From 9341679e870714dce0f5527dbc28c6c5ef6ef951 Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 16 Nov 2020 14:48:53 +0000 Subject: [PATCH 01/18] Remove iRODS 4.1.12 and add iRODS 4.2.8 iRODS 4.2.8 is marked as an expected failure because we have not yet built a Conda package of irods-icommands for iRODS 4.2.8 --- .travis.yml | 13 +++++++++++-- scripts/travis_install.sh | 17 +---------------- 2 files changed, 12 insertions(+), 18 deletions(-) diff --git a/.travis.yml b/.travis.yml index 28db8df..418f2b2 100644 --- a/.travis.yml +++ b/.travis.yml @@ -9,13 +9,22 @@ go: - "1.13" - "1.14" +_iRODS_4_2_8: &iRODS_4_2_8 DOCKER_IMAGE="wsinpg/ub-18.04-irods-4.2.8:latest" IRODS_VERSION="==4.2.8" BATON_VERSION=">2.0.1" + env: global: - GO111MODULE=on - WSI_CONDA_CHANNEL="https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic" - matrix: - - DOCKER_IMAGE="wsinpg/ub-12.04-irods-4.1:latest" IRODS_VERSION="==4.1.12" BATON_VERSION="==2.0.1" + jobs: - DOCKER_IMAGE="wsinpg/ub-16.04-irods-4.2.7:latest" IRODS_VERSION="==4.2.7" BATON_VERSION=">2.0.1" + - *iRODS_4_2_8 + +jobs: + allow_failures: + - go: "1.13" + env: *iRODS_4_2_8 + - go: "1.14" + env: *iRODS_4_2_8 cache: directories: diff --git a/scripts/travis_install.sh b/scripts/travis_install.sh index 9d0181d..eafd87c 100755 --- a/scripts/travis_install.sh +++ b/scripts/travis_install.sh @@ -22,31 +22,16 @@ conda install -y baton"$BATON_VERSION" mkdir -p ~/.irods -if [[ "$IRODS_VERSION" =~ 4\.1\.12 ]] -then - cat < ~/.irods/irods_environment.json +cat <<'EOF' > ~/.irods/irods_environment.json { "irods_host": "localhost", "irods_port": 1247, "irods_user_name": "irods", "irods_zone_name": "testZone", "irods_home": "/testZone/home/irods", - "irods_plugins_home": "$HOME/miniconda/envs/travis/lib/irods/plugins/", "irods_default_resource": "testResc" } EOF -else - cat <<'EOF' > ~/.irods/irods_environment.json -{ - "irods_host": "localhost", - "irods_port": 1247, - "irods_user_name": "irods", - "irods_zone_name": "testZone", - "irods_home": "/testZone/home/irods", - "irods_default_resource": "testResc" -} -EOF -fi go get github.com/onsi/ginkgo/ginkgo go get github.com/onsi/gomega/... From 666497ac26129c01ad7a7a80f805b1607621a139 Mon Sep 17 00:00:00 2001 From: Keith James Date: Thu, 25 Feb 2021 15:47:26 +0000 Subject: [PATCH 02/18] Relocate repository from github.com/kjsanger to github.com/wtsi-npg --- .travis.yml | 6 ++-- cmd/archive.go | 4 +-- cmd/archive_annotate.go | 10 +++--- cmd/archive_create.go | 10 +++--- cmd/checksum.go | 2 +- cmd/checksum_create.go | 6 ++-- cmd/checksum_status.go | 6 ++-- cmd/valet.go | 10 +++--- go.mod | 22 ++++++------- go.sum | 67 ++++++++++++++++++++------------------- main.go | 4 +-- scripts/travis_install.sh | 4 +-- valet/channels.go | 4 +-- valet/helpers_test.go | 8 ++--- valet/pathfind.go | 4 +-- valet/pathproc.go | 4 +-- valet/pathprune.go | 2 +- valet/pathwatch.go | 8 ++--- valet/predicates.go | 6 ++-- valet/predicates_test.go | 2 +- valet/report.go | 4 +-- valet/report_test.go | 4 +-- valet/suite_test.go | 6 ++-- valet/valet_suite_test.go | 6 ++-- valet/workfunc.go | 8 ++--- valet/workfunc_test.go | 8 ++--- 26 files changed, 114 insertions(+), 111 deletions(-) diff --git a/.travis.yml b/.travis.yml index 418f2b2..01f5361 100644 --- a/.travis.yml +++ b/.travis.yml @@ -6,8 +6,8 @@ services: language: go go: - - "1.13" - "1.14" + - "1.15" _iRODS_4_2_8: &iRODS_4_2_8 DOCKER_IMAGE="wsinpg/ub-18.04-irods-4.2.8:latest" IRODS_VERSION="==4.2.8" BATON_VERSION=">2.0.1" @@ -21,10 +21,10 @@ env: jobs: allow_failures: - - go: "1.13" - env: *iRODS_4_2_8 - go: "1.14" env: *iRODS_4_2_8 + - go: "1.15" + env: *iRODS_4_2_8 cache: directories: diff --git a/cmd/archive.go b/cmd/archive.go index 6d995ad..fb7f000 100644 --- a/cmd/archive.go +++ b/cmd/archive.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -23,8 +23,8 @@ package cmd import ( "os" - logs "github.com/kjsanger/logshim" "github.com/spf13/cobra" + logs "github.com/wtsi-npg/logshim" ) var archiveCmd = &cobra.Command{ diff --git a/cmd/archive_annotate.go b/cmd/archive_annotate.go index cfab4f5..b93fe81 100644 --- a/cmd/archive_annotate.go +++ b/cmd/archive_annotate.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -23,13 +23,13 @@ package cmd import ( "os" - ex "github.com/kjsanger/extendo/v2" - logs "github.com/kjsanger/logshim" "github.com/pkg/errors" "github.com/spf13/cobra" + ex "github.com/wtsi-npg/extendo/v2" + logs "github.com/wtsi-npg/logshim" - "github.com/kjsanger/valet/utilities" - "github.com/kjsanger/valet/valet" + "github.com/wtsi-npg/valet/utilities" + "github.com/wtsi-npg/valet/valet" ) var archAnnotateFlags = &dataFileCliFlags{} diff --git a/cmd/archive_create.go b/cmd/archive_create.go index 93aa158..f256bd5 100644 --- a/cmd/archive_create.go +++ b/cmd/archive_create.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -25,12 +25,12 @@ import ( "os" "time" - ex "github.com/kjsanger/extendo/v2" - logs "github.com/kjsanger/logshim" "github.com/spf13/cobra" + ex "github.com/wtsi-npg/extendo/v2" + logs "github.com/wtsi-npg/logshim" - "github.com/kjsanger/valet/utilities" - "github.com/kjsanger/valet/valet" + "github.com/wtsi-npg/valet/utilities" + "github.com/wtsi-npg/valet/valet" ) diff --git a/cmd/checksum.go b/cmd/checksum.go index 29cf5dd..660b3f7 100644 --- a/cmd/checksum.go +++ b/cmd/checksum.go @@ -23,8 +23,8 @@ package cmd import ( "os" - logs "github.com/kjsanger/logshim" "github.com/spf13/cobra" + logs "github.com/wtsi-npg/logshim" ) var checksumFlags = &dataDirCliFlags{} diff --git a/cmd/checksum_create.go b/cmd/checksum_create.go index 97f2d01..ec4497b 100644 --- a/cmd/checksum_create.go +++ b/cmd/checksum_create.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -25,10 +25,10 @@ import ( "os" "time" - logs "github.com/kjsanger/logshim" "github.com/spf13/cobra" + logs "github.com/wtsi-npg/logshim" - "github.com/kjsanger/valet/valet" + "github.com/wtsi-npg/valet/valet" ) var checksumCreateCmd = &cobra.Command{ diff --git a/cmd/checksum_status.go b/cmd/checksum_status.go index 92a2383..6e167b1 100644 --- a/cmd/checksum_status.go +++ b/cmd/checksum_status.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -25,10 +25,10 @@ import ( "os" "sync" - logs "github.com/kjsanger/logshim" "github.com/spf13/cobra" + logs "github.com/wtsi-npg/logshim" - "github.com/kjsanger/valet/valet" + "github.com/wtsi-npg/valet/valet" ) var checksumStatusCmd = &cobra.Command{ diff --git a/cmd/valet.go b/cmd/valet.go index 7da09ba..67c1ad9 100644 --- a/cmd/valet.go +++ b/cmd/valet.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -35,11 +35,11 @@ import ( "github.com/rs/zerolog" "github.com/spf13/cobra" - "github.com/kjsanger/valet/utilities" - "github.com/kjsanger/valet/valet" + "github.com/wtsi-npg/valet/utilities" + "github.com/wtsi-npg/valet/valet" - logs "github.com/kjsanger/logshim" - "github.com/kjsanger/logshim-zerolog/zlog" + logs "github.com/wtsi-npg/logshim" + "github.com/wtsi-npg/logshim-zerolog/zlog" ) type baseCliFlags struct { diff --git a/go.mod b/go.mod index 84bcc74..828d1ef 100644 --- a/go.mod +++ b/go.mod @@ -1,21 +1,21 @@ -module github.com/kjsanger/valet +module github.com/wtsi-npg/valet -go 1.13 +go 1.14 require ( - github.com/kjsanger/extendo/v2 v2.2.0 - github.com/kjsanger/fsnotify v1.4.8-0.20190705153444-45ca73e9793a - github.com/kjsanger/logshim v1.1.0 - github.com/kjsanger/logshim-zerolog v1.1.0 github.com/klauspost/compress v1.9.1 // indirect github.com/klauspost/pgzip v1.2.1 - github.com/onsi/ginkgo v1.12.3 - github.com/onsi/gomega v1.10.1 + github.com/onsi/ginkgo v1.15.0 + github.com/onsi/gomega v1.10.5 github.com/pkg/errors v0.9.1 github.com/rs/zerolog v1.19.0 github.com/spf13/cobra v0.0.5 - github.com/stretchr/testify v1.6.1 - golang.org/x/crypto v0.0.0-20190701094942-4def268fd1a4 + github.com/stretchr/testify v1.7.0 + github.com/wtsi-npg/extendo/v2 v2.3.0 + github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a + github.com/wtsi-npg/logshim v1.2.0 + github.com/wtsi-npg/logshim-zerolog v1.2.0 + golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9 ) -// replace github.com/kjsanger/extendo/v2 => ../extendo +// replace github.com/wtsi-npg/extendo/v2 => ../extendo diff --git a/go.sum b/go.sum index 0430380..0e5e8a1 100644 --- a/go.sum +++ b/go.sum @@ -19,26 +19,17 @@ github.com/golang/protobuf v1.4.0-rc.1.0.20200221234624-67d41d38c208/go.mod h1:x github.com/golang/protobuf v1.4.0-rc.2/go.mod h1:LlEzMj4AhA7rCAGe4KMBDvJI+AwstrUpVNzEA03Pprs= github.com/golang/protobuf v1.4.0-rc.4.0.20200313231945-b860323f09d0/go.mod h1:WU3c8KckQ9AFe+yFwt9sWVRKCVIyN9cPHBJSNnbL67w= github.com/golang/protobuf v1.4.0/go.mod h1:jodUvKwWbYaEsadDk5Fwe5c77LiNKVO9IDvqG2KuDX0= +github.com/golang/protobuf v1.4.2 h1:+Z5KGCizgyZCbGh1KZqA0fcLLkwbsjIzS4aV2v7wJX0= github.com/golang/protobuf v1.4.2/go.mod h1:oDoupMAO8OvCJWAcko0GGGIgR6R6ocIYbsSw735rRwI= github.com/google/go-cmp v0.3.0/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU= github.com/google/go-cmp v0.3.1/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU= +github.com/google/go-cmp v0.4.0 h1:xsAVV57WRhGj6kEIi8ReJzQlHHqcBYCElAvkovg3B/4= github.com/google/go-cmp v0.4.0/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= github.com/hashicorp/hcl v1.0.0/go.mod h1:E5yfLk+7swimpb2L/Alb/PJmXilQ/rhwaUYs4T20WEQ= github.com/hpcloud/tail v1.0.0 h1:nfCOvKYfkgYP8hkirhJocXT2+zOD8yUNjXaWfTlyFKI= github.com/hpcloud/tail v1.0.0/go.mod h1:ab1qPbhIpdTxEkNHXyeSf5vhxWSCs/tWer42PpOxQnU= github.com/inconshreveable/mousetrap v1.0.0 h1:Z8tu5sraLXCXIcARxBp/8cbvlwVa7Z1NHg9XEKhtSvM= github.com/inconshreveable/mousetrap v1.0.0/go.mod h1:PxqpIevigyE2G7u3NXJIT2ANytuPF1OarO4DADm73n8= -github.com/kjsanger/extendo/v2 v2.1.0 h1:gfQV0ifaVTEXTVk4S1KM/PsVChTnFs7oSpAQCM7TpGc= -github.com/kjsanger/extendo/v2 v2.1.0/go.mod h1:A0USxUEy/SfwCpj/DMaU3pYX/zSi1bl33jwb7TU6h+Y= -github.com/kjsanger/extendo/v2 v2.2.0 h1:81quL5c4OCjNWVVk/v079KRUdq4M/fpX6I/vZITh6rU= -github.com/kjsanger/extendo/v2 v2.2.0/go.mod h1:OjfcuhiYzg0yvbYfSmq+tnMC07eFHKtO+qafsOqecwk= -github.com/kjsanger/fsnotify v1.4.8-0.20190705153444-45ca73e9793a h1:eEXk79VRqIscsPHonU4g+oCU1KSt1zbJlOjQHU1RgOE= -github.com/kjsanger/fsnotify v1.4.8-0.20190705153444-45ca73e9793a/go.mod h1:4sKo+f997RhF5HZNa2h3t/N7TD7RNcbGzRO7xFpRBYM= -github.com/kjsanger/logshim v1.0.0/go.mod h1:a0VpOYrCQgfvQUqympQP5mTuGWz766IAbtPwHeA6PEE= -github.com/kjsanger/logshim v1.1.0 h1:43+UWmayDVVzTSuDYVeZrCZCwKyE+iahIODsxbtWVvk= -github.com/kjsanger/logshim v1.1.0/go.mod h1:drKALnhjaOKRtZjagdHMa4k6kgd8k03+rw93ShsNiCI= -github.com/kjsanger/logshim-zerolog v1.1.0 h1:gwpvOtJd17IE1GbVLgakbZDzNaUrEf96AlZeNdqnCEE= -github.com/kjsanger/logshim-zerolog v1.1.0/go.mod h1:U5/BO2owB1e49IJn4hTaoSatqnfA91izLrj7mbjXYI4= github.com/klauspost/compress v1.9.1 h1:TWy0o9J9c6LK9C8t7Msh6IAJNXbsU/nvKLTQUU5HdaY= github.com/klauspost/compress v1.9.1/go.mod h1:RyIbtBH6LamlWaDj8nUwkbUhJ87Yi3uG0guNDohfE1A= github.com/klauspost/pgzip v1.2.1 h1:oIPZROsWuPHpOdMVWLuJZXwgjhrW8r1yEX8UqMyeNHM= @@ -49,16 +40,14 @@ github.com/mitchellh/mapstructure v1.1.2/go.mod h1:FVVH3fgwuzCH5S8UJGiWEs2h04kUh github.com/nxadm/tail v1.4.4 h1:DQuhQpB1tVlglWS2hLQ5OV6B5r8aGxSrPc5Qo6uTN78= github.com/nxadm/tail v1.4.4/go.mod h1:kenIhsEOeOJmVchQTgglprH7qJGnHDVpk1VPCcaMI8A= github.com/onsi/ginkgo v1.6.0/go.mod h1:lLunBs/Ym6LB5Z9jYTR76FiuTmxDTDusOGeTQH+WWjE= -github.com/onsi/ginkgo v1.12.0 h1:Iw5WCbBcaAAd0fpRb1c9r5YCylv4XDoCSigm1zLevwU= -github.com/onsi/ginkgo v1.12.0/go.mod h1:oUhWkIvk5aDxtKvDDuw8gItl8pKl42LzjC9KZE0HfGg= github.com/onsi/ginkgo v1.12.1/go.mod h1:zj2OWP4+oCPe1qIXoGWkgMRwljMUYCdkwsT2108oapk= -github.com/onsi/ginkgo v1.12.3 h1:+RYp9QczoWz9zfUyLP/5SLXQVhfr6gZOoKGfQqHuLZQ= -github.com/onsi/ginkgo v1.12.3/go.mod h1:iSB4RoI2tjJc9BBv4NKIKWKya62Rps+oPG/Lv9klQyY= +github.com/onsi/ginkgo v1.15.0 h1:1V1NfVQR87RtWAgp1lv9JZJ5Jap+XFGKPi00andXGi4= +github.com/onsi/ginkgo v1.15.0/go.mod h1:hF8qUzuuC8DJGygJH3726JnCZX4MYbRB8yFfISqnKUg= github.com/onsi/gomega v1.7.1/go.mod h1:XdKZgCCFLUoM/7CFJVPcG8C1xQ1AJ0vpAezJrB7JYyY= -github.com/onsi/gomega v1.9.0 h1:R1uwffexN6Pr340GtYRIdZmAiN4J+iw6WG4wog1DUXg= -github.com/onsi/gomega v1.9.0/go.mod h1:Ho0h+IUsWyvy1OpqCwxlQ/21gkhVunqlU8fDGcoTdcA= github.com/onsi/gomega v1.10.1 h1:o0+MgICZLuZ7xjH7Vx6zS/zcu93/BEp1VwkIW1mEXCE= github.com/onsi/gomega v1.10.1/go.mod h1:iN09h71vgCQne3DLsj+A5owkum+a2tYe+TOCB1ybHNo= +github.com/onsi/gomega v1.10.5 h1:7n6FEkpFmfCoo2t+YYqXH0evK+a9ICQz0xcAy9dYcaQ= +github.com/onsi/gomega v1.10.5/go.mod h1:gza4q3jKQJijlu05nKWRCW/GavJumGt8aNRxWg7mt48= github.com/pelletier/go-toml v1.2.0/go.mod h1:5z9KED0ma1S8pY6P1sdut58dfprrGBbd/94hg7ilaic= github.com/pkg/errors v0.8.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0= github.com/pkg/errors v0.9.1 h1:FEBLx1zS214owpjy7qsBeixbURkuhQAwrK5UwLGTwt4= @@ -67,8 +56,6 @@ github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZb github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4= github.com/rs/xid v1.2.1/go.mod h1:+uKXf+4Djp6Md1KODXJxgGQPKngRmWyn10oCKFzNHOQ= github.com/rs/zerolog v1.17.2/go.mod h1:9nvC1axdVrAHcu/s9taAVfBuIdTZLVQmKQyvrUjF5+I= -github.com/rs/zerolog v1.18.0 h1:CbAm3kP2Tptby1i9sYy2MGRg0uxIN9cyDb59Ys7W8z8= -github.com/rs/zerolog v1.18.0/go.mod h1:9nvC1axdVrAHcu/s9taAVfBuIdTZLVQmKQyvrUjF5+I= github.com/rs/zerolog v1.19.0 h1:hYz4ZVdUgjXTBUmrkrw55j1nHx68LfOKIQk5IYtyScg= github.com/rs/zerolog v1.19.0/go.mod h1:IzD0RJ65iWH0w97OQQebJEvTZYvsCUm9WVLWBQrJRjo= github.com/russross/blackfriday v1.5.2/go.mod h1:JO/DiYxRf+HjHt06OyowR9PTA263kcR/rfWxYHBV53g= @@ -82,29 +69,38 @@ github.com/spf13/pflag v1.0.3/go.mod h1:DYY7MBk1bdzusC3SYhjObp+wFpr4gzcvqqNjLnIn github.com/spf13/viper v1.3.2/go.mod h1:ZiWeW+zYFKm7srdB9IoDzzZXaJaI5eL9QjNiN/DMA2s= github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs= -github.com/stretchr/testify v1.3.0/go.mod h1:M5WIy9Dh21IEIfnGCwXGc5bZfKNJtfHm1UVUgZn+9EI= -github.com/stretchr/testify v1.4.0 h1:2E4SXV/wtOkTonXsotYi4li6zVWxYlZuYNCXe9XRJyk= -github.com/stretchr/testify v1.4.0/go.mod h1:j7eGeouHqKxXV5pUuKE4zz7dFj8WfuZ+81PSLYec5m4= -github.com/stretchr/testify v1.5.1 h1:nOGnQDM7FYENwehXlg/kFVnos3rEvtKTjRvOWSzb6H4= -github.com/stretchr/testify v1.5.1/go.mod h1:5W2xD1RspED5o8YsWQXVCued0rvSQ+mT+I5cxcmMvtA= -github.com/stretchr/testify v1.6.1 h1:hDPOHmpOpP40lSULcqw7IrRb/u7w6RpDC9399XyoNd0= -github.com/stretchr/testify v1.6.1/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg= +github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg= github.com/ugorji/go/codec v0.0.0-20181204163529-d75b2dcb6bc8/go.mod h1:VFNgLljTbGfSG7qAOspJ7OScBnGdDN/yBr0sguwnwf0= +github.com/wtsi-npg/extendo/v2 v2.3.0 h1:sKlABJFbFtuQB2LOmlBTX4oMbhfAM7HbdreMU81YeRc= +github.com/wtsi-npg/extendo/v2 v2.3.0/go.mod h1:K0EdJrVoWbZbJAYiUxiSzaemYXzfKXwO36nNYCM1mHM= +github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a h1:LmzJGJXUS8U69eZ08MjwKwii8mos8630pV3aSZRdmc0= +github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a/go.mod h1:/ux2ROeuYmj0JshWH6r5f+gvLIJP2ZbMutVFrW6/8Pg= +github.com/wtsi-npg/logshim v1.2.0 h1:d9y9XvBRkYB2bUsN07zGJWhGCu13PKoxIxQE97Q9aZw= +github.com/wtsi-npg/logshim v1.2.0/go.mod h1:1JRn1t/rlx1/oAtv3LOcshcpjDDvHGHCK8p8ua0Hrss= +github.com/wtsi-npg/logshim-zerolog v1.2.0 h1:b1HpB1h8OO9XBg/m9r6ycmHRUDNZLnpTmfjWrhmeaT4= +github.com/wtsi-npg/logshim-zerolog v1.2.0/go.mod h1:xyahqnZDG2utxSUAQKYjgEdzQz74wfPY7+JttEie41k= github.com/xordataexchange/crypt v0.0.3-0.20170626215501-b2862e3d0a77/go.mod h1:aYKd//L2LvnjZzWKhF00oedf4jCCReLcmhLdhm1A27Q= +github.com/yuin/goldmark v1.2.1/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74= github.com/zenazn/goji v0.9.0/go.mod h1:7S9M489iMyHBNxwZnk9/EHS098H4/F6TATF2mIxtB1Q= golang.org/x/crypto v0.0.0-20181203042331-505ab145d0a9/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4= golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w= -golang.org/x/crypto v0.0.0-20190701094942-4def268fd1a4 h1:HuIa8hRrWRSrqYzx1qI49NNxhdi2PrY7gxVSq1JjLDc= -golang.org/x/crypto v0.0.0-20190701094942-4def268fd1a4/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI= +golang.org/x/crypto v0.0.0-20191011191535-87dc89f01550/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI= +golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9 h1:psW17arqaxU48Z5kZ0CQnkZWQJsqcURM6tKiBApRjXI= +golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9/go.mod h1:LzIPMQfyMNhhGPhUkYOs5KpL4U8rLKemX1yGLhDgUto= +golang.org/x/mod v0.3.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA= golang.org/x/net v0.0.0-20180906233101-161cd47e91fd/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= golang.org/x/net v0.0.0-20190620200207-3b0461eec859 h1:R/3boaszxrf1GEUWTVDzSKVwLmSJpwZ1yqXm8j0v2QI= golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s= golang.org/x/net v0.0.0-20200520004742-59133d7f0dd7 h1:AeiKBIuRw3UomYXSbLy0Mc2dDLfdtbT/IVn4keq83P0= golang.org/x/net v0.0.0-20200520004742-59133d7f0dd7/go.mod h1:qpuaurCH72eLCgpAm/N6yyVIVM9cpaDIP3A8BGJEC5A= +golang.org/x/net v0.0.0-20201021035429-f5854403a974/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU= +golang.org/x/net v0.0.0-20201202161906-c7110b5ffcbb h1:eBmm0M9fYhWpKZLjQUUKka/LtIxf46G4fxeEz5KJr9U= +golang.org/x/net v0.0.0-20201202161906-c7110b5ffcbb/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU= golang.org/x/sync v0.0.0-20180314180146-1d60e4601c6f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20190423024810-112230192c58 h1:8gQV6CLnAEikrhgkHFbMAEhagSSnXWGV915qUMm9mrU= golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= +golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sys v0.0.0-20180909124046-d0be0721c37e/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= golang.org/x/sys v0.0.0-20181205085412-a5c9d58dba9a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= @@ -114,23 +110,30 @@ golang.org/x/sys v0.0.0-20191005200804-aed5e4c7ecf9/go.mod h1:h1NjWce9XRLGQEsW7w golang.org/x/sys v0.0.0-20191120155948-bd437916bb0e h1:N7DeIrjYszNmSW409R3frPPwglRwMkXSBzwVbkOjLLA= golang.org/x/sys v0.0.0-20191120155948-bd437916bb0e/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20200323222414-85ca7c5b95cd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20200519105757-fe76b779f299 h1:DYfZAGf2WMFjMxbgTjaC+2HC7NkNAQs+6Q8b9WEB/F4= -golang.org/x/sys v0.0.0-20200519105757-fe76b779f299/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= +golang.org/x/sys v0.0.0-20200930185726-fdedc70b468f/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= +golang.org/x/sys v0.0.0-20210112080510-489259a85091 h1:DMyOG0U+gKfu8JZzg2UQe9MeaC1X+xQWlAKcRnjxjCw= +golang.org/x/sys v0.0.0-20210112080510-489259a85091/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/text v0.3.0 h1:g61tztE5qeGQ89tm6NTjjM9VPIm088od1l6aSorWRWg= golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= -golang.org/x/text v0.3.2 h1:tW2bmiBqwgJj/UpqtC8EpXEZVYOwU0yG4iWbprSVAcs= -golang.org/x/text v0.3.2/go.mod h1:bEr9sfX3Q8Zfm5fL9x+3itogRgK3+ptLWKqgva+5dAk= +golang.org/x/text v0.3.3 h1:cokOdA+Jmi5PJGXLlLllQSgYigAEfHXJAERHVMaCc2k= +golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= golang.org/x/tools v0.0.0-20190828213141-aed303cbaa74/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= +golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= +golang.org/x/tools v0.0.0-20201224043029-2b0845dc783e/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7 h1:9zdDQZ7Thm29KFXgAX/+yaf3eVbP7djjWp/dXAppNCc= golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= +golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543 h1:E7g+9GITq07hpfrRu66IVDexMakfv52eLZ2CXBWiKr4= golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= +golang.org/x/xerrors v0.0.0-20200804184101-5ec99f83aff1 h1:go1bK/D/BFZV2I8cIQd1NKEZ+0owSTG1fDTci4IqFcE= +golang.org/x/xerrors v0.0.0-20200804184101-5ec99f83aff1/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= google.golang.org/protobuf v0.0.0-20200109180630-ec00e32a8dfd/go.mod h1:DFci5gLYBciE7Vtevhsrf46CRTquxDuWsQurQQe4oz8= google.golang.org/protobuf v0.0.0-20200221191635-4d8936d0db64/go.mod h1:kwYJMbMJ01Woi6D6+Kah6886xMZcty6N08ah7+eCXa0= google.golang.org/protobuf v0.0.0-20200228230310-ab0ca4ff8a60/go.mod h1:cfTl7dwQJ+fmap5saPgwCLgHXTUD7jkjRqWcaiX5VyM= google.golang.org/protobuf v1.20.1-0.20200309200217-e05f789c0967/go.mod h1:A+miEFZTKqfCUM6K7xSMQL9OKL/b6hQv+e19PK+JZNE= google.golang.org/protobuf v1.21.0/go.mod h1:47Nbq4nVaFHyn7ilMalzfO3qCViNmqZ2kzikPIcrTAo= +google.golang.org/protobuf v1.23.0 h1:4MY060fB1DLGMB/7MBTLnwQUY6+F09GEiz6SsrNqyzM= google.golang.org/protobuf v1.23.0/go.mod h1:EGpADcykh3NcUnDUJcl1+ZksZNG86OlYog2l/sGQquU= gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405 h1:yhCVgyC4o1eVCa2tZl7eS0r+SDo693bJlVdllGtEeKM= gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= diff --git a/main.go b/main.go index 8202188..67e487b 100644 --- a/main.go +++ b/main.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -21,7 +21,7 @@ package main import ( - "github.com/kjsanger/valet/cmd" + "github.com/wtsi-npg/valet/cmd" ) func main() { diff --git a/scripts/travis_install.sh b/scripts/travis_install.sh index eafd87c..fc6aef5 100755 --- a/scripts/travis_install.sh +++ b/scripts/travis_install.sh @@ -12,8 +12,8 @@ echo "conda activate base" >> ~/.bashrc . ~/miniconda/etc/profile.d/conda.sh conda activate base conda config --set auto_update_conda False -conda config --add channels "$WSI_CONDA_CHANNEL" -conda config --add channels conda-forge +conda config --prepend channels "$WSI_CONDA_CHANNEL" +conda config --append channels conda-forge conda create -y -n travis conda activate travis diff --git a/valet/channels.go b/valet/channels.go index da633ee..3380eb7 100644 --- a/valet/channels.go +++ b/valet/channels.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -20,7 +20,7 @@ package valet -import "github.com/kjsanger/logshim" +import "github.com/wtsi-npg/logshim" // MergeFileChannels merges values from its two input channels x and y for as // long as at least one of them is open. One both x and y have been closed, the diff --git a/valet/helpers_test.go b/valet/helpers_test.go index 1e8aa94..489639f 100644 --- a/valet/helpers_test.go +++ b/valet/helpers_test.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -27,11 +27,11 @@ import ( "os" "path/filepath" - ex "github.com/kjsanger/extendo/v2" . "github.com/onsi/ginkgo" + ex "github.com/wtsi-npg/extendo/v2" - "github.com/kjsanger/valet/utilities" - "github.com/kjsanger/valet/valet" + "github.com/wtsi-npg/valet/utilities" + "github.com/wtsi-npg/valet/valet" ) type itemPathTransform func(i []ex.RodsItem) []string diff --git a/valet/pathfind.go b/valet/pathfind.go index 93afb46..7ad317e 100644 --- a/valet/pathfind.go +++ b/valet/pathfind.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -26,7 +26,7 @@ import ( "path/filepath" "time" - logs "github.com/kjsanger/logshim" + logs "github.com/wtsi-npg/logshim" ) const DefaultSweep = 5 * time.Minute diff --git a/valet/pathproc.go b/valet/pathproc.go index 1b0ea93..49839b7 100644 --- a/valet/pathproc.go +++ b/valet/pathproc.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -25,8 +25,8 @@ import ( "sync" "time" - logs "github.com/kjsanger/logshim" "github.com/pkg/errors" + logs "github.com/wtsi-npg/logshim" ) type token struct{} diff --git a/valet/pathprune.go b/valet/pathprune.go index 399de6d..397eef2 100644 --- a/valet/pathprune.go +++ b/valet/pathprune.go @@ -23,7 +23,7 @@ package valet import ( "path/filepath" - logs "github.com/kjsanger/logshim" + logs "github.com/wtsi-npg/logshim" ) // Directory names within the root MinKNOW data directory (typically /data) diff --git a/valet/pathwatch.go b/valet/pathwatch.go index 4cfd058..18b0064 100644 --- a/valet/pathwatch.go +++ b/valet/pathwatch.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -25,11 +25,11 @@ import ( "os" "path/filepath" - "github.com/kjsanger/fsnotify" - logs "github.com/kjsanger/logshim" "github.com/pkg/errors" + "github.com/wtsi-npg/fsnotify" + logs "github.com/wtsi-npg/logshim" - "github.com/kjsanger/valet/utilities" + "github.com/wtsi-npg/valet/utilities" ) // WatchFiles reports filesystem events on the directories below root. Watches diff --git a/valet/predicates.go b/valet/predicates.go index 6eca27c..efe65f4 100644 --- a/valet/predicates.go +++ b/valet/predicates.go @@ -26,11 +26,11 @@ import ( "path/filepath" "regexp" - ex "github.com/kjsanger/extendo/v2" - logs "github.com/kjsanger/logshim" "github.com/pkg/errors" + ex "github.com/wtsi-npg/extendo/v2" + logs "github.com/wtsi-npg/logshim" - "github.com/kjsanger/valet/utilities" + "github.com/wtsi-npg/valet/utilities" ) type FilePredicate func(path FilePath) (bool, error) diff --git a/valet/predicates_test.go b/valet/predicates_test.go index 75aa6e9..c795225 100644 --- a/valet/predicates_test.go +++ b/valet/predicates_test.go @@ -29,7 +29,7 @@ import ( "github.com/stretchr/testify/assert" - "github.com/kjsanger/valet/utilities" + "github.com/wtsi-npg/valet/utilities" ) func TestIsDir(t *testing.T) { diff --git a/valet/report.go b/valet/report.go index e39992e..751b672 100644 --- a/valet/report.go +++ b/valet/report.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -26,8 +26,8 @@ import ( "regexp" "strings" - ex "github.com/kjsanger/extendo/v2" "github.com/pkg/errors" + ex "github.com/wtsi-npg/extendo/v2" ) const dutyTimeField = "Duty Time" diff --git a/valet/report_test.go b/valet/report_test.go index 1ec60ac..b4c77a5 100644 --- a/valet/report_test.go +++ b/valet/report_test.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -23,8 +23,8 @@ package valet import ( "testing" - ex "github.com/kjsanger/extendo/v2" "github.com/stretchr/testify/assert" + ex "github.com/wtsi-npg/extendo/v2" ) func TestParsePromethIONReport(t *testing.T) { diff --git a/valet/suite_test.go b/valet/suite_test.go index 7cfe366..03af408 100644 --- a/valet/suite_test.go +++ b/valet/suite_test.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -25,12 +25,12 @@ import ( "testing" "time" - "github.com/kjsanger/logshim-zerolog/zlog" . "github.com/onsi/ginkgo" . "github.com/onsi/gomega" "github.com/rs/zerolog" + "github.com/wtsi-npg/logshim-zerolog/zlog" - logs "github.com/kjsanger/logshim" + logs "github.com/wtsi-npg/logshim" ) func TestValet(t *testing.T) { diff --git a/valet/valet_suite_test.go b/valet/valet_suite_test.go index 4c953e0..49d7d97 100644 --- a/valet/valet_suite_test.go +++ b/valet/valet_suite_test.go @@ -29,12 +29,12 @@ import ( "sync" "time" - ex "github.com/kjsanger/extendo/v2" . "github.com/onsi/ginkgo" . "github.com/onsi/gomega" + ex "github.com/wtsi-npg/extendo/v2" - "github.com/kjsanger/valet/cmd" - "github.com/kjsanger/valet/valet" + "github.com/wtsi-npg/valet/cmd" + "github.com/wtsi-npg/valet/valet" ) var _ = Describe("Find directories)", func() { diff --git a/valet/workfunc.go b/valet/workfunc.go index 9e4fc83..210b065 100644 --- a/valet/workfunc.go +++ b/valet/workfunc.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -32,13 +32,13 @@ import ( "sort" "strings" - ex "github.com/kjsanger/extendo/v2" "github.com/klauspost/pgzip" "github.com/pkg/errors" + ex "github.com/wtsi-npg/extendo/v2" - "github.com/kjsanger/valet/utilities" + "github.com/wtsi-npg/valet/utilities" - logs "github.com/kjsanger/logshim" + logs "github.com/wtsi-npg/logshim" ) // WorkFunc is a worker function used by DoProcessFiles. diff --git a/valet/workfunc_test.go b/valet/workfunc_test.go index fbaf47e..a088762 100644 --- a/valet/workfunc_test.go +++ b/valet/workfunc_test.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -33,13 +33,13 @@ import ( "testing" "time" - logs "github.com/kjsanger/logshim" - "github.com/kjsanger/logshim-zerolog/zlog" "github.com/pkg/errors" "github.com/rs/zerolog" "github.com/stretchr/testify/assert" + logs "github.com/wtsi-npg/logshim" + "github.com/wtsi-npg/logshim-zerolog/zlog" - "github.com/kjsanger/valet/utilities" + "github.com/wtsi-npg/valet/utilities" ) func TestMain(m *testing.M) { From 1f175f6a6bf447ef3e3ca027e15e0f5f2a037a7e Mon Sep 17 00:00:00 2001 From: Keith James Date: Wed, 24 Feb 2021 19:15:53 +0000 Subject: [PATCH 03/18] Improve recognition of files to be processed and archived Add support for TSV files. Add support for compressing CSV files. Use path.UncompressedFilename() more liberally to streamline adding compression to other file types. Add new all ONT-specific paths to the exclusion list. Add the /data/laboratory WSI-specific path to the exclusion list. --- README.md | 36 ++++++++++-------- scripts/valet_archive_create.sh | 4 +- valet/pathprune.go | 8 +++- valet/predicates.go | 34 ++++++++++------- valet/predicates_test.go | 16 +++++++- .../barcode_alignment_FAL01979_43578c8f.tsv | 1 + valet/testdata/valet/1/ancillary.csv.gz | Bin 0 -> 38 bytes valet/valet_suite_test.go | 12 ++++-- 8 files changed, 74 insertions(+), 37 deletions(-) create mode 100644 valet/testdata/platform/ont/minknow/gridion/66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/barcode_alignment_FAL01979_43578c8f.tsv create mode 100644 valet/testdata/valet/1/ancillary.csv.gz diff --git a/README.md b/README.md index 4713ff7..eb5a7ad 100644 --- a/README.md +++ b/README.md @@ -3,8 +3,8 @@ ## Overview `valet` is a utility for performing data management tasks automatically. Once -started, `valet` will continue working until interrupted by SIGINT (^C) or -SIGTERM (kill), when it will stop gracefully. +started, `valet` will continue working until interrupted by `SIGINT` (^C) or +`SIGTERM` (kill), when it will stop gracefully. It monitors filesystem events and also performs filesystem walks to ensure that tasks are done in a timely fashion. @@ -21,23 +21,27 @@ disks filling. #### Compressing files Some versions of MinKNOW to do not compress fastq files and no version -compresses the large sequencing_summary.txt files. `valet` compresses both of -these types with a simple gzip. +compresses the large sequencing_summary.txt files. `valet` compresses +some files with gzip. - File patterns supported - - *.fastq$ - - *.txt$ + - `*.csv` + - `*.fastq` + - `*.txt` #### Archiving files - Files patterns supported - - *.csv$ - - *.fast5$ - - *.gz$ - - *.md$ - - *.pdf$ + - `*.csv` + - `*.fast5` + - `*.fastq` + - `*.gz` + - `*.md` + - `*.pdf` + - `*.tsv` + - `*.txt` #### Creating up-to-date checksum files @@ -55,7 +59,7 @@ it recognises for archiving. - Checksum file patterns supported - - (data file name).md5 + - `.md5` `valet` will monitor a directory hierarchy and locate data files within it that have no accompanying checksum file, or have a checksum file that is stale. @@ -64,7 +68,7 @@ have no accompanying checksum file, or have a checksum file that is stale. ### Operation `valet` is a command-line program with online help. Once launched it will -continue to run until signalled with SIGINT (^C) or SIGTERM (kill), when it +continue to run until signalled with `SIGINT` (^C) or `SIGTERM` (kill), when it will stop by cancelling the filesystem monitor and waiting for any running jobs to exit. @@ -116,16 +120,16 @@ function, or another) from operating on a particular file concurrently. ### Bugs -- See [GitHub issues](https://github.com/kjsanger/valet/issues?q=is%3Aissue+is%3Aopen+label%3Abug) +- See [GitHub issues](https://github.com/wtsi-npg/valet/issues?q=is%3Aissue+is%3Aopen+label%3Abug) #### Status -[![Build Status](https://travis-ci.org/kjsanger/valet.svg?branch=devel)](https://travis-ci.org/kjsanger/valet) +[![Build Status](https://travis-ci.com/wtsi-npg/valet.svg?branch=devel)](https://travis-ci.com/wtsi-npg/valet) #### Dependencies: -https://github.com/kjsanger/extendo +https://github.com/wtsi-npg/extendo Versions >= 2.0.0 diff --git a/scripts/valet_archive_create.sh b/scripts/valet_archive_create.sh index c7a709e..b33d5e3 100755 --- a/scripts/valet_archive_create.sh +++ b/scripts/valet_archive_create.sh @@ -54,9 +54,9 @@ conda activate "$CONDA_ENV" && \ --root "$DATA_ROOT" \ --archive-root "$ARCHIVE_ROOT" \ --exclude "$SAFE_ROOT" \ - --exclude "$DATA_ROOT/pings" \ - --exclude "$DATA_ROOT/reports" \ + --exclude "$DATA_ROOT/laboratory" \ --max-proc "$MAX_PROC" \ --interval "$INTERVAL" \ --delete-on-archive \ --verbose >> "$LOG_FILE" 2>&1 + diff --git a/valet/pathprune.go b/valet/pathprune.go index 397eef2..da061b7 100644 --- a/valet/pathprune.go +++ b/valet/pathprune.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -29,13 +29,19 @@ import ( // Directory names within the root MinKNOW data directory (typically /data) // that we will ignore by default. var MinKNOWIgnore = []string{ + "core-dump-db", + "devices", "epi2me_inside", "intermediate", + "logs", + "lost+found", + "network", "npg", "pings", "queued_reads", "reads", "reports", + "user_scripts", } // DefaultIgnorePatterns returns glob patterns matching directories in the root diff --git a/valet/predicates.go b/valet/predicates.go index efe65f4..c680c27 100644 --- a/valet/predicates.go +++ b/valet/predicates.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -40,18 +40,20 @@ const FastqSuffix string = "fastq" // The recognised suffix for fastq files const CSVSuffix string = "csv" const MarkdownSuffix string = "md" const TxtSuffix string = "txt" +const TsvSuffix string = "tsv" const PDFSuffix string = "pdf" const MD5Suffix string = "md5" // The recognised suffix for MD5 checksum files const GzipSuffix string = "gz" -var fast5Regex = regexp.MustCompile(fmt.Sprintf(".*[.]%s$", Fast5Suffix)) -var fastqRegex = regexp.MustCompile(fmt.Sprintf(".*[.]%s$", FastqSuffix)) -var txtRegex = regexp.MustCompile(fmt.Sprintf(".*[.]%s$", TxtSuffix)) -var markdownRegex = regexp.MustCompile(fmt.Sprintf(".*[.]%s$", MarkdownSuffix)) -var pdfRegex = regexp.MustCompile(fmt.Sprintf(".*[.]%s$", PDFSuffix)) -var csvRegex = regexp.MustCompile(fmt.Sprintf(".*[.]%s$", CSVSuffix)) -var gzipRegex = regexp.MustCompile(fmt.Sprintf(".*[.]%s$", GzipSuffix)) -var reportRegex = regexp.MustCompile(fmt.Sprintf("report.*[.]%s$", MarkdownSuffix)) +var fast5Regex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", Fast5Suffix)) +var fastqRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", FastqSuffix)) +var txtRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", TxtSuffix)) +var tsvRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", TsvSuffix)) +var markdownRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", MarkdownSuffix)) +var pdfRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", PDFSuffix)) +var csvRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", CSVSuffix)) +var gzipRegex = regexp.MustCompile(fmt.Sprintf("(?i).*[.]%s$", GzipSuffix)) +var reportRegex = regexp.MustCompile(fmt.Sprintf("(?i)report.*[.]%s$", MarkdownSuffix)) // Matches the run ID of MinKNOW c. August 2019 for GridION and PromethION // i.e. of the form: @@ -64,9 +66,10 @@ var RequiresCopying = Or( IsFast5, And(IsFastq, IsCompressed), And(IsTxt, IsCompressed), + And(IsCSV, IsCompressed), IsMarkdown, IsPDF, - IsCSV) + IsTSV) // RequiresChecksum returns true if the argument is a regular file that is // recognised as a checksum target and either has no checksum file, or has a @@ -79,7 +82,7 @@ var RequiresChecksum = And( var HasValidChecksumFile = Not(HasStaleChecksumFile) var RequiresCompression = And( - Or(IsFastq, IsTxt), + Or(IsFastq, IsTxt, IsCSV), Not(IsCompressed), Not(HasCompressedVersion)) @@ -171,7 +174,7 @@ func IsTxt(path FilePath) (bool, error) { // IsMarkdown returns true if path matches the recognised markdown file // pattern. func IsMarkdown(path FilePath) (bool, error) { - return markdownRegex.MatchString(path.Location), nil + return markdownRegex.MatchString(path.UncompressedFilename()), nil } // IsPDF returns true if path matches the recognised PDF file pattern. @@ -181,7 +184,12 @@ func IsPDF(path FilePath) (bool, error) { // IsCSV returns true if path matches the recognised CSV file pattern. func IsCSV(path FilePath) (bool, error) { - return csvRegex.MatchString(path.Location), nil + return csvRegex.MatchString(path.UncompressedFilename()), nil +} + +// IsTSV returns true if path matches the recognised TSV file pattern. +func IsTSV(path FilePath) (bool, error) { + return tsvRegex.MatchString(path.UncompressedFilename()), nil } // IsCompressed returns true if the path matches the recognised compressed file diff --git a/valet/predicates_test.go b/valet/predicates_test.go index c795225..9f2c8af 100644 --- a/valet/predicates_test.go +++ b/valet/predicates_test.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -102,6 +102,20 @@ func TestIsGzipFastqMatch(t *testing.T) { } } +func TestIsGzipCSVMatch(t *testing.T) { + csv, _ := NewFilePath("./testdata/valet/1/ancillarey.csv.gz") + + ok, err := IsCompressed(csv) + if assert.NoError(t, err) { + assert.True(t, ok, "expected true for a gzipped CSV file") + } + + ok, err = IsCSV(csv) + if assert.NoError(t, err) { + assert.True(t, ok, "expected true for a gzipped CSV file") + } +} + func TestIsCompressed(t *testing.T) { fq1, _ := NewFilePath("./testdata/valet/1/reads/fastq/reads1.fastq") ok1, err1 := IsCompressed(fq1) diff --git a/valet/testdata/platform/ont/minknow/gridion/66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/barcode_alignment_FAL01979_43578c8f.tsv b/valet/testdata/platform/ont/minknow/gridion/66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/barcode_alignment_FAL01979_43578c8f.tsv new file mode 100644 index 0000000..f1e8d0f --- /dev/null +++ b/valet/testdata/platform/ont/minknow/gridion/66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/barcode_alignment_FAL01979_43578c8f.tsv @@ -0,0 +1 @@ +f1f11e36-76c8-11eb-a698-d789d03e9d9a diff --git a/valet/testdata/valet/1/ancillary.csv.gz b/valet/testdata/valet/1/ancillary.csv.gz new file mode 100644 index 0000000000000000000000000000000000000000..33ae7e68b6ddcb7eb8b1988609cfc57da0e5a874 GIT binary patch literal 38 ucmb2|=HPIcZI-T*k0^#hOP<43}zNJ!D~EU;qI1Mh$EL literal 0 HcmV?d00001 diff --git a/valet/valet_suite_test.go b/valet/valet_suite_test.go index 49d7d97..375913f 100644 --- a/valet/valet_suite_test.go +++ b/valet/valet_suite_test.go @@ -1,5 +1,5 @@ /* - * Copyright (C) 2019, 2020. Genome Research Ltd. All rights reserved. + * Copyright (C) 2019, 2020, 2021. Genome Research Ltd. All rights reserved. * * 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 @@ -111,6 +111,7 @@ var _ = Describe("Find regular files)", func() { When("using a file predicate", func() { It("should find files", func() { expectedPaths := []string{ + "1/ancillary.csv.gz", "1/reads/fast5/reads1.fast5", "1/reads/fast5/reads1.fast5.md5", "1/reads/fast5/reads2.fast5", @@ -280,6 +281,7 @@ var _ = Describe("Find files at intervals", func() { dataDir = "testdata/valet" expectedPaths = []string{ + "1/ancillary.csv.gz", "1/reads/fast5/reads1.fast5", "1/reads/fast5/reads1.fast5.md5", "1/reads/fast5/reads2.fast5", @@ -863,10 +865,12 @@ var _ = Describe("Archive MINKnow files", func() { "DN585561I_A1_sequencing_summary.txt.gz", "66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/" + "final_summary.txt.gz", - "66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/duty_time.csv", + "66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/duty_time.csv.gz", "66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/report.md", "66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/report.pdf", - "66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/throughput.csv", + "66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/throughput.csv.gz", + "66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/" + + "barcode_alignment_FAL01979_43578c8f.tsv", // Fast5 fail "66/DN585561I_A1/20190904_1514_GA20000_FAL01979_43578c8f/fast5_fail/" + @@ -1050,7 +1054,7 @@ var _ = Describe("Archive MINKnow files", func() { var _ = Describe("Count files without a checksum", func() { var ( numFilesFound uint64 - numFilesExpected uint64 = 5 // fast5, fastq.gz and md (reports) + numFilesExpected uint64 = 6 // csv, fast5, fastq.gz and md (reports) ) BeforeEach(func() { From 67af4604a69cd48e13e44f7a1fe17fd427d436c1 Mon Sep 17 00:00:00 2001 From: Keith James <47220353+kjsanger@users.noreply.github.com> Date: Mon, 15 Mar 2021 17:04:51 +0000 Subject: [PATCH 04/18] Create dependabot.yml --- .github/dependabot.yml | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 .github/dependabot.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..b7b54e5 --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,6 @@ +version: 2 +updates: + - package-ecosystem: "gomod" + directory: "/" + schedulee: + interval: "weekly" From b681fbad4078c0318eab58fc7d35f62dbe185cea Mon Sep 17 00:00:00 2001 From: Keith James <47220353+kjsanger@users.noreply.github.com> Date: Mon, 15 Mar 2021 17:08:28 +0000 Subject: [PATCH 05/18] Update dependabot.yml Fix typo --- .github/dependabot.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index b7b54e5..54fb6e6 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -2,5 +2,5 @@ version: 2 updates: - package-ecosystem: "gomod" directory: "/" - schedulee: + schedule: interval: "weekly" From 1ed1387298a3a10c10c9fed4fe4fd34cf7e25dfe Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 15 Mar 2021 17:10:57 +0000 Subject: [PATCH 06/18] Bump github.com/onsi/ginkgo from 1.15.0 to 1.15.1 Bumps [github.com/onsi/ginkgo](https://github.com/onsi/ginkgo) from 1.15.0 to 1.15.1. - [Release notes](https://github.com/onsi/ginkgo/releases) - [Changelog](https://github.com/onsi/ginkgo/blob/master/CHANGELOG.md) - [Commits](https://github.com/onsi/ginkgo/compare/v1.15.0...v1.15.1) Signed-off-by: dependabot[bot] --- go.mod | 2 +- go.sum | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/go.mod b/go.mod index 828d1ef..0022638 100644 --- a/go.mod +++ b/go.mod @@ -5,7 +5,7 @@ go 1.14 require ( github.com/klauspost/compress v1.9.1 // indirect github.com/klauspost/pgzip v1.2.1 - github.com/onsi/ginkgo v1.15.0 + github.com/onsi/ginkgo v1.15.1 github.com/onsi/gomega v1.10.5 github.com/pkg/errors v0.9.1 github.com/rs/zerolog v1.19.0 diff --git a/go.sum b/go.sum index 0e5e8a1..3e84f48 100644 --- a/go.sum +++ b/go.sum @@ -39,10 +39,14 @@ github.com/mitchellh/go-homedir v1.1.0/go.mod h1:SfyaCUpYCn1Vlf4IUYiD9fPX4A5wJrk github.com/mitchellh/mapstructure v1.1.2/go.mod h1:FVVH3fgwuzCH5S8UJGiWEs2h04kUh9fWfEaFds41c1Y= github.com/nxadm/tail v1.4.4 h1:DQuhQpB1tVlglWS2hLQ5OV6B5r8aGxSrPc5Qo6uTN78= github.com/nxadm/tail v1.4.4/go.mod h1:kenIhsEOeOJmVchQTgglprH7qJGnHDVpk1VPCcaMI8A= +github.com/nxadm/tail v1.4.8 h1:nPr65rt6Y5JFSKQO7qToXr7pePgD6Gwiw05lkbyAQTE= +github.com/nxadm/tail v1.4.8/go.mod h1:+ncqLTQzXmGhMZNUePPaPqPvBxHAIsmXswZKocGu+AU= github.com/onsi/ginkgo v1.6.0/go.mod h1:lLunBs/Ym6LB5Z9jYTR76FiuTmxDTDusOGeTQH+WWjE= github.com/onsi/ginkgo v1.12.1/go.mod h1:zj2OWP4+oCPe1qIXoGWkgMRwljMUYCdkwsT2108oapk= github.com/onsi/ginkgo v1.15.0 h1:1V1NfVQR87RtWAgp1lv9JZJ5Jap+XFGKPi00andXGi4= github.com/onsi/ginkgo v1.15.0/go.mod h1:hF8qUzuuC8DJGygJH3726JnCZX4MYbRB8yFfISqnKUg= +github.com/onsi/ginkgo v1.15.1 h1:DsXNrKujDlkMS9Rsxmd+Fg7S6Kc5lhE+qX8tY6laOxc= +github.com/onsi/ginkgo v1.15.1/go.mod h1:Dd6YFfwBW84ETqqtL0CPyPXillHgY6XhQH3uuCCTr/o= github.com/onsi/gomega v1.7.1/go.mod h1:XdKZgCCFLUoM/7CFJVPcG8C1xQ1AJ0vpAezJrB7JYyY= github.com/onsi/gomega v1.10.1 h1:o0+MgICZLuZ7xjH7Vx6zS/zcu93/BEp1VwkIW1mEXCE= github.com/onsi/gomega v1.10.1/go.mod h1:iN09h71vgCQne3DLsj+A5owkum+a2tYe+TOCB1ybHNo= @@ -69,6 +73,7 @@ github.com/spf13/pflag v1.0.3/go.mod h1:DYY7MBk1bdzusC3SYhjObp+wFpr4gzcvqqNjLnIn github.com/spf13/viper v1.3.2/go.mod h1:ZiWeW+zYFKm7srdB9IoDzzZXaJaI5eL9QjNiN/DMA2s= github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs= +github.com/stretchr/testify v1.7.0 h1:nwc3DEeHmmLAfoZucVR881uASk0Mfjw8xYJ99tb5CcY= github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg= github.com/ugorji/go/codec v0.0.0-20181204163529-d75b2dcb6bc8/go.mod h1:VFNgLljTbGfSG7qAOspJ7OScBnGdDN/yBr0sguwnwf0= github.com/wtsi-npg/extendo/v2 v2.3.0 h1:sKlABJFbFtuQB2LOmlBTX4oMbhfAM7HbdreMU81YeRc= From 183a5fa1ec58f975a6f6bc9809a485bb93ac96a9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 17 Mar 2021 17:47:32 +0000 Subject: [PATCH 07/18] Bump github.com/onsi/gomega from 1.10.5 to 1.11.0 Bumps [github.com/onsi/gomega](https://github.com/onsi/gomega) from 1.10.5 to 1.11.0. - [Release notes](https://github.com/onsi/gomega/releases) - [Changelog](https://github.com/onsi/gomega/blob/master/CHANGELOG.md) - [Commits](https://github.com/onsi/gomega/compare/v1.10.5...v1.11.0) Signed-off-by: dependabot[bot] --- go.mod | 2 +- go.sum | 24 ++++++------------------ 2 files changed, 7 insertions(+), 19 deletions(-) diff --git a/go.mod b/go.mod index 0022638..db70187 100644 --- a/go.mod +++ b/go.mod @@ -6,7 +6,7 @@ require ( github.com/klauspost/compress v1.9.1 // indirect github.com/klauspost/pgzip v1.2.1 github.com/onsi/ginkgo v1.15.1 - github.com/onsi/gomega v1.10.5 + github.com/onsi/gomega v1.11.0 github.com/pkg/errors v0.9.1 github.com/rs/zerolog v1.19.0 github.com/spf13/cobra v0.0.5 diff --git a/go.sum b/go.sum index 3e84f48..ef66172 100644 --- a/go.sum +++ b/go.sum @@ -8,25 +8,23 @@ github.com/cpuguy83/go-md2man v1.0.10/go.mod h1:SmD6nW6nTyfqj6ABTjUi3V3JVMnlJmwc github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c= github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= -github.com/fsnotify/fsnotify v1.4.7 h1:IXs+QLmnXW2CcXuY+8Mzv/fWEsPGWxqefPtCP5CnV9I= github.com/fsnotify/fsnotify v1.4.7/go.mod h1:jwhsz4b93w/PPRr/qN1Yymfu8t87LnFCMoQvtojpjFo= github.com/fsnotify/fsnotify v1.4.9 h1:hsms1Qyu0jgnwNXIxa+/V/PDsU6CfLf6CNO8H7IWoS4= github.com/fsnotify/fsnotify v1.4.9/go.mod h1:znqG4EE+3YCdAaPaxE2ZRY/06pZUdp0tY4IgpuI1SZQ= -github.com/golang/protobuf v1.2.0 h1:P3YflyNX/ehuJFLhxviNdFxQPkGK5cDcApsge1SqnvM= github.com/golang/protobuf v1.2.0/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U= github.com/golang/protobuf v1.4.0-rc.1/go.mod h1:ceaxUfeHdC40wWswd/P6IGgMaK3YpKi5j83Wpe3EHw8= github.com/golang/protobuf v1.4.0-rc.1.0.20200221234624-67d41d38c208/go.mod h1:xKAWHe0F5eneWXFV3EuXVDTCmh+JuBKY0li0aMyXATA= github.com/golang/protobuf v1.4.0-rc.2/go.mod h1:LlEzMj4AhA7rCAGe4KMBDvJI+AwstrUpVNzEA03Pprs= github.com/golang/protobuf v1.4.0-rc.4.0.20200313231945-b860323f09d0/go.mod h1:WU3c8KckQ9AFe+yFwt9sWVRKCVIyN9cPHBJSNnbL67w= github.com/golang/protobuf v1.4.0/go.mod h1:jodUvKwWbYaEsadDk5Fwe5c77LiNKVO9IDvqG2KuDX0= -github.com/golang/protobuf v1.4.2 h1:+Z5KGCizgyZCbGh1KZqA0fcLLkwbsjIzS4aV2v7wJX0= github.com/golang/protobuf v1.4.2/go.mod h1:oDoupMAO8OvCJWAcko0GGGIgR6R6ocIYbsSw735rRwI= +github.com/golang/protobuf v1.4.3 h1:JjCZWpVbqXDqFVmTfYWEVTMIYrL/NPdPSCHPJ0T/raM= +github.com/golang/protobuf v1.4.3/go.mod h1:oDoupMAO8OvCJWAcko0GGGIgR6R6ocIYbsSw735rRwI= github.com/google/go-cmp v0.3.0/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU= github.com/google/go-cmp v0.3.1/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU= github.com/google/go-cmp v0.4.0 h1:xsAVV57WRhGj6kEIi8ReJzQlHHqcBYCElAvkovg3B/4= github.com/google/go-cmp v0.4.0/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= github.com/hashicorp/hcl v1.0.0/go.mod h1:E5yfLk+7swimpb2L/Alb/PJmXilQ/rhwaUYs4T20WEQ= -github.com/hpcloud/tail v1.0.0 h1:nfCOvKYfkgYP8hkirhJocXT2+zOD8yUNjXaWfTlyFKI= github.com/hpcloud/tail v1.0.0/go.mod h1:ab1qPbhIpdTxEkNHXyeSf5vhxWSCs/tWer42PpOxQnU= github.com/inconshreveable/mousetrap v1.0.0 h1:Z8tu5sraLXCXIcARxBp/8cbvlwVa7Z1NHg9XEKhtSvM= github.com/inconshreveable/mousetrap v1.0.0/go.mod h1:PxqpIevigyE2G7u3NXJIT2ANytuPF1OarO4DADm73n8= @@ -37,21 +35,19 @@ github.com/klauspost/pgzip v1.2.1/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQ github.com/magiconair/properties v1.8.0/go.mod h1:PppfXfuXeibc/6YijjN8zIbojt8czPbwD3XqdrwzmxQ= github.com/mitchellh/go-homedir v1.1.0/go.mod h1:SfyaCUpYCn1Vlf4IUYiD9fPX4A5wJrkLzIz1N1q0pr0= github.com/mitchellh/mapstructure v1.1.2/go.mod h1:FVVH3fgwuzCH5S8UJGiWEs2h04kUh9fWfEaFds41c1Y= -github.com/nxadm/tail v1.4.4 h1:DQuhQpB1tVlglWS2hLQ5OV6B5r8aGxSrPc5Qo6uTN78= github.com/nxadm/tail v1.4.4/go.mod h1:kenIhsEOeOJmVchQTgglprH7qJGnHDVpk1VPCcaMI8A= github.com/nxadm/tail v1.4.8 h1:nPr65rt6Y5JFSKQO7qToXr7pePgD6Gwiw05lkbyAQTE= github.com/nxadm/tail v1.4.8/go.mod h1:+ncqLTQzXmGhMZNUePPaPqPvBxHAIsmXswZKocGu+AU= github.com/onsi/ginkgo v1.6.0/go.mod h1:lLunBs/Ym6LB5Z9jYTR76FiuTmxDTDusOGeTQH+WWjE= github.com/onsi/ginkgo v1.12.1/go.mod h1:zj2OWP4+oCPe1qIXoGWkgMRwljMUYCdkwsT2108oapk= -github.com/onsi/ginkgo v1.15.0 h1:1V1NfVQR87RtWAgp1lv9JZJ5Jap+XFGKPi00andXGi4= github.com/onsi/ginkgo v1.15.0/go.mod h1:hF8qUzuuC8DJGygJH3726JnCZX4MYbRB8yFfISqnKUg= github.com/onsi/ginkgo v1.15.1 h1:DsXNrKujDlkMS9Rsxmd+Fg7S6Kc5lhE+qX8tY6laOxc= github.com/onsi/ginkgo v1.15.1/go.mod h1:Dd6YFfwBW84ETqqtL0CPyPXillHgY6XhQH3uuCCTr/o= github.com/onsi/gomega v1.7.1/go.mod h1:XdKZgCCFLUoM/7CFJVPcG8C1xQ1AJ0vpAezJrB7JYyY= -github.com/onsi/gomega v1.10.1 h1:o0+MgICZLuZ7xjH7Vx6zS/zcu93/BEp1VwkIW1mEXCE= github.com/onsi/gomega v1.10.1/go.mod h1:iN09h71vgCQne3DLsj+A5owkum+a2tYe+TOCB1ybHNo= -github.com/onsi/gomega v1.10.5 h1:7n6FEkpFmfCoo2t+YYqXH0evK+a9ICQz0xcAy9dYcaQ= github.com/onsi/gomega v1.10.5/go.mod h1:gza4q3jKQJijlu05nKWRCW/GavJumGt8aNRxWg7mt48= +github.com/onsi/gomega v1.11.0 h1:+CqWgvj0OZycCaqclBD1pxKHAU+tOkHmQIWvDHq2aug= +github.com/onsi/gomega v1.11.0/go.mod h1:azGKhqFUon9Vuj0YmTfLSmx0FUwqXYSTl5re8lQLTUg= github.com/pelletier/go-toml v1.2.0/go.mod h1:5z9KED0ma1S8pY6P1sdut58dfprrGBbd/94hg7ilaic= github.com/pkg/errors v0.8.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0= github.com/pkg/errors v0.9.1 h1:FEBLx1zS214owpjy7qsBeixbURkuhQAwrK5UwLGTwt4= @@ -95,15 +91,12 @@ golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9/go.mod h1:LzIPMQfyMNhhGPh golang.org/x/mod v0.3.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA= golang.org/x/net v0.0.0-20180906233101-161cd47e91fd/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= -golang.org/x/net v0.0.0-20190620200207-3b0461eec859 h1:R/3boaszxrf1GEUWTVDzSKVwLmSJpwZ1yqXm8j0v2QI= golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s= -golang.org/x/net v0.0.0-20200520004742-59133d7f0dd7 h1:AeiKBIuRw3UomYXSbLy0Mc2dDLfdtbT/IVn4keq83P0= golang.org/x/net v0.0.0-20200520004742-59133d7f0dd7/go.mod h1:qpuaurCH72eLCgpAm/N6yyVIVM9cpaDIP3A8BGJEC5A= golang.org/x/net v0.0.0-20201021035429-f5854403a974/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU= golang.org/x/net v0.0.0-20201202161906-c7110b5ffcbb h1:eBmm0M9fYhWpKZLjQUUKka/LtIxf46G4fxeEz5KJr9U= golang.org/x/net v0.0.0-20201202161906-c7110b5ffcbb/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU= golang.org/x/sync v0.0.0-20180314180146-1d60e4601c6f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= -golang.org/x/sync v0.0.0-20190423024810-112230192c58 h1:8gQV6CLnAEikrhgkHFbMAEhagSSnXWGV915qUMm9mrU= golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sys v0.0.0-20180909124046-d0be0721c37e/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= @@ -112,13 +105,11 @@ golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5h golang.org/x/sys v0.0.0-20190412213103-97732733099d/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20190904154756-749cb33beabd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20191005200804-aed5e4c7ecf9/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20191120155948-bd437916bb0e h1:N7DeIrjYszNmSW409R3frPPwglRwMkXSBzwVbkOjLLA= golang.org/x/sys v0.0.0-20191120155948-bd437916bb0e/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20200323222414-85ca7c5b95cd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20200930185726-fdedc70b468f/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20210112080510-489259a85091 h1:DMyOG0U+gKfu8JZzg2UQe9MeaC1X+xQWlAKcRnjxjCw= golang.org/x/sys v0.0.0-20210112080510-489259a85091/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/text v0.3.0 h1:g61tztE5qeGQ89tm6NTjjM9VPIm088od1l6aSorWRWg= golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= golang.org/x/text v0.3.3 h1:cokOdA+Jmi5PJGXLlLllQSgYigAEfHXJAERHVMaCc2k= golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= @@ -126,10 +117,8 @@ golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGm golang.org/x/tools v0.0.0-20190828213141-aed303cbaa74/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20201224043029-2b0845dc783e/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= -golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7 h1:9zdDQZ7Thm29KFXgAX/+yaf3eVbP7djjWp/dXAppNCc= golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= -golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543 h1:E7g+9GITq07hpfrRu66IVDexMakfv52eLZ2CXBWiKr4= golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= golang.org/x/xerrors v0.0.0-20200804184101-5ec99f83aff1 h1:go1bK/D/BFZV2I8cIQd1NKEZ+0owSTG1fDTci4IqFcE= golang.org/x/xerrors v0.0.0-20200804184101-5ec99f83aff1/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= @@ -142,14 +131,13 @@ google.golang.org/protobuf v1.23.0 h1:4MY060fB1DLGMB/7MBTLnwQUY6+F09GEiz6SsrNqyz google.golang.org/protobuf v1.23.0/go.mod h1:EGpADcykh3NcUnDUJcl1+ZksZNG86OlYog2l/sGQquU= gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405 h1:yhCVgyC4o1eVCa2tZl7eS0r+SDo693bJlVdllGtEeKM= gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= -gopkg.in/fsnotify.v1 v1.4.7 h1:xOHLXZwVvI9hhs+cLKq5+I5onOuwQLhQwiu63xxlHs4= gopkg.in/fsnotify.v1 v1.4.7/go.mod h1:Tz8NjZHkW78fSQdbUxIjBTcgA1z1m8ZHf0WmKUhAMys= gopkg.in/tomb.v1 v1.0.0-20141024135613-dd632973f1e7 h1:uRGJdciOHaEIrze2W8Q3AKkepLTh2hOroT7a+7czfdQ= gopkg.in/tomb.v1 v1.0.0-20141024135613-dd632973f1e7/go.mod h1:dt/ZhP58zS4L8KSrWDmTeBkI65Dw0HsyUHuEVlX15mw= gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= -gopkg.in/yaml.v2 v2.2.4 h1:/eiJrUcujPVeJ3xlSWaiNi3uSVmDGBK1pDHUHAnao1I= gopkg.in/yaml.v2 v2.2.4/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= -gopkg.in/yaml.v2 v2.3.0 h1:clyUAQHOM3G0M3f5vQj7LuJrETvjVot3Z5el9nffUtU= gopkg.in/yaml.v2 v2.3.0/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= +gopkg.in/yaml.v2 v2.4.0 h1:D8xgwECY7CYvx+Y2n4sBz93Jn9JRvxdiyyo8CTfuKaY= +gopkg.in/yaml.v2 v2.4.0/go.mod h1:RDklbk79AGWmwhnvt/jBztapEOGDOx6ZbXqjP6csGnQ= gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c h1:dUUwHk2QECo/6vqA44rthZ8ie2QXMNeKRTHCNY2nXvo= gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM= From 0cae21601c9bf77fb10d215cc1989e42f064f571 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 19 Mar 2021 09:53:24 +0000 Subject: [PATCH 08/18] Bump github.com/klauspost/pgzip from 1.2.1 to 1.2.5 Bumps [github.com/klauspost/pgzip](https://github.com/klauspost/pgzip) from 1.2.1 to 1.2.5. - [Release notes](https://github.com/klauspost/pgzip/releases) - [Commits](https://github.com/klauspost/pgzip/compare/v1.2.1...v1.2.5) Signed-off-by: dependabot[bot] --- go.mod | 2 +- go.sum | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/go.mod b/go.mod index db70187..b8aac93 100644 --- a/go.mod +++ b/go.mod @@ -4,7 +4,7 @@ go 1.14 require ( github.com/klauspost/compress v1.9.1 // indirect - github.com/klauspost/pgzip v1.2.1 + github.com/klauspost/pgzip v1.2.5 github.com/onsi/ginkgo v1.15.1 github.com/onsi/gomega v1.11.0 github.com/pkg/errors v0.9.1 diff --git a/go.sum b/go.sum index ef66172..5d29037 100644 --- a/go.sum +++ b/go.sum @@ -30,8 +30,8 @@ github.com/inconshreveable/mousetrap v1.0.0 h1:Z8tu5sraLXCXIcARxBp/8cbvlwVa7Z1NH github.com/inconshreveable/mousetrap v1.0.0/go.mod h1:PxqpIevigyE2G7u3NXJIT2ANytuPF1OarO4DADm73n8= github.com/klauspost/compress v1.9.1 h1:TWy0o9J9c6LK9C8t7Msh6IAJNXbsU/nvKLTQUU5HdaY= github.com/klauspost/compress v1.9.1/go.mod h1:RyIbtBH6LamlWaDj8nUwkbUhJ87Yi3uG0guNDohfE1A= -github.com/klauspost/pgzip v1.2.1 h1:oIPZROsWuPHpOdMVWLuJZXwgjhrW8r1yEX8UqMyeNHM= -github.com/klauspost/pgzip v1.2.1/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs= +github.com/klauspost/pgzip v1.2.5 h1:qnWYvvKqedOF2ulHpMG72XQol4ILEJ8k2wwRl/Km8oE= +github.com/klauspost/pgzip v1.2.5/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs= github.com/magiconair/properties v1.8.0/go.mod h1:PppfXfuXeibc/6YijjN8zIbojt8czPbwD3XqdrwzmxQ= github.com/mitchellh/go-homedir v1.1.0/go.mod h1:SfyaCUpYCn1Vlf4IUYiD9fPX4A5wJrkLzIz1N1q0pr0= github.com/mitchellh/mapstructure v1.1.2/go.mod h1:FVVH3fgwuzCH5S8UJGiWEs2h04kUh9fWfEaFds41c1Y= From 9b9e104411b04dfc74d5ee94a5ca4f285ad71fb7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 19 Mar 2021 11:33:58 +0000 Subject: [PATCH 09/18] Bump github.com/spf13/cobra from 0.0.5 to 0.0.7 Bumps [github.com/spf13/cobra](https://github.com/spf13/cobra) from 0.0.5 to 0.0.7. - [Release notes](https://github.com/spf13/cobra/releases) - [Changelog](https://github.com/spf13/cobra/blob/master/CHANGELOG.md) - [Commits](https://github.com/spf13/cobra/compare/0.0.5...0.0.7) Signed-off-by: dependabot[bot] --- go.mod | 2 +- go.sum | 111 +++++++++++++++++++++++++++++++++++++++++++++++++++------ 2 files changed, 102 insertions(+), 11 deletions(-) diff --git a/go.mod b/go.mod index b8aac93..64fa7a4 100644 --- a/go.mod +++ b/go.mod @@ -9,7 +9,7 @@ require ( github.com/onsi/gomega v1.11.0 github.com/pkg/errors v0.9.1 github.com/rs/zerolog v1.19.0 - github.com/spf13/cobra v0.0.5 + github.com/spf13/cobra v0.0.7 github.com/stretchr/testify v1.7.0 github.com/wtsi-npg/extendo/v2 v2.3.0 github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a diff --git a/go.sum b/go.sum index 5d29037..bceaa20 100644 --- a/go.sum +++ b/go.sum @@ -1,17 +1,39 @@ +cloud.google.com/go v0.26.0/go.mod h1:aQUYkXzVsufM+DwF1aE+0xfcU+56JwCaLick0ClmMTw= github.com/BurntSushi/toml v0.3.1/go.mod h1:xHWCNGjB5oqiDr8zfno3MHue2Ht5sIBksp03qcyfWMU= +github.com/OneOfOne/xxhash v1.2.2/go.mod h1:HSdplMjZKSmBqAxg5vPj2TmRDmfkzw+cTzAElWljhcU= +github.com/alecthomas/template v0.0.0-20160405071501-a0175ee3bccc/go.mod h1:LOuyumcjzFXgccqObfd/Ljyb9UuFJ6TxHnclSeseNhc= +github.com/alecthomas/units v0.0.0-20151022065526-2efee857e7cf/go.mod h1:ybxpYRFXyAe+OPACYpWeL0wqObRcbAqCMya13uyzqw0= github.com/armon/consul-api v0.0.0-20180202201655-eb2c6b5be1b6/go.mod h1:grANhF5doyWs3UAsr3K4I6qtAmlQcZDesFNEHPZAzj8= +github.com/beorn7/perks v0.0.0-20180321164747-3a771d992973/go.mod h1:Dwedo/Wpr24TaqPxmxbtue+5NUziq4I4S80YR8gNf3Q= +github.com/beorn7/perks v1.0.0/go.mod h1:KWe93zE9D1o94FZ5RNwFwVgaQK1VOXiVxmqh+CedLV8= +github.com/cespare/xxhash v1.1.0/go.mod h1:XrSqR1VqqWfGrhpAt58auRo0WTKS1nRRg3ghfAqPWnc= +github.com/client9/misspell v0.3.4/go.mod h1:qj6jICC3Q7zFZvVWo7KLAzC3yx5G7kyvSDkc90ppPyw= +github.com/coreos/bbolt v1.3.2/go.mod h1:iRUV2dpdMOn7Bo10OQBFzIJO9kkE559Wcmn+qkEiiKk= github.com/coreos/etcd v3.3.10+incompatible/go.mod h1:uF7uidLiAD3TWHmW31ZFd/JWoc32PjwdhPthX9715RE= -github.com/coreos/go-etcd v2.0.0+incompatible/go.mod h1:Jez6KQU2B/sWsbdaef3ED8NzMklzPG4d5KIOhIy30Tk= github.com/coreos/go-semver v0.2.0/go.mod h1:nnelYz7RCh+5ahJtPPxZlU+153eP4D4r3EedlOD2RNk= github.com/coreos/go-systemd v0.0.0-20190321100706-95778dfbb74e/go.mod h1:F5haX7vjVVG0kc13fIWeqUViNPyEJxv/OmvnBo0Yme4= -github.com/cpuguy83/go-md2man v1.0.10/go.mod h1:SmD6nW6nTyfqj6ABTjUi3V3JVMnlJmwcJI5acqYI6dE= +github.com/coreos/pkg v0.0.0-20180928190104-399ea9e2e55f/go.mod h1:E3G3o1h8I7cfcXa63jLwjI0eiQQMgzzUDFVpN/nH/eA= +github.com/cpuguy83/go-md2man/v2 v2.0.0/go.mod h1:maD7wRr/U5Z6m/iR4s+kqSMx2CaBsrgA7czyZG/E6dU= github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c= github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38= +github.com/dgrijalva/jwt-go v3.2.0+incompatible/go.mod h1:E3ru+11k8xSBh+hMPgOLZmtrrCbhqsmaPHjLKYnJCaQ= +github.com/dgryski/go-sip13 v0.0.0-20181026042036-e10d5fee7954/go.mod h1:vAd38F8PWV+bWy6jNmig1y/TA+kYO4g3RSRF0IAv0no= github.com/fsnotify/fsnotify v1.4.7/go.mod h1:jwhsz4b93w/PPRr/qN1Yymfu8t87LnFCMoQvtojpjFo= github.com/fsnotify/fsnotify v1.4.9 h1:hsms1Qyu0jgnwNXIxa+/V/PDsU6CfLf6CNO8H7IWoS4= github.com/fsnotify/fsnotify v1.4.9/go.mod h1:znqG4EE+3YCdAaPaxE2ZRY/06pZUdp0tY4IgpuI1SZQ= +github.com/ghodss/yaml v1.0.0/go.mod h1:4dBDuWmgqj2HViK6kFavaiC9ZROes6MMH2rRYeMEF04= +github.com/go-kit/kit v0.8.0/go.mod h1:xBxKIO96dXMWWy0MnWVtmwkA9/13aqxPnvrjFYMA2as= +github.com/go-logfmt/logfmt v0.3.0/go.mod h1:Qt1PoO58o5twSAckw1HlFXLmHsOX5/0LbT9GBnD5lWE= +github.com/go-logfmt/logfmt v0.4.0/go.mod h1:3RMwSq7FuexP4Kalkev3ejPJsZTpXXBr9+V4qmtdjCk= +github.com/go-stack/stack v1.8.0/go.mod h1:v0f6uXyyMGvRgIKkXu+yp6POWl0qKG85gN/melR3HDY= +github.com/gogo/protobuf v1.1.1/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ= +github.com/gogo/protobuf v1.2.1/go.mod h1:hp+jE20tsWTFYpLwKvXlhS1hjn+gTNwPg2I6zVXpSg4= +github.com/golang/glog v0.0.0-20160126235308-23def4e6c14b/go.mod h1:SBH7ygxi8pfUlaOkMMuAQtPIUF8ecWP5IEl/CR7VP2Q= +github.com/golang/groupcache v0.0.0-20190129154638-5b532d6fd5ef/go.mod h1:cIg4eruTrX1D+g88fzRXU5OdNfaM+9IcxsU14FzY7Hc= +github.com/golang/mock v1.1.1/go.mod h1:oTYuIxOrZwtPieC+H1uAHpcLFnEyAGVDL/k47Jfbm0A= github.com/golang/protobuf v1.2.0/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U= +github.com/golang/protobuf v1.3.1/go.mod h1:6lQm79b+lXiMfvg/cZm0SGofjICqVBUtrP5yJMmIC1U= github.com/golang/protobuf v1.4.0-rc.1/go.mod h1:ceaxUfeHdC40wWswd/P6IGgMaK3YpKi5j83Wpe3EHw8= github.com/golang/protobuf v1.4.0-rc.1.0.20200221234624-67d41d38c208/go.mod h1:xKAWHe0F5eneWXFV3EuXVDTCmh+JuBKY0li0aMyXATA= github.com/golang/protobuf v1.4.0-rc.2/go.mod h1:LlEzMj4AhA7rCAGe4KMBDvJI+AwstrUpVNzEA03Pprs= @@ -20,24 +42,44 @@ github.com/golang/protobuf v1.4.0/go.mod h1:jodUvKwWbYaEsadDk5Fwe5c77LiNKVO9IDvq github.com/golang/protobuf v1.4.2/go.mod h1:oDoupMAO8OvCJWAcko0GGGIgR6R6ocIYbsSw735rRwI= github.com/golang/protobuf v1.4.3 h1:JjCZWpVbqXDqFVmTfYWEVTMIYrL/NPdPSCHPJ0T/raM= github.com/golang/protobuf v1.4.3/go.mod h1:oDoupMAO8OvCJWAcko0GGGIgR6R6ocIYbsSw735rRwI= +github.com/google/btree v1.0.0/go.mod h1:lNA+9X1NB3Zf8V7Ke586lFgjr2dZNuvo3lPJSGZ5JPQ= +github.com/google/go-cmp v0.2.0/go.mod h1:oXzfMopK8JAjlY9xF4vHSVASa0yLyX7SntLO5aqRK0M= github.com/google/go-cmp v0.3.0/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU= github.com/google/go-cmp v0.3.1/go.mod h1:8QqcDgzrUqlUb/G2PQTWiueGozuR1884gddMywk6iLU= github.com/google/go-cmp v0.4.0 h1:xsAVV57WRhGj6kEIi8ReJzQlHHqcBYCElAvkovg3B/4= github.com/google/go-cmp v0.4.0/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE= +github.com/gorilla/websocket v1.4.0/go.mod h1:E7qHFY5m1UJ88s3WnNqhKjPHQ0heANvMoAMk2YaljkQ= +github.com/grpc-ecosystem/go-grpc-middleware v1.0.0/go.mod h1:FiyG127CGDf3tlThmgyCl78X/SZQqEOJBCDaAfeWzPs= +github.com/grpc-ecosystem/go-grpc-prometheus v1.2.0/go.mod h1:8NvIoxWQoOIhqOTXgfV/d3M/q6VIi02HzZEHgUlZvzk= +github.com/grpc-ecosystem/grpc-gateway v1.9.0/go.mod h1:vNeuVxBJEsws4ogUvrchl83t/GYV9WGTSLVdBhOQFDY= github.com/hashicorp/hcl v1.0.0/go.mod h1:E5yfLk+7swimpb2L/Alb/PJmXilQ/rhwaUYs4T20WEQ= github.com/hpcloud/tail v1.0.0/go.mod h1:ab1qPbhIpdTxEkNHXyeSf5vhxWSCs/tWer42PpOxQnU= github.com/inconshreveable/mousetrap v1.0.0 h1:Z8tu5sraLXCXIcARxBp/8cbvlwVa7Z1NHg9XEKhtSvM= github.com/inconshreveable/mousetrap v1.0.0/go.mod h1:PxqpIevigyE2G7u3NXJIT2ANytuPF1OarO4DADm73n8= +github.com/jonboulle/clockwork v0.1.0/go.mod h1:Ii8DK3G1RaLaWxj9trq07+26W01tbo22gdxWY5EU2bo= +github.com/julienschmidt/httprouter v1.2.0/go.mod h1:SYymIcj16QtmaHHD7aYtjjsJG7VTCxuUUipMqKk8s4w= +github.com/kisielk/errcheck v1.1.0/go.mod h1:EZBBE59ingxPouuu3KfxchcWSUPOHkagtvWXihfKN4Q= +github.com/kisielk/gotool v1.0.0/go.mod h1:XhKaO+MFFWcvkIS/tQcRk01m1F5IRFswLeQ+oQHNcck= github.com/klauspost/compress v1.9.1 h1:TWy0o9J9c6LK9C8t7Msh6IAJNXbsU/nvKLTQUU5HdaY= github.com/klauspost/compress v1.9.1/go.mod h1:RyIbtBH6LamlWaDj8nUwkbUhJ87Yi3uG0guNDohfE1A= github.com/klauspost/pgzip v1.2.5 h1:qnWYvvKqedOF2ulHpMG72XQol4ILEJ8k2wwRl/Km8oE= github.com/klauspost/pgzip v1.2.5/go.mod h1:Ch1tH69qFZu15pkjo5kYi6mth2Zzwzt50oCQKQE9RUs= +github.com/konsorten/go-windows-terminal-sequences v1.0.1/go.mod h1:T0+1ngSBFLxvqU3pZ+m/2kptfBszLMUkC4ZK/EgS/cQ= +github.com/kr/logfmt v0.0.0-20140226030751-b84e30acd515/go.mod h1:+0opPa2QZZtGFBFZlji/RkVcI2GknAs/DXo4wKdlNEc= +github.com/kr/pretty v0.1.0 h1:L/CwN0zerZDmRFUapSPitk6f+Q3+0za1rQkzVuMiMFI= +github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo= +github.com/kr/pty v1.1.1/go.mod h1:pFQYn66WHrOpPYNljwOMqo10TkYh1fy3cYio2l3bCsQ= +github.com/kr/text v0.1.0 h1:45sCR5RtlFHMR4UwH9sdQ5TC8v0qDQCHnXt+kaKSTVE= +github.com/kr/text v0.1.0/go.mod h1:4Jbv+DJW3UT/LiOwJeYQe1efqtUx/iVham/4vfdArNI= github.com/magiconair/properties v1.8.0/go.mod h1:PppfXfuXeibc/6YijjN8zIbojt8czPbwD3XqdrwzmxQ= +github.com/matttproud/golang_protobuf_extensions v1.0.1/go.mod h1:D8He9yQNgCq6Z5Ld7szi9bcBfOoFv/3dc6xSMkL2PC0= github.com/mitchellh/go-homedir v1.1.0/go.mod h1:SfyaCUpYCn1Vlf4IUYiD9fPX4A5wJrkLzIz1N1q0pr0= github.com/mitchellh/mapstructure v1.1.2/go.mod h1:FVVH3fgwuzCH5S8UJGiWEs2h04kUh9fWfEaFds41c1Y= +github.com/mwitkow/go-conntrack v0.0.0-20161129095857-cc309e4a2223/go.mod h1:qRWi+5nqEBWmkhHvq77mSJWrCKwh8bxhgT7d/eI7P4U= github.com/nxadm/tail v1.4.4/go.mod h1:kenIhsEOeOJmVchQTgglprH7qJGnHDVpk1VPCcaMI8A= github.com/nxadm/tail v1.4.8 h1:nPr65rt6Y5JFSKQO7qToXr7pePgD6Gwiw05lkbyAQTE= github.com/nxadm/tail v1.4.8/go.mod h1:+ncqLTQzXmGhMZNUePPaPqPvBxHAIsmXswZKocGu+AU= +github.com/oklog/ulid v1.3.1/go.mod h1:CirwcVhetQ6Lv90oh/F+FBtV6XMibvdAFo93nm5qn4U= github.com/onsi/ginkgo v1.6.0/go.mod h1:lLunBs/Ym6LB5Z9jYTR76FiuTmxDTDusOGeTQH+WWjE= github.com/onsi/ginkgo v1.12.1/go.mod h1:zj2OWP4+oCPe1qIXoGWkgMRwljMUYCdkwsT2108oapk= github.com/onsi/ginkgo v1.15.0/go.mod h1:hF8qUzuuC8DJGygJH3726JnCZX4MYbRB8yFfISqnKUg= @@ -49,29 +91,46 @@ github.com/onsi/gomega v1.10.5/go.mod h1:gza4q3jKQJijlu05nKWRCW/GavJumGt8aNRxWg7 github.com/onsi/gomega v1.11.0 h1:+CqWgvj0OZycCaqclBD1pxKHAU+tOkHmQIWvDHq2aug= github.com/onsi/gomega v1.11.0/go.mod h1:azGKhqFUon9Vuj0YmTfLSmx0FUwqXYSTl5re8lQLTUg= github.com/pelletier/go-toml v1.2.0/go.mod h1:5z9KED0ma1S8pY6P1sdut58dfprrGBbd/94hg7ilaic= +github.com/pkg/errors v0.8.0/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0= github.com/pkg/errors v0.8.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0= github.com/pkg/errors v0.9.1 h1:FEBLx1zS214owpjy7qsBeixbURkuhQAwrK5UwLGTwt4= github.com/pkg/errors v0.9.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0= github.com/pmezard/go-difflib v1.0.0 h1:4DBwDE0NGyQoBHbLQYPwSUPoCMWR5BEzIk/f1lZbAQM= github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4= +github.com/prometheus/client_golang v0.9.1/go.mod h1:7SWBe2y4D6OKWSNQJUaRYU/AaXPKyh/dDVn+NZz0KFw= +github.com/prometheus/client_golang v0.9.3/go.mod h1:/TN21ttK/J9q6uSwhBd54HahCDft0ttaMvbicHlPoso= +github.com/prometheus/client_model v0.0.0-20180712105110-5c3871d89910/go.mod h1:MbSGuTsp3dbXC40dX6PRTWyKYBIrTGTE9sqQNg2J8bo= +github.com/prometheus/client_model v0.0.0-20190129233127-fd36f4220a90/go.mod h1:xMI15A0UPsDsEKsMN9yxemIoYk6Tm2C1GtYGdfGttqA= +github.com/prometheus/common v0.0.0-20181113130724-41aa239b4cce/go.mod h1:daVV7qP5qjZbuso7PdcryaAu0sAZbrN9i7WWcTMWvro= +github.com/prometheus/common v0.4.0/go.mod h1:TNfzLD0ON7rHzMJeJkieUDPYmFC7Snx/y86RQel1bk4= +github.com/prometheus/procfs v0.0.0-20181005140218-185b4288413d/go.mod h1:c3At6R/oaqEKCNdg8wHV1ftS6bRYblBhIjjI8uT2IGk= +github.com/prometheus/procfs v0.0.0-20190507164030-5867b95ac084/go.mod h1:TjEm7ze935MbeOT/UhFTIMYKhuLP4wbCsTZCD3I8kEA= +github.com/prometheus/tsdb v0.7.1/go.mod h1:qhTCs0VvXwvX/y3TZrWD7rabWM+ijKTux40TwIPHuXU= +github.com/rogpeppe/fastuuid v0.0.0-20150106093220-6724a57986af/go.mod h1:XWv6SoW27p1b0cqNHllgS5HIMJraePCO15w5zCzIWYg= github.com/rs/xid v1.2.1/go.mod h1:+uKXf+4Djp6Md1KODXJxgGQPKngRmWyn10oCKFzNHOQ= github.com/rs/zerolog v1.17.2/go.mod h1:9nvC1axdVrAHcu/s9taAVfBuIdTZLVQmKQyvrUjF5+I= github.com/rs/zerolog v1.19.0 h1:hYz4ZVdUgjXTBUmrkrw55j1nHx68LfOKIQk5IYtyScg= github.com/rs/zerolog v1.19.0/go.mod h1:IzD0RJ65iWH0w97OQQebJEvTZYvsCUm9WVLWBQrJRjo= -github.com/russross/blackfriday v1.5.2/go.mod h1:JO/DiYxRf+HjHt06OyowR9PTA263kcR/rfWxYHBV53g= +github.com/russross/blackfriday/v2 v2.0.1/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM= +github.com/shurcooL/sanitized_anchor_name v1.0.0/go.mod h1:1NzhyTcUVG4SuEtjjoZeVRXNmyL/1OwPU0+IJeTBvfc= +github.com/sirupsen/logrus v1.2.0/go.mod h1:LxeOpSwHxABJmUn/MG1IvRgCAasNZTLOkJPxbbu5VWo= +github.com/soheilhy/cmux v0.1.4/go.mod h1:IM3LyeVVIOuxMH7sFAkER9+bJ4dT7Ms6E4xg4kGIyLM= +github.com/spaolacci/murmur3 v0.0.0-20180118202830-f09979ecbc72/go.mod h1:JwIasOWyU6f++ZhiEuf87xNszmSA2myDM2Kzu9HwQUA= github.com/spf13/afero v1.1.2/go.mod h1:j4pytiNVoe2o6bmDsKpLACNPDBIoEAkihy7loJ1B0CQ= github.com/spf13/cast v1.3.0/go.mod h1:Qx5cxh0v+4UWYiBimWS+eyWzqEqokIECu5etghLkUJE= -github.com/spf13/cobra v0.0.5 h1:f0B+LkLX6DtmRH1isoNA9VTtNUK9K8xYd28JNNfOv/s= -github.com/spf13/cobra v0.0.5/go.mod h1:3K3wKZymM7VvHMDS9+Akkh4K60UwM26emMESw8tLCHU= +github.com/spf13/cobra v0.0.7 h1:FfTH+vuMXOas8jmfb5/M7dzEYx7LpcLb7a0LPe34uOU= +github.com/spf13/cobra v0.0.7/go.mod h1:/6GTrnGXV9HjY+aR4k0oJ5tcvakLuG6EuKReYlHNrgE= github.com/spf13/jwalterweatherman v1.0.0/go.mod h1:cQK4TGJAtQXfYWX+Ddv3mKDzgVb68N+wFjFa4jdeBTo= github.com/spf13/pflag v1.0.3 h1:zPAT6CGy6wXeQ7NtTnaTerfKOsV6V6F8agHXFiazDkg= github.com/spf13/pflag v1.0.3/go.mod h1:DYY7MBk1bdzusC3SYhjObp+wFpr4gzcvqqNjLnInEg4= -github.com/spf13/viper v1.3.2/go.mod h1:ZiWeW+zYFKm7srdB9IoDzzZXaJaI5eL9QjNiN/DMA2s= +github.com/spf13/viper v1.4.0/go.mod h1:PTJ7Z/lr49W6bUbkmS1V3by4uWynFiR9p7+dSq/yZzE= github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= +github.com/stretchr/objx v0.1.1/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs= github.com/stretchr/testify v1.7.0 h1:nwc3DEeHmmLAfoZucVR881uASk0Mfjw8xYJ99tb5CcY= github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg= -github.com/ugorji/go/codec v0.0.0-20181204163529-d75b2dcb6bc8/go.mod h1:VFNgLljTbGfSG7qAOspJ7OScBnGdDN/yBr0sguwnwf0= +github.com/tmc/grpc-websocket-proxy v0.0.0-20190109142713-0ad062ec5ee5/go.mod h1:ncp9v5uamzpCO7NfCPTXjqaC+bZgJeR0sMTm6dMHP7U= +github.com/ugorji/go v1.1.4/go.mod h1:uQMGLiO92mf5W77hV/PUCpI3pbzQx3CRekS0kk+RGrc= github.com/wtsi-npg/extendo/v2 v2.3.0 h1:sKlABJFbFtuQB2LOmlBTX4oMbhfAM7HbdreMU81YeRc= github.com/wtsi-npg/extendo/v2 v2.3.0/go.mod h1:K0EdJrVoWbZbJAYiUxiSzaemYXzfKXwO36nNYCM1mHM= github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a h1:LmzJGJXUS8U69eZ08MjwKwii8mos8630pV3aSZRdmc0= @@ -80,27 +139,45 @@ github.com/wtsi-npg/logshim v1.2.0 h1:d9y9XvBRkYB2bUsN07zGJWhGCu13PKoxIxQE97Q9aZ github.com/wtsi-npg/logshim v1.2.0/go.mod h1:1JRn1t/rlx1/oAtv3LOcshcpjDDvHGHCK8p8ua0Hrss= github.com/wtsi-npg/logshim-zerolog v1.2.0 h1:b1HpB1h8OO9XBg/m9r6ycmHRUDNZLnpTmfjWrhmeaT4= github.com/wtsi-npg/logshim-zerolog v1.2.0/go.mod h1:xyahqnZDG2utxSUAQKYjgEdzQz74wfPY7+JttEie41k= +github.com/xiang90/probing v0.0.0-20190116061207-43a291ad63a2/go.mod h1:UETIi67q53MR2AWcXfiuqkDkRtnGDLqkBTpCHuJHxtU= github.com/xordataexchange/crypt v0.0.3-0.20170626215501-b2862e3d0a77/go.mod h1:aYKd//L2LvnjZzWKhF00oedf4jCCReLcmhLdhm1A27Q= github.com/yuin/goldmark v1.2.1/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74= github.com/zenazn/goji v0.9.0/go.mod h1:7S9M489iMyHBNxwZnk9/EHS098H4/F6TATF2mIxtB1Q= -golang.org/x/crypto v0.0.0-20181203042331-505ab145d0a9/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4= +go.etcd.io/bbolt v1.3.2/go.mod h1:IbVyRI1SCnLcuJnV2u8VeU0CEYM7e686BmAb1XKL+uU= +go.uber.org/atomic v1.4.0/go.mod h1:gD2HeocX3+yG+ygLZcrzQJaqmWj9AIm7n08wl/qW/PE= +go.uber.org/multierr v1.1.0/go.mod h1:wR5kodmAFQ0UK8QlbwjlSNy0Z68gJhDJUG5sjR94q/0= +go.uber.org/zap v1.10.0/go.mod h1:vwi/ZaCAaUcBkycHslxD9B2zi4UTXhF60s6SWpuDF0Q= +golang.org/x/crypto v0.0.0-20180904163835-0709b304e793/go.mod h1:6SG95UA2DQfeDnfUPMdvaQW0Q7yPrPDi9nlGo2tz2b4= golang.org/x/crypto v0.0.0-20190308221718-c2843e01d9a2/go.mod h1:djNgcEr1/C05ACkg1iLfiJU5Ep61QUkGW8qpdssI0+w= golang.org/x/crypto v0.0.0-20191011191535-87dc89f01550/go.mod h1:yigFU9vqHzYiE8UmvKecakEJjdnWj3jj499lnFckfCI= golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9 h1:psW17arqaxU48Z5kZ0CQnkZWQJsqcURM6tKiBApRjXI= golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9/go.mod h1:LzIPMQfyMNhhGPhUkYOs5KpL4U8rLKemX1yGLhDgUto= +golang.org/x/lint v0.0.0-20181026193005-c67002cb31c3/go.mod h1:UVdnD1Gm6xHRNCYTkRU2/jEulfH38KcIWyp/GAMgvoE= +golang.org/x/lint v0.0.0-20190313153728-d0100b6bd8b3/go.mod h1:6SW0HCj/g11FgYtHlgUYUwCkIfeOF89ocIRzGO/8vkc= golang.org/x/mod v0.3.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA= +golang.org/x/net v0.0.0-20180826012351-8a410e7b638d/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= golang.org/x/net v0.0.0-20180906233101-161cd47e91fd/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= +golang.org/x/net v0.0.0-20181114220301-adae6a3d119a/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= +golang.org/x/net v0.0.0-20181220203305-927f97764cc3/go.mod h1:mL1N/T3taQHkDXs73rZJwtUhF3w3ftmwwsq0BUmARs4= +golang.org/x/net v0.0.0-20190311183353-d8887717615a/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= golang.org/x/net v0.0.0-20190404232315-eb5bcb51f2a3/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg= +golang.org/x/net v0.0.0-20190522155817-f3200d17e092/go.mod h1:HSz+uSET+XFnRR8LxR5pz3Of3rY3CfYBVs4xY44aLks= golang.org/x/net v0.0.0-20190620200207-3b0461eec859/go.mod h1:z5CRVTTTmAJ677TzLLGU+0bjPO0LkuOLi4/5GtJWs/s= golang.org/x/net v0.0.0-20200520004742-59133d7f0dd7/go.mod h1:qpuaurCH72eLCgpAm/N6yyVIVM9cpaDIP3A8BGJEC5A= golang.org/x/net v0.0.0-20201021035429-f5854403a974/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU= golang.org/x/net v0.0.0-20201202161906-c7110b5ffcbb h1:eBmm0M9fYhWpKZLjQUUKka/LtIxf46G4fxeEz5KJr9U= golang.org/x/net v0.0.0-20201202161906-c7110b5ffcbb/go.mod h1:sp8m0HH+o8qH0wwXwYZr8TS3Oi6o0r6Gce1SSxlDquU= +golang.org/x/oauth2 v0.0.0-20180821212333-d2e6202438be/go.mod h1:N/0e6XlmueqKjAGxoOufVs8QHGRruUQn6yWY3a++T0U= golang.org/x/sync v0.0.0-20180314180146-1d60e4601c6f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= +golang.org/x/sync v0.0.0-20181108010431-42b317875d0f/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= +golang.org/x/sync v0.0.0-20181221193216-37e7f081c4d4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20190423024810-112230192c58/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM= +golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= +golang.org/x/sys v0.0.0-20180905080454-ebe1bf3edb33/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= golang.org/x/sys v0.0.0-20180909124046-d0be0721c37e/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= -golang.org/x/sys v0.0.0-20181205085412-a5c9d58dba9a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= +golang.org/x/sys v0.0.0-20181107165924-66b7b1311ac8/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= +golang.org/x/sys v0.0.0-20181116152217-5ac8a444bdc5/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= golang.org/x/sys v0.0.0-20190215142949-d0b11bdaac8a/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY= golang.org/x/sys v0.0.0-20190412213103-97732733099d/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20190904154756-749cb33beabd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= @@ -113,7 +190,11 @@ golang.org/x/sys v0.0.0-20210112080510-489259a85091/go.mod h1:h1NjWce9XRLGQEsW7w golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= golang.org/x/text v0.3.3 h1:cokOdA+Jmi5PJGXLlLllQSgYigAEfHXJAERHVMaCc2k= golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= +golang.org/x/time v0.0.0-20190308202827-9d24e82272b4/go.mod h1:tRJNPiyCQ0inRvYxbN9jk5I+vvW/OXSQhTDSoE431IQ= +golang.org/x/tools v0.0.0-20180221164845-07fd8470d635/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= +golang.org/x/tools v0.0.0-20190114222345-bf090417da8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= +golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs= golang.org/x/tools v0.0.0-20190828213141-aed303cbaa74/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20201224043029-2b0845dc783e/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= @@ -122,6 +203,10 @@ golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8T golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= golang.org/x/xerrors v0.0.0-20200804184101-5ec99f83aff1 h1:go1bK/D/BFZV2I8cIQd1NKEZ+0owSTG1fDTci4IqFcE= golang.org/x/xerrors v0.0.0-20200804184101-5ec99f83aff1/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= +google.golang.org/appengine v1.1.0/go.mod h1:EbEs0AVv82hx2wNQdGPgUI5lhzA/G0D9YwlJXL52JkM= +google.golang.org/genproto v0.0.0-20180817151627-c66870c02cf8/go.mod h1:JiN7NxoALGmiZfu7CAH4rXhgtRTLTxftemlI0sWmxmc= +google.golang.org/grpc v1.19.0/go.mod h1:mqu4LbDTu4XGKhr4mRzUsmM4RtVoemTSY81AxZiDr8c= +google.golang.org/grpc v1.21.0/go.mod h1:oYelfM1adQP15Ek0mdvEgi9Df8B9CZIaU1084ijfRaM= google.golang.org/protobuf v0.0.0-20200109180630-ec00e32a8dfd/go.mod h1:DFci5gLYBciE7Vtevhsrf46CRTquxDuWsQurQQe4oz8= google.golang.org/protobuf v0.0.0-20200221191635-4d8936d0db64/go.mod h1:kwYJMbMJ01Woi6D6+Kah6886xMZcty6N08ah7+eCXa0= google.golang.org/protobuf v0.0.0-20200228230310-ab0ca4ff8a60/go.mod h1:cfTl7dwQJ+fmap5saPgwCLgHXTUD7jkjRqWcaiX5VyM= @@ -129,11 +214,16 @@ google.golang.org/protobuf v1.20.1-0.20200309200217-e05f789c0967/go.mod h1:A+miE google.golang.org/protobuf v1.21.0/go.mod h1:47Nbq4nVaFHyn7ilMalzfO3qCViNmqZ2kzikPIcrTAo= google.golang.org/protobuf v1.23.0 h1:4MY060fB1DLGMB/7MBTLnwQUY6+F09GEiz6SsrNqyzM= google.golang.org/protobuf v1.23.0/go.mod h1:EGpADcykh3NcUnDUJcl1+ZksZNG86OlYog2l/sGQquU= -gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405 h1:yhCVgyC4o1eVCa2tZl7eS0r+SDo693bJlVdllGtEeKM= +gopkg.in/alecthomas/kingpin.v2 v2.2.6/go.mod h1:FMv+mEhP44yOT+4EoQTLFTRgOQ1FBLkstjWtayDeSgw= gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= +gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127 h1:qIbj1fsPNlZgppZ+VLlY7N33q108Sa+fhmuc+sWQYwY= +gopkg.in/check.v1 v1.0.0-20180628173108-788fd7840127/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0= gopkg.in/fsnotify.v1 v1.4.7/go.mod h1:Tz8NjZHkW78fSQdbUxIjBTcgA1z1m8ZHf0WmKUhAMys= +gopkg.in/resty.v1 v1.12.0/go.mod h1:mDo4pnntr5jdWRML875a/NmxYqAlA73dVijT2AXvQQo= gopkg.in/tomb.v1 v1.0.0-20141024135613-dd632973f1e7 h1:uRGJdciOHaEIrze2W8Q3AKkepLTh2hOroT7a+7czfdQ= gopkg.in/tomb.v1 v1.0.0-20141024135613-dd632973f1e7/go.mod h1:dt/ZhP58zS4L8KSrWDmTeBkI65Dw0HsyUHuEVlX15mw= +gopkg.in/yaml.v2 v2.0.0-20170812160011-eb3733d160e7/go.mod h1:JAlM8MvJe8wmxCU4Bli9HhUf9+ttbYbLASfIpnQbh74= +gopkg.in/yaml.v2 v2.2.1/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v2 v2.2.2/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v2 v2.2.4/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= gopkg.in/yaml.v2 v2.3.0/go.mod h1:hI93XBmqTisBFMUTm0b8Fm+jr3Dg1NNxqwp+5A1VGuI= @@ -141,3 +231,4 @@ gopkg.in/yaml.v2 v2.4.0 h1:D8xgwECY7CYvx+Y2n4sBz93Jn9JRvxdiyyo8CTfuKaY= gopkg.in/yaml.v2 v2.4.0/go.mod h1:RDklbk79AGWmwhnvt/jBztapEOGDOx6ZbXqjP6csGnQ= gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c h1:dUUwHk2QECo/6vqA44rthZ8ie2QXMNeKRTHCNY2nXvo= gopkg.in/yaml.v3 v3.0.0-20200313102051-9f266ea9e77c/go.mod h1:K4uyk7z7BCEPqu6E+C64Yfv1cQ7kz7rIZviUmN+EgEM= +honnef.co/go/tools v0.0.0-20190102054323-c2f93a96b099/go.mod h1:rf3lG4BRIbNafJWhAfAdb/ePZxsR/4RtNHQocxwk9r4= From 09dbc68dedcd843cc906ef986ef3f46693ee7c3c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 19 Mar 2021 12:05:56 +0000 Subject: [PATCH 10/18] Bump github.com/rs/zerolog from 1.19.0 to 1.20.0 Bumps [github.com/rs/zerolog](https://github.com/rs/zerolog) from 1.19.0 to 1.20.0. - [Release notes](https://github.com/rs/zerolog/releases) - [Commits](https://github.com/rs/zerolog/compare/v1.19.0...v1.20.0) Signed-off-by: dependabot[bot] --- go.mod | 2 +- go.sum | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/go.mod b/go.mod index 64fa7a4..379719b 100644 --- a/go.mod +++ b/go.mod @@ -8,7 +8,7 @@ require ( github.com/onsi/ginkgo v1.15.1 github.com/onsi/gomega v1.11.0 github.com/pkg/errors v0.9.1 - github.com/rs/zerolog v1.19.0 + github.com/rs/zerolog v1.20.0 github.com/spf13/cobra v0.0.7 github.com/stretchr/testify v1.7.0 github.com/wtsi-npg/extendo/v2 v2.3.0 diff --git a/go.sum b/go.sum index bceaa20..58ed3b6 100644 --- a/go.sum +++ b/go.sum @@ -109,8 +109,9 @@ github.com/prometheus/tsdb v0.7.1/go.mod h1:qhTCs0VvXwvX/y3TZrWD7rabWM+ijKTux40T github.com/rogpeppe/fastuuid v0.0.0-20150106093220-6724a57986af/go.mod h1:XWv6SoW27p1b0cqNHllgS5HIMJraePCO15w5zCzIWYg= github.com/rs/xid v1.2.1/go.mod h1:+uKXf+4Djp6Md1KODXJxgGQPKngRmWyn10oCKFzNHOQ= github.com/rs/zerolog v1.17.2/go.mod h1:9nvC1axdVrAHcu/s9taAVfBuIdTZLVQmKQyvrUjF5+I= -github.com/rs/zerolog v1.19.0 h1:hYz4ZVdUgjXTBUmrkrw55j1nHx68LfOKIQk5IYtyScg= github.com/rs/zerolog v1.19.0/go.mod h1:IzD0RJ65iWH0w97OQQebJEvTZYvsCUm9WVLWBQrJRjo= +github.com/rs/zerolog v1.20.0 h1:38k9hgtUBdxFwE34yS8rTHmHBa4eN16E4DJlv177LNs= +github.com/rs/zerolog v1.20.0/go.mod h1:IzD0RJ65iWH0w97OQQebJEvTZYvsCUm9WVLWBQrJRjo= github.com/russross/blackfriday/v2 v2.0.1/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM= github.com/shurcooL/sanitized_anchor_name v1.0.0/go.mod h1:1NzhyTcUVG4SuEtjjoZeVRXNmyL/1OwPU0+IJeTBvfc= github.com/sirupsen/logrus v1.2.0/go.mod h1:LxeOpSwHxABJmUn/MG1IvRgCAasNZTLOkJPxbbu5VWo= From f0a6f8010dd6dbe57d755ac06242602b84749c42 Mon Sep 17 00:00:00 2001 From: Keith James <47220353+kjsanger@users.noreply.github.com> Date: Wed, 24 Mar 2021 09:15:36 +0000 Subject: [PATCH 11/18] Update README.md Co-authored-by: dkj --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index eb5a7ad..23ef714 100644 --- a/README.md +++ b/README.md @@ -20,7 +20,7 @@ disks filling. #### Compressing files -Some versions of MinKNOW to do not compress fastq files and no version +Some versions of MinKNOW do not compress fastq files and no version compresses the large sequencing_summary.txt files. `valet` compresses some files with gzip. From 64207e6f60ce403d3e2a38bcf3e0f8113068b24a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 29 Mar 2021 07:32:17 +0000 Subject: [PATCH 12/18] Bump github.com/rs/zerolog from 1.20.0 to 1.21.0 Bumps [github.com/rs/zerolog](https://github.com/rs/zerolog) from 1.20.0 to 1.21.0. - [Release notes](https://github.com/rs/zerolog/releases) - [Commits](https://github.com/rs/zerolog/compare/v1.20.0...v1.21.0) Signed-off-by: dependabot[bot] --- go.mod | 2 +- go.sum | 8 +++++--- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/go.mod b/go.mod index 379719b..790ae34 100644 --- a/go.mod +++ b/go.mod @@ -8,7 +8,7 @@ require ( github.com/onsi/ginkgo v1.15.1 github.com/onsi/gomega v1.11.0 github.com/pkg/errors v0.9.1 - github.com/rs/zerolog v1.20.0 + github.com/rs/zerolog v1.21.0 github.com/spf13/cobra v0.0.7 github.com/stretchr/testify v1.7.0 github.com/wtsi-npg/extendo/v2 v2.3.0 diff --git a/go.sum b/go.sum index 58ed3b6..c397727 100644 --- a/go.sum +++ b/go.sum @@ -110,8 +110,8 @@ github.com/rogpeppe/fastuuid v0.0.0-20150106093220-6724a57986af/go.mod h1:XWv6So github.com/rs/xid v1.2.1/go.mod h1:+uKXf+4Djp6Md1KODXJxgGQPKngRmWyn10oCKFzNHOQ= github.com/rs/zerolog v1.17.2/go.mod h1:9nvC1axdVrAHcu/s9taAVfBuIdTZLVQmKQyvrUjF5+I= github.com/rs/zerolog v1.19.0/go.mod h1:IzD0RJ65iWH0w97OQQebJEvTZYvsCUm9WVLWBQrJRjo= -github.com/rs/zerolog v1.20.0 h1:38k9hgtUBdxFwE34yS8rTHmHBa4eN16E4DJlv177LNs= -github.com/rs/zerolog v1.20.0/go.mod h1:IzD0RJ65iWH0w97OQQebJEvTZYvsCUm9WVLWBQrJRjo= +github.com/rs/zerolog v1.21.0 h1:Q3vdXlfLNT+OftyBHsU0Y445MD+8m8axjKgf2si0QcM= +github.com/rs/zerolog v1.21.0/go.mod h1:ZPhntP/xmq1nnND05hhpAh2QMhSsA4UN3MGZ6O2J3hM= github.com/russross/blackfriday/v2 v2.0.1/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM= github.com/shurcooL/sanitized_anchor_name v1.0.0/go.mod h1:1NzhyTcUVG4SuEtjjoZeVRXNmyL/1OwPU0+IJeTBvfc= github.com/sirupsen/logrus v1.2.0/go.mod h1:LxeOpSwHxABJmUn/MG1IvRgCAasNZTLOkJPxbbu5VWo= @@ -186,8 +186,9 @@ golang.org/x/sys v0.0.0-20191005200804-aed5e4c7ecf9/go.mod h1:h1NjWce9XRLGQEsW7w golang.org/x/sys v0.0.0-20191120155948-bd437916bb0e/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20200323222414-85ca7c5b95cd/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/sys v0.0.0-20200930185726-fdedc70b468f/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= -golang.org/x/sys v0.0.0-20210112080510-489259a85091 h1:DMyOG0U+gKfu8JZzg2UQe9MeaC1X+xQWlAKcRnjxjCw= golang.org/x/sys v0.0.0-20210112080510-489259a85091/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= +golang.org/x/sys v0.0.0-20210119212857-b64e53b001e4 h1:myAQVi0cGEoqQVR5POX+8RR2mrocKqNN1hmeMqhX27k= +golang.org/x/sys v0.0.0-20210119212857-b64e53b001e4/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs= golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ= golang.org/x/text v0.3.3 h1:cokOdA+Jmi5PJGXLlLllQSgYigAEfHXJAERHVMaCc2k= golang.org/x/text v0.3.3/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ= @@ -199,6 +200,7 @@ golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3 golang.org/x/tools v0.0.0-20190828213141-aed303cbaa74/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20201224043029-2b0845dc783e/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= +golang.org/x/tools v0.1.0/go.mod h1:xkSsbof2nBLbhDlRMhhhyNLN/zl3eTqcnHD5viDpcZ0= golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= golang.org/x/xerrors v0.0.0-20191011141410-1b5146add898/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= golang.org/x/xerrors v0.0.0-20191204190536-9bdfabe68543/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0= From 75662f90424dcffb927dc68321afe82556a2f889 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 5 Apr 2021 07:54:04 +0000 Subject: [PATCH 13/18] Bump github.com/onsi/ginkgo from 1.15.1 to 1.16.0 Bumps [github.com/onsi/ginkgo](https://github.com/onsi/ginkgo) from 1.15.1 to 1.16.0. - [Release notes](https://github.com/onsi/ginkgo/releases) - [Changelog](https://github.com/onsi/ginkgo/blob/master/CHANGELOG.md) - [Commits](https://github.com/onsi/ginkgo/compare/v1.15.1...v1.16.0) Signed-off-by: dependabot[bot] --- go.mod | 2 +- go.sum | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/go.mod b/go.mod index 790ae34..1087b4b 100644 --- a/go.mod +++ b/go.mod @@ -5,7 +5,7 @@ go 1.14 require ( github.com/klauspost/compress v1.9.1 // indirect github.com/klauspost/pgzip v1.2.5 - github.com/onsi/ginkgo v1.15.1 + github.com/onsi/ginkgo v1.16.0 github.com/onsi/gomega v1.11.0 github.com/pkg/errors v0.9.1 github.com/rs/zerolog v1.21.0 diff --git a/go.sum b/go.sum index c397727..712d4a3 100644 --- a/go.sum +++ b/go.sum @@ -27,6 +27,7 @@ github.com/go-kit/kit v0.8.0/go.mod h1:xBxKIO96dXMWWy0MnWVtmwkA9/13aqxPnvrjFYMA2 github.com/go-logfmt/logfmt v0.3.0/go.mod h1:Qt1PoO58o5twSAckw1HlFXLmHsOX5/0LbT9GBnD5lWE= github.com/go-logfmt/logfmt v0.4.0/go.mod h1:3RMwSq7FuexP4Kalkev3ejPJsZTpXXBr9+V4qmtdjCk= github.com/go-stack/stack v1.8.0/go.mod h1:v0f6uXyyMGvRgIKkXu+yp6POWl0qKG85gN/melR3HDY= +github.com/go-task/slim-sprig v0.0.0-20210107165309-348f09dbbbc0/go.mod h1:fyg7847qk6SyHyPtNmDHnmrv/HOrqktSC+C9fM+CJOE= github.com/gogo/protobuf v1.1.1/go.mod h1:r8qH/GZQm5c6nD/R0oafs1akxWv10x8SbQlK7atdtwQ= github.com/gogo/protobuf v1.2.1/go.mod h1:hp+jE20tsWTFYpLwKvXlhS1hjn+gTNwPg2I6zVXpSg4= github.com/golang/glog v0.0.0-20160126235308-23def4e6c14b/go.mod h1:SBH7ygxi8pfUlaOkMMuAQtPIUF8ecWP5IEl/CR7VP2Q= @@ -83,8 +84,8 @@ github.com/oklog/ulid v1.3.1/go.mod h1:CirwcVhetQ6Lv90oh/F+FBtV6XMibvdAFo93nm5qn github.com/onsi/ginkgo v1.6.0/go.mod h1:lLunBs/Ym6LB5Z9jYTR76FiuTmxDTDusOGeTQH+WWjE= github.com/onsi/ginkgo v1.12.1/go.mod h1:zj2OWP4+oCPe1qIXoGWkgMRwljMUYCdkwsT2108oapk= github.com/onsi/ginkgo v1.15.0/go.mod h1:hF8qUzuuC8DJGygJH3726JnCZX4MYbRB8yFfISqnKUg= -github.com/onsi/ginkgo v1.15.1 h1:DsXNrKujDlkMS9Rsxmd+Fg7S6Kc5lhE+qX8tY6laOxc= -github.com/onsi/ginkgo v1.15.1/go.mod h1:Dd6YFfwBW84ETqqtL0CPyPXillHgY6XhQH3uuCCTr/o= +github.com/onsi/ginkgo v1.16.0 h1:NBrNLB37exjJLxXtFOktx6CISBdS1aF8+7MwKlTV8U4= +github.com/onsi/ginkgo v1.16.0/go.mod h1:CObGmKUOKaSC0RjmoAK7tKyn4Azo5P2IWuoMnvwxz1E= github.com/onsi/gomega v1.7.1/go.mod h1:XdKZgCCFLUoM/7CFJVPcG8C1xQ1AJ0vpAezJrB7JYyY= github.com/onsi/gomega v1.10.1/go.mod h1:iN09h71vgCQne3DLsj+A5owkum+a2tYe+TOCB1ybHNo= github.com/onsi/gomega v1.10.5/go.mod h1:gza4q3jKQJijlu05nKWRCW/GavJumGt8aNRxWg7mt48= @@ -128,6 +129,7 @@ github.com/spf13/viper v1.4.0/go.mod h1:PTJ7Z/lr49W6bUbkmS1V3by4uWynFiR9p7+dSq/y github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= github.com/stretchr/objx v0.1.1/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME= github.com/stretchr/testify v1.2.2/go.mod h1:a8OnRcib4nhh0OaRAV+Yts87kKdq0PP7pXfy6kDkUVs= +github.com/stretchr/testify v1.5.1/go.mod h1:5W2xD1RspED5o8YsWQXVCued0rvSQ+mT+I5cxcmMvtA= github.com/stretchr/testify v1.7.0 h1:nwc3DEeHmmLAfoZucVR881uASk0Mfjw8xYJ99tb5CcY= github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg= github.com/tmc/grpc-websocket-proxy v0.0.0-20190109142713-0ad062ec5ee5/go.mod h1:ncp9v5uamzpCO7NfCPTXjqaC+bZgJeR0sMTm6dMHP7U= From 333ac4d4407153a7404bb3ec6a4ca5610176388f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 12 Apr 2021 07:54:16 +0000 Subject: [PATCH 14/18] Bump github.com/onsi/ginkgo from 1.16.0 to 1.16.1 Bumps [github.com/onsi/ginkgo](https://github.com/onsi/ginkgo) from 1.16.0 to 1.16.1. - [Release notes](https://github.com/onsi/ginkgo/releases) - [Changelog](https://github.com/onsi/ginkgo/blob/master/CHANGELOG.md) - [Commits](https://github.com/onsi/ginkgo/compare/v1.16.0...v1.16.1) Signed-off-by: dependabot[bot] --- go.mod | 2 +- go.sum | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/go.mod b/go.mod index 1087b4b..1ff2ab4 100644 --- a/go.mod +++ b/go.mod @@ -5,7 +5,7 @@ go 1.14 require ( github.com/klauspost/compress v1.9.1 // indirect github.com/klauspost/pgzip v1.2.5 - github.com/onsi/ginkgo v1.16.0 + github.com/onsi/ginkgo v1.16.1 github.com/onsi/gomega v1.11.0 github.com/pkg/errors v0.9.1 github.com/rs/zerolog v1.21.0 diff --git a/go.sum b/go.sum index 712d4a3..6f4ae8c 100644 --- a/go.sum +++ b/go.sum @@ -84,8 +84,8 @@ github.com/oklog/ulid v1.3.1/go.mod h1:CirwcVhetQ6Lv90oh/F+FBtV6XMibvdAFo93nm5qn github.com/onsi/ginkgo v1.6.0/go.mod h1:lLunBs/Ym6LB5Z9jYTR76FiuTmxDTDusOGeTQH+WWjE= github.com/onsi/ginkgo v1.12.1/go.mod h1:zj2OWP4+oCPe1qIXoGWkgMRwljMUYCdkwsT2108oapk= github.com/onsi/ginkgo v1.15.0/go.mod h1:hF8qUzuuC8DJGygJH3726JnCZX4MYbRB8yFfISqnKUg= -github.com/onsi/ginkgo v1.16.0 h1:NBrNLB37exjJLxXtFOktx6CISBdS1aF8+7MwKlTV8U4= -github.com/onsi/ginkgo v1.16.0/go.mod h1:CObGmKUOKaSC0RjmoAK7tKyn4Azo5P2IWuoMnvwxz1E= +github.com/onsi/ginkgo v1.16.1 h1:foqVmeWDD6yYpK+Yz3fHyNIxFYNxswxqNFjSKe+vI54= +github.com/onsi/ginkgo v1.16.1/go.mod h1:CObGmKUOKaSC0RjmoAK7tKyn4Azo5P2IWuoMnvwxz1E= github.com/onsi/gomega v1.7.1/go.mod h1:XdKZgCCFLUoM/7CFJVPcG8C1xQ1AJ0vpAezJrB7JYyY= github.com/onsi/gomega v1.10.1/go.mod h1:iN09h71vgCQne3DLsj+A5owkum+a2tYe+TOCB1ybHNo= github.com/onsi/gomega v1.10.5/go.mod h1:gza4q3jKQJijlu05nKWRCW/GavJumGt8aNRxWg7mt48= From 319f65dc1e142b31885a66256a7c0c585194b7cc Mon Sep 17 00:00:00 2001 From: Keith James Date: Mon, 12 Apr 2021 17:53:36 +0100 Subject: [PATCH 15/18] Add Github Actions test workflow --- .github/dependabot.yml | 2 +- .github/workflows/run-tests.yml | 105 ++++++++++++++++++++++++++++++++ 2 files changed, 106 insertions(+), 1 deletion(-) create mode 100644 .github/workflows/run-tests.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml index 54fb6e6..f1b219b 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -1,5 +1,5 @@ version: 2 -updates: +updates: - package-ecosystem: "gomod" directory: "/" schedule: diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml new file mode 100644 index 0000000..55d123d --- /dev/null +++ b/.github/workflows/run-tests.yml @@ -0,0 +1,105 @@ +name: "Unit tests" + +on: [push, pull_request] + +jobs: + build: + runs-on: ubuntu-18.04 + continue-on-error: ${{ matrix.experimental }} # Experimental builds may fail + + defaults: + run: + shell: bash -l -e -o pipefail {0} + + env: + WSI_CONDA_CHANNEL: "https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic" + CONDA_TEST_ENVIRONMENT: "testenv" + + strategy: + matrix: + go: [ "1.16" ] + baton: [ "2.1.0" ] + experimental: [false] + include: + - irods: "4.2.7" + server_image: "wsinpg/ub-16.04-irods-4.2.7:latest" + experimental: false + - irods: "4.2.8" + server_image: "wsinpg/ub-18.04-irods-4.2.8:latest" + experimental: true + + services: + irods: + image: ${{ matrix.server_image }} + ports: + - 1247:1247 + + steps: + - uses: actions/checkout@v2 + + - name: "Set up Go ${{ matrix.go }}" + uses: actions/setup-go@v2 + with: + go-version: ${{ matrix.go }} + + - name: "Initialize Miniconda" + run: | + echo 'source $CONDA/etc/profile.d/conda.sh' >> "$HOME/.bash_profile" + + - name: "Configure Miniconda" + run: | + conda config --prepend pkgs_dirs "$HOME/conda/pkgs" + conda config --prepend envs_dirs "$HOME/conda/envs" + + conda config --set auto_update_conda False + conda config --prepend channels "$WSI_CONDA_CHANNEL" + conda config --append channels conda-forge + conda info + + - name: "Install iRODS clients" + run: | + conda create -y -n "$CONDA_TEST_ENVIRONMENT" + conda install -y -n "$CONDA_TEST_ENVIRONMENT" "irods-icommands ==${{ matrix.irods }}" + conda install -y -n "$CONDA_TEST_ENVIRONMENT" "baton ==${{ matrix.baton }}" + + - name: "Configure iRODS clients" + run: | + conda activate "$CONDA_TEST_ENVIRONMENT" + + mkdir -p "$HOME/.irods" + cat <<'EOF' > "$HOME/.irods/irods_environment.json" + { + "irods_host": "localhost", + "irods_port": 1247, + "irods_user_name": "irods", + "irods_zone_name": "testZone", + "irods_home": "/testZone/home/irods", + "irods_default_resource": "testResc" + } + EOF + + echo "irods" | script -q -c "iinit" /dev/null + ienv + ils + + baton-do --version + + - name: "Cache Go modules" + uses: actions/cache@v2 + with: + path: | + "$HOME/go/pkg/mod" + "$HOME/.cache/go-build" + key: ${{ runner.os }}-go-${{ hashFiles('**/go.sum') }} + restore-keys: | + ${{ runner.os }}-go- + + - name: "Install test runner" + run: | + go get github.com/onsi/ginkgo/ginkgo + go get github.com/onsi/gomega/... + + - name: "Run tests" + run: | + conda activate "$CONDA_TEST_ENVIRONMENT" + make test From 271c576916ed4141b1ef97cd753dc25cbc1b2e97 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 13 Apr 2021 09:55:26 +0100 Subject: [PATCH 16/18] Replace kjsanger with wtsi-npg in URLs --- Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 1348e3d..cffbdf4 100644 --- a/Makefile +++ b/Makefile @@ -1,5 +1,5 @@ VERSION := $(shell git describe --always --tags --dirty) -ldflags := "-X github.com/kjsanger/valet/valet.Version=${VERSION}" +ldflags := "-X github.com/wtsi-npg/valet/valet.Version=${VERSION}" build_path = "build/valet-${VERSION}" .PHONY: build coverage dist install lint test check clean @@ -11,7 +11,7 @@ install: build: mkdir -p ${build_path} - go build -v -ldflags ${ldflags} -o ${build_path}/valet github.com/kjsanger/valet + go build -v -ldflags ${ldflags} -o ${build_path}/valet github.com/wtsi-npg/valet lint: golangci-lint run ./... From 0d0fdf599c8522668f97cf623ce3d1808f4b35d0 Mon Sep 17 00:00:00 2001 From: Keith James Date: Tue, 13 Apr 2021 11:08:19 +0100 Subject: [PATCH 17/18] Update README and CHANGELOG --- CHANGELOG.md | 10 +++++----- README.md | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 303098e..617d242 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [Unreleased] - [![Build Status](https://travis-ci.org/kjsanger/valet.svg?branch=devel)](https://travis-ci.org/kjsanger/valet) +## [Unreleased] - [![Unit tests](https://github.com/wtsi-npg/valet/actions/workflows/run-tests.yml/badge.svg)](https://github.com/wtsi-npg/valet/actions/workflows/run-tests.yml) ## [1.4.0] - 2020-09-14 @@ -16,7 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed -- Bump github.com/kjsanger/extendo from 2.1.0 to 2.2.0 +- Bump github.com/wtsi-npg/extendo from 2.1.0 to 2.2.0 ## [1.3.0] - 2020-06-02 @@ -26,7 +26,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed -- Bump github.com/kjsanger/extendo from 2.0.0 to 2.1.0 +- Bump github.com/wtsi-npg//extendo from 2.0.0 to 2.1.0 - Bump github.com/stretchr/testify from 1.5.1 to 1.6.0 - Bump github.com/onsi/ginkgo from 1.12.0 to 1.12.2 @@ -43,7 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Improve verbose level logging for consistency and information. - Add to default paths to ignore in the data root. -- Bump github.com/kjsanger/extendo from 1.1.0 to 2.0.0 +- Bump github.com/wtsi-npg//extendo from 1.1.0 to 2.0.0 - Bump github.com/onsi/ginkgo from 1.10.3 to 1.12.0 - Bump github.com/onsi/gomega from 1.7.1 to 1.9.0 @@ -68,7 +68,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## Changed -- Bump github.com/kjsanger/extendo from 1.0.0 to 1.1.0 +- Bump github.com/wtsi-npg//extendo from 1.0.0 to 1.1.0 - Bump github.com/onsi/gomega from 1.5.0 to 1.7.1 - Bump github.com/onsi/ginkgo from 1.8.0 to 1.10.3 - Bump github.com/rs/zerolog from 1.14.3 to 1.17.2 diff --git a/README.md b/README.md index 23ef714..c97686c 100644 --- a/README.md +++ b/README.md @@ -125,7 +125,7 @@ function, or another) from operating on a particular file concurrently. #### Status -[![Build Status](https://travis-ci.com/wtsi-npg/valet.svg?branch=devel)](https://travis-ci.com/wtsi-npg/valet) +[![Unit tests](https://github.com/wtsi-npg/valet/actions/workflows/run-tests.yml/badge.svg)](https://github.com/wtsi-npg/valet/actions/workflows/run-tests.yml) #### Dependencies: From fc43fd27768890dad2a1f012070f61042429fca8 Mon Sep 17 00:00:00 2001 From: Keith James Date: Thu, 15 Apr 2021 15:24:04 +0100 Subject: [PATCH 18/18] Update dependencies and changelog --- CHANGELOG.md | 33 ++++++++++++++++++++++++++++++--- go.mod | 8 ++++---- go.sum | 16 ++++++---------- 3 files changed, 40 insertions(+), 17 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 617d242..2cf57d4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,33 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## [Unreleased] - [![Unit tests](https://github.com/wtsi-npg/valet/actions/workflows/run-tests.yml/badge.svg)](https://github.com/wtsi-npg/valet/actions/workflows/run-tests.yml) +### Added + +- Add Github Actions test workflow +- Improve recognition of files to be processed and archived +- Add support for TSV files. +- Add support for compressing CSV files. +- Add new all ONT-specific paths to the exclusion list. +- Add the /data/laboratory WSI-specific path to the exclusion list. +- Add iRODS 4.2.8 support + +### Removed + +- Remove iRODS 4.1.12 support + +### Changed + +- Relocate repository from github.com/kjsanger to github.com/wtsi-npg + +- Bump github.com/wtsi-npg/extendo/v2 from 2.2.0 to 2.4.0 +- Bump github.com/wtsi-npg/logshim from to 1.1.0 to 1.3.0 +- Bump github.com/wtsi-npg/logshim-zerolog from 1.1.0 to 1.3.0 +- Bump github.com/klauspost/pgzip from 1.2.1 to 1.2.5 +- Bump github.com/onsi/ginkgo from 1.12.3 to 1.16.1 +- Bump github.com/onsi/gomega from 1.10.1 to 1.11.0 +- Bump github.com/rs/zerolog from 1.19.1 to 1.21.0 +- Bump github.com/spf13/cobra from 0.0.5 to 0.0.7 + ## [1.4.0] - 2020-09-14 ### Added @@ -26,7 +53,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Changed -- Bump github.com/wtsi-npg//extendo from 2.0.0 to 2.1.0 +- Bump github.com/wtsi-npg/extendo from 2.0.0 to 2.1.0 - Bump github.com/stretchr/testify from 1.5.1 to 1.6.0 - Bump github.com/onsi/ginkgo from 1.12.0 to 1.12.2 @@ -43,7 +70,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Improve verbose level logging for consistency and information. - Add to default paths to ignore in the data root. -- Bump github.com/wtsi-npg//extendo from 1.1.0 to 2.0.0 +- Bump github.com/wtsi-npg/extendo from 1.1.0 to 2.0.0 - Bump github.com/onsi/ginkgo from 1.10.3 to 1.12.0 - Bump github.com/onsi/gomega from 1.7.1 to 1.9.0 @@ -68,7 +95,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## Changed -- Bump github.com/wtsi-npg//extendo from 1.0.0 to 1.1.0 +- Bump github.com/wtsi-npg/extendo from 1.0.0 to 1.1.0 - Bump github.com/onsi/gomega from 1.5.0 to 1.7.1 - Bump github.com/onsi/ginkgo from 1.8.0 to 1.10.3 - Bump github.com/rs/zerolog from 1.14.3 to 1.17.2 diff --git a/go.mod b/go.mod index 1ff2ab4..c29159e 100644 --- a/go.mod +++ b/go.mod @@ -1,6 +1,6 @@ module github.com/wtsi-npg/valet -go 1.14 +go 1.16 require ( github.com/klauspost/compress v1.9.1 // indirect @@ -11,10 +11,10 @@ require ( github.com/rs/zerolog v1.21.0 github.com/spf13/cobra v0.0.7 github.com/stretchr/testify v1.7.0 - github.com/wtsi-npg/extendo/v2 v2.3.0 + github.com/wtsi-npg/extendo/v2 v2.4.0 github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a - github.com/wtsi-npg/logshim v1.2.0 - github.com/wtsi-npg/logshim-zerolog v1.2.0 + github.com/wtsi-npg/logshim v1.3.0 + github.com/wtsi-npg/logshim-zerolog v1.3.0 golang.org/x/crypto v0.0.0-20200622213623-75b288015ac9 ) diff --git a/go.sum b/go.sum index 6f4ae8c..84c4e00 100644 --- a/go.sum +++ b/go.sum @@ -83,12 +83,10 @@ github.com/nxadm/tail v1.4.8/go.mod h1:+ncqLTQzXmGhMZNUePPaPqPvBxHAIsmXswZKocGu+ github.com/oklog/ulid v1.3.1/go.mod h1:CirwcVhetQ6Lv90oh/F+FBtV6XMibvdAFo93nm5qn4U= github.com/onsi/ginkgo v1.6.0/go.mod h1:lLunBs/Ym6LB5Z9jYTR76FiuTmxDTDusOGeTQH+WWjE= github.com/onsi/ginkgo v1.12.1/go.mod h1:zj2OWP4+oCPe1qIXoGWkgMRwljMUYCdkwsT2108oapk= -github.com/onsi/ginkgo v1.15.0/go.mod h1:hF8qUzuuC8DJGygJH3726JnCZX4MYbRB8yFfISqnKUg= github.com/onsi/ginkgo v1.16.1 h1:foqVmeWDD6yYpK+Yz3fHyNIxFYNxswxqNFjSKe+vI54= github.com/onsi/ginkgo v1.16.1/go.mod h1:CObGmKUOKaSC0RjmoAK7tKyn4Azo5P2IWuoMnvwxz1E= github.com/onsi/gomega v1.7.1/go.mod h1:XdKZgCCFLUoM/7CFJVPcG8C1xQ1AJ0vpAezJrB7JYyY= github.com/onsi/gomega v1.10.1/go.mod h1:iN09h71vgCQne3DLsj+A5owkum+a2tYe+TOCB1ybHNo= -github.com/onsi/gomega v1.10.5/go.mod h1:gza4q3jKQJijlu05nKWRCW/GavJumGt8aNRxWg7mt48= github.com/onsi/gomega v1.11.0 h1:+CqWgvj0OZycCaqclBD1pxKHAU+tOkHmQIWvDHq2aug= github.com/onsi/gomega v1.11.0/go.mod h1:azGKhqFUon9Vuj0YmTfLSmx0FUwqXYSTl5re8lQLTUg= github.com/pelletier/go-toml v1.2.0/go.mod h1:5z9KED0ma1S8pY6P1sdut58dfprrGBbd/94hg7ilaic= @@ -109,8 +107,6 @@ github.com/prometheus/procfs v0.0.0-20190507164030-5867b95ac084/go.mod h1:TjEm7z github.com/prometheus/tsdb v0.7.1/go.mod h1:qhTCs0VvXwvX/y3TZrWD7rabWM+ijKTux40TwIPHuXU= github.com/rogpeppe/fastuuid v0.0.0-20150106093220-6724a57986af/go.mod h1:XWv6SoW27p1b0cqNHllgS5HIMJraePCO15w5zCzIWYg= github.com/rs/xid v1.2.1/go.mod h1:+uKXf+4Djp6Md1KODXJxgGQPKngRmWyn10oCKFzNHOQ= -github.com/rs/zerolog v1.17.2/go.mod h1:9nvC1axdVrAHcu/s9taAVfBuIdTZLVQmKQyvrUjF5+I= -github.com/rs/zerolog v1.19.0/go.mod h1:IzD0RJ65iWH0w97OQQebJEvTZYvsCUm9WVLWBQrJRjo= github.com/rs/zerolog v1.21.0 h1:Q3vdXlfLNT+OftyBHsU0Y445MD+8m8axjKgf2si0QcM= github.com/rs/zerolog v1.21.0/go.mod h1:ZPhntP/xmq1nnND05hhpAh2QMhSsA4UN3MGZ6O2J3hM= github.com/russross/blackfriday/v2 v2.0.1/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM= @@ -134,18 +130,19 @@ github.com/stretchr/testify v1.7.0 h1:nwc3DEeHmmLAfoZucVR881uASk0Mfjw8xYJ99tb5Cc github.com/stretchr/testify v1.7.0/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg= github.com/tmc/grpc-websocket-proxy v0.0.0-20190109142713-0ad062ec5ee5/go.mod h1:ncp9v5uamzpCO7NfCPTXjqaC+bZgJeR0sMTm6dMHP7U= github.com/ugorji/go v1.1.4/go.mod h1:uQMGLiO92mf5W77hV/PUCpI3pbzQx3CRekS0kk+RGrc= -github.com/wtsi-npg/extendo/v2 v2.3.0 h1:sKlABJFbFtuQB2LOmlBTX4oMbhfAM7HbdreMU81YeRc= -github.com/wtsi-npg/extendo/v2 v2.3.0/go.mod h1:K0EdJrVoWbZbJAYiUxiSzaemYXzfKXwO36nNYCM1mHM= +github.com/wtsi-npg/extendo/v2 v2.4.0 h1:rbBbVklHGoobwQiovcfs1d7znaniBVlempgBAL0uEUI= +github.com/wtsi-npg/extendo/v2 v2.4.0/go.mod h1:/mi30w9nekV6fYUGb1T7zvX3Kspy9HQKh2IzSQIJIOw= github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a h1:LmzJGJXUS8U69eZ08MjwKwii8mos8630pV3aSZRdmc0= github.com/wtsi-npg/fsnotify v1.4.8-0.20190705153444-45ca73e9793a/go.mod h1:/ux2ROeuYmj0JshWH6r5f+gvLIJP2ZbMutVFrW6/8Pg= github.com/wtsi-npg/logshim v1.2.0 h1:d9y9XvBRkYB2bUsN07zGJWhGCu13PKoxIxQE97Q9aZw= github.com/wtsi-npg/logshim v1.2.0/go.mod h1:1JRn1t/rlx1/oAtv3LOcshcpjDDvHGHCK8p8ua0Hrss= -github.com/wtsi-npg/logshim-zerolog v1.2.0 h1:b1HpB1h8OO9XBg/m9r6ycmHRUDNZLnpTmfjWrhmeaT4= -github.com/wtsi-npg/logshim-zerolog v1.2.0/go.mod h1:xyahqnZDG2utxSUAQKYjgEdzQz74wfPY7+JttEie41k= +github.com/wtsi-npg/logshim v1.3.0 h1:J4JIzWrEVC6RghSdnhadjviOwAwQ4BUqG7hveqxrisY= +github.com/wtsi-npg/logshim v1.3.0/go.mod h1:O1IqtDB3IiWuIpEE42IznMkJD8d++UFp40gBSjps3ac= +github.com/wtsi-npg/logshim-zerolog v1.3.0 h1:7BoTUhTKtBwuduc+8mCcsYVWCAptqFY1CT1Y3pSjoaw= +github.com/wtsi-npg/logshim-zerolog v1.3.0/go.mod h1:yWGzgCuHUkg1tcKcF0DBKi2laec69EIUMkXl77P2yII= github.com/xiang90/probing v0.0.0-20190116061207-43a291ad63a2/go.mod h1:UETIi67q53MR2AWcXfiuqkDkRtnGDLqkBTpCHuJHxtU= github.com/xordataexchange/crypt v0.0.3-0.20170626215501-b2862e3d0a77/go.mod h1:aYKd//L2LvnjZzWKhF00oedf4jCCReLcmhLdhm1A27Q= github.com/yuin/goldmark v1.2.1/go.mod h1:3hX8gzYuyVAZsxl0MRgGTJEmQBFcNTphYh9decYSb74= -github.com/zenazn/goji v0.9.0/go.mod h1:7S9M489iMyHBNxwZnk9/EHS098H4/F6TATF2mIxtB1Q= go.etcd.io/bbolt v1.3.2/go.mod h1:IbVyRI1SCnLcuJnV2u8VeU0CEYM7e686BmAb1XKL+uU= go.uber.org/atomic v1.4.0/go.mod h1:gD2HeocX3+yG+ygLZcrzQJaqmWj9AIm7n08wl/qW/PE= go.uber.org/multierr v1.1.0/go.mod h1:wR5kodmAFQ0UK8QlbwjlSNy0Z68gJhDJUG5sjR94q/0= @@ -199,7 +196,6 @@ golang.org/x/tools v0.0.0-20180221164845-07fd8470d635/go.mod h1:n7NCudcB/nEzxVGm golang.org/x/tools v0.0.0-20180917221912-90fa682c2a6e/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= golang.org/x/tools v0.0.0-20190114222345-bf090417da8b/go.mod h1:n7NCudcB/nEzxVGmLbDWY5pfWTLqBcC2KZ6jyYvM4mQ= golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs= -golang.org/x/tools v0.0.0-20190828213141-aed303cbaa74/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20191119224855-298f0cb1881e/go.mod h1:b+2E5dAYhXwXZwtnZ6UAqBI28+e2cm9otk0dWdXHAEo= golang.org/x/tools v0.0.0-20201224043029-2b0845dc783e/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA= golang.org/x/tools v0.1.0/go.mod h1:xkSsbof2nBLbhDlRMhhhyNLN/zl3eTqcnHD5viDpcZ0=