Diff of the two buildlogs: -- --- b1/build.log 2021-10-12 08:48:51.856191768 +0000 +++ b2/build.log 2021-10-12 08:50:05.309683314 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Mon Nov 14 03:08:38 -12 2022 -I: pbuilder-time-stamp: 1668438518 +I: Current time: Tue Oct 12 22:48:53 +14 2021 +I: pbuilder-time-stamp: 1634028533 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration @@ -17,7 +17,7 @@ I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error -gpgv: Signature made Wed Oct 31 06:17:57 2018 -12 +gpgv: Signature made Thu Nov 1 08:17:57 2018 +14 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key @@ -27,136 +27,170 @@ dpkg-source: info: unpacking python-pbcommand_1.1.1-1.debian.tar.xz I: using fakeroot in build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/388208/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/3974162/tmp/hooks/D01_modify_environment starting +debug: Running on ionos1-amd64. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' +Adding 'diversion of /bin/sh to /bin/sh.distrib by bash' +Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' +Adding 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by bash' +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/3974162/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/3974162/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='amd64' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=16' - DISTRIBUTION='' - HOME='/root' - HOST_ARCH='amd64' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:hostcomplete:interactive_comments:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="0" [2]="3" [3]="1" [4]="release" [5]="x86_64-pc-linux-gnu") + BASH_VERSION='5.0.3(1)-release' + BUILDDIR=/build + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=amd64 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15' + DIRSTACK=() + DISTRIBUTION= + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=x86_64 + HOST_ARCH=amd64 IFS=' ' - INVOCATION_ID='9b93e91e4a4d4fb8b75b9bba21412e6a' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='388208' - PS1='# ' - PS2='> ' + INVOCATION_ID=e6701c70395d4017954ecbb344b23be3 + LANG=C + LANGUAGE=et_EE:et + LC_ALL=C + MACHTYPE=x86_64-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=3974162 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.XLbuBZMoNE/pbuilderrc_9OcD --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.XLbuBZMoNE/b1 --logfile b1/build.log python-pbcommand_1.1.1-1.dsc' - SUDO_GID='111' - SUDO_UID='106' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://85.184.249.68:3128' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.XLbuBZMoNE/pbuilderrc_feqw --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.XLbuBZMoNE/b2 --logfile b2/build.log python-pbcommand_1.1.1-1.dsc' + SUDO_GID=110 + SUDO_UID=105 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://78.137.99.97:3128 I: uname -a - Linux ionos15-amd64 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 5.10.0-9-amd64 #1 SMP Debian 5.10.70-1 (2021-09-30) x86_64 GNU/Linux I: ls -l /bin total 5116 - -rwxr-xr-x 1 root root 1168776 Apr 17 2019 bash - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bunzip2 - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzcat - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff - -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep - -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep - -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep - -rwxr-xr-x 3 root root 38984 Jul 10 2019 bzip2 - -rwxr-xr-x 1 root root 14328 Jul 10 2019 bzip2recover - lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore - -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore - -rwxr-xr-x 1 root root 43744 Feb 28 2019 cat - -rwxr-xr-x 1 root root 64320 Feb 28 2019 chgrp - -rwxr-xr-x 1 root root 64288 Feb 28 2019 chmod - -rwxr-xr-x 1 root root 72512 Feb 28 2019 chown - -rwxr-xr-x 1 root root 146880 Feb 28 2019 cp - -rwxr-xr-x 1 root root 121464 Jan 17 2019 dash - -rwxr-xr-x 1 root root 109408 Feb 28 2019 date - -rwxr-xr-x 1 root root 76712 Feb 28 2019 dd - -rwxr-xr-x 1 root root 93744 Feb 28 2019 df - -rwxr-xr-x 1 root root 138856 Feb 28 2019 dir - -rwxr-xr-x 1 root root 84288 Jan 9 2019 dmesg - lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname - lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname - -rwxr-xr-x 1 root root 39520 Feb 28 2019 echo - -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep - -rwxr-xr-x 1 root root 35424 Feb 28 2019 false - -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep - -rwxr-xr-x 1 root root 68880 Jan 9 2019 findmnt - -rwsr-xr-x 1 root root 34896 Apr 22 2020 fusermount - -rwxr-xr-x 1 root root 198976 Jan 7 2019 grep - -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip - -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe - -rwxr-xr-x 1 root root 98048 Jan 5 2019 gzip - -rwxr-xr-x 1 root root 26696 Sep 26 2018 hostname - -rwxr-xr-x 1 root root 68552 Feb 28 2019 ln - -rwxr-xr-x 1 root root 56760 Jul 26 2018 login - -rwxr-xr-x 1 root root 138856 Feb 28 2019 ls - -rwxr-xr-x 1 root root 108624 Jan 9 2019 lsblk - -rwxr-xr-x 1 root root 89088 Feb 28 2019 mkdir - -rwxr-xr-x 1 root root 68544 Feb 28 2019 mknod - -rwxr-xr-x 1 root root 43808 Feb 28 2019 mktemp - -rwxr-xr-x 1 root root 43008 Jan 9 2019 more - -rwsr-xr-x 1 root root 51280 Jan 9 2019 mount - -rwxr-xr-x 1 root root 14408 Jan 9 2019 mountpoint - -rwxr-xr-x 1 root root 138728 Feb 28 2019 mv - lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname - lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 - -rwxr-xr-x 1 root root 39616 Feb 28 2019 pwd - lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash - -rwxr-xr-x 1 root root 47776 Feb 28 2019 readlink - -rwxr-xr-x 1 root root 68416 Feb 28 2019 rm - -rwxr-xr-x 1 root root 47776 Feb 28 2019 rmdir - -rwxr-xr-x 1 root root 23312 Jan 21 2019 run-parts - -rwxr-xr-x 1 root root 122224 Dec 22 2018 sed - lrwxrwxrwx 1 root root 4 Nov 9 02:47 sh -> dash - -rwxr-xr-x 1 root root 39552 Feb 28 2019 sleep - -rwxr-xr-x 1 root root 80672 Feb 28 2019 stty - -rwsr-xr-x 1 root root 63568 Jan 9 2019 su - -rwxr-xr-x 1 root root 35488 Feb 28 2019 sync - -rwxr-xr-x 1 root root 445560 Apr 23 2019 tar - -rwxr-xr-x 1 root root 14440 Jan 21 2019 tempfile - -rwxr-xr-x 1 root root 97152 Feb 28 2019 touch - -rwxr-xr-x 1 root root 35424 Feb 28 2019 true - -rwxr-xr-x 1 root root 14328 Apr 22 2020 ulockmgr_server - -rwsr-xr-x 1 root root 34888 Jan 9 2019 umount - -rwxr-xr-x 1 root root 39584 Feb 28 2019 uname - -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress - -rwxr-xr-x 1 root root 138856 Feb 28 2019 vdir - -rwxr-xr-x 1 root root 34896 Jan 9 2019 wdctl - -rwxr-xr-x 1 root root 946 Jan 21 2019 which - lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname - -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat - -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp - -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff - -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep - -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep - -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce - -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep - -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless - -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore - -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew -I: user script /srv/workspace/pbuilder/388208/tmp/hooks/D02_print_environment finished + -rwxr-xr-x 1 root root 1168776 Apr 18 2019 bash + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bunzip2 + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzcat + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzcmp -> bzdiff + -rwxr-xr-x 1 root root 2227 Jul 11 2019 bzdiff + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzegrep -> bzgrep + -rwxr-xr-x 1 root root 4877 Jun 25 2019 bzexe + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzfgrep -> bzgrep + -rwxr-xr-x 1 root root 3641 Jul 11 2019 bzgrep + -rwxr-xr-x 3 root root 38984 Jul 11 2019 bzip2 + -rwxr-xr-x 1 root root 14328 Jul 11 2019 bzip2recover + lrwxrwxrwx 1 root root 6 Jul 11 2019 bzless -> bzmore + -rwxr-xr-x 1 root root 1297 Jul 11 2019 bzmore + -rwxr-xr-x 1 root root 43744 Mar 1 2019 cat + -rwxr-xr-x 1 root root 64320 Mar 1 2019 chgrp + -rwxr-xr-x 1 root root 64288 Mar 1 2019 chmod + -rwxr-xr-x 1 root root 72512 Mar 1 2019 chown + -rwxr-xr-x 1 root root 146880 Mar 1 2019 cp + -rwxr-xr-x 1 root root 121464 Jan 18 2019 dash + -rwxr-xr-x 1 root root 109408 Mar 1 2019 date + -rwxr-xr-x 1 root root 76712 Mar 1 2019 dd + -rwxr-xr-x 1 root root 93744 Mar 1 2019 df + -rwxr-xr-x 1 root root 138856 Mar 1 2019 dir + -rwxr-xr-x 1 root root 84288 Jan 10 2019 dmesg + lrwxrwxrwx 1 root root 8 Sep 27 2018 dnsdomainname -> hostname + lrwxrwxrwx 1 root root 8 Sep 27 2018 domainname -> hostname + -rwxr-xr-x 1 root root 39520 Mar 1 2019 echo + -rwxr-xr-x 1 root root 28 Jan 8 2019 egrep + -rwxr-xr-x 1 root root 35424 Mar 1 2019 false + -rwxr-xr-x 1 root root 28 Jan 8 2019 fgrep + -rwxr-xr-x 1 root root 68880 Jan 10 2019 findmnt + -rwsr-xr-x 1 root root 34896 Apr 23 2020 fusermount + -rwxr-xr-x 1 root root 198976 Jan 8 2019 grep + -rwxr-xr-x 2 root root 2345 Jan 6 2019 gunzip + -rwxr-xr-x 1 root root 6375 Jan 6 2019 gzexe + -rwxr-xr-x 1 root root 98048 Jan 6 2019 gzip + -rwxr-xr-x 1 root root 26696 Sep 27 2018 hostname + -rwxr-xr-x 1 root root 68552 Mar 1 2019 ln + -rwxr-xr-x 1 root root 56760 Jul 27 2018 login + -rwxr-xr-x 1 root root 138856 Mar 1 2019 ls + -rwxr-xr-x 1 root root 108624 Jan 10 2019 lsblk + -rwxr-xr-x 1 root root 89088 Mar 1 2019 mkdir + -rwxr-xr-x 1 root root 68544 Mar 1 2019 mknod + -rwxr-xr-x 1 root root 43808 Mar 1 2019 mktemp + -rwxr-xr-x 1 root root 43008 Jan 10 2019 more + -rwsr-xr-x 1 root root 51280 Jan 10 2019 mount + -rwxr-xr-x 1 root root 14408 Jan 10 2019 mountpoint + -rwxr-xr-x 1 root root 138728 Mar 1 2019 mv + lrwxrwxrwx 1 root root 8 Sep 27 2018 nisdomainname -> hostname + lrwxrwxrwx 1 root root 14 Feb 15 2019 pidof -> /sbin/killall5 + -rwxr-xr-x 1 root root 39616 Mar 1 2019 pwd + lrwxrwxrwx 1 root root 4 Apr 18 2019 rbash -> bash + -rwxr-xr-x 1 root root 47776 Mar 1 2019 readlink + -rwxr-xr-x 1 root root 68416 Mar 1 2019 rm + -rwxr-xr-x 1 root root 47776 Mar 1 2019 rmdir + -rwxr-xr-x 1 root root 23312 Jan 22 2019 run-parts + -rwxr-xr-x 1 root root 122224 Dec 23 2018 sed + lrwxrwxrwx 1 root root 4 Oct 12 22:48 sh -> bash + lrwxrwxrwx 1 root root 4 Oct 7 22:25 sh.distrib -> dash + -rwxr-xr-x 1 root root 39552 Mar 1 2019 sleep + -rwxr-xr-x 1 root root 80672 Mar 1 2019 stty + -rwsr-xr-x 1 root root 63568 Jan 10 2019 su + -rwxr-xr-x 1 root root 35488 Mar 1 2019 sync + -rwxr-xr-x 1 root root 445560 Apr 24 2019 tar + -rwxr-xr-x 1 root root 14440 Jan 22 2019 tempfile + -rwxr-xr-x 1 root root 97152 Mar 1 2019 touch + -rwxr-xr-x 1 root root 35424 Mar 1 2019 true + -rwxr-xr-x 1 root root 14328 Apr 23 2020 ulockmgr_server + -rwsr-xr-x 1 root root 34888 Jan 10 2019 umount + -rwxr-xr-x 1 root root 39584 Mar 1 2019 uname + -rwxr-xr-x 2 root root 2345 Jan 6 2019 uncompress + -rwxr-xr-x 1 root root 138856 Mar 1 2019 vdir + -rwxr-xr-x 1 root root 34896 Jan 10 2019 wdctl + -rwxr-xr-x 1 root root 946 Jan 22 2019 which + lrwxrwxrwx 1 root root 8 Sep 27 2018 ypdomainname -> hostname + -rwxr-xr-x 1 root root 1983 Jan 6 2019 zcat + -rwxr-xr-x 1 root root 1677 Jan 6 2019 zcmp + -rwxr-xr-x 1 root root 5879 Jan 6 2019 zdiff + -rwxr-xr-x 1 root root 29 Jan 6 2019 zegrep + -rwxr-xr-x 1 root root 29 Jan 6 2019 zfgrep + -rwxr-xr-x 1 root root 2080 Jan 6 2019 zforce + -rwxr-xr-x 1 root root 7584 Jan 6 2019 zgrep + -rwxr-xr-x 1 root root 2205 Jan 6 2019 zless + -rwxr-xr-x 1 root root 1841 Jan 6 2019 zmore + -rwxr-xr-x 1 root root 4552 Jan 6 2019 znew +I: user script /srv/workspace/pbuilder/3974162/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -315,7 +349,7 @@ Get: 99 http://deb.debian.org/debian buster/main amd64 python-pbcore all 1.6.5+dfsg-1 [9100 kB] Get: 100 http://deb.debian.org/debian buster/main amd64 python-urllib3 all 1.24.1-1 [97.0 kB] Get: 101 http://deb.debian.org/debian buster/main amd64 python-requests all 2.21.0-1 [67.1 kB] -Fetched 50.3 MB in 2s (27.2 MB/s) +Fetched 50.3 MB in 1s (59.7 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19195 files and directories currently installed.) @@ -757,7 +791,8 @@ fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package -I: Running cd /build/python-pbcommand-1.1.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../python-pbcommand_1.1.1-1_source.changes +hostname: Name or service not known +I: Running cd /build/python-pbcommand-1.1.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../python-pbcommand_1.1.1-1_source.changes dpkg-buildpackage: info: source package python-pbcommand dpkg-buildpackage: info: source version 1.1.1-1 dpkg-buildpackage: info: source distribution unstable @@ -876,163 +911,163 @@ make[1]: Entering directory '/build/python-pbcommand-1.1.1' PYTHONPATH=/build/python-pbcommand-1.1.1 \ nosetests -s --verbose --logging-config log_nose.cfg --where=tests -test_01 (tests.test_common_cmdline_core.SimpleTest) ... [INFO] 2022-11-14 15:11:12,874Z [tests.test_common_cmdline_core _pacbio_main_runner 130] Using pbcommand v1.1.1 -[INFO] 2022-11-14 15:11:12,874Z [tests.test_common_cmdline_core _pacbio_main_runner 131] completed setting up logger with -[INFO] 2022-11-14 15:11:12,874Z [tests.test_common_cmdline_core _pacbio_main_runner 132] log opts {'file_name': None, 'level': 10} -[INFO] 2022-11-14 15:11:12,874Z [tests.test_common_cmdline_core args_runner 14] Running args: (Namespace(debug=True, example_file='/path/to/my_fake_file.txt'),) -[INFO] 2022-11-14 15:11:12,874Z [tests.test_common_cmdline_core _pacbio_main_runner 155] exiting with return code 0 in 0.00 sec. +test_01 (tests.test_common_cmdline_core.SimpleTest) ... [INFO] 2021-10-12 08:49:53,045Z [tests.test_common_cmdline_core _pacbio_main_runner 130] Using pbcommand v1.1.1 +[INFO] 2021-10-12 08:49:53,045Z [tests.test_common_cmdline_core _pacbio_main_runner 131] completed setting up logger with +[INFO] 2021-10-12 08:49:53,045Z [tests.test_common_cmdline_core _pacbio_main_runner 132] log opts {'file_name': None, 'level': 10} +[INFO] 2021-10-12 08:49:53,045Z [tests.test_common_cmdline_core args_runner 14] Running args: (Namespace(debug=True, example_file='/path/to/my_fake_file.txt'),) +[INFO] 2021-10-12 08:49:53,045Z [tests.test_common_cmdline_core _pacbio_main_runner 155] exiting with return code 0 in 0.00 sec. ok test_run_e2e (tests.test_e2e_example_apps.PbTestApp) ... ok -test_run_e2e (tests.test_e2e_example_apps.TestBadChoiceValue) ... [DEBUG] 2022-11-14 15:11:12,879Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_mixed_app --emit-tool-contract -[DEBUG] 2022-11-14 15:11:12,879Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] -[DEBUG] 2022-11-14 15:11:12,879Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpp88thU-rtc-test -[DEBUG] 2022-11-14 15:11:13,135Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpp88thU-rtc-test/tmpX19L99-TestBadChoiceValue-tool_contract.json -[INFO] 2022-11-14 15:11:13,136Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC -ok -test_run_e2e (tests.test_e2e_example_apps.TestOptionTypes) ... [DEBUG] 2022-11-14 15:11:13,138Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_mixed_app --emit-tool-contract -[DEBUG] 2022-11-14 15:11:13,138Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] -[DEBUG] 2022-11-14 15:11:13,138Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpCQkfQQ-rtc-test -[DEBUG] 2022-11-14 15:11:13,557Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpCQkfQQ-rtc-test/tmpr6hxJB-TestOptionTypes-tool_contract.json -[INFO] 2022-11-14 15:11:13,559Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC -[INFO] 2022-11-14 15:11:13,560Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpCQkfQQ-rtc-test/tmp5bRbb7resolved_tool_contract.json -[INFO] 2022-11-14 15:11:13,560Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_mixed_app --resolved-tool-contract /tmp/tmpCQkfQQ-rtc-test/tmp5bRbb7resolved_tool_contract.json' -[INFO] 2022-11-14 15:11:13,766Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_mixed_app --emit-tool-contract -[DEBUG] 2022-11-14 15:11:13,767Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from -[DEBUG] 2022-11-14 15:11:13,767Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_mixed_app -[DEBUG] 2022-11-14 15:11:13,767Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpCQkfQQ-rtc-test/example.report.json'] -ok -test_run_e2e (tests.test_e2e_example_apps.TestQuickCustomTxtCustomOuts) ... [DEBUG] 2022-11-14 15:11:13,773Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_txt_custom_outs -[DEBUG] 2022-11-14 15:11:13,774Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] -[DEBUG] 2022-11-14 15:11:13,774Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpQS_TtN-rtc-test -[DEBUG] 2022-11-14 15:11:14,032Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpQS_TtN-rtc-test/tmp1VMYOz-TestQuickCustomTxtCustomOuts-tool_contract.json -[INFO] 2022-11-14 15:11:14,033Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC -[INFO] 2022-11-14 15:11:14,034Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpQS_TtN-rtc-test/tmpe0sF_fresolved_tool_contract.json -[INFO] 2022-11-14 15:11:14,035Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_quick_hello_world run-rtc /tmp/tmpQS_TtN-rtc-test/tmpe0sF_fresolved_tool_contract.json' -[INFO] 2022-11-14 15:11:14,364Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_txt_custom_outs -[DEBUG] 2022-11-14 15:11:14,365Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from -[DEBUG] 2022-11-14 15:11:14,365Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_txt_custom_outs -[DEBUG] 2022-11-14 15:11:14,365Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpQS_TtN-rtc-test/PacBio.FileTypes.txt_file_0.txt', '/tmp/tmpQS_TtN-rtc-test/PacBio.FileTypes.txt_file_1.txt'] -ok -test_run_e2e (tests.test_e2e_example_apps.TestQuickDevHelloWorld) ... [DEBUG] 2022-11-14 15:11:14,367Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_qhello_world -[DEBUG] 2022-11-14 15:11:14,367Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] -[DEBUG] 2022-11-14 15:11:14,367Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpPW7i16-rtc-test -[DEBUG] 2022-11-14 15:11:14,856Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpPW7i16-rtc-test/tmpKm4LDY-TestQuickDevHelloWorld-tool_contract.json -[INFO] 2022-11-14 15:11:14,857Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC -[INFO] 2022-11-14 15:11:14,858Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpPW7i16-rtc-test/tmpYNpXiaresolved_tool_contract.json -[INFO] 2022-11-14 15:11:14,858Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_quick_hello_world run-rtc /tmp/tmpPW7i16-rtc-test/tmpYNpXiaresolved_tool_contract.json' -[INFO] 2022-11-14 15:11:15,364Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_qhello_world -[DEBUG] 2022-11-14 15:11:15,365Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from -[DEBUG] 2022-11-14 15:11:15,365Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_qhello_world -[DEBUG] 2022-11-14 15:11:15,365Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpPW7i16-rtc-test/file.fasta'] -ok -test_run_e2e (tests.test_e2e_example_apps.TestQuickOptionTypes) ... [DEBUG] 2022-11-14 15:11:15,367Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_test_options -[DEBUG] 2022-11-14 15:11:15,367Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] -[DEBUG] 2022-11-14 15:11:15,367Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpJwxW3A-rtc-test -[DEBUG] 2022-11-14 15:11:15,768Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpJwxW3A-rtc-test/tmpSrrf7a-TestQuickOptionTypes-tool_contract.json -[INFO] 2022-11-14 15:11:15,769Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC -[INFO] 2022-11-14 15:11:15,770Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpJwxW3A-rtc-test/tmp2a4dqcresolved_tool_contract.json -[INFO] 2022-11-14 15:11:15,770Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_quick_hello_world run-rtc /tmp/tmpJwxW3A-rtc-test/tmp2a4dqcresolved_tool_contract.json' -[INFO] 2022-11-14 15:11:16,136Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_test_options -[DEBUG] 2022-11-14 15:11:16,137Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from -[DEBUG] 2022-11-14 15:11:16,137Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_test_options -[DEBUG] 2022-11-14 15:11:16,137Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpJwxW3A-rtc-test/file.txt'] -ok -test_run_e2e (tests.test_e2e_example_apps.TestQuickTxt) ... [DEBUG] 2022-11-14 15:11:16,139Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_txt_hello -[DEBUG] 2022-11-14 15:11:16,139Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] -[DEBUG] 2022-11-14 15:11:16,139Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpdrY8Ir-rtc-test -[DEBUG] 2022-11-14 15:11:16,605Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpdrY8Ir-rtc-test/tmpkk9w7b-TestQuickTxt-tool_contract.json -[INFO] 2022-11-14 15:11:16,606Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC -[INFO] 2022-11-14 15:11:16,607Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpdrY8Ir-rtc-test/tmpNxxJlGresolved_tool_contract.json -[INFO] 2022-11-14 15:11:16,607Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_quick_hello_world run-rtc /tmp/tmpdrY8Ir-rtc-test/tmpNxxJlGresolved_tool_contract.json' -[INFO] 2022-11-14 15:11:16,882Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_txt_hello -[DEBUG] 2022-11-14 15:11:16,882Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from -[DEBUG] 2022-11-14 15:11:16,882Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_txt_hello -[DEBUG] 2022-11-14 15:11:16,883Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpdrY8Ir-rtc-test/file.txt', '/tmp/tmpdrY8Ir-rtc-test/file-1.txt'] -ok -test_run_e2e (tests.test_e2e_example_apps.TestRunDevApp) ... [DEBUG] 2022-11-14 15:11:16,884Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_app --emit-tool-contract -[DEBUG] 2022-11-14 15:11:16,884Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.fasta'] -[DEBUG] 2022-11-14 15:11:16,884Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpmGgpvc-rtc-test -[DEBUG] 2022-11-14 15:11:17,484Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpmGgpvc-rtc-test/tmpXC6OMp-TestRunDevApp-tool_contract.json -[INFO] 2022-11-14 15:11:17,485Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC -[INFO] 2022-11-14 15:11:17,486Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpmGgpvc-rtc-test/tmpWTToMTresolved_tool_contract.json -[INFO] 2022-11-14 15:11:17,486Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_app --resolved-tool-contract /tmp/tmpmGgpvc-rtc-test/tmpWTToMTresolved_tool_contract.json' -[INFO] 2022-11-14 15:11:18,248Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_app --emit-tool-contract -[DEBUG] 2022-11-14 15:11:18,249Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from -[DEBUG] 2022-11-14 15:11:18,249Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_app -[DEBUG] 2022-11-14 15:11:18,249Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpmGgpvc-rtc-test/filter.fasta'] -ok -test_run_e2e (tests.test_e2e_example_apps.TestTxtDevApp) ... [DEBUG] 2022-11-14 15:11:18,251Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_txt_app --emit-tool-contract -[DEBUG] 2022-11-14 15:11:18,251Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] -[DEBUG] 2022-11-14 15:11:18,251Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpHdkEbb-rtc-test -[DEBUG] 2022-11-14 15:11:18,508Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpHdkEbb-rtc-test/tmpp_8gJm-TestTxtDevApp-tool_contract.json -[INFO] 2022-11-14 15:11:18,509Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC -[INFO] 2022-11-14 15:11:18,510Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpHdkEbb-rtc-test/tmpHMrD_Aresolved_tool_contract.json -[INFO] 2022-11-14 15:11:18,510Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_txt_app --resolved-tool-contract /tmp/tmpHdkEbb-rtc-test/tmpHMrD_Aresolved_tool_contract.json' -[INFO] 2022-11-14 15:11:18,976Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_txt_app --emit-tool-contract -[DEBUG] 2022-11-14 15:11:18,977Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from -[DEBUG] 2022-11-14 15:11:18,977Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_txt_app -[DEBUG] 2022-11-14 15:11:18,977Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpHdkEbb-rtc-test/output.txt'] -ok -test_simple_run_cmd (tests.test_engine_runner.RunnerSmokeTest) ... [DEBUG] 2022-11-14 15:11:19,012Z [pbcommand.engine.runner run_cmd 45] calling cmd 'cat /tmp/tmpXAeTyzsimple-cmd/tmp_TwwmY.txt > /tmp/tmpXAeTyzsimple-cmd/tmpBXCeV_*.txt' on ionos15-amd64 -[DEBUG] 2022-11-14 15:11:19,340Z [pbcommand.engine.runner run_cmd 76] returncode is 0 in 0.36 sec. +test_run_e2e (tests.test_e2e_example_apps.TestBadChoiceValue) ... [DEBUG] 2021-10-12 08:49:53,050Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_mixed_app --emit-tool-contract +[DEBUG] 2021-10-12 08:49:53,050Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] +[DEBUG] 2021-10-12 08:49:53,050Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpTxGhVM-rtc-test +[DEBUG] 2021-10-12 08:49:53,279Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpTxGhVM-rtc-test/tmpdI6VIx-TestBadChoiceValue-tool_contract.json +[INFO] 2021-10-12 08:49:53,281Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC +ok +test_run_e2e (tests.test_e2e_example_apps.TestOptionTypes) ... [DEBUG] 2021-10-12 08:49:53,282Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_mixed_app --emit-tool-contract +[DEBUG] 2021-10-12 08:49:53,282Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] +[DEBUG] 2021-10-12 08:49:53,282Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpsQJZZa-rtc-test +[DEBUG] 2021-10-12 08:49:53,533Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpsQJZZa-rtc-test/tmpGSfuJi-TestOptionTypes-tool_contract.json +[INFO] 2021-10-12 08:49:53,535Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC +[INFO] 2021-10-12 08:49:53,536Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpsQJZZa-rtc-test/tmpVWblkxresolved_tool_contract.json +[INFO] 2021-10-12 08:49:53,536Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_mixed_app --resolved-tool-contract /tmp/tmpsQJZZa-rtc-test/tmpVWblkxresolved_tool_contract.json' +[INFO] 2021-10-12 08:49:53,755Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_mixed_app --emit-tool-contract +[DEBUG] 2021-10-12 08:49:53,755Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from +[DEBUG] 2021-10-12 08:49:53,755Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_mixed_app +[DEBUG] 2021-10-12 08:49:53,756Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpsQJZZa-rtc-test/example.report.json'] +ok +test_run_e2e (tests.test_e2e_example_apps.TestQuickCustomTxtCustomOuts) ... [DEBUG] 2021-10-12 08:49:53,758Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_txt_custom_outs +[DEBUG] 2021-10-12 08:49:53,758Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] +[DEBUG] 2021-10-12 08:49:53,758Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpYcMNeZ-rtc-test +[DEBUG] 2021-10-12 08:49:53,964Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpYcMNeZ-rtc-test/tmpA68Ty6-TestQuickCustomTxtCustomOuts-tool_contract.json +[INFO] 2021-10-12 08:49:53,965Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC +[INFO] 2021-10-12 08:49:53,966Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpYcMNeZ-rtc-test/tmp5KO88Bresolved_tool_contract.json +[INFO] 2021-10-12 08:49:53,966Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_quick_hello_world run-rtc /tmp/tmpYcMNeZ-rtc-test/tmp5KO88Bresolved_tool_contract.json' +[INFO] 2021-10-12 08:49:54,189Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_txt_custom_outs +[DEBUG] 2021-10-12 08:49:54,189Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from +[DEBUG] 2021-10-12 08:49:54,189Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_txt_custom_outs +[DEBUG] 2021-10-12 08:49:54,189Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpYcMNeZ-rtc-test/PacBio.FileTypes.txt_file_0.txt', '/tmp/tmpYcMNeZ-rtc-test/PacBio.FileTypes.txt_file_1.txt'] +ok +test_run_e2e (tests.test_e2e_example_apps.TestQuickDevHelloWorld) ... [DEBUG] 2021-10-12 08:49:54,191Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_qhello_world +[DEBUG] 2021-10-12 08:49:54,191Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] +[DEBUG] 2021-10-12 08:49:54,191Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpVQpFKJ-rtc-test +[DEBUG] 2021-10-12 08:49:54,440Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpVQpFKJ-rtc-test/tmp8x8Icx-TestQuickDevHelloWorld-tool_contract.json +[INFO] 2021-10-12 08:49:54,441Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC +[INFO] 2021-10-12 08:49:54,442Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpVQpFKJ-rtc-test/tmpJjT0Fhresolved_tool_contract.json +[INFO] 2021-10-12 08:49:54,442Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_quick_hello_world run-rtc /tmp/tmpVQpFKJ-rtc-test/tmpJjT0Fhresolved_tool_contract.json' +[INFO] 2021-10-12 08:49:54,660Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_qhello_world +[DEBUG] 2021-10-12 08:49:54,660Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from +[DEBUG] 2021-10-12 08:49:54,660Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_qhello_world +[DEBUG] 2021-10-12 08:49:54,661Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpVQpFKJ-rtc-test/file.fasta'] +ok +test_run_e2e (tests.test_e2e_example_apps.TestQuickOptionTypes) ... [DEBUG] 2021-10-12 08:49:54,662Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_test_options +[DEBUG] 2021-10-12 08:49:54,662Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] +[DEBUG] 2021-10-12 08:49:54,662Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpxYDeoT-rtc-test +[DEBUG] 2021-10-12 08:49:54,886Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpxYDeoT-rtc-test/tmpcgjxq9-TestQuickOptionTypes-tool_contract.json +[INFO] 2021-10-12 08:49:54,888Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC +[INFO] 2021-10-12 08:49:54,888Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpxYDeoT-rtc-test/tmpGQ8lohresolved_tool_contract.json +[INFO] 2021-10-12 08:49:54,889Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_quick_hello_world run-rtc /tmp/tmpxYDeoT-rtc-test/tmpGQ8lohresolved_tool_contract.json' +[INFO] 2021-10-12 08:49:55,119Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_test_options +[DEBUG] 2021-10-12 08:49:55,119Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from +[DEBUG] 2021-10-12 08:49:55,120Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_test_options +[DEBUG] 2021-10-12 08:49:55,120Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpxYDeoT-rtc-test/file.txt'] +ok +test_run_e2e (tests.test_e2e_example_apps.TestQuickTxt) ... [DEBUG] 2021-10-12 08:49:55,121Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_txt_hello +[DEBUG] 2021-10-12 08:49:55,121Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] +[DEBUG] 2021-10-12 08:49:55,121Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpESzldJ-rtc-test +[DEBUG] 2021-10-12 08:49:55,328Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpESzldJ-rtc-test/tmpSXjeZc-TestQuickTxt-tool_contract.json +[INFO] 2021-10-12 08:49:55,329Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC +[INFO] 2021-10-12 08:49:55,330Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpESzldJ-rtc-test/tmpTgEekcresolved_tool_contract.json +[INFO] 2021-10-12 08:49:55,330Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_quick_hello_world run-rtc /tmp/tmpESzldJ-rtc-test/tmpTgEekcresolved_tool_contract.json' +[INFO] 2021-10-12 08:49:55,531Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_quick_hello_world emit-tool-contract pbcommand.tasks.dev_txt_hello +[DEBUG] 2021-10-12 08:49:55,531Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from +[DEBUG] 2021-10-12 08:49:55,531Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_txt_hello +[DEBUG] 2021-10-12 08:49:55,531Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpESzldJ-rtc-test/file.txt', '/tmp/tmpESzldJ-rtc-test/file-1.txt'] +ok +test_run_e2e (tests.test_e2e_example_apps.TestRunDevApp) ... [DEBUG] 2021-10-12 08:49:55,533Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_app --emit-tool-contract +[DEBUG] 2021-10-12 08:49:55,533Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.fasta'] +[DEBUG] 2021-10-12 08:49:55,533Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpPUNFpV-rtc-test +[DEBUG] 2021-10-12 08:49:55,965Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpPUNFpV-rtc-test/tmpaC6iJl-TestRunDevApp-tool_contract.json +[INFO] 2021-10-12 08:49:55,966Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC +[INFO] 2021-10-12 08:49:55,967Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpPUNFpV-rtc-test/tmpa5HCyRresolved_tool_contract.json +[INFO] 2021-10-12 08:49:55,968Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_app --resolved-tool-contract /tmp/tmpPUNFpV-rtc-test/tmpa5HCyRresolved_tool_contract.json' +[INFO] 2021-10-12 08:49:56,453Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_app --emit-tool-contract +[DEBUG] 2021-10-12 08:49:56,454Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from +[DEBUG] 2021-10-12 08:49:56,454Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_app +[DEBUG] 2021-10-12 08:49:56,454Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpPUNFpV-rtc-test/filter.fasta'] +ok +test_run_e2e (tests.test_e2e_example_apps.TestTxtDevApp) ... [DEBUG] 2021-10-12 08:49:56,455Z [pbcommand.testkit.core test_run_e2e 94] Driver python -m pbcommand.cli.examples.dev_txt_app --emit-tool-contract +[DEBUG] 2021-10-12 08:49:56,455Z [pbcommand.testkit.core test_run_e2e 95] input files ['/build/python-pbcommand-1.1.1/tests/data/example.txt'] +[DEBUG] 2021-10-12 08:49:56,456Z [pbcommand.testkit.core test_run_e2e 96] running in /tmp/tmpKGQZ5o-rtc-test +[DEBUG] 2021-10-12 08:49:56,682Z [pbcommand.testkit.core test_run_e2e 104] Loading tool-contract from /tmp/tmpKGQZ5o-rtc-test/tmpX45brE-TestTxtDevApp-tool_contract.json +[INFO] 2021-10-12 08:49:56,683Z [pbcommand.testkit.core test_run_e2e 107] Resolving tool contract to RTC +[INFO] 2021-10-12 08:49:56,685Z [pbcommand.testkit.core test_run_e2e 130] running resolved contract /tmp/tmpKGQZ5o-rtc-test/tmpi5eY4oresolved_tool_contract.json +[INFO] 2021-10-12 08:49:56,685Z [pbcommand.testkit.core test_run_e2e 133] Running exe 'python -m pbcommand.cli.examples.dev_txt_app --resolved-tool-contract /tmp/tmpKGQZ5o-rtc-test/tmpi5eY4oresolved_tool_contract.json' +[INFO] 2021-10-12 08:49:56,940Z [pbcommand.testkit.core test_run_e2e 142] Successfully completed running e2e for python -m pbcommand.cli.examples.dev_txt_app --emit-tool-contract +[DEBUG] 2021-10-12 08:49:56,940Z [pbcommand.testkit.core _test_outputs_exists 64] validating output file existence from +[DEBUG] 2021-10-12 08:49:56,940Z [pbcommand.testkit.core _test_outputs_exists 65] Resolved Output files from pbcommand.tasks.dev_txt_app +[DEBUG] 2021-10-12 08:49:56,940Z [pbcommand.testkit.core _test_outputs_exists 66] ['/tmp/tmpKGQZ5o-rtc-test/output.txt'] +ok +test_simple_run_cmd (tests.test_engine_runner.RunnerSmokeTest) ... [DEBUG] 2021-10-12 08:49:56,953Z [pbcommand.engine.runner run_cmd 45] calling cmd 'cat /tmp/tmpFQQublsimple-cmd/tmpN1vP6t.txt > /tmp/tmpFQQublsimple-cmd/tmpEc4g5R*.txt' on i-capture-the-hostname +[DEBUG] 2021-10-12 08:49:57,267Z [pbcommand.engine.runner run_cmd 76] returncode is 0 in 0.32 sec. ok -test_01 (tests.test_load_resolved_tool_contract.TestLoadResolvedContract) ... [INFO] 2022-11-14 15:11:19,352Z [tests.test_load_resolved_tool_contract test_01 33] +test_01 (tests.test_load_resolved_tool_contract.TestLoadResolvedContract) ... [INFO] 2021-10-12 08:49:57,270Z [tests.test_load_resolved_tool_contract test_01 33] ok -test_01 (tests.test_load_resolved_tool_contract.TestResolveContract) ... [INFO] 2022-11-14 15:11:19,369Z [tests.test_load_resolved_tool_contract test_01 50] -[DEBUG] 2022-11-14 15:11:19,369Z [tests.test_load_resolved_tool_contract test_01 55] Resources [, , ] +test_01 (tests.test_load_resolved_tool_contract.TestResolveContract) ... [INFO] 2021-10-12 08:49:57,271Z [tests.test_load_resolved_tool_contract test_01 50] +[DEBUG] 2021-10-12 08:49:57,271Z [tests.test_load_resolved_tool_contract test_01 55] Resources [, , ] ok -test_datastore_file (tests.test_models_common.TestDataStore) ... [INFO] 2022-11-14 15:11:19,371Z [tests.test_models_common test_datastore_file 33] DataStoreFile: +test_datastore_file (tests.test_models_common.TestDataStore) ... [INFO] 2021-10-12 08:49:57,273Z [tests.test_models_common test_datastore_file 33] DataStoreFile: ok test_datastore_paths (tests.test_models_common.TestDataStore) ... ok test_file_types (tests.test_models_common.TestLoadFileTypes) ... ok test_is_valid (tests.test_models_common.TestLoadFileTypes) ... ok test_bad_invalid_choice (tests.test_models_common_pacbio_options.TestPacBioBasicChoiceTest) ... ok test_sanity_choice_option (tests.test_models_common_pacbio_options.TestPacBioBasicChoiceTest) ... ok -test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioBasicChoiceTest) ... [DEBUG] 2022-11-14 15:11:19,384Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option +test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioBasicChoiceTest) ... [DEBUG] 2021-10-12 08:49:57,276Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option ok -test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioBasicOptionTest) ... [DEBUG] 2022-11-14 15:11:19,385Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option +test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioBasicOptionTest) ... [DEBUG] 2021-10-12 08:49:57,277Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option ok test_bad_value_float (tests.test_models_common_pacbio_options.TestPacBioBooleanOptionTest) ... ok test_bad_value_int (tests.test_models_common_pacbio_options.TestPacBioBooleanOptionTest) ... ok test_bad_value_string (tests.test_models_common_pacbio_options.TestPacBioBooleanOptionTest) ... ok -test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioBooleanOptionTest) ... [DEBUG] 2022-11-14 15:11:19,387Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option +test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioBooleanOptionTest) ... [DEBUG] 2021-10-12 08:49:57,278Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option ok test_bad_invalid_choice (tests.test_models_common_pacbio_options.TestPacBioChoiceStringOptionTest) ... ok test_sanity_choice_option (tests.test_models_common_pacbio_options.TestPacBioChoiceStringOptionTest) ... ok -test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioChoiceStringOptionTest) ... [DEBUG] 2022-11-14 15:11:19,392Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option +test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioChoiceStringOptionTest) ... [DEBUG] 2021-10-12 08:49:57,279Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option ok test_bad_choices (tests.test_models_common_pacbio_options.TestPacBioFloatChoiceOptionTest) ... ok test_bad_invalid_choice (tests.test_models_common_pacbio_options.TestPacBioFloatChoiceOptionTest) ... ok test_coerce_float_choices (tests.test_models_common_pacbio_options.TestPacBioFloatChoiceOptionTest) ... ok test_sanity_choice_option (tests.test_models_common_pacbio_options.TestPacBioFloatChoiceOptionTest) ... ok -test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioFloatChoiceOptionTest) ... [DEBUG] 2022-11-14 15:11:19,394Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option +test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioFloatChoiceOptionTest) ... [DEBUG] 2021-10-12 08:49:57,281Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option ok test_bad_value_boolean (tests.test_models_common_pacbio_options.TestPacBioFloatOptionTest) ... ok test_bad_value_float_tuple (tests.test_models_common_pacbio_options.TestPacBioFloatOptionTest) ... ok test_bad_value_string (tests.test_models_common_pacbio_options.TestPacBioFloatOptionTest) ... ok test_coerced_value_int (tests.test_models_common_pacbio_options.TestPacBioFloatOptionTest) ... ok -test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioFloatOptionTest) ... [DEBUG] 2022-11-14 15:11:19,396Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option +test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioFloatOptionTest) ... [DEBUG] 2021-10-12 08:49:57,282Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option ok test_bad_invalid_choice (tests.test_models_common_pacbio_options.TestPacBioIntChoiceOptionTest) ... ok test_sanity_choice_option (tests.test_models_common_pacbio_options.TestPacBioIntChoiceOptionTest) ... ok -test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioIntChoiceOptionTest) ... [DEBUG] 2022-11-14 15:11:19,401Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option +test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioIntChoiceOptionTest) ... [DEBUG] 2021-10-12 08:49:57,283Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option ok test_bad_value_boolean (tests.test_models_common_pacbio_options.TestPacBioIntOptionTest) ... ok test_bad_value_float (tests.test_models_common_pacbio_options.TestPacBioIntOptionTest) ... ok test_bad_value_string (tests.test_models_common_pacbio_options.TestPacBioIntOptionTest) ... ok -test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioIntOptionTest) ... [DEBUG] 2022-11-14 15:11:19,403Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option +test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioIntOptionTest) ... [DEBUG] 2021-10-12 08:49:57,285Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option ok Test that unicode values are not Supported ... ok test_bad_value_float (tests.test_models_common_pacbio_options.TestPacBioStringOptionTest) ... ok test_bad_value_int (tests.test_models_common_pacbio_options.TestPacBioStringOptionTest) ... ok -test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioStringOptionTest) ... [DEBUG] 2022-11-14 15:11:19,408Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option +test_sanity_option (tests.test_models_common_pacbio_options.TestPacBioStringOptionTest) ... [DEBUG] 2021-10-12 08:49:57,286Z [tests.test_models_common_pacbio_options test_sanity_option 37] Created option ok test_bad_01 (tests.test_models_report.TestMalformedReport) ... ok Can't add elements with the same id. ... a plot with id 'a' has already been added to . -[ERROR] 2022-11-14 15:11:19,416Z [pbcommand.models.report is_unique 115] a plot with id 'a' has already been added to . +[ERROR] 2021-10-12 08:49:57,288Z [pbcommand.models.report is_unique 115] a plot with id 'a' has already been added to . ok test_empty_id (tests.test_models_report.TestReportModel) ... id '' for Report must contain only lower-case alphanumeric or underscore characters -[ERROR] 2022-11-14 15:11:19,417Z [pbcommand.models.report __init__ 100] id '' for Report must contain only lower-case alphanumeric or underscore characters +[ERROR] 2021-10-12 08:49:57,288Z [pbcommand.models.report __init__ 100] id '' for Report must contain only lower-case alphanumeric or underscore characters ok test_from_simple_dict (tests.test_models_report.TestReportModel) ... ok test_get_attribute_by_id (tests.test_models_report.TestReportModel) ... ok @@ -1046,18 +1081,18 @@ test_get_table_by_id (tests.test_models_report.TestReportModel) ... ok test_get_table_by_id_with_bad_id (tests.test_models_report.TestReportModel) ... ok Ids must be alphanumberic with underscores ... id 'a b' for Attribute must contain only lower-case alphanumeric or underscore characters -[ERROR] 2022-11-14 15:11:19,424Z [pbcommand.models.report __init__ 100] id 'a b' for Attribute must contain only lower-case alphanumeric or underscore characters +[ERROR] 2021-10-12 08:49:57,291Z [pbcommand.models.report __init__ 100] id 'a b' for Attribute must contain only lower-case alphanumeric or underscore characters ok test_merge (tests.test_models_report.TestReportModel) ... ok -test_merge_tables (tests.test_models_report.TestReportModel) ... [INFO] 2022-11-14 15:11:19,425Z [tests.test_models_report _to_report 22] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/laa_report1.json -[INFO] 2022-11-14 15:11:19,437Z [tests.test_models_report _to_report 22] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/laa_report2.json +test_merge_tables (tests.test_models_report.TestReportModel) ... [INFO] 2021-10-12 08:49:57,292Z [tests.test_models_report _to_report 22] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/laa_report1.json +[INFO] 2021-10-12 08:49:57,292Z [tests.test_models_report _to_report 22] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/laa_report2.json ok Can't create a report with an empty namespace. ... id '' for Report must contain only lower-case alphanumeric or underscore characters -[ERROR] 2022-11-14 15:11:19,438Z [pbcommand.models.report __init__ 100] id '' for Report must contain only lower-case alphanumeric or underscore characters +[ERROR] 2021-10-12 08:49:57,293Z [pbcommand.models.report __init__ 100] id '' for Report must contain only lower-case alphanumeric or underscore characters ok Can't create a report without a namespace. ... ok -The id of report sub elements is prepended with the id of the parent ... [DEBUG] 2022-11-14 15:11:19,446Z [tests.test_models_report test_to_dict 95] -{'_comment': 'Generated with pbcommand version 1.1.1 at 2022-11-14T03:11:19.439160', +The id of report sub elements is prepended with the id of the parent ... [DEBUG] 2021-10-12 08:49:57,297Z [tests.test_models_report test_to_dict 95] +{'_comment': 'Generated with pbcommand version 1.1.1 at 2021-10-12T22:49:57.294471', 'attributes': [{'id': 'redfang.a', 'name': None, 'value': 'b'}, {'id': 'redfang.a2', 'name': None, 'value': 'b2'}], 'dataset_uuids': [], @@ -1082,47 +1117,47 @@ 'id': 'redfang.tabid', 'title': None}], 'title': 'Report redfang', - 'uuid': '23ab409a-f32a-4996-bae3-3a20d5f6f6b1', + 'uuid': '22ff97cf-dfc8-4986-ae82-08370af80f7e', 'version': '1.0.1'} ok -Multiple complex elements. ... [DEBUG] 2022-11-14 15:11:19,447Z [tests.test_models_report test_to_dict_multi 151] {'tables': [{'id': 'redfang.tabid', 'columns': [{'header': None, 'values': [], 'id': 'redfang.tabid.c1'}], 'title': None}, {'id': 'redfang.tabid2', 'columns': [{'header': None, 'values': [], 'id': 'redfang.tabid2.c2'}], 'title': None}], 'uuid': 'e1af68d8-a58a-495f-8f48-f75375ec5cba', 'title': 'Report redfang', '_comment': 'Generated with pbcommand version 1.1.1 at 2022-11-14T03:11:19.447680', 'dataset_uuids': [], 'version': '1.0.1', 'attributes': [{'name': None, 'value': 'b', 'id': 'redfang.a'}, {'name': None, 'value': 'b2', 'id': 'redfang.a2'}], 'id': 'redfang', 'plotGroups': [{'id': 'redfang.pgid', 'thumbnail': None, 'plots': [{'id': 'redfang.pgid.pid', 'caption': None, 'image': 'anImg', 'plotType': 'image', 'title': None}, {'id': 'redfang.pgid.pid2', 'caption': None, 'image': 'anImg2', 'plotType': 'image', 'title': None}], 'legend': None, 'title': None}, {'id': 'redfang.pgid2', 'thumbnail': None, 'plots': [{'id': 'redfang.pgid2.pid2', 'caption': None, 'image': 'anImg2', 'plotType': 'image', 'title': None}, {'id': 'redfang.pgid2.pid22', 'caption': None, 'image': 'anImg22', 'plotType': 'image', 'title': None}], 'legend': None, 'title': None}]} -[INFO] 2022-11-14 15:11:19,448Z [tests.test_models_report test_to_dict_multi 177] +Multiple complex elements. ... [DEBUG] 2021-10-12 08:49:57,297Z [tests.test_models_report test_to_dict_multi 151] {'tables': [{'id': 'redfang.tabid', 'columns': [{'header': None, 'values': [], 'id': 'redfang.tabid.c1'}], 'title': None}, {'id': 'redfang.tabid2', 'columns': [{'header': None, 'values': [], 'id': 'redfang.tabid2.c2'}], 'title': None}], 'uuid': 'd4e61ac7-cde9-42ba-884f-848dde1c18c9', 'title': 'Report redfang', '_comment': 'Generated with pbcommand version 1.1.1 at 2021-10-12T22:49:57.297713', 'dataset_uuids': [], 'version': '1.0.1', 'attributes': [{'name': None, 'value': 'b', 'id': 'redfang.a'}, {'name': None, 'value': 'b2', 'id': 'redfang.a2'}], 'id': 'redfang', 'plotGroups': [{'id': 'redfang.pgid', 'thumbnail': None, 'plots': [{'id': 'redfang.pgid.pid', 'caption': None, 'image': 'anImg', 'plotType': 'image', 'title': None}, {'id': 'redfang.pgid.pid2', 'caption': None, 'image': 'anImg2', 'plotType': 'image', 'title': None}], 'legend': None, 'title': None}, {'id': 'redfang.pgid2', 'thumbnail': None, 'plots': [{'id': 'redfang.pgid2.pid2', 'caption': None, 'image': 'anImg2', 'plotType': 'image', 'title': None}, {'id': 'redfang.pgid2.pid22', 'caption': None, 'image': 'anImg22', 'plotType': 'image', 'title': None}], 'legend': None, 'title': None}]} +[INFO] 2021-10-12 08:49:57,297Z [tests.test_models_report test_to_dict_multi 177] ok test_uppercase_id (tests.test_models_report.TestReportModel) ... id 'A' for Report must contain only lower-case alphanumeric or underscore characters -[ERROR] 2022-11-14 15:11:19,452Z [pbcommand.models.report __init__ 100] id 'A' for Report must contain only lower-case alphanumeric or underscore characters +[ERROR] 2021-10-12 08:49:57,298Z [pbcommand.models.report __init__ 100] id 'A' for Report must contain only lower-case alphanumeric or underscore characters ok -test_version_and_changelist (tests.test_models_report.TestReportModel) ... [INFO] 2022-11-14 15:11:19,453Z [tests.test_models_report test_version_and_changelist 113] -{'_comment': 'Generated with pbcommand version 1.1.1 at 2022-11-14T03:11:19.453135', +test_version_and_changelist (tests.test_models_report.TestReportModel) ... [INFO] 2021-10-12 08:49:57,298Z [tests.test_models_report test_version_and_changelist 113] +{'_comment': 'Generated with pbcommand version 1.1.1 at 2021-10-12T22:49:57.298359', 'attributes': [], 'dataset_uuids': [], 'id': 'example', 'plotGroups': [], 'tables': [], 'title': 'Report example', - 'uuid': '6de30e3c-da70-4fd0-bc05-36d68583482e', + 'uuid': 'cb2c85ee-8b82-4639-ad2c-b97690cd6ab4', 'version': '1.0.1'} ok -test_sanity (tests.test_models_report.TestReportSchemaVersion100) ... [INFO] 2022-11-14 15:11:19,454Z [tests.test_models_report _to_report 22] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/example_version_1_0_0.json +test_sanity (tests.test_models_report.TestReportSchemaVersion100) ... [INFO] 2021-10-12 08:49:57,299Z [tests.test_models_report _to_report 22] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/example_version_1_0_0.json ok -test_apply_view (tests.test_models_report.TestReportSpec) ... [INFO] 2022-11-14 15:11:19,478Z [tests.test_models_report _to_report 22] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/test_report2.json +test_apply_view (tests.test_models_report.TestReportSpec) ... [INFO] 2021-10-12 08:49:57,302Z [tests.test_models_report _to_report 22] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/test_report2.json ok test_format_metric (tests.test_models_report.TestReportSpec) ... ok -test_report_validation (tests.test_models_report.TestReportSpec) ... [INFO] 2022-11-14 15:11:19,487Z [tests.test_models_report _to_report 22] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/test_report.json +test_report_validation (tests.test_models_report.TestReportSpec) ... [INFO] 2021-10-12 08:49:57,304Z [tests.test_models_report _to_report 22] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/test_report.json ok test_sanity (tests.test_models_report.TestRepotSchemaVersion100WithPlots) ... Report test_report failed validation against spec: Attribute attribute1 has value of type float (expected ) Attribute attribute5 not found in spec -[INFO] 2022-11-14 15:11:19,489Z [tests.test_models_report _to_report 22] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/example_with_plot.json +[INFO] 2021-10-12 08:49:57,306Z [tests.test_models_report _to_report 22] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/example_with_plot.json ok Test exception of handling Attribute with int ids ... ok Can't create an attribute without an id. ... ok test_eq (tests.test_models_report_attribute.TestAttribute) ... ok -test_repr (tests.test_models_report_attribute.TestAttribute) ... [INFO] 2022-11-14 15:11:19,498Z [tests.test_models_report_attribute test_repr 45] +test_repr (tests.test_models_report_attribute.TestAttribute) ... [INFO] 2021-10-12 08:49:57,307Z [tests.test_models_report_attribute test_repr 45] ok Test attribute to_dict function ... ok Test: Can't create a Column without an id. ... ok test_repr (tests.test_models_report_column.TestColumn) ... ok -Initial with thumbnail ... [INFO] 2022-11-14 15:11:19,503Z [tests.test_models_report_plot test_init_with_thumbnail 42] {'caption': 'Awesome image', +Initial with thumbnail ... [INFO] 2021-10-12 08:49:57,310Z [tests.test_models_report_plot test_init_with_thumbnail 42] {'caption': 'Awesome image', 'id': 'plot_1', 'image': 'my_image.png', 'plotType': 'image', @@ -1131,20 +1166,20 @@ Can't create an plot without an id. ... ok Can't create an plot without an image. ... ok test_plotly_plot (tests.test_models_report_plot.TestPlot) ... ok -Test plot to dictionary method ... [INFO] 2022-11-14 15:11:19,503Z [tests.test_models_report_plot test_to_dict 31] { 'caption': 'foo is the caption', +Test plot to dictionary method ... [INFO] 2021-10-12 08:49:57,311Z [tests.test_models_report_plot test_to_dict 31] { 'caption': 'foo is the caption', 'id': '123', 'image': 'foo', 'plotType': 'image', 'title': None} -[INFO] 2022-11-14 15:11:19,504Z [tests.test_models_report_plot test_to_dict 32] +[INFO] 2021-10-12 08:49:57,311Z [tests.test_models_report_plot test_to_dict 32] ok Validate type when adding Plots. ... ok Test constructor with kwargs ... ok Can't add plots with duplicate ids. ... a plot with id 'id' has already been added to . -[ERROR] 2022-11-14 15:11:19,510Z [pbcommand.models.report is_unique 115] a plot with id 'id' has already been added to . +[ERROR] 2021-10-12 08:49:57,312Z [pbcommand.models.report is_unique 115] a plot with id 'id' has already been added to . ok Can't create an plotGroup without an id. ... ok -Test plotGroup to_dict function. ... [DEBUG] 2022-11-14 15:11:19,511Z [tests.test_models_report_plotgroup test_to_dict 42] {'id': '123', +Test plotGroup to_dict function. ... [DEBUG] 2021-10-12 08:49:57,313Z [tests.test_models_report_plotgroup test_to_dict 42] {'id': '123', 'legend': 'foo legend', 'plots': [{'caption': 'a caption', 'id': '123.id', @@ -1153,11 +1188,11 @@ 'title': None}], 'thumbnail': 'foo thumbnail', 'title': 'foo title'} -[INFO] 2022-11-14 15:11:19,511Z [tests.test_models_report_plotgroup test_to_dict 49] +[INFO] 2021-10-12 08:49:57,313Z [tests.test_models_report_plotgroup test_to_dict 49] ok Basic check for column values ... ok Test Columns ... ok -Smoke test for conversion to str ... [INFO] 2022-11-14 15:11:19,518Z [tests.test_models_report_table test_str 61] +Smoke test for conversion to str ... [INFO] 2021-10-12 08:49:57,315Z [tests.test_models_report_table test_str 61] Table id:my_table_with_values --------------------- One Two Three @@ -1167,20 +1202,20 @@ 2 c file3 ok test_to_csv (tests.test_models_report_table.TestBasicTable) ... ok -Conversion to dictionary ... [INFO] 2022-11-14 15:11:19,519Z [tests.test_models_report_table test_to_dict 76] {'id': 'my_table_with_values', 'columns': [{'header': 'One', 'values': [0, 1, 2], 'id': 'my_table_with_values.one'}, {'header': 'Two', 'values': ['a', 'b', 'c'], 'id': 'my_table_with_values.two'}, {'header': 'Three', 'values': ['file1', 'file2', 'file3'], 'id': 'my_table_with_values.three'}], 'title': None} +Conversion to dictionary ... [INFO] 2021-10-12 08:49:57,316Z [tests.test_models_report_table test_to_dict 76] {'id': 'my_table_with_values', 'columns': [{'header': 'One', 'values': [0, 1, 2], 'id': 'my_table_with_values.one'}, {'header': 'Two', 'values': ['a', 'b', 'c'], 'id': 'my_table_with_values.two'}, {'header': 'Three', 'values': ['file1', 'file2', 'file3'], 'id': 'my_table_with_values.three'}], 'title': None} ok Basic check for column values ... ok Test Columns ... ok -Smoke test for conversion to str ... [INFO] 2022-11-14 15:11:19,525Z [tests.test_models_report_table test_str 23] +Smoke test for conversion to str ... [INFO] 2021-10-12 08:49:57,317Z [tests.test_models_report_table test_str 23] Table id:my_table --------------------- One Two Three --------------------- ok -Conversion to dictionary ... [INFO] 2022-11-14 15:11:19,525Z [tests.test_models_report_table test_to_dict 38] {'id': 'my_table', 'columns': [{'header': 'One', 'values': [], 'id': 'my_table.one'}, {'header': 'Two', 'values': [], 'id': 'my_table.two'}, {'header': 'Three', 'values': [], 'id': 'my_table.three'}], 'title': None} +Conversion to dictionary ... [INFO] 2021-10-12 08:49:57,318Z [tests.test_models_report_table test_to_dict 38] {'id': 'my_table', 'columns': [{'header': 'One', 'values': [], 'id': 'my_table.one'}, {'header': 'Two', 'values': [], 'id': 'my_table.two'}, {'header': 'Three', 'values': [], 'id': 'my_table.three'}], 'title': None} ok Cannot add column with duplicate id. ... a plot with id '2' has already been added to . -[ERROR] 2022-11-14 15:11:19,526Z [pbcommand.models.report is_unique 115] a plot with id '2' has already been added to . +[ERROR] 2021-10-12 08:49:57,318Z [pbcommand.models.report is_unique 115] a plot with id '2' has already been added to . ok Added data values by column identifier. ... ok Append data to columns by index. ... ok @@ -1188,25 +1223,25 @@ test_catch_output_file_extension (tests.test_parsers.TestParsers) ... ok test_input_output_files (tests.test_parsers.TestParsers) ... ok test_misc_parser_types (tests.test_parsers.TestParsers) ... ok -test_write_chunks (tests.test_pb_io_common.TestWriteChunk) ... [DEBUG] 2022-11-14 15:11:19,548Z [tests.test_pb_io_common test_write_chunks 26] [, , , , ] -[DEBUG] 2022-11-14 15:11:19,549Z [pbcommand.pb_io.common write_pipeline_chunks 28] Write 5 chunks to /tmp/tmpVjHxnbpipeline-chunks/tmplJcRcR_chunk.json +test_write_chunks (tests.test_pb_io_common.TestWriteChunk) ... [DEBUG] 2021-10-12 08:49:57,326Z [tests.test_pb_io_common test_write_chunks 26] [, , , , ] +[DEBUG] 2021-10-12 08:49:57,327Z [pbcommand.pb_io.common write_pipeline_chunks 28] Write 5 chunks to /tmp/tmpoRIJBipipeline-chunks/tmp3RoVZa_chunk.json ok -[INFO] 2022-11-14 15:11:19,551Z [tests.test_pb_io_conditions _loader 18] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-conditions/reseq-conditions-01.json -test_condition_a (tests.test_pb_io_conditions.TestSerializationOfResequencingConditions) ... [INFO] 2022-11-14 15:11:19,561Z [tests.test_pb_io_conditions test_condition_a 35] ReseqConditions(conditions=[ReseqCondition(cond_id='cond_alpha', subreadset='/path/to/subreadset-01.xml', alignmentset='/path/to/alignmentset-A.xml', referenceset='/path/to/reference.xml'), ReseqCondition(cond_id='cond_alpha', subreadset='/path/to/subreadset-02.xml', alignmentset='/path/to/alignmentset-B.xml', referenceset='/path/to/reference.xml'), ReseqCondition(cond_id='cond_beta', subreadset='/path/to/subreadset-03.xml', alignmentset='/path/to/alignmentset-C.xml', referenceset='/path/to/reference.xml')]) +[INFO] 2021-10-12 08:49:57,328Z [tests.test_pb_io_conditions _loader 18] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-conditions/reseq-conditions-01.json +test_condition_a (tests.test_pb_io_conditions.TestSerializationOfResequencingConditions) ... [INFO] 2021-10-12 08:49:57,328Z [tests.test_pb_io_conditions test_condition_a 35] ReseqConditions(conditions=[ReseqCondition(cond_id='cond_alpha', subreadset='/path/to/subreadset-01.xml', alignmentset='/path/to/alignmentset-A.xml', referenceset='/path/to/reference.xml'), ReseqCondition(cond_id='cond_alpha', subreadset='/path/to/subreadset-02.xml', alignmentset='/path/to/alignmentset-B.xml', referenceset='/path/to/reference.xml'), ReseqCondition(cond_id='cond_beta', subreadset='/path/to/subreadset-03.xml', alignmentset='/path/to/alignmentset-C.xml', referenceset='/path/to/reference.xml')]) ok test_condition_n (tests.test_pb_io_conditions.TestSerializationOfResequencingConditions) ... ok test_condition_paths_abs (tests.test_pb_io_conditions.TestSerializationOfResequencingConditions) ... ok -[INFO] 2022-11-14 15:11:19,562Z [tests.test_pb_io_conditions _loader 18] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-conditions/reseq-conditions-02.json -test_condition_a (tests.test_pb_io_conditions.TestSerializationOfResequencingConditionsWithRelativePath) ... [INFO] 2022-11-14 15:11:19,562Z [tests.test_pb_io_conditions test_condition_a 35] ReseqConditions(conditions=[ReseqCondition(cond_id='cond_alpha', subreadset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/subreadset-01.xml', alignmentset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/alignmentset-A.xml', referenceset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/reference.xml'), ReseqCondition(cond_id='cond_alpha', subreadset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/subreadset-02.xml', alignmentset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/alignmentset-B.xml', referenceset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/reference.xml'), ReseqCondition(cond_id='cond_beta', subreadset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/subreadset-03.xml', alignmentset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/alignmentset-C.xml', referenceset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/reference.xml')]) +[INFO] 2021-10-12 08:49:57,329Z [tests.test_pb_io_conditions _loader 18] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-conditions/reseq-conditions-02.json +test_condition_a (tests.test_pb_io_conditions.TestSerializationOfResequencingConditionsWithRelativePath) ... [INFO] 2021-10-12 08:49:57,329Z [tests.test_pb_io_conditions test_condition_a 35] ReseqConditions(conditions=[ReseqCondition(cond_id='cond_alpha', subreadset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/subreadset-01.xml', alignmentset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/alignmentset-A.xml', referenceset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/reference.xml'), ReseqCondition(cond_id='cond_alpha', subreadset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/subreadset-02.xml', alignmentset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/alignmentset-B.xml', referenceset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/reference.xml'), ReseqCondition(cond_id='cond_beta', subreadset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/subreadset-03.xml', alignmentset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/alignmentset-C.xml', referenceset='/build/python-pbcommand-1.1.1/tests/data/example-conditions/reference.xml')]) ok test_condition_n (tests.test_pb_io_conditions.TestSerializationOfResequencingConditionsWithRelativePath) ... ok test_condition_paths_abs (tests.test_pb_io_conditions.TestSerializationOfResequencingConditionsWithRelativePath) ... ok -[INFO] 2022-11-14 15:11:19,567Z [tests.test_pb_io_report _to_report 19] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/filter_reports_adapters.json +[INFO] 2021-10-12 08:49:57,331Z [tests.test_pb_io_report _to_report 19] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/filter_reports_adapters.json test_attributes (tests.test_pb_io_report.TestSerializationAdapterReport) ... ok test_id (tests.test_pb_io_report.TestSerializationAdapterReport) ... ok test_plotgroups (tests.test_pb_io_report.TestSerializationAdapterReport) ... ok test_plots (tests.test_pb_io_report.TestSerializationAdapterReport) ... ok -[INFO] 2022-11-14 15:11:19,578Z [tests.test_pb_io_report _to_report 19] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/overview.json +[INFO] 2021-10-12 08:49:57,332Z [tests.test_pb_io_report _to_report 19] loading json report from /build/python-pbcommand-1.1.1/tests/data/example-reports/overview.json test_attributes (tests.test_pb_io_report.TestSerializationOverviewReport) ... ok test_id (tests.test_pb_io_report.TestSerializationOverviewReport) ... ok test_title (tests.test_pb_io_report.TestSerializationOverviewReport) ... ok @@ -1215,7 +1250,7 @@ test_shorthand_options (tests.test_pb_io_tool_contract.TestLoadPipelinePresets) ... ok test_01 (tests.test_pb_io_tool_contract.TestLoadToolContract) ... ok test_tc_no_inputs (tests.test_pb_io_tool_contract.TestMalformedToolContract) ... ok -test_01 (tests.test_pb_io_tool_contract.TestWriteResolvedToolContractAvro) ... [DEBUG] 2022-11-14 15:11:19,613Z [pbcommand.pb_io.tool_contract_io _write_records_to_avro 388] Write avro file to /tmp/tmpxK3OFbrtc-app/tmpH_QLWE-resolved-tool-contract.avro +test_01 (tests.test_pb_io_tool_contract.TestWriteResolvedToolContractAvro) ... [DEBUG] 2021-10-12 08:49:57,339Z [pbcommand.pb_io.tool_contract_io _write_records_to_avro 388] Write avro file to /tmp/tmpzIchkyrtc-app/tmpdrPOrH-resolved-tool-contract.avro ok test_01 (tests.test_pb_io_tool_contract_v1.TestLoadToolContract) ... ok test_tc_no_inputs (tests.test_pb_io_tool_contract_v1.TestMalformedToolContract) ... ok @@ -1223,44 +1258,44 @@ test_failure_modes (tests.test_resolver.TestResolver) ... ok test_sanity (tests.test_resolver.TestResolver) ... ok test_sanity (tests.test_resolver.TestScatterResolver) ... ok -test_validate_pipeline_datastore_view_rules (tests.test_schema_validation.ValidateDataStoreViewRules) ... [INFO] 2022-11-14 15:11:19,650Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/pipeline-datastore-view-rules/rules_01.json' -[INFO] 2022-11-14 15:11:19,650Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/pipeline-datastore-view-rules/rules_01.json +test_validate_pipeline_datastore_view_rules (tests.test_schema_validation.ValidateDataStoreViewRules) ... [INFO] 2021-10-12 08:49:57,347Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/pipeline-datastore-view-rules/rules_01.json' +[INFO] 2021-10-12 08:49:57,347Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/pipeline-datastore-view-rules/rules_01.json ok -test_validate_pipeline_presets (tests.test_schema_validation.ValidatePipelinePreset) ... [INFO] 2022-11-14 15:11:19,656Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/pipeline-presets/example-pipeline-presets.json' -[INFO] 2022-11-14 15:11:19,656Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/pipeline-presets/example-pipeline-presets.json -[INFO] 2022-11-14 15:11:19,657Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/pipeline-presets/example-pipeline-presets-typed.json' -[INFO] 2022-11-14 15:11:19,657Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/pipeline-presets/example-pipeline-presets-typed.json +test_validate_pipeline_presets (tests.test_schema_validation.ValidatePipelinePreset) ... [INFO] 2021-10-12 08:49:57,348Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/pipeline-presets/example-pipeline-presets.json' +[INFO] 2021-10-12 08:49:57,348Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/pipeline-presets/example-pipeline-presets.json +[INFO] 2021-10-12 08:49:57,349Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/pipeline-presets/example-pipeline-presets-typed.json' +[INFO] 2021-10-12 08:49:57,349Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/pipeline-presets/example-pipeline-presets-typed.json ok test_validate_report_spec (tests.test_schema_validation.ValidateReportSpec) ... ok -test_validate_resolved_tool_contracts (tests.test_schema_validation.ValidateResolvedToolContracts) ... [INFO] 2022-11-14 15:11:19,660Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/resolved_tool_contract_dev_app.json' -[INFO] 2022-11-14 15:11:19,664Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/resolved_tool_contract_dev_app.json -[INFO] 2022-11-14 15:11:19,664Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/resolved_contract_01.json' -[INFO] 2022-11-14 15:11:19,665Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/resolved_contract_01.json -[INFO] 2022-11-14 15:11:19,665Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/dev_mixed_app_resolved_tool_contract.json' -[INFO] 2022-11-14 15:11:19,665Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/dev_mixed_app_resolved_tool_contract.json -[INFO] 2022-11-14 15:11:19,665Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/dev_example_resolved_tool_contract.json' -[INFO] 2022-11-14 15:11:19,665Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/dev_example_resolved_tool_contract.json -ok -test_validate_tool_contracts (tests.test_schema_validation.ValidateToolContracts) ... [INFO] 2022-11-14 15:11:19,676Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_txt_hello_tool_contract.json' -[INFO] 2022-11-14 15:11:19,676Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_txt_hello_tool_contract.json -[INFO] 2022-11-14 15:11:19,684Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_txt_custom_outs_tool_contract.json' -[INFO] 2022-11-14 15:11:19,684Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_txt_custom_outs_tool_contract.json -[INFO] 2022-11-14 15:11:19,685Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_qhello_world_tool_contract.json' -[INFO] 2022-11-14 15:11:19,685Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_qhello_world_tool_contract.json -[INFO] 2022-11-14 15:11:19,686Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_fastq2fasta_tool_contract.json' -[INFO] 2022-11-14 15:11:19,686Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_fastq2fasta_tool_contract.json -[INFO] 2022-11-14 15:11:19,692Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_app_tool_contract.json' -[INFO] 2022-11-14 15:11:19,692Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_app_tool_contract.json -[INFO] 2022-11-14 15:11:19,693Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_scatter_fasta_app_tool_contract.json' -[INFO] 2022-11-14 15:11:19,693Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_scatter_fasta_app_tool_contract.json -[INFO] 2022-11-14 15:11:19,694Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_mixed_app_tool_contract.json' -[INFO] 2022-11-14 15:11:19,694Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_mixed_app_tool_contract.json -[INFO] 2022-11-14 15:11:19,695Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_gather_fasta_app_tool_contract.json' -[INFO] 2022-11-14 15:11:19,695Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_gather_fasta_app_tool_contract.json -[INFO] 2022-11-14 15:11:19,695Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_example_tool_contract.json' -[INFO] 2022-11-14 15:11:19,696Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_example_tool_contract.json -[INFO] 2022-11-14 15:11:19,696Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_example_dev_txt_app_tool_contract.json' -[INFO] 2022-11-14 15:11:19,696Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_example_dev_txt_app_tool_contract.json +test_validate_resolved_tool_contracts (tests.test_schema_validation.ValidateResolvedToolContracts) ... [INFO] 2021-10-12 08:49:57,351Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/resolved_tool_contract_dev_app.json' +[INFO] 2021-10-12 08:49:57,351Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/resolved_tool_contract_dev_app.json +[INFO] 2021-10-12 08:49:57,352Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/resolved_contract_01.json' +[INFO] 2021-10-12 08:49:57,352Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/resolved_contract_01.json +[INFO] 2021-10-12 08:49:57,352Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/dev_mixed_app_resolved_tool_contract.json' +[INFO] 2021-10-12 08:49:57,352Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/dev_mixed_app_resolved_tool_contract.json +[INFO] 2021-10-12 08:49:57,352Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/dev_example_resolved_tool_contract.json' +[INFO] 2021-10-12 08:49:57,352Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/resolved-tool-contracts/dev_example_resolved_tool_contract.json +ok +test_validate_tool_contracts (tests.test_schema_validation.ValidateToolContracts) ... [INFO] 2021-10-12 08:49:57,353Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_txt_hello_tool_contract.json' +[INFO] 2021-10-12 08:49:57,354Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_txt_hello_tool_contract.json +[INFO] 2021-10-12 08:49:57,354Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_txt_custom_outs_tool_contract.json' +[INFO] 2021-10-12 08:49:57,354Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_txt_custom_outs_tool_contract.json +[INFO] 2021-10-12 08:49:57,355Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_qhello_world_tool_contract.json' +[INFO] 2021-10-12 08:49:57,355Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_qhello_world_tool_contract.json +[INFO] 2021-10-12 08:49:57,355Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_fastq2fasta_tool_contract.json' +[INFO] 2021-10-12 08:49:57,355Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_fastq2fasta_tool_contract.json +[INFO] 2021-10-12 08:49:57,356Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_app_tool_contract.json' +[INFO] 2021-10-12 08:49:57,356Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/pbcommand.tasks.dev_app_tool_contract.json +[INFO] 2021-10-12 08:49:57,356Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_scatter_fasta_app_tool_contract.json' +[INFO] 2021-10-12 08:49:57,357Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_scatter_fasta_app_tool_contract.json +[INFO] 2021-10-12 08:49:57,357Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_mixed_app_tool_contract.json' +[INFO] 2021-10-12 08:49:57,357Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_mixed_app_tool_contract.json +[INFO] 2021-10-12 08:49:57,358Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_gather_fasta_app_tool_contract.json' +[INFO] 2021-10-12 08:49:57,358Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_gather_fasta_app_tool_contract.json +[INFO] 2021-10-12 08:49:57,358Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_example_tool_contract.json' +[INFO] 2021-10-12 08:49:57,358Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_example_tool_contract.json +[INFO] 2021-10-12 08:49:57,358Z [tests.test_schema_validation test_is_validate 40] Attempting to validate '/build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_example_dev_txt_app_tool_contract.json' +[INFO] 2021-10-12 08:49:57,359Z [tests.test_schema_validation test_is_validate 42] is-valid? True /build/python-pbcommand-1.1.1/tests/data/tool-contracts/dev_example_dev_txt_app_tool_contract.json ok Test that the pb_requirements decorator monkey-patches test methods ... ok test_empty_list (tests.test_utils.TestCompose) ... ok @@ -1271,19 +1306,19 @@ test_basic (tests.test_utils.TestSingleton) ... ok test_get_dataset_metadata (tests.test_utils.TestUtils) ... SKIP: pbtestdata not available, skipping Test: Return abspath if file found ... ok -Test: Raise IOError if file not found ... ls: cannot access 'this_file_does_not_exist': No such file or directory +Test: Raise IOError if file not found ... ls: 'this_file_does_not_exist' ei saa kasutada: No such file or directory ok Test: Return abspath if file found and not empty ... ok -Test: Raise IOError if file found but empty ... ls: cannot access '/tmp/tmpsNJOMQempty': No such file or directory +Test: Raise IOError if file found but empty ... ls: '/tmp/tmpnU5Rjcempty' ei saa kasutada: No such file or directory ok -Test: Raise IOError if output does not exist ... ls: cannot access '/whatev': No such file or directory +Test: Raise IOError if output does not exist ... ls: '/whatev' ei saa kasutada: No such file or directory ok test_validate_report (tests.test_validators.TestValidators) ... ok test_validate_report_fails (tests.test_validators.TestValidators) ... ok Test: Raise ValueError if report has path sep ... ok ---------------------------------------------------------------------- -Ran 157 tests in 6.982s +Ran 157 tests in 4.367s OK (SKIP=1) make[1]: Leaving directory '/build/python-pbcommand-1.1.1' @@ -1499,12 +1534,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: including full source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/3974162/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/3974162/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/388208 and its subdirectories -I: Current time: Mon Nov 14 03:11:51 -12 2022 -I: pbuilder-time-stamp: 1668438711 +I: removing directory /srv/workspace/pbuilder/3974162 and its subdirectories +I: Current time: Tue Oct 12 22:50:04 +14 2021 +I: pbuilder-time-stamp: 1634028604