; - to_remove = ['split stats phix', 'spatial filter', 'split stats']; + to_remove = ['split stats phix', 'spatial filter', 'split stats', 'rna seqc']; IF !run_view; to_remove.push('qX yield', 'gc fraction'); END; From e764ce680064461b2d7cf269948b1b74d8936323 Mon Sep 17 00:00:00 2001 From: mgcam Date: Mon, 21 Nov 2016 11:56:12 +0000 Subject: [PATCH 3/5] fix release number --- Changes | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Changes b/Changes index 9c3cc9eb2..c051d2535 100644 --- a/Changes +++ b/Changes @@ -1,6 +1,6 @@ LIST OF CHANGES FOR NPG-QC PACKAGE -release 63.5 +release 62.5 - a very concise replacement for NPG_QC pages - no templates rna_seqc results - we should not try rendering From a7ebec05e024ba8e8031b60759590ed381225b76 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 24 Nov 2016 10:45:01 +0000 Subject: [PATCH 4/5] Force comparison as numbers so 0 and 0.00 are considered equal --- t/10-model-cache_query.t | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) diff --git a/t/10-model-cache_query.t b/t/10-model-cache_query.t index e9390b1bf..2386eac2f 100644 --- a/t/10-model-cache_query.t +++ b/t/10-model-cache_query.t @@ -5,12 +5,10 @@ use strict; use warnings; -use Test::More tests => 37; +use Test::More tests => 77; use Test::Exception; -use Test::Deep; use IO::Scalar; use t::util; -use npg_qc::model::cache_query; use_ok('npg_qc::model::cache_query'); @@ -128,7 +126,26 @@ subtest q[testing no nulls] => sub { lives_ok { $model->cache_lane_summary(37) } 'cache lane summary lives'; my $rows_ref; lives_ok { $rows_ref = $model->get_cache_by_id_type_end() } 'get lane summary lives'; - is_deeply($rows_ref, [{'clusters_pf' => '66598','lane_yield' => '7392','perc_pf_clusters_sd' => '0.00','perc_pf_align_sd' => undef,'clusters_pf_sd' => '0','perc_pf_clusters' => '79.88','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '0','perc_error_rate_sd' => undef,'clusters_raw_sd' => '0','perc_int_20_cycles_sd' => '0.00','first_cycle_int' => '159','lane' => '1','clusters_raw' => '83372','end' => '1','perc_int_20_cycles' => '99.06','align_score_sd' => undef},{'clusters_pf' => '66598','lane_yield' => '2464','perc_pf_clusters_sd' => '0.00','perc_pf_align_sd' => undef,'clusters_pf_sd' => '0','perc_pf_clusters' => '79.88','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '0','perc_error_rate_sd' => undef,'clusters_raw_sd' => '0','perc_int_20_cycles_sd' => '0.00','first_cycle_int' => '159','lane' => '2','clusters_raw' => '83372','end' => '1','perc_int_20_cycles' => '99.06','align_score_sd' => undef}] , 'get correct cache summary'); + + my $expected = [{'clusters_pf' => '66598','lane_yield' => '7392','perc_pf_clusters_sd' => '0.00','perc_pf_align_sd' => undef,'clusters_pf_sd' => '0','perc_pf_clusters' => '79.88','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '0','perc_error_rate_sd' => undef,'clusters_raw_sd' => '0','perc_int_20_cycles_sd' => '0','first_cycle_int' => '159','lane' => '1','clusters_raw' => '83372','end' => '1','perc_int_20_cycles' => '99.06','align_score_sd' => undef},{'clusters_pf' => '66598','lane_yield' => '2464','perc_pf_clusters_sd' => '0.00','perc_pf_align_sd' => undef,'clusters_pf_sd' => '0','perc_pf_clusters' => '79.88','align_score' => undef,'perc_pf_align' => undef,'perc_error_rate' => undef,'first_cycle_int_sd' => '0','perc_error_rate_sd' => undef,'clusters_raw_sd' => '0','perc_int_20_cycles_sd' => '0.00','first_cycle_int' => '159','lane' => '2','clusters_raw' => '83372','end' => '1','perc_int_20_cycles' => '99.06','align_score_sd' => undef}]; + + my $num_results = 2; + is (scalar @{$rows_ref}, $num_results, 'two results returned'); + my $i = 0; + while ($i < $num_results) { + my $row = $rows_ref->[$i]; + my $erow = $expected->[$i]; + my @keys = sort keys %{$row}; + is (join(q[:], @keys), join(q[:], sort keys %{$erow}), 'correct set of fields'); + # Force comparison as numbers so '0' and '0.00' are considered equal + foreach my $key (@keys) { + defined $row->{$key} ? + ok ( defined $erow->{$key} && ($row->{$key} == $erow->{$key}), $key) : + ok (!defined $erow->{$key}, $key); + } + + $i++; + } } { From f447b5a4c40305bf8865aa30cd382be5a0c70b55 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Thu, 24 Nov 2016 13:50:08 +0000 Subject: [PATCH 5/5] update Changes --- Changes | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Changes b/Changes index c051d2535..e2106ab77 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,7 @@ LIST OF CHANGES FOR NPG-QC PACKAGE + - back to testing with mysql 5.7.13 in travis + release 62.5 - a very concise replacement for NPG_QC pages - no templates rna_seqc results - we should not try rendering