Update for new CDS API

[pixalytics]

@bgruening Sorry, but I've got another pull request. Yesterday, ECMWF released the new version of the API https://confluence.ecmwf.int/display/CKB/Please+read%3A+CDS+and+ADS+migrating+to+new+infrastructure%3A+Common+Data+Store+%28CDS%29+Engine so older versions of the CDS API call don't work.

I've updated the tool to comply with the new API, primarily up versioning the Python libraries, but also a slight change in how the data is called. I've updated the documentation.

The current test doesn't actually test if data is downloaded, just that the API call text is as expected. So, I'm not sure if this needs an improvement.

[bgruening]

Outch, they break API? This is not good :(

Thanks for fixing it that quickly!

[bgruening]

I would assume that they keep the versioned APIs?

Is there a v3 now that we can use?

[pixalytics]

It's a new CDS with a backwards-compatible API. In their guidance for usage they have dropped the v2

[bgruening]

We only have type bibtex and type doi ...

When you use bibtex you can do some freetext if you like. https://github.com/bgruening/galaxytools/blob/master/tools/whisper/whisper.xml#L349

[pixalytics]

@bgruening Thanks, I've used that approach to encode the text

[bgruening]

Thanks a lot!

[annefou]

@pixalytics Thanks a lot for fixing this tool!

it was written a while ago and does not follow the recommended practices for EDAM annotations. I think that you need to move them for instance after the description of the tool.

[bgruening]

Suggested change

	This tool is a wrapper to retrieve data from the Copernicus Climate Data Store.
	- It allows to retrieve data from the Copernicus climate Data Store.
	- Any user willing to use this tool needs to `create a new account <https://cds.climate.copernicus.eu/user/register?destination=%2F%23!%2Fhome>`_.
	- Any user willing to use this tool needs to `create a new account <https://cds.climate.copernicus.eu/>`_.
	- Set your CDS API Key via: User -> Preferences -> Manage Information"
	- Documentation on where to get the CDS API key can be found `here <https://cds.climate.copernicus.eu/api-how-to>`_.
	- Compose your request directly on C3S and copy/paste it in the input field "Request" or save it in a file.
	- Be aware that for being able to download dataset from C3S, users also need to agree to their term of use (Licence to use Copernicus Products) on the C3S website.
	- Documentation on where to get the CDS API key can be found `here <https://cds.climate.copernicus.eu/how-to-api>`_.
	- Compose your request directly on C3S and extract the relevant information, which should be put in the input field "Request" or saved in a file. The format should be, for example:
	import cdsapi
	c = cdsapi.Client()
	c.retrieve(
	'reanalysis-era5-single-levels-monthly-means',
	{
	'data_format': 'netcdf',
	'product_type': 'monthly_averaged_reanalysis',
	'variable': '2m_temperature',
	'year': '2020',
	'month': '12',
	'time': '00:00',
	'area': [60, 10, 59.5, 10.5],
	},
	'download.nc')
	- Be aware that for being able to download dataset from C3S, users also need to agree to licensing terms for each dataset of interest on the C3S website.
	License:
	~~~~~~~~
	This tool is a wrapper to retrieve data from the Copernicus Climate Data Store.
	- It allows to retrieve data from the Copernicus climate Data Store.
	- Any user willing to use this tool needs to `create a new account <https://cds.climate.copernicus.eu/>`_.
	- Set your CDS API Key via: User -> Preferences -> Manage Information"
	- Documentation on where to get the CDS API key can be found `here <https://cds.climate.copernicus.eu/how-to-api>`_.
	- Compose your request directly on C3S and extract the relevant information, which should be put in the input field "Request" or saved in a file. The format should be, for example::
	import cdsapi
	c = cdsapi.Client()
	c.retrieve(
	'reanalysis-era5-single-levels-monthly-means',
	{
	'data_format': 'netcdf',
	'product_type': 'monthly_averaged_reanalysis',
	'variable': '2m_temperature',
	'year': '2020',
	'month': '12',
	'time': '00:00',
	'area': [60, 10, 59.5, 10.5],
	},
	'download.nc')
	- Be aware that for being able to download dataset from C3S, users also need to agree to licensing terms for each dataset of interest on the C3S website.
	License:
	~~~~~~~~

This should hopefully fix the RST warning.

[pixalytics]

Thanks, I was trying to work out how to get the formatting right...

[bgruening]

@pixalytics sorry I still can not push to your branch. Can you maybe provide commit access to your fork. I can then handle the lining issues. They are not your fault, our listing just got stricter since the tool was last modified and I would take the opportunity to fix the linting.

[bgruening]

Thanks a lot. This version will be installed over the weekend. If you need it earlier, please let me know.