rabix/composer

A graphical editor for CWL documents

chi-chi weng

@wcc526

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.

https://github.com/arvados/composer/tree/feature/web-app this node version is ?

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

Hadley King

@HadleyKing

Hi all!
I am experimenting with the composer and had an issue. The example I am running through says to use the following:

requirements:
  - class: DockerRequirement
    dockerPull: biocontainers/bwa

but the docker pull fails unless I put the SPECIFIC tag desired in the line dockerPull: biocontainers/bwa:v0.7.17_cv1
I tried using dockerPull: biocontainers/bwa:latest as well and that failed. Is the tutorial outdated or is it a Docker issue or something else? I know I heard that Docker is changing things up...

Michael R. Crusoe

@mr-c

@HadleyKing What failure message do you get?

Probably best to use quay.io/biocontainers/bwa:0.7.8--hed695b0_5 instead

@TMiguelT Where can we send a PR to update https://www.melbournebioinformatics.org.au/tutorials/tutorials/cwl/media/#1 ?

Michael Milton

@TMiguelT

Haha that's a very old tutorial

But if you would like to, it's located at: https://www.github.com/melbournebioinformatics/MelBioInf_docs/tree/master/docs%2Ftutorials%2Fcwl

Hadley King

@HadleyKing

@mr-c the failure message is:

[2020-12-01 08:33:25.051] [DEBUG] Pulling docker image
[2020-12-01 08:33:25.051] [INFO] Pulling docker image biocontainers/bwa:latest
[2020-12-01 08:33:25.052] [DEBUG] Using configfile: /Users/hadley/.docker/config.json
[2020-12-01 08:33:25.063] [WARN] Could not find auth field for https://index.docker.io/v1/
[2020-12-01 08:33:26.451] [INFO] Failed to pull docker image. Retrying in 30 seconds
[2020-12-01 08:33:26.451] [INFO] Composer: {"status": "DOCKER_PULL_FAILED",  "retry": 30, "image": "biocontainers/bwa:latest","message": "Request error: POST unix://localhost:80/images/create?fromImage=biocontainers/bwa&tag=latest: 404"}
[2020-12-01 08:33:26.456] [ERROR] Method invocation failed. Method public synchronized void org.rabix.executor.container.impl.DockerContainerHandler$DockerClientLockDecorator.pull(java.lang.String,com.spotify.docker.client.messages.AuthConfig) throws com.spotify.docker.client.exceptions.DockerException,java.lang.InterruptedException
java.util.concurrent.ExecutionException: java.lang.Exception: com.spotify.docker.client.exceptions.DockerRequestException: Request error: POST unix://localhost:80/images/create?fromImage=biocontainers/bwa&tag=latest: 404
    at java.util.concurrent.FutureTask.report(FutureTask.java:122) ~[na:1.8.0_191]

TLDR: Failed to pull docker image. Retrying in 30 seconds

@TMiguelT I thought that that tutorial was VERY well done and it is a top hit for Google search so it would be worth maintaining IMO.

Michael R. Crusoe

@mr-c

@TMiguelT melbournebioinformatics/MelBioInf_docs#116 :-)

Michael Milton

@TMiguelT

Thank you both!

If the Composer gets updated I will also happily remove this workaround

Bruno Grande

@BrunoGrandePhD

I was given a CWL workflow with over 16,000 lines (after removing the sbg:* fields and collapsing long JS expressions to single lines), and I would like to visualize it. Its size is mostly because it's nested, i.e. sub-workflows are defined within the CWL file rather than using external references. I tried using Rabix Composer to visualize the workflow, but I can't seem to inspect the sub-workflows.

Does anyone here have suggestions on how to visualize a nested workflow in either Rabix Composer or another tool? Thanks in advance!

Bruno Grande

@BrunoGrandePhD

I tried using the "Benten: CWL preview" feature in the VS Code extension, but I ran into the following error:

Command 'Benten: CWL preview' resulted in an error (command 'cwl.show_graph' not found)

If folks here can confirm that they expect this cwl.show_graph command to work on nested workflows, then I can dig deeper to resolve this issue. Any pointers would be appreciated!

Kaushik Ghose

@kaushik-work

Hi @BrunoGrandePhD for Benten 1. It will handle nested workflows bu 2. Will only show the first level.

It should not generate any errors

@BrunoGrandePhD if you are using the latest versions of Benten and the VS Code extension, please open an issue in the repo, thanks!

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