Argo data tool

[Marie59]

1st batch tool for the Earth-System subdomain ! This tool allows user to retrieve argo data in netcdf file. It will be part of the ocean part of the Earth System. I think it should go in the section Get Data of the tool pannel.
I am not sure if I filed the .shed.yml correctly.
What do you think of it ?

[bgruening]

can you use the argparse library for that script?

[Marie59]

Yes I think I can just need to check how it works ;)

[Marie59]

Is it good now ?

[bgruening]

Do those emojis work? :)

[Marie59]

Yes they do I really like the style ;)

[Marie59]

I see that I need to add a category Earth-system somewhere with this warning message .. WARNING: Categories [['Earth-system']] unknown.
But I search in the repo github here and I don't find where I am supposed to do that. Could you give me a hand @yvanlebras or @bgruening ?

[Marie59]

Weird my planemo t is working locally but it's not here...

[bgruening]

The warning about the missing category is because this category does not exist in the ToolShed. Use a different one from the TS please. https://toolshed.g2.bx.psu.edu/

[bgruening]

Are you running the tests locall with planemo test --biocontainers?

[yvanlebras]

Yes, categoris are toolshed ones. You can use the ecology one

[Marie59]

Are you running the tests locall with planemo test --biocontainers?

I was not using the option --biocontainers so I tried with it and I do have the same error. I search and tried out some stuffs and I think my tool is searching for a "galaxy user" to run and is not able to find it (because it does not exist I think). I don't really know how to fix that. I tried to add a user in the Cheetah but I don't know how to do it and it may not be the right thing to do.
Does one have you has an idea @bgruening and @yvanlebras ?

[Marie59]

The warning about the missing category is because this category does not exist in the ToolShed. Use a different one from the TS please. https://toolshed.g2.bx.psu.edu/

Am I gonna be able to have this tool to one of the sections I have implemented in the earth system subdomain ? Because I don't want to be forced to add the entire set of ecology tools in the earth system...
Thinking about it maybe I should just add it in the 'Source Data' category ? and it will be in the 'Get Data' tool section ?

[bgruening]

ToolShed sections are independent of Galaxy tool panel sections. So don't worry about it here.

[bgruening]

Job in error state.. tool_id: argo_getdata, exit_code: 1, stderr: Traceback (most recent call last):
  File "/home/runner/work/tools-ecology/tools-ecology/tools/ocean/argo_getdata.py", line 187, in <module>
    argo_data = argo_data.load().data
                ^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/argopy/fetchers.py", line 643, in load
    self._data = self.to_xarray(**kwargs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/argopy/fetchers.py", line 490, in to_xarray
    xds = self.fetcher.to_xarray(**kwargs)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/argopy/data_fetchers/erddap_data.py", line 716, in to_xarray
    results = self.post_process(results, add_dm=add_dm, URI=URI)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/site-packages/argopy/data_fetchers/erddap_data.py", line 681, in post_process
    this_ds.attrs["Fetched_by"] = getpass.getuser()
                                  ^^^^^^^^^^^^^^^^^
  File "/usr/local/lib/python3.12/getpass.py", line 169, in getuser
    return pwd.getpwuid(os.getuid())[0]
           ^^^^^^^^^^^^^^^^^^^^^^^^^
KeyError: 'getpwuid(): uid not found: 1001'

This looks really like an upstream problem of erddap_data.py

[bgruening]

I assume it is this line: https://github.com/euroargodev/argopy/blob/master/argopy/data_fetchers/erddap_data.py#L686

The function wants to get Return the password database entry for the given numeric user ID. not sure why this is needed. But in container settings and on HPC this is not a valid assumption.

[Marie59]

So, I need to contact the authors of erddap to ask if they can modify that ?

[bgruening]

I think so. Otherwise we need to hack around this problem on our side :(

[Marie59]

OOOH can I start my happy dance @bgruening ?

[bgruening]

should this be still expcluded?

[Marie59]

I think I took all your @bgruening suggestions into account. Is there anything else that needs improvement ?

[bgruening]

Looks great!