Mercurial > repos > climate > c3s
changeset 3:d7b62d55f8dd draft default tip
planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 706e03c8e81940b6e10d3fd7b412d30b46b46ce7
| author | climate |
|---|---|
| date | Mon, 09 Mar 2026 14:11:43 +0000 |
| parents | 21e8386cf36f |
| children | |
| files | c3s.xml c3s_retrieve.py |
| diffstat | 2 files changed, 42 insertions(+), 43 deletions(-) [+] |
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--- a/c3s.xml Fri Sep 27 19:34:36 2024 +0000 +++ b/c3s.xml Mon Mar 09 14:11:43 2026 +0000 @@ -1,4 +1,4 @@ -<tool id="c3s" name="Copernicus Climate Data Store" version="0.3.0" profile="23.0"> +<tool id="c3s" name="Copernicus Climate Data Store" version="0.3.1" profile="25.1"> <description>for retrieving climate data</description> <edam_topics> <edam_topic>topic_3855</edam_topic> @@ -15,15 +15,17 @@ <requirement type="package" version="2.4.4">cdo</requirement> <requirement type="package" version="1.34">tar</requirement> <requirement type="package" version="6.0">unzip</requirement> + <credentials name="c3s_cds_apikey" version="1.0" label="CDS API key" description="Credential for accessing Copernicus climate Data Store API."> + <secret name="key" inject_as_env="CDS_API_KEY" optional="false" label="CDS API key" description="Your Copernicus climate Data Store API key."/> + </credentials> </requirements> + <required_files> + <include path="c3s_retrieve.py"/> + <include path="c3s.sh"/> + </required_files> <command detect_errors="exit_code"><![CDATA[ export HOME=`pwd` && - #set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "") - #if $c3s_cds_apikey == "" - echo "Error. Set your credentials via: User -> Preferences -> Manage Information" && - #else - cp '$cds_key_file' .cdsapirc && - #end if + #if str($is_file.has_req).strip() == 'yes' python3 '$__tool_directory__/c3s_retrieve.py' --request '$is_file.api_req_file' --output request.txt && @@ -35,11 +37,6 @@ echo "C3S data retrieval is done" ]]></command> <configfiles> - <configfile name="cds_key_file"><![CDATA[ -#set $c3s_cds_apikey = $__user__.extra_preferences.get('c3s_account|c3s_cds_apikey', "") - url: https://cds.climate.copernicus.eu/api - key: $c3s_cds_apikey - ]]></configfile> <configfile name="req_from_paste"><![CDATA[ #if str($is_file.has_req).strip() == 'no' $is_file.api_req_text @@ -52,11 +49,11 @@ <option value="yes" selected="true">yes</option> <option value="no">no</option> </param> - <when value="yes"> - <param name="api_req_file" type="data" label="API Request filename" format="txt"/> + <when value="yes"> + <param name="api_req_file" type="data" label="API Request filename" format="txt"/> </when> - <when value="no"> - <param name="api_req_text" type="text" label="Paste API Request" area="true" /> + <when value="no"> + <param name="api_req_text" type="text" label="Paste API Request" area="true" /> </when> </conditional> </inputs> @@ -65,26 +62,14 @@ <data name="ofilename" format="netcdf" from_work_dir="tmp.nc" label="${tool.name} on ${on_string}: NC"/> </outputs> <tests> - <test> - <param name="api_req_file" value="input.txt" /> - <output name="request" ftype="txt"> - <assert_contents> - <has_text text="dataset to retrieve: reanalysis-era5-single-levels-monthly-means" /> - <has_text text="'data_format': 'netcdf'" /> - <has_text text="'product_type': 'monthly_averaged_reanalysis'" /> - <has_text text="'variable': '2m_temperature'" /> - <has_text text="'year': '2020'" /> - <has_text text="'month': '12'" /> - <has_text text="'time': '00:00'" /> - <has_text text="'area': [" /> - <has_text text="60," /> - <has_text text="10," /> - <has_text text="59.5," /> - <has_text text="10.5," /> - <has_text text="]" /> - <has_text text="output filename: download.nc" /> - </assert_contents> - </output> + <test expect_failure="true"> + <conditional name="is_file"> + <param name="has_req" value="yes"/> + <param name="api_req_file" value="input.txt" /> + </conditional> + <assert_stderr> + <has_text text="CDS retrieval failed, make sure you filled in your CDS API Key"/> + </assert_stderr> </test> </tests> <help><![CDATA[ @@ -96,11 +81,10 @@ - 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" +- Set your CDS API Key in the Credentials - 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()
--- a/c3s_retrieve.py Fri Sep 27 19:34:36 2024 +0000 +++ b/c3s_retrieve.py Mon Mar 09 14:11:43 2026 +0000 @@ -1,5 +1,6 @@ import argparse import ast +import sys from os import environ, path import cdsapi @@ -47,14 +48,28 @@ print("start retrieving data...") -cdapi_file = path.join(environ.get('HOME'), '.cdsapirc') +api_key = environ.get("CDS_API_KEY") -if path.isfile(cdapi_file): - c = cdsapi.Client() +if not api_key: + sys.stderr.write( + "CDS retrieval failed, make sure you filled in your CDS API Key\n" + ) + sys.exit(1) + +try: + c = cdsapi.Client( + url="https://cds.climate.copernicus.eu/api", + key=api_key + ) c.retrieve( c3s_type, c3s_req_dict, - c3s_output) - + c3s_output + ) print("data retrieval successful") +except Exception: + sys.stderr.write( + "CDS retrieval failed, make sure you filled in your CDS API Key\n" + ) + sys.exit(1)