Fix new bugs

[richardreeve]

• fixes fair pull is registering external DataProducts as file_type py #68 and registers file types correctly
• fixes Register a Namespace entry in fair init #69 and registers user namespace automatically in fair init
• fixes remote_repo is missing from the working config #70 and adds remote_repo: to run_metadata:
• fixes run_metadata: write_data_store: value needs to end in a slash #71 and adds a path separator to folder names

@soniamitchell - can you check this works please?

[soniamitchell]

Testing:

• fixes fair pull is registering external DataProducts as file_type py and registers file types correctly
• fixes Register a Namespace entry in fair init and registers user namespace automatically in fair init
• fixes remote_repo is missing from the working config and adds remote_repo: to run_metadata:
• fixes run_metadata: write_data_store: value needs to end in a slash and adds a path separator to folder names

[soniamitchell]

• when write_data_store is included in the user-written config, fair run doesn't check whether it ends in a slash
• fair init --using sonia.yaml no longer works correctly (and so checking the Namespace entry is incomplete) - fair is unable to find the registry:

Initialised empty fair repository in /Users/Soniam/Desktop/git/FAIRDataPipeline/rSimpleModel/.fair
Error: Failed to find local registry executable      
'/Users/runner/work/SimpleModel/SimpleModel/.fair/registry/scripts/start_fair_registry', is the FAIR data pipeline properly    installed on this system?  

• when running through fair init, curser keys / tab complete are inoperable - I'd like to be able to paste and edit
• after fair init is complete:

Initialised empty fair repository in /Users/Soniam/Desktop/git/FAIRDataPipeline/rSimpleModel/.fair
Traceback (most recent call last):
  File "/Users/Soniam/Library/Caches/pypoetry/virtualenvs/fair-cli-kJcAWAhH-py3.7/bin/fair", line 5, in <module>
    cli()
  File "/Users/Soniam/Library/Caches/pypoetry/virtualenvs/fair-cli-kJcAWAhH-py3.7/lib/python3.7/site-packages/click/core.py", line 1137, in __call__
    return self.main(*args, **kwargs)
  File "/Users/Soniam/Library/Caches/pypoetry/virtualenvs/fair-cli-kJcAWAhH-py3.7/lib/python3.7/site-packages/click/core.py", line 1062, in main
    rv = self.invoke(ctx)
  File "/Users/Soniam/Library/Caches/pypoetry/virtualenvs/fair-cli-kJcAWAhH-py3.7/lib/python3.7/site-packages/click/core.py", line 1668, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/Soniam/Library/Caches/pypoetry/virtualenvs/fair-cli-kJcAWAhH-py3.7/lib/python3.7/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/Soniam/Library/Caches/pypoetry/virtualenvs/fair-cli-kJcAWAhH-py3.7/lib/python3.7/site-packages/click/core.py", line 763, in invoke
    return __callback(*args, **kwargs)
  File "/Users/Soniam/Desktop/git/FAIRDataPipeline/FAIR-CLI/fair/cli.py", line 120, in init
    export_as=export
  File "/Users/Soniam/Desktop/git/FAIRDataPipeline/FAIR-CLI/fair/session.py", line 605, in initialise
    _uri
  File "/Users/Soniam/Desktop/git/FAIRDataPipeline/FAIR-CLI/fair/registry/storage.py", line 349, in store_namespace
    uri, "namespace", data=_data, params={"name": namespace_label}
  File "/Users/Soniam/Desktop/git/FAIRDataPipeline/FAIR-CLI/fair/registry/requests.py", line 407, in post_else_get
    token = local_token()
  File "/Users/Soniam/Desktop/git/FAIRDataPipeline/FAIR-CLI/fair/registry/requests.py", line 65, in local_token
    _local_token_file = os.path.join(fdp_com.registry_home(), "token")
  File "/Users/Soniam/Desktop/git/FAIRDataPipeline/FAIR-CLI/fair/common.py", line 53, in registry_home
    _glob_conf = yaml.safe_load(open(global_fdpconfig()))
FileNotFoundError: [Errno 2] No such file or directory: '/Users/Soniam/.fair/cli/cli-config.yaml'

[richardreeve]

• when write_data_store is included in the user-written config, fair run doesn't check whether it ends in a slash
  @soniamitchell - hopefully this is fixed now.

[richardreeve]

• fair init --using sonia.yaml no longer works correctly (and so checking the Namespace entry is incomplete) - fair is unable to find the registry:

Initialised empty fair repository in /Users/Soniam/Desktop/git/FAIRDataPipeline/rSimpleModel/.fair
Error: Failed to find local registry executable      
'/Users/runner/work/SimpleModel/SimpleModel/.fair/registry/scripts/start_fair_registry', is the FAIR data pipeline properly    installed on this system?  

If that problem is mine, could you give me your sonia.yaml via Zulip, because I can't reproduce it... thanks! Also:

• when running through fair init, curser keys / tab complete are inoperable - I'd like to be able to paste and edit

This isn't fixable (at least by me!), sorry...

[soniamitchell]

Turns out it works fine 👍 it was a problem with local: data_store: and local: directory:, perhaps a check could be made as to whether local: directory: is accurate prior to initialising the empty fair repository?

[richardreeve]

Turns out it works fine 👍 it was a problem with local: data_store: and local: directory:, perhaps a check could be made as to whether local: directory: is accurate prior to initialising the empty fair repository?

Great. Maybe add a new issue for this because I can't fix it now though...

[richardreeve]

@soniamitchell - okay, maybe(?!) fixed now. This may also accidentally fix #74 btw.

[richardreeve]

Nope - maybe not. Fixed a few problems, but created a new one...

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
3 Code Smells

No Coverage information
0.0% Duplication

[richardreeve]

Okay - trying this again @soniamitchell - I think it really is fixed now. This may also accidentally fix #74 btw. It gives inscrutable errors when you do things in the wrong order sadly, but otherwise I hope good?