fairagro / m4.4_sciwin_client

🦀 SciWIn Client: Reproducible computational Workflows made easy!

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Implement `s4n tool create` aka `s4n run` #2

Closed hvwaldow closed 1 month ago

hvwaldow commented 1 month ago

Input: Command line to run tool.
Distinguish from command line (parsing):
- script
- file
- positional
- flag
- argument
Implement explicit markup of cli tokens to support funny scripts.
File: toolname.cwl in /workflows/toolname/toolname.cwl
Initially: Check if Git is available, if everything is commited
Finally: Identify output, write cwl accordingly, commit.

JensKrumsieck commented 1 month ago

Development happening in feature/tool_create-branch

JensKrumsieck commented 1 month ago

Achieved first successful conversion from CLI command to cwl - not all requirements are met, but it is starting to work 🤩 https://github.com/fairagro/m4.4_sciwin_client/commit/4ca62a289e889f5679e1d259608ea19786dc95d5

JensKrumsieck commented 1 month ago

Status report

Does work:

[x] Use command tool create with run as synonym
[x] check if repo exists and if state is good
[x] Parse command and determine input and baseCommand
[x] run command and determine output files
[x] create (basic) CWL from command (and output CWL file)
[x] Basic unit/integration testing
[x] fluent CWL API (for CommandLineTool)
...

Does not work, yet

[x] infer input type
[x] Docker support
[x] commit after cwl creation
[x] save cwl in correct location
[ ] support for "funny" scripts
~[ ] CWL API not capable of doing everything CWL could do~
...

Needs improvement

[x] condense out interim tool structure and use CWL in memory representation in the first place
...

JensKrumsieck commented 1 month ago

PR: https://github.com/fairagro/m4.4_sciwin_client/pull/9