Update script to match result of FDP_SCRIPT

[kzscisoft]

The CLI will in future provide the variable FDP_SCRIPT pointing to the path of the script during a run, this should be used to determine the script file type in:
https://github.com/FAIRDataPipeline/pyDataPipeline/blob/dev/fairdatapipeline/pipeline.py#L178

Related to FAIRDataPipeline/FAIR-CLI#197.

[bobturneruk]

pyDataPipeline/data_pipeline_api/pipeline.py

Line 178 in 9fb64a9

# TODO: Change to Batch?

[kzscisoft]

This relates to the fact that the CLI provides the environment variable FDP_SCRIPT which should be used by the API for retrieval of the working script:
https://github.com/FAIRDataPipeline/FAIR-CLI/blob/346ca2db58aedd504704fb4a428decdddf225dc4/fair/user_config/__init__.py#L677

[bobturneruk]

Thanks @kzscisoft! Myself, @bruvio and @RyanJField will have a chat about this.

[bruvio]

ok. I still do not understand all this. but it is ok

[bobturneruk]

Thanks for noting that @bruvio. Sorry to disturb you again, but is there any documentation we can look at @kzscisoft to better understand this issue, please?

[RyanJField]

Currently pipeline.py registers the script file extension as .py: Pipeline Line 184. However when using fair run and the script: block in a yaml, the script runs through a shell script (.sh) and needs to be registered as one (script.sh). Therefore pipeline.py needs to read the file extension when registering the script to the registry.