Mercurial > repos > climate > cads
changeset 1:67a7303bc5c9 draft default tip
planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 7cb1c1196b3e8998743e3b4b949290e95c5d3be1
| author | climate |
|---|---|
| date | Fri, 06 Mar 2026 13:39:23 +0000 |
| parents | b768e517a7d0 |
| children | |
| files | cads.sh cads.xml cads_retrieve.py test-data/req-timeseries.txt test-data/req.txt |
| diffstat | 5 files changed, 99 insertions(+), 98 deletions(-) [+] |
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--- a/cads.sh Sat Jun 19 18:35:50 2021 +0000 +++ b/cads.sh Fri Mar 06 13:39:23 2026 +0000 @@ -1,19 +1,19 @@ #!/usr/bin/env bash -if [ -f download.tar.gz ]; then - tar zxvf download.tar.gz +if [ -f *.tar.gz ]; then + tar zxvf *.tar.gz cat *.grib > tmp.grib cdo setgridtype,regular tmp.grib tmpg.grib cdo -f nc -t ecmwf copy tmpg.grib tmp.nc -elif [ -f download.zip ]; then - unzip download.zip +elif [ -f *.zip ]; then + unzip *.zip cat *.grib > tmp.grib cdo setgridtype,regular tmp.grib tmpg.grib cdo -f nc -t ecmwf copy tmpg.grib tmp.nc -elif [ -f download.grib ]; then - cdo -f nc -t ecmwf copy download.grib tmp.nc -elif [ -f download.nc ]; then - mv download.nc tmp.nc +elif [ -f *.grib ]; then + cdo -f nc -t ecmwf copy *.grib tmp.nc +elif [ -f *.nc ]; then + mv *.nc tmp.nc else echo "No data found! Check your request and/or credentials." fi
--- a/cads.xml Sat Jun 19 18:35:50 2021 +0000 +++ b/cads.xml Fri Mar 06 13:39:23 2026 +0000 @@ -1,22 +1,30 @@ -<tool id="cads" name="Copernicus Atmosphere Data Store" version="0.1.0" profile="20.05"> +<tool id="cads" name="Copernicus Atmosphere Data Store" version="0.1.1" profile="25.1"> <description>for retrieving data from the Atmosphere Monitoring Service</description> + <edam_topics> + <edam_topic>topic_3855</edam_topic> + <edam_topic>topic_3318</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_2422</edam_operation> + <edam_operation>operation_3357</edam_operation> + <edam_operation>operation_0335</edam_operation> + </edam_operations> <requirements> - <requirement type="package" version="3">python</requirement> - <requirement type="package" version="0.5.1">cdsapi</requirement> - <requirement type="package" version="1.9.9">cdo</requirement> + <requirement type="package" version="3.8">python</requirement> + <requirement type="package" version="0.7.3">cdsapi</requirement> + <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="cads_apikey" version="1.0" label="CADS API key" description="Credential for accessing Copernicus atmosphere Data Store API."> + <secret name="key" inject_as_env="CADS_API_KEY" optional="false" label="CADS API key" description="Your Copernicus atmosphere Data Store API key."/> + </credentials> </requirements> - <command detect_errors="exit_code"><![CDATA[ + <required_files> + <include path="cads_retrieve.py" /> + <include path="cads.sh" /> + </required_files> + <command detect_errors="exit_code"><![CDATA[ export HOME=`pwd` && - #set $cads_apikey = $__user__.extra_preferences.get('cads_account|cads_apikey', "") - #if $cads_apikey == '' - echo 'Error. Set your CADS credentials via: User -> Preferences -> Manage Information' && - echo 'Will try to use tool adsapirc file (used for testing)' && - cp '$__tool_directory__/adsapirc.cfg' .cdsapirc && - #else - cp '$cads_key_file' .cdsapirc && - #end if python3 '$__tool_directory__/cads_retrieve.py' #if str($is_file.has_req).strip() == 'yes' @@ -29,14 +37,9 @@ echo "Data retrieval from Copernicus Atmosphere Data Store is done" ]]></command> <configfiles> - <configfile name="cads_key_file"><![CDATA[ -#set $cads_apikey = $__user__.extra_preferences.get('cads_account|cads_apikey', "") - url: https://ads.atmosphere.copernicus.eu/api/v2 - key: $cads_apikey - ]]></configfile> <configfile name="req_from_paste"><![CDATA[ #if str($is_file.has_req).strip() == 'no' -$is_file.api_req_text + $is_file.api_req_text #end if ]]></configfile> </configfiles> @@ -55,25 +58,27 @@ </conditional> </inputs> <outputs> - <data name="request" format="txt" from_work_dir="request.txt"/> - <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/> + <data name="request" format="txt" from_work_dir="request.txt" label="Request"/> + <data name="filename" format="netcdf" from_work_dir="tmp.nc" label="Netcdf file"/> </outputs> <tests> - <test> + <test expect_failure="true"> <conditional name="is_file"> <param name="has_req" value="yes" /> <param name="api_req_file" ftype="txt" value="req.txt" /> </conditional> - <output name="request" value="req_out.txt" compare="sim_size" delta="10"/> - <output name="ofilename" ftype="netcdf" value="output.nc" compare="sim_size" delta="100"/> + <assert_stderr> + <has_text text="CADS retrieval failed, make sure you filled in your CADS API Key"/> + </assert_stderr> </test> - <test> + <test expect_failure="true"> <conditional name="is_file"> <param name="has_req" value="yes" /> <param name="api_req_file" ftype="txt" value="req-timeseries.txt" /> </conditional> - <output name="request" value="timeseries_out.txt" compare="sim_size" delta="10"/> - <output name="ofilename" ftype="netcdf" value="timeseries.nc" compare="sim_size" delta="100"/> + <assert_stderr> + <has_text text="CADS retrieval failed, make sure you filled in your CADS API Key"/> + </assert_stderr> </test> </tests> <help><![CDATA[ @@ -84,10 +89,10 @@ This tool is a wrapper to retrieve data from the Copernicus Atmosphere Data Store. - It allows to retrieve data from the Copernicus Atmosphere Monitoring Service. -- Any user willing to use this tool needs to `create a new account <https://ads.atmosphere.copernicus.eu/user/register?destination=/api-how-to|>`_. -- Set your CADS 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 Copernicus Atmosphere Data Store and copy/paste it in the input field "Request" or save it in a file. +- Any user willing to use this tool needs to `create a new account here <https://ads.atmosphere.copernicus.eu/>`_. +- Set your CADS API Key in the credentials +- Your CADS API key can be found `here <https://ads.atmosphere.copernicus.eu/profile>`_. +- Compose your request directly on Copernicus Atmosphere Data Store and copy/paste it in the input field "Request" or save it in a file mor information on how to proceed in the `documentation <https://ads.atmosphere.copernicus.eu/user-guide>` . - Be aware that for being able to download dataset from ADS, users also need to agree to their term of use (Licence to use Copernicus Products) on the ADS website. License: @@ -98,14 +103,6 @@ that may be made of the Copernicus information or data it contains. ]]></help> <citations> + <citation type="bibtex">@misc{CADS,author={Copernicus Atmosphere Data Store}}</citation> </citations> - <edam_topics> - <edam_topic>topic_3855</edam_topic> - <edam_topic>topic_3318</edam_topic> - </edam_topics> - <edam_operations> - <edam_operation>operation_2422</edam_operation> - <edam_operation>operation_3357</edam_operation> - <edam_operation>operation_0335</edam_operation> - </edam_operations> </tool>
--- a/cads_retrieve.py Sat Jun 19 18:35:50 2021 +0000 +++ b/cads_retrieve.py Fri Mar 06 13:39:23 2026 +0000 @@ -1,6 +1,7 @@ import argparse import ast -from os import environ, path +import sys +from os import environ import cdsapi @@ -31,26 +32,35 @@ req = req.replace(value, key) print("req = ", req) -c3s_type = req.split('c.retrieve')[1].split('(')[1].split(',')[0].strip(' "\'\t\r\n') -c3s_req = '{' + req.split('{', 1)[1].rsplit('}', 1)[0].replace('\n', '') + '}' +c3s_type = req.split('dataset')[1].split('=')[1].split('\n')[0].strip(' "\'\t\r\n') +c3s_req = '{' + req.split('request', 1)[1].split('{', 1)[1].rsplit('}', 1)[0].replace('\n', '') + '}' c3s_req_dict = ast.literal_eval(c3s_req) -c3s_output = req.rsplit('}', 1)[1].split(',')[1].split(')')[0].strip(' "\'\t\r\n') - -with open(args.output, "w") as f: - f.write(f'dataset to retrieve: {c3s_type}\nrequest: {c3s_req}\noutput filename: {c3s_output}') - print("start retrieving data...") -cdapi_file = path.join(environ.get('HOME'), '.cdsapirc') +api_key = environ.get("CADS_API_KEY") -if path.isfile(cdapi_file): - c = cdsapi.Client() +if not api_key: + sys.stderr.write( + "CADS retrieval failed, make sure you filled in your CADS API Key\n" + ) + sys.exit(1) - c.retrieve( - c3s_type, - c3s_req_dict, - c3s_output) +try: + c = cdsapi.Client( + url="https://ads.atmosphere.copernicus.eu/api", + key=api_key + ) + + result = c.retrieve(c3s_type, c3s_req_dict) + c3s_output = result.download() print("data retrieval successful") +except Exception: + raise RuntimeError( + "CADS retrieval failed, make sure you filled in your CADS API Key" + ) + +with open(args.output, "w") as f: + f.write(f'dataset to retrieve: {c3s_type}\nrequest: {c3s_req}\noutput filename: {c3s_output}')
--- a/test-data/req-timeseries.txt Sat Jun 19 18:35:50 2021 +0000 +++ b/test-data/req-timeseries.txt Fri Mar 06 13:39:23 2026 +0000 @@ -1,19 +1,15 @@ import cdsapi - -c = cdsapi.Client() -c.retrieve( - 'cams-solar-radiation-timeseries', - { - 'sky_type': 'clear', - 'location': { - 'latitude': 60, - 'longitude': 11, - }, - 'altitude': '-999.', - 'date': '2021-06-17/2021-06-17', - 'time_step': '15minute', - 'time_reference': 'universal_time', - 'format': 'netcdf', - }, - 'download.nc') +dataset = "cams-solar-radiation-timeseries" +request = { + "sky_type": "clear", + "location": {"longitude": 11, "latitude": 60}, + "altitude": ["-999"], + "date": ["2026-03-04/2026-03-04"], + "time_step": "15minute", + "time_reference": "universal_time", + "data_format": "netcdf" +} + +client = cdsapi.Client() +client.retrieve(dataset, request).download()
--- a/test-data/req.txt Sat Jun 19 18:35:50 2021 +0000 +++ b/test-data/req.txt Fri Mar 06 13:39:23 2026 +0000 @@ -1,21 +1,19 @@ import cdsapi -c = cdsapi.Client() +dataset = "cams-global-reanalysis-eac4" +request = { + "variable": [ + "total_column_carbon_monoxide", + "total_column_nitric_acid" + ], + "date": ["2025-08-01/2025-08-31"], + "time": [ + "00:00", "03:00", "06:00", + "09:00", "12:00", "15:00", + "18:00", "21:00" + ], + "data_format": "grib" +} -c.retrieve( - 'cams-europe-air-quality-forecasts', - { - 'variable': 'nitrogen_dioxide', - 'model': 'ensemble', - 'level': '0', - 'date': '2021-06-16/2021-06-16', - 'type': 'analysis', - 'time': '00:00', - 'leadtime_hour': '0', - 'format': 'netcdf', - 'area': [ - 59.96, 10.66, 59.87, - 10.9, - ], - }, - 'download.nc') +client = cdsapi.Client() +client.retrieve(dataset, request).download()