0s autopkgtest [06:36:17]: starting date and time: 2024-05-05 06:36:17+0000 0s autopkgtest [06:36:17]: git checkout: 699e7f9f ssh-setup/nova: explicitely set 'fqdn' in cloud-init 0s autopkgtest [06:36:17]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6brsplk3/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@bos03-arm64-18.secgroup --name adt-oracular-arm64-ctdconverter-20240505-063617-juju-7f2275-prod-proposed-migration-environment-3-c32ce91c-3bb2-43e7-9a53-677a236dcfdd --image adt/ubuntu-oracular-arm64-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://ftpmaster.internal/ubuntu/ 266s autopkgtest [06:40:43]: testbed dpkg architecture: arm64 266s autopkgtest [06:40:43]: testbed apt version: 2.7.14build2 266s autopkgtest [06:40:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 267s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [64.7 kB] 267s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [2800 B] 267s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [1708 kB] 267s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [23.5 kB] 267s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [110 kB] 267s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [188 kB] 267s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [13.1 kB] 267s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [1288 kB] 268s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [22.1 kB] 268s Fetched 3420 kB in 1s (2798 kB/s) 268s Reading package lists... 271s Reading package lists... 272s Building dependency tree... 272s Reading state information... 273s Calculating upgrade... 274s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 274s Reading package lists... 274s Building dependency tree... 274s Reading state information... 275s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 276s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease 276s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease 276s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease 276s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 278s Reading package lists... 278s Reading package lists... 278s Building dependency tree... 278s Reading state information... 279s Calculating upgrade... 280s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 280s Reading package lists... 281s Building dependency tree... 281s Reading state information... 283s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 286s autopkgtest [06:41:03]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 286s autopkgtest [06:41:03]: @@@@@@@@@@@@@@@@@@@@ apt-source ctdconverter 288s Get:1 http://ftpmaster.internal/ubuntu oracular/universe ctdconverter 2.1-6 (dsc) [2138 B] 288s Get:2 http://ftpmaster.internal/ubuntu oracular/universe ctdconverter 2.1-6 (tar) [38.1 kB] 288s Get:3 http://ftpmaster.internal/ubuntu oracular/universe ctdconverter 2.1-6 (diff) [7340 B] 288s gpgv: Signature made Thu Jul 13 15:37:57 2023 UTC 288s gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 288s gpgv: issuer "tille@debian.org" 288s gpgv: Can't check signature: No public key 288s dpkg-source: warning: cannot verify inline signature for ./ctdconverter_2.1-6.dsc: no acceptable signature found 289s autopkgtest [06:41:06]: testing package ctdconverter version 2.1-6 289s autopkgtest [06:41:06]: build not needed 289s autopkgtest [06:41:06]: test run-unit-test: preparing testbed 290s Reading package lists... 291s Building dependency tree... 291s Reading state information... 291s Starting pkgProblemResolver with broken count: 0 291s Starting 2 pkgProblemResolver with broken count: 0 291s Done 292s The following additional packages will be installed: 292s ctdconverter libxslt1.1 python3-ctdopts python3-lxml python3-ruamel.yaml 292s python3-ruamel.yaml.clib 292s Suggested packages: 292s cwl-runner python-lxml-doc 292s Recommended packages: 292s python3-bs4 python3-cssselect python3-html5lib 292s The following NEW packages will be installed: 292s autopkgtest-satdep ctdconverter libxslt1.1 python3-ctdopts python3-lxml 292s python3-ruamel.yaml python3-ruamel.yaml.clib 292s 0 upgraded, 7 newly installed, 0 to remove and 0 not upgraded. 292s Need to get 1649 kB/1650 kB of archives. 292s After this operation, 6493 kB of additional disk space will be used. 292s Get:1 /tmp/autopkgtest.m9RWIf/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [708 B] 293s Get:2 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-ctdopts all 1.5-2 [22.5 kB] 293s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libxslt1.1 arm64 1.1.39-0exp1build1 [166 kB] 293s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-lxml arm64 5.2.1-1 [1179 kB] 293s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 python3-ruamel.yaml.clib arm64 0.2.8+ds-1 [127 kB] 293s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 python3-ruamel.yaml all 0.18.6+ds-3 [126 kB] 293s Get:7 http://ftpmaster.internal/ubuntu oracular/universe arm64 ctdconverter all 2.1-6 [28.1 kB] 294s Fetched 1649 kB in 1s (2328 kB/s) 294s Selecting previously unselected package python3-ctdopts. 294s (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 ... 77729 files and directories currently installed.) 294s Preparing to unpack .../0-python3-ctdopts_1.5-2_all.deb ... 294s Unpacking python3-ctdopts (1.5-2) ... 294s Selecting previously unselected package libxslt1.1:arm64. 294s Preparing to unpack .../1-libxslt1.1_1.1.39-0exp1build1_arm64.deb ... 294s Unpacking libxslt1.1:arm64 (1.1.39-0exp1build1) ... 294s Selecting previously unselected package python3-lxml:arm64. 294s Preparing to unpack .../2-python3-lxml_5.2.1-1_arm64.deb ... 294s Unpacking python3-lxml:arm64 (5.2.1-1) ... 294s Selecting previously unselected package python3-ruamel.yaml.clib:arm64. 294s Preparing to unpack .../3-python3-ruamel.yaml.clib_0.2.8+ds-1_arm64.deb ... 294s Unpacking python3-ruamel.yaml.clib:arm64 (0.2.8+ds-1) ... 294s Selecting previously unselected package python3-ruamel.yaml. 294s Preparing to unpack .../4-python3-ruamel.yaml_0.18.6+ds-3_all.deb ... 294s Unpacking python3-ruamel.yaml (0.18.6+ds-3) ... 294s Selecting previously unselected package ctdconverter. 294s Preparing to unpack .../5-ctdconverter_2.1-6_all.deb ... 294s Unpacking ctdconverter (2.1-6) ... 294s Selecting previously unselected package autopkgtest-satdep. 294s Preparing to unpack .../6-1-autopkgtest-satdep.deb ... 294s Unpacking autopkgtest-satdep (0) ... 294s Setting up python3-ctdopts (1.5-2) ... 294s Setting up python3-ruamel.yaml.clib:arm64 (0.2.8+ds-1) ... 294s Setting up python3-ruamel.yaml (0.18.6+ds-3) ... 295s Setting up libxslt1.1:arm64 (1.1.39-0exp1build1) ... 295s Setting up python3-lxml:arm64 (5.2.1-1) ... 295s Setting up ctdconverter (2.1-6) ... 295s Setting up autopkgtest-satdep (0) ... 295s Processing triggers for man-db (2.12.0-4build2) ... 296s Processing triggers for libc-bin (2.39-0ubuntu8) ... 300s (Reading database ... 77962 files and directories currently installed.) 300s Removing autopkgtest-satdep (0) ... 300s autopkgtest [06:41:17]: test run-unit-test: [----------------------- 301s CTDConverter - A project from the WorkflowConversion family (https://github.com/WorkflowConversion/CTDConverter) 301s 301s Copyright 2017, WorklfowConversion 301s 301s Licensed under the Apache License, Version 2.0 (the "License"); 301s you may not use this file except in compliance with the License. 301s You may obtain a copy of the License at 301s 301s http://www.apache.org/licenses/LICENSE-2.0 301s 301s Unless required by applicable law or agreed to in writing, software 301s distributed under the License is distributed on an "AS IS" BASIS, 301s WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 301s See the License for the specific language governing permissions and 301s limitations under the License. 301s 301s 301s USAGE: 301s 301s $ CTDConverter [FORMAT] [ARGUMENTS ...] 301s 301s FORMAT can be either one of the supported output formats: cwl, galaxy. 301s 301s There is one converter for each supported FORMAT, each taking a different set of arguments. Please consult the detailed 301s documentation for each of the converters. Nevertheless, all converters have the following common parameters/options: 301s 301s 301s I - Parsing a single CTD file and convert it: 301s 301s $ CTDConverter [FORMAT] -i [INPUT_FILE] -o [OUTPUT_FILE] 301s 301s 301s II - Parsing several CTD files, output converted wrappers in a given folder: 301s 301s $ CTDConverter [FORMAT] -i [INPUT_FILES] -o [OUTPUT_DIRECTORY] 301s 301s 301s III - Hardcoding parameters 301s 301s It is possible to hardcode parameters. This makes sense if you want to set a tool in 'quiet' mode or if your tools 301s support multi-threading and accept the number of threads via a parameter, without giving end users the chance to 301s change the values for these parameters. 301s 301s In order to generate hardcoded parameters, you need to provide a simple file. Each line of this file contains 301s two or three columns separated by whitespace. Any line starting with a '#' will be ignored. The first column contains 301s the name of the parameter, the second column contains the value that will always be set for this parameter. Only the 301s first two columns are mandatory. 301s 301s If the parameter is to be hardcoded only for a set of tools, then a third column can be added. This column contains 301s a comma-separated list of tool names for which the parameter will be hardcoded. If a third column is not present, 301s then all processed tools containing the given parameter will get a hardcoded value for it. 301s 301s The following is an example of a valid file: 301s 301s ##################################### HARDCODED PARAMETERS example ##################################### 301s # Every line starting with a # will be handled as a comment and will not be parsed. 301s # The first column is the name of the parameter and the second column is the value that will be used. 301s 301s # Parameter name # Value # Tool(s) 301s threads 8 301s mode quiet 301s xtandem_executable xtandem XTandemAdapter 301s verbosity high Foo, Bar 301s 301s ######################################################################################################### 301s 301s Using the above file will produce a command-line similar to: 301s 301s [TOOL] ... -threads 8 -mode quiet ... 301s 301s for all tools. For XTandemAdapter, however, the command-line will look like: 301s 301s XtandemAdapter ... -threads 8 -mode quiet -xtandem_executable xtandem ... 301s 301s And for tools Foo and Bar, the command-line will be similar to: 301s 301s Foo -threads 8 -mode quiet -verbosity high ... 301s 301s 301s IV - Engine-specific parameters 301s 301s i - Galaxy 301s 301s a. Providing file formats, mimetypes 301s 301s Galaxy supports the concept of file format in order to connect compatible ports, that is, input ports of a 301s certain data format will be able to receive data from a port from the same format. This converter allows you 301s to provide a personalized file in which you can relate the CTD data formats with supported Galaxy data formats. 301s The layout of this file consists of lines, each of either one or four columns separated by any amount of 301s whitespace. The content of each column is as follows: 301s 301s * 1st column: file extension 301s * 2nd column: data type, as listed in Galaxy 301s * 3rd column: full-named Galaxy data type, as it will appear on datatypes_conf.xml 301s * 4th column: mimetype (optional) 301s 301s The following is an example of a valid "file formats" file: 301s 301s ########################################## FILE FORMATS example ########################################## 301s # Every line starting with a # will be handled as a comment and will not be parsed. 301s # The first column is the file format as given in the CTD and second column is the Galaxy data format. The 301s # second, third, fourth and fifth columns can be left empty if the data type has already been registered 301s # in Galaxy, otherwise, all but the mimetype must be provided. 301s 301s # CTD type # Galaxy type # Long Galaxy data type # Mimetype 301s csv tabular galaxy.datatypes.data:Text 301s fasta 301s ini txt galaxy.datatypes.data:Text 301s txt 301s idxml txt galaxy.datatypes.xml:GenericXml application/xml 301s options txt galaxy.datatypes.data:Text 301s grid grid galaxy.datatypes.data:Grid 301s ########################################################################################################## 301s 301s Note that each line consists precisely of either one, three or four columns. In the case of data types already 301s registered in Galaxy (such as fasta and txt in the above example), only the first column is needed. In the 301s case of data types that haven't been yet registered in Galaxy, the first three columns are needed 301s (mimetype is optional). 301s 301s For information about Galaxy data types and subclasses, see the following page: 301s https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes 301s 301s 301s b. Finer control over which tools will be converted 301s 301s Sometimes only a subset of CTDs needs to be converted. It is possible to either explicitly specify which tools 301s will be converted or which tools will not be converted. 301s 301s The value of the -s/--skip-tools parameter is a file in which each line will be interpreted as the name of a 301s tool that will not be converted. Conversely, the value of the -r/--required-tools is a file in which each line 301s will be interpreted as a tool that is required. Only one of these parameters can be specified at a given time. 301s 301s The format of both files is exactly the same. As stated before, each line will be interpreted as the name of a 301s tool. Any line starting with a '#' will be ignored. 301s 301s 301s ii - CWL 301s 301s There are, for now, no CWL-specific parameters or options. 301s 301s 301s 301s autopkgtest [06:41:18]: test run-unit-test: -----------------------] 302s autopkgtest [06:41:19]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 302s run-unit-test PASS (superficial) 302s autopkgtest [06:41:19]: @@@@@@@@@@@@@@@@@@@@ summary 302s run-unit-test PASS (superficial) 306s Creating nova instance adt-oracular-arm64-ctdconverter-20240505-063617-juju-7f2275-prod-proposed-migration-environment-3-c32ce91c-3bb2-43e7-9a53-677a236dcfdd from image adt/ubuntu-oracular-arm64-server-20240505.img (UUID cab8e143-b89e-42dc-afbd-61eafce7a271)...