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    Peter Amstutz
    @tetron
    now I'm wondering if the package building does something strange
    uh, arvados-workbench_1.4.3-1_amd64.deb is not the same as arvados-workbench-server_1.4.3-1_amd64.deb ?
    Dante Tsang
    @dantetwc
    Ignore the version for workbench as I haven't update it for the specified version in the package
    It is 1.16.6 for api
    Peter Amstutz
    @tetron
    ah, got it
    Peter Amstutz
    @tetron
    I'm very confused. maybe bundler wants to load an old version of itself depending on the version in the Gemfile.lock ?
    bundler is supposed to solve problems but lately it has mostly been causing them
    @dantetwc what happens if you do gem install bundler --version 2.0.2 before you try to install a Rails package
    Peter Amstutz
    @tetron
    @dantetwc do you work with topayito_gitlab?
    Dante Tsang
    @dantetwc
    
    RUN gem install bundler --version 2.0.2 && \
        apt-get install arvados-workbench
    produce same error
    @tetron Nope, I am not working with Antonio
    Peter Amstutz
    @tetron
    oh okay, I just asked because I noticed "FROM codex-arvados-base" and he had mentioned something about a 'codex' when he was here earlier, I thought it might be the name of a specific project, or maybe just coincidence
    Dante Tsang
    @dantetwc
    Haha maybe. The company I am working for is called Codex based in Hong Kong
    Peter Amstutz
    @tetron
    'codex' means 'book' in latin so it is not that unusual in english
    ok, so, I'm glad you found a workaround
    I am working on the 1.5 release and am hoping to start building a release candidate and testing next week
    Dante Tsang
    @dantetwc
    @tetron Thanks for the hard work and look forward to 1.5 release
    Peter Amstutz
    @tetron
    I should mention if your company is looking for professional support or feature development to contact info@curii.com
    Dante Tsang
    @dantetwc
    Will do so once our platform is live on production
    Peter Amstutz
    @tetron
    great!
    Dante Tsang
    @dantetwc
    @tetron is is possible to start a cwl using API?
    Wanted to integrated with other tools of our company and automatically start a task by using API
    Moritz Gilsdorf
    @gilsdom1
    @dantetwc Yes, this is working of course. The workbench2 is doing this since it is, as a single page application, relying only on the API. I also have a python example for doing this if you are interested.
    Dante Tsang
    @dantetwc
    @gilsdom1 Thanks, may you share the example for python?
    Moritz Gilsdorf
    @gilsdom1
    @dantetwc This is quite old and I'm not sure if it still works. @tetron maybe something for the cookbook? Any improvements are welcome
    Dante Tsang
    @dantetwc
    @gilsdom1 Much Appreciated, will test now
    Peter Amstutz
    @tetron
    @dantetwc as @gilsdom1 pointed out it is certainly possible (that's how workbench and the arvados-cwl-runner clients work) but the current API is very low level
    Peter Amstutz
    @tetron
    @dantetwc also, there is https://github.com/common-workflow-language/workflow-service which implements the GA4GH Workflow Execution Service API using Arvados
    Peter Amstutz
    @tetron
    @dantetwc https://bundler.io/blog/2019/05/14/solutions-for-cant-find-gem-bundler-with-executable-bundle.html there's a note about needing to update gem along with bundler and that bundler 2.0 has a new version switching behavior
    Peter Amstutz
    @tetron
    @dantetwc ok, so I think you want to make sure either you're using bundler 1.16, or if you install bundler 2.x you also need to do "gem update ---system" to update RubyGems
    bundler 2.0 seems to require RubyGems 3.0
    Jacoberts
    @Jacoberts

    Hi @tetron,

    When I bring up workbench, I am getting an error that makes me think my application.yml file isn't recognized, although I've confirmed that a symlink exists at /var/www/arvados-workbench/current/config/application.yml. I'm having difficulty figuring out what's failing in the load_config.rb. Does you know off hand of any gotchas I should look out for, or have you seen this error message before?

    2020-01-21T21:16:00.4286668Z App 1315 output: The following configuration settings must be specified in
    2020-01-21T21:16:00.428671167Z App 1315 output: config/application.yml:
    2020-01-21T21:16:00.428674283Z App 1315 output: * arvados_login_base
    2020-01-21T21:16:00.42867761Z App 1315 output: * arvados_v1_base
    2020-01-21T21:16:00.42868134Z App 1315 output: * arvados_insecure_https
    2020-01-21T21:16:00.428721642Z App 1315 output: * secret_token
    Peter Amstutz
    @tetron
    hmm
    @Jacoberts I believe it makes a symlink from /var/www/arvados-workbench/current/config/application.yml to /etc/arvados/api/application.yml (or similar)
    those keys need to be in the 'common' or 'production' section of the yml file
    Dante Tsang
    @dantetwc
     Dante  …  user  cwl  bwa-mem  arvados-cwl-runner --create-workflow bwa-mem.cwl bwa-mem-template.yml                                                                                                         master
    2020-01-22 17:47:08 cwltool INFO: /Users/Dante/Library/Python/2.7/bin/arvados-cwl-runner 1.4.2, arvados-python-client 1.4.2, cwltool 1.0.20181217162649
    2020-01-22 17:47:08 cwltool INFO: Resolved 'bwa-mem.cwl' to 'file:///Users/Dante/Downloads/arvados/doc/user/cwl/bwa-mem/bwa-mem.cwl'
    2020-01-22 17:47:09 arvados.arv-run INFO: Using empty collection d41d8cd98f00b204e9800998ecf8427e+0
    2020-01-22 17:47:09 arvados.arv-run INFO: Using empty collection d41d8cd98f00b204e9800998ecf8427e+0
    2020-01-22 17:47:09 arvados.arv-run INFO: Using empty collection d41d8cd98f00b204e9800998ecf8427e+0
    arv01-7fd4e-r2vhghpwkybtkn5
    2020-01-22 17:47:09 cwltool INFO: Final process status is success
     Dante  …  user  cwl  bwa-mem  arvados-cwl-runner --debug arv01-7fd4e-r2vhghpwkybtkn5                                                                                                                        master
    2020-01-22 17:47:22 cwltool INFO: /Users/Dante/Library/Python/2.7/bin/arvados-cwl-runner 1.4.2, arvados-python-client 1.4.2, cwltool 1.0.20181217162649
    2020-01-22 17:47:22 cwltool INFO: Resolved 'arv01-7fd4e-r2vhghpwkybtkn5' to 'arvwf:arv01-7fd4e-r2vhghpwkybtkn5#main'
    2020-01-22 17:47:22 cwltool ERROR: I'm sorry, I couldn't load this CWL file.
    The error was:
    Traceback (most recent call last):
      File "/Users/Dante/Library/Python/2.7/lib/python/site-packages/cwltool/main.py", line 646, in main
        fetcher_constructor=loadingContext.fetcher_constructor)
      File "/Users/Dante/Library/Python/2.7/lib/python/site-packages/cwltool/load_tool.py", line 117, in fetch_document
        workflowobj = document_loader.fetch(fileuri)
      File "/Users/Dante/Library/Python/2.7/lib/python/site-packages/schema_salad/ref_resolver.py", line 961, in fetch
        result = yaml.round_trip_load(textIO, preserve_quotes=True)
      File "/usr/local/Cellar/python@2/2.7.17_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ruamel/yaml/main.py", line 144, in round_trip_load
        return load(stream, RoundTripLoader, version, preserve_quotes=preserve_quotes)
      File "/usr/local/Cellar/python@2/2.7.17_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ruamel/yaml/main.py", line 95, in load
        return loader._constructor.get_single_data()
      File "/usr/local/Cellar/python@2/2.7.17_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ruamel/yaml/constructor.py", line 86, in get_single_data
        node = self.composer.get_single_node()
      File "/usr/local/Cellar/python@2/2.7.17_1/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/ruamel/yaml/composer.py", line 79, in get_single_node
        event.start_mark)
    ComposerError: expected a single document in the stream
      in "arvwf:arv01-7fd4e-r2vhghpwkybtkn5", line 1, column 1
    but found another document
      in "arvwf:arv01-7fd4e-r2vhghpwkybtkn5", line 128, column 1
     Dante  …  user  cwl  bwa-mem 
    trying to create a workflow following the guide here https://doc.arvados.org/master/user/tutorials/writing-cwl-workflow.html
    but it didn't work
    any insight?
    Peter Amstutz
    @tetron
    That's odd
    @dantetwc I'll have to try it later and see what result I get
    Looks like you are running it on OS X?
    Evan Clark
    @djevo1_gitlab
    @tetron trying to install arvados manually and am getting this error when trying to update the repo
    http://rpm.arvados.org/CentOS/2/os/x86_64/repodata/repomd.xml: [Errno 14] HTTP Error 404 - Not Found
    Trying other mirror.
    Nevermind I found the issue