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chi-chi weng
@wcc526
There is dockerfile for the composer web service?
It would be more convernient for host it on the web
Andrey Kartashov
@portah
It might be. The idea behind composer to enable researchers assemble workflow, usually on a computer they use for work
Peter Amstutz
@tetron
the code that I linked is integrated with Arvados. it is a web app but it is not standalone either. there is a docker build of Arvados that includes composer https://doc.arvados.org/v2.0/install/arvbox.html
Andrey Kartashov
@portah
Web means you probably would like to have workflows on a server
For that reason, you can probably have NX to the server
chi-chi weng
@wcc526
em,My purpose is integrated with StackStorm https://docs.stackstorm.com/overview.html
StackStorm workflow editor is commercial.
Peter Amstutz
@tetron
StackStorm runs CWL?
why did that turn into a highlighted box
(silly gitter)
chi-chi weng
@wcc526
My plan is transfer CWL between St2 yaml
Peter Amstutz
@tetron
I see
chi-chi weng
@wcc526

ersion: 1.0

description: Calculates (a + b) * (c + d)

input:

  • a: 0 # Defaults to value of 0 if input is not provided.
  • b: 0
  • c: 0
  • d: 0

tasks:
task1:

# Fully qualified name (pack.name) for the action.
action: math.add

# Assign input arguments to the action from the context.
input:
  operand1: <% ctx(a) %>
  operand2: <% ctx(b) %>

# Specify what to run next after the task is completed.
next:
  - # Specify the condition in YAQL or Jinja that is required
    # for this task to transition to the next set of tasks.
    when: <% succeeded() %>

    # Publish variables on task transition. This allows for
    # variables to be published based on the task state and
    # its result.
    publish:
      - msg: task1 done
      - ab: <% result() %>

    # List the tasks to run next. Each task will be invoked
    # sequentially. If more than one tasks transition to the
    # same task and a join is specified at the subsequent
    # task (i.e task1 and task2 transition to task3 in this
    # case), then the subsequent task becomes a barrier and
    # will be invoked when condition of prior tasks are met.
    do:
      - log
      - task3

task2:

# Short hand is supported for input arguments. Arguments can be
# delimited either by space, comma, or semicolon.
action: math.add operand1=<% ctx("c") %> operand2=<% ctx("d") %>
next:
  - when: <% succeeded() %>

    # Short hand is supported for publishing variables. Variables
    # can be delimited either by space, comma, or semicolon.
    publish: msg="task2 done", cd=<% result() %>

    # Short hand with comma delimited list is supported.
    do: log, task3

task3:

# Join is specified for this task. This task will be invoked
# when the condition of all inbound task transitions are met.
join: all
action: math.multiple operand1=<% ctx('ab') %> operand2=<% ctx('cd') %>
next:
  - when: <% succeeded() %>
    publish: msg="task3 done" abcd=<% result() %>
    do: log

Define a reusable task to log progress. Although this task is

referenced by multiple tasks, since there is no join defined,

this task is not a barrier and will be invoked separately.

log:
action: core.log message=<% ctx(msg) %>

output:

  • result: <% ctx().abcd %>
sorry,the code is not formated.
chi-chi weng
@wcc526
@tetron where is the composer code in the https://github.com/arvados/arvados.git?
How do you deploy and update composer code with dockerfile?
chi-chi weng
@wcc526
TypeError: write() argument must be str, not bytes while trying to load binding.gyp
gyp ERR! configure error
gyp ERR! stack Error: gyp failed with exit code: 1
gyp ERR! stack at ChildProcess.onCpExit (/root/.nvm/versions/node/v10.19.0/lib/node_modules/npm/node_modules/node-gyp/lib/configure.js:351:16)
gyp ERR! stack at ChildProcess.emit (events.js:198:13)
gyp ERR! stack at Process.ChildProcess._handle.onexit (internal/child_process.js:248:12)
gyp ERR! System Linux 4.4.0-173-generic
gyp ERR! command "/root/.nvm/versions/node/v10.19.0/bin/node" "/root/.nvm/versions/node/v10.19.0/lib/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js" "rebuild"
gyp ERR! cwd /root/composer/electron/node_modules/keytar
gyp ERR! node -v v10.19.0
gyp ERR! node-gyp -v v5.0.5
gyp ERR! not ok
info Visit https://yarnpkg.com/en/docs/cli/install for documentation about this command.
error Command failed with exit code 1.
info Visit https://yarnpkg.com/en/docs/cli/install for documentation about this command.
Andrey Kartashov
@portah
@wcc526 I believe there is no stand alone solution to run rabix composer in web
so if the idea to integrate you either tearing apart original rabix composer (easier to get cwl-svg package and add some code from rabix) or organize your work with what already exist like sharing directories or just converting CWLs to stackstorm
chi-chi weng
@wcc526
Could rabix/composer run on MacOS ?
git clone https://github.com/rabix/composer
cd composer
yarn install
yarn run serve // starts the dev server
yarn run compile:electron // compiles electron backend
yarn run start:electron // opens the app shell
I run these command on MacOS ,but there is only blank page.
chi-chi weng
@wcc526
Module build failed: Error: Cannot find module 'node-sass'
at Function.Module._resolveFilename (internal/modules/cjs/loader.js:636:15)
at Function.Module._load (internal/modules/cjs/loader.js:562:25)
at Module.require (internal/modules/cjs/loader.js:692:17)
at require (internal/modules/cjs/helpers.js:25:18)
Michael R. Crusoe
@mr-c
@wcc526 There is a dmg for macOS at https://github.com/rabix/composer/releases
@wcc526 Great to hear that you want to work on StackStorm & CWL! Please let me know how I can help mrc@commonwl.org ; note, I can't provide help with the Rabix Composer itself, alas
chi-chi weng
@wcc526
@mr-c now I'm trying to workon on StackStorm & WALKOFF. The WLAKOFF has a basic web ui.
Michael R. Crusoe
@mr-c
@wcc526 Cool, I hadn't seen that one before. The interface reminds me of Galaxy
Ben
@tirohia
Is it possible to run rabix locally and have the tools, data and execution on a remote server? Adding a local project is easy, but I get the impression that the only way to do remote work is through one of seven bridges, cancer genomics cloud or cavatica?
Kaushik Ghose
@kaushik-work
Hi @tirohia no there is no way, or plan, to add integrations with other platforms for Rabix Composer. A planned release will add support for selectable CWL runners instead of rabix-executor. You could write a small stub that acts like a cwl-runner and invokes cloude resources and then you could do that. How to refer to cloud resources (files) is a different problem.
Ben
@tirohia
I'm not after a method to access a cloud platform - the data that I'm working with is belongs to indigenous populations and will never touch the cloud. We have a local server is all, that I'd like to have the workflows on. I tried running it from command line with X11 forwarding on, but that doesn't appear to work.
Kaushik Ghose
@kaushik-work
You would have to run the workflows separately using, say, toil or some other CWL executor. You could still develop the workflows using Rabix Composer by mounting a remote folder and pointing RC to that.
Ben
@tirohia
Thanks @kaushik-work, I'll try to work something out.
Evan Clark
@djevo1_gitlab
@kaushik-work noticing some issues with the latest composer, mainly any workflow marked as v1.1 won't render.
And this error randomly appears
Model error: e.requirements.forEach is not a function
Kaushik Ghose
@kaushik-work
Hi @djevo1_gitlab we haven't released 1.1 support for Desktop Composer yet, unfortunately.
I think a lot of the work has been done, we have to push it, QA it and then create a release. I'm hoping we can bundle this with the custom executor support. I'm hoping we can get this done in July.
Evan Clark
@djevo1_gitlab
@kaushik-work Ok great, also benten is giving this error when previewing a 1.0 script: Command 'Benten: CWL preview' resulted in an error (Running the contributed command: 'cwl.show_graph' failed.)
Kaushik Ghose
@kaushik-work
@djevo1_gitlab that error also happened to me. Could you check if that happens to you for other plugins with a preview? I had a horrendous time with none of my plugin previews working. I still don't know how it resolved, but I got rid of my extensions directory and reinstalled VS Code and finally it came all back.
@djevo1_gitlab with my issue, it happened with the built in markdown preview too.
Evan Clark
@djevo1_gitlab
@kaushik-work the markdown preview works and that's the only other preview extension I have.
Kaushik Ghose
@kaushik-work
@djevo1_gitlab could you open an issue on the repo with details of your os, VS code and plugin version? Thank you!
@djevo1_gitlab I need to update the VS Code component anyway - it hasn't been touched in a while.

I'm on

Version: 1.45.1
Commit: 5763d909d5f12fe19f215cbfdd29a91c0fa9208a
Date: 2020-05-14T08:33:47.663Z (2 wks ago)
Electron: 7.2.4
Chrome: 78.0.3904.130
Node.js: 12.8.1
V8: 7.8.279.23-electron.0
OS: Darwin x64 19.4.0

With Benten VS Code version 2019.12.3

Kaushik Ghose
@kaushik-work
@djevo1_gitlab I've published a new version of the extension, updating the dependencies. Please tell me if that solves your issue. It's been working fine on my end even with the old version.
Evan Clark
@djevo1_gitlab
@kaushik-work I just updated, have the same issue, will open a ticket