0s autopkgtest [04:12:41]: starting date and time: 2024-05-06 04:12:41+0000 0s autopkgtest [04:12:41]: git checkout: 699e7f9f ssh-setup/nova: explicitely set 'fqdn' in cloud-init 0s autopkgtest [04:12:41]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.gpp370ub/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:ruamel.yaml,src:monty,src:ruamel.yaml.clib --apt-upgrade ctdconverter --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=ruamel.yaml/0.18.6+ds-3 monty/2024.4.17-1 ruamel.yaml.clib/0.2.8+ds-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-ppc64el-4.secgroup --name adt-oracular-ppc64el-ctdconverter-20240506-041241-juju-7f2275-prod-proposed-migration-environment-3-24f5358d-33f8-471b-b650-8e5fd1d173d0 --image adt/ubuntu-oracular-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://us.ports.ubuntu.com/ubuntu-ports/ 220s autopkgtest [04:16:21]: testbed dpkg architecture: ppc64el 221s autopkgtest [04:16:22]: testbed apt version: 2.7.14build2 221s autopkgtest [04:16:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 222s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] 222s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [110 kB] 222s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [1647 kB] 222s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [2800 B] 222s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [23.5 kB] 222s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [182 kB] 222s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1260 B] 222s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [1269 kB] 222s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [22.6 kB] 223s Fetched 3322 kB in 1s (2593 kB/s) 223s Reading package lists... 225s Reading package lists... 225s Building dependency tree... 225s Reading state information... 226s Calculating upgrade... 226s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 226s Reading package lists... 226s Building dependency tree... 226s Reading state information... 226s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 227s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 227s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 227s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 227s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 228s Reading package lists... 228s Reading package lists... 228s Building dependency tree... 228s Reading state information... 228s Calculating upgrade... 228s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 228s Reading package lists... 229s Building dependency tree... 229s Reading state information... 229s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 232s autopkgtest [04:16:33]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024 232s autopkgtest [04:16:33]: @@@@@@@@@@@@@@@@@@@@ apt-source ctdconverter 233s Get:1 http://ftpmaster.internal/ubuntu oracular/universe ctdconverter 2.1-6 (dsc) [2138 B] 233s Get:2 http://ftpmaster.internal/ubuntu oracular/universe ctdconverter 2.1-6 (tar) [38.1 kB] 233s Get:3 http://ftpmaster.internal/ubuntu oracular/universe ctdconverter 2.1-6 (diff) [7340 B] 234s gpgv: Signature made Thu Jul 13 15:37:57 2023 UTC 234s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 234s gpgv: issuer "tille@debian.org" 234s gpgv: Can't check signature: No public key 234s dpkg-source: warning: cannot verify inline signature for ./ctdconverter_2.1-6.dsc: no acceptable signature found 234s autopkgtest [04:16:35]: testing package ctdconverter version 2.1-6 234s autopkgtest [04:16:35]: build not needed 234s autopkgtest [04:16:35]: test run-unit-test: preparing testbed 235s Reading package lists... 236s Building dependency tree... 236s Reading state information... 236s Starting pkgProblemResolver with broken count: 0 236s Starting 2 pkgProblemResolver with broken count: 0 236s Done 236s The following additional packages will be installed: 236s ctdconverter libxslt1.1 python3-ctdopts python3-lxml python3-ruamel.yaml 236s python3-ruamel.yaml.clib 236s Suggested packages: 236s cwl-runner python-lxml-doc 236s Recommended packages: 236s python3-bs4 python3-cssselect python3-html5lib 236s The following NEW packages will be installed: 236s autopkgtest-satdep ctdconverter libxslt1.1 python3-ctdopts python3-lxml 236s python3-ruamel.yaml python3-ruamel.yaml.clib 236s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 236s Need to get 1776 kB/1777 kB of archives. 236s After this operation, 7608 kB of additional disk space will be used. 236s Get:1 /tmp/autopkgtest.yXW4tp/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [712 B] 236s Get:2 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-ctdopts all 1.5-2 [22.5 kB] 236s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1build1 [192 kB] 237s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-lxml ppc64el 5.2.1-1 [1250 kB] 237s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el python3-ruamel.yaml.clib ppc64el 0.2.8+ds-1 [158 kB] 237s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el python3-ruamel.yaml all 0.18.6+ds-3 [126 kB] 237s Get:7 http://ftpmaster.internal/ubuntu oracular/universe ppc64el ctdconverter all 2.1-6 [28.1 kB] 237s Fetched 1776 kB in 1s (2052 kB/s) 237s Selecting previously unselected package python3-ctdopts. 238s (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 ... 72141 files and directories currently installed.) 238s Preparing to unpack .../0-python3-ctdopts_1.5-2_all.deb ... 238s Unpacking python3-ctdopts (1.5-2) ... 238s Selecting previously unselected package libxslt1.1:ppc64el. 238s Preparing to unpack .../1-libxslt1.1_1.1.39-0exp1build1_ppc64el.deb ... 238s Unpacking libxslt1.1:ppc64el (1.1.39-0exp1build1) ... 238s Selecting previously unselected package python3-lxml:ppc64el. 238s Preparing to unpack .../2-python3-lxml_5.2.1-1_ppc64el.deb ... 238s Unpacking python3-lxml:ppc64el (5.2.1-1) ... 238s Selecting previously unselected package python3-ruamel.yaml.clib:ppc64el. 238s Preparing to unpack .../3-python3-ruamel.yaml.clib_0.2.8+ds-1_ppc64el.deb ... 238s Unpacking python3-ruamel.yaml.clib:ppc64el (0.2.8+ds-1) ... 238s Selecting previously unselected package python3-ruamel.yaml. 238s Preparing to unpack .../4-python3-ruamel.yaml_0.18.6+ds-3_all.deb ... 238s Unpacking python3-ruamel.yaml (0.18.6+ds-3) ... 238s Selecting previously unselected package ctdconverter. 238s Preparing to unpack .../5-ctdconverter_2.1-6_all.deb ... 238s Unpacking ctdconverter (2.1-6) ... 238s Selecting previously unselected package autopkgtest-satdep. 238s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 238s Unpacking autopkgtest-satdep (0) ... 238s Setting up python3-ctdopts (1.5-2) ... 238s Setting up python3-ruamel.yaml.clib:ppc64el (0.2.8+ds-1) ... 238s Setting up python3-ruamel.yaml (0.18.6+ds-3) ... 238s Setting up libxslt1.1:ppc64el (1.1.39-0exp1build1) ... 238s Setting up python3-lxml:ppc64el (5.2.1-1) ... 238s Setting up ctdconverter (2.1-6) ... 239s Setting up autopkgtest-satdep (0) ... 239s Processing triggers for man-db (2.12.0-4build2) ... 239s Processing triggers for libc-bin (2.39-0ubuntu8) ... 241s (Reading database ... 72374 files and directories currently installed.) 241s Removing autopkgtest-satdep (0) ... 242s autopkgtest [04:16:43]: test run-unit-test: [----------------------- 242s CTDConverter - A project from the WorkflowConversion family (https://github.com/WorkflowConversion/CTDConverter) 242s 242s Copyright 2017, WorklfowConversion 242s 242s Licensed under the Apache License, Version 2.0 (the "License"); 242s you may not use this file except in compliance with the License. 242s You may obtain a copy of the License at 242s 242s http://www.apache.org/licenses/LICENSE-2.0 242s 242s Unless required by applicable law or agreed to in writing, software 242s distributed under the License is distributed on an "AS IS" BASIS, 242s WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 242s See the License for the specific language governing permissions and 242s limitations under the License. 242s 242s 242s USAGE: 242s 242s $ CTDConverter [FORMAT] [ARGUMENTS ...] 242s 242s FORMAT can be either one of the supported output formats: cwl, galaxy. 242s 242s There is one converter for each supported FORMAT, each taking a different set of arguments. Please consult the detailed 242s documentation for each of the converters. Nevertheless, all converters have the following common parameters/options: 242s 242s 242s I - Parsing a single CTD file and convert it: 242s 242s $ CTDConverter [FORMAT] -i [INPUT_FILE] -o [OUTPUT_FILE] 242s 242s 242s II - Parsing several CTD files, output converted wrappers in a given folder: 242s 242s $ CTDConverter [FORMAT] -i [INPUT_FILES] -o [OUTPUT_DIRECTORY] 242s 242s 242s III - Hardcoding parameters 242s 242s It is possible to hardcode parameters. This makes sense if you want to set a tool in 'quiet' mode or if your tools 242s support multi-threading and accept the number of threads via a parameter, without giving end users the chance to 242s change the values for these parameters. 242s 242s In order to generate hardcoded parameters, you need to provide a simple file. Each line of this file contains 242s two or three columns separated by whitespace. Any line starting with a '#' will be ignored. The first column contains 242s the name of the parameter, the second column contains the value that will always be set for this parameter. Only the 242s first two columns are mandatory. 242s 242s If the parameter is to be hardcoded only for a set of tools, then a third column can be added. This column contains 242s a comma-separated list of tool names for which the parameter will be hardcoded. If a third column is not present, 242s then all processed tools containing the given parameter will get a hardcoded value for it. 242s 242s The following is an example of a valid file: 242s 242s ##################################### HARDCODED PARAMETERS example ##################################### 242s # Every line starting with a # will be handled as a comment and will not be parsed. 242s # The first column is the name of the parameter and the second column is the value that will be used. 242s 242s # Parameter name # Value # Tool(s) 242s threads 8 242s mode quiet 242s xtandem_executable xtandem XTandemAdapter 242s verbosity high Foo, Bar 242s 242s ######################################################################################################### 242s 242s Using the above file will produce a command-line similar to: 242s 242s [TOOL] ... -threads 8 -mode quiet ... 242s 242s for all tools. For XTandemAdapter, however, the command-line will look like: 242s 242s XtandemAdapter ... -threads 8 -mode quiet -xtandem_executable xtandem ... 242s 242s And for tools Foo and Bar, the command-line will be similar to: 242s 242s Foo -threads 8 -mode quiet -verbosity high ... 242s 242s 242s IV - Engine-specific parameters 242s 242s i - Galaxy 242s 242s a. Providing file formats, mimetypes 242s 242s Galaxy supports the concept of file format in order to connect compatible ports, that is, input ports of a 242s certain data format will be able to receive data from a port from the same format. This converter allows you 242s to provide a personalized file in which you can relate the CTD data formats with supported Galaxy data formats. 242s The layout of this file consists of lines, each of either one or four columns separated by any amount of 242s whitespace. The content of each column is as follows: 242s 242s * 1st column: file extension 242s * 2nd column: data type, as listed in Galaxy 242s * 3rd column: full-named Galaxy data type, as it will appear on datatypes_conf.xml 242s * 4th column: mimetype (optional) 242s 242s The following is an example of a valid "file formats" file: 242s 242s ########################################## FILE FORMATS example ########################################## 242s # Every line starting with a # will be handled as a comment and will not be parsed. 242s # The first column is the file format as given in the CTD and second column is the Galaxy data format. The 242s # second, third, fourth and fifth columns can be left empty if the data type has already been registered 242s # in Galaxy, otherwise, all but the mimetype must be provided. 242s 242s # CTD type # Galaxy type # Long Galaxy data type # Mimetype 242s csv tabular galaxy.datatypes.data:Text 242s fasta 242s ini txt galaxy.datatypes.data:Text 242s txt 242s idxml txt galaxy.datatypes.xml:GenericXml application/xml 242s options txt galaxy.datatypes.data:Text 242s grid grid galaxy.datatypes.data:Grid 242s ########################################################################################################## 242s 242s Note that each line consists precisely of either one, three or four columns. In the case of data types already 242s registered in Galaxy (such as fasta and txt in the above example), only the first column is needed. In the 242s case of data types that haven't been yet registered in Galaxy, the first three columns are needed 242s (mimetype is optional). 242s 242s For information about Galaxy data types and subclasses, see the following page: 242s https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes 242s 242s 242s b. Finer control over which tools will be converted 242s 242s Sometimes only a subset of CTDs needs to be converted. It is possible to either explicitly specify which tools 242s will be converted or which tools will not be converted. 242s 242s The value of the -s/--skip-tools parameter is a file in which each line will be interpreted as the name of a 242s tool that will not be converted. Conversely, the value of the -r/--required-tools is a file in which each line 242s will be interpreted as a tool that is required. Only one of these parameters can be specified at a given time. 242s 242s The format of both files is exactly the same. As stated before, each line will be interpreted as the name of a 242s tool. Any line starting with a '#' will be ignored. 242s 242s 242s ii - CWL 242s 242s There are, for now, no CWL-specific parameters or options. 242s 242s 242s 243s autopkgtest [04:16:44]: test run-unit-test: -----------------------] 243s run-unit-test PASS (superficial) 243s autopkgtest [04:16:44]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 244s autopkgtest [04:16:45]: @@@@@@@@@@@@@@@@@@@@ summary 244s run-unit-test PASS (superficial) 324s Creating nova instance adt-oracular-ppc64el-ctdconverter-20240506-041241-juju-7f2275-prod-proposed-migration-environment-3-24f5358d-33f8-471b-b650-8e5fd1d173d0 from image adt/ubuntu-oracular-ppc64el-server-20240505.img (UUID 5f2b29ba-0f78-4fea-bb4b-40e2e923a051)...