Mercurial > repos > climate > cds_essential_variability
changeset 0:5c0ab9932311 draft
planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables commit 49926d09bb7d28f07b24050d25c40f2ae875d6f7
| author | climate |
|---|---|
| date | Fri, 03 May 2019 15:11:01 -0400 |
| parents | |
| children | 8b30be2cef81 |
| files | README.md ecv_retrieve.py essential_climate_variables.xml test-data/prep_seaice.nc test-data/soil_moisture.nc |
| diffstat | 5 files changed, 329 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri May 03 15:11:01 2019 -0400 @@ -0,0 +1,17 @@ + +# Copernicus Essential Climate Variables for assessing climate variability + +This tool allows you to retrieve Copernicus **Essential Climate Variables** for assessing climate variability from the [Copernicus Climate Data Store](https://cds.climate.copernicus.eu/#!/home). + +Copernicus ECV for assessing climate variability is available from the Copernicus portal at https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview + +To be able to retrieve data, you would need to register and get your [CDS API key](https://cds.climate.copernicus.eu/api-how-to). + +The CDS API Key needs to be: + - located in a file called `.cdsapirc`in the HOME area + (as defined the `HOME` environment variable). + - or passed in an enviroment variable called `GALAXY_COPERNICUS_CDSAPIRC`. + When passed in `GALAXY_COPERNICUS_CDSAPIRC`, make sure the key does not contain + the string `key: ` but the key itself only (starting with a number). The file + `.cdsapirc` will then be created and placed in the HOME area (using HOME + environment variable).
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ecv_retrieve.py Fri May 03 15:11:01 2019 -0400 @@ -0,0 +1,145 @@ +# Retrieve Copernicus ECV +# (Essential climate Variables) + +import argparse +import os +import shutil +import tarfile +import tempfile +import warnings + +import cdsapi + + +class ECV (): + def __init__(self, archive, variable, product_type, year, + month, time_aggregation, area, format, output, + verbose=False + ): + self.archive = archive + self.variable = variable.split(',') + if product_type == '': + self.product_type = 'climatology' + else: + self.product_type = product_type + if year == '': + self.year = '2019' + else: + self.year = year.split(',') + if month == '': + self.month = '01' + else: + self.month = month.split(',') + if time_aggregation == '': + self.time_aggregation = '1_month' + else: + self.time_aggregation = time_aggregation + self.area = area + if format == '': + self.format = 'tgz' + else: + self.format = format + if output == '': + self.outputfile = "donwload." + self.format + else: + self.outputfile = output + if verbose: + print("archive: ", self.archive) + print("variable: ", self.variable) + print("year: ", self.year) + print("month: ", self.month) + self.cdsapi = cdsapi.Client() + + def retrieve(self): + + self.cdsapi.retrieve( + self.archive, { + 'variable': self.variable, + 'year': self.year, + 'month': self.month, + 'area': self.area, + 'format': self.format, + 'product_type': self.product_type, + 'time_aggregation': self.time_aggregation, + }, + self.outputfile) + + def checktar(self): + is_grib = False + with open(self.outputfile, 'rb') as ofile: + is_grib = ofile.read(4) + if (is_grib == b'GRIB' and self.format == 'tgz'): + # we create a tgz to be consistent + newfilename = tempfile.NamedTemporaryFile() + gribfile = os.path.basename(newfilename.name) + '.grib' + shutil.copyfile(self.outputfile, gribfile) + newfilename.close() + tar = tarfile.open(self.outputfile, 'w:gz') + tar.add(gribfile) + tar.close() + + +if __name__ == '__main__': + warnings.filterwarnings("ignore") + parser = argparse.ArgumentParser() + + remove_apikey = False + current_pwd = os.environ['HOME'] + if 'GALAXY_COPERNICUS_CDSAPIRC_KEY' in os.environ and \ + not os.path.isfile('.cdsapirc'): + with open(".cdsapirc", "w+") as apikey: + apikey.write("url: https://cds.climate.copernicus.eu/api/v2\n") + apikey.write( + "key: " + os.environ['GALAXY_COPERNICUS_CDSAPIRC_KEY']) + remove_apikey = True + + parser.add_argument( + 'archive', + help='Archive name' + ) + parser.add_argument( + 'variable', + help='Specify which variable to retrieve' + ) + parser.add_argument( + '--product_type', + help='Type of product (climatology or anomaly)' + ) + parser.add_argument( + '--year', + help='Year(s) to retrieve.' + ) + parser.add_argument( + '--month', + help='List of months to retrieve.' + ) + parser.add_argument( + '--time_aggregation', + help='Time range over which data is aggregated (monthly/yearly).' + ) + parser.add_argument( + '--area', + help='Desired sub-area to extract (North/West/South/East)' + ) + parser.add_argument( + '--format', + help='Output file format (GRIB or netCDF or tgz)' + ) + parser.add_argument( + '--output', + help='output filename' + ) + parser.add_argument( + "-v", "--verbose", + help="switch on verbose mode", + action="store_true") + args = parser.parse_args() + + p = ECV(args.archive, args.variable, args.product_type, + args.year, args.month, args.time_aggregation, args.area, + args.format, args.output, args.verbose) + p.retrieve() + p.checktar() + # remove api key file if it was created + if remove_apikey and os.getcwd() == current_pwd: + os.remove(os.path.join(current_pwd, '.cdsapirc'))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/essential_climate_variables.xml Fri May 03 15:11:01 2019 -0400 @@ -0,0 +1,167 @@ +<tool id="cds_essential_variability" name="Copernicus Essential Climate Variables" version="0.1.4"> + <description>for assessing climate variability</description> + <requirements> + <requirement type="package" version="3">python</requirement> + <requirement type="package" version="0.1.4">cdsapi</requirement> + <requirement type="package" version="1.9.6">cdo</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + HOME=`pwd` && + python3 '$__tool_directory__/ecv_retrieve.py' + 'ecv-for-climate-change' '$variable' + --year '$year' + #if str($time_aggregation.selector) == '1_month' + --month '$time_aggregation.month' + #else + --month '01' + #end if + --time_aggregation '$time_aggregation.selector' + --product_type '$product_type' + --format 'tgz' --output 'tmp.tgz' + --verbose && + tar zxvf tmp.tgz && + cat *.grib > tmp.grib && + cdo -f nc -t ecmwf copy tmp.grib tmp.nc + ]]></command> + <inputs> + <param name="variable" type="select" multiple="true" label="Variable(s)"> + <option value="surface_air_temperature" selected="true">Surface air temperature</option> + <option value="surface_air_relative_humidity" selected="true">Surface air relative humidity</option> + <option value="0_7cm_volumetric_soil_moisture" selected="true">0-7cm volumetric soil moisture</option> + <option value="precipitation" selected="true">Precipitation</option> + <option value="sea_ice" selected="true">Sea-ice</option> + </param> + <param name="product_type" type="select" label="Select type of data"> + <option value="climatology" selected="true">Climatology</option> + <option value="anomaly">Anomaly</option> + </param> + <conditional name="time_aggregation"> + <param name="selector" type="select" label="Time aggregation"> + <option value="12_month" selected="true">yearly</option> + <option value="1_month">monthly</option> + </param> + <when value="1_month"> + <param name="month" type="select" multiple="true" label="Select month(s)"> + <option value="01" selected="true">January</option> + <option value="02" selected="true">February</option> + <option value="03" selected="true">March</option> + <option value="04" selected="true">April</option> + <option value="05" selected="true">May</option> + <option value="06" selected="true">June</option> + <option value="07" selected="true">July</option> + <option value="08" selected="true">August</option> + <option value="09" selected="true">September</option> + <option value="10" selected="true">October</option> + <option value="11" selected="true">November</option> + <option value="12" selected="true">December</option> + </param> + </when> + </conditional> + + <param name="year" type="select" multiple="true" label="Select year(s)"> + <option value="1979">1979</option> + <option value="1980">1980</option> + <option value="1981">1981</option> + <option value="1982">1982</option> + <option value="1983">1983</option> + <option value="1984">1984</option> + <option value="1985">1985</option> + <option value="1986">1986</option> + <option value="1987">1987</option> + <option value="1988">1988</option> + <option value="1989">1989</option> + <option value="1990">1990</option> + <option value="1991">1991</option> + <option value="1992">1992</option> + <option value="1993">1993</option> + <option value="1994">1994</option> + <option value="1995">1995</option> + <option value="1996">1996</option> + <option value="1997">1997</option> + <option value="1998">1998</option> + <option value="1999">1999</option> + <option value="2000">2000</option> + <option value="2001">2001</option> + <option value="2002">2002</option> + <option value="2003">2003</option> + <option value="2004">2004</option> + <option value="2005">2005</option> + <option value="2006">2006</option> + <option value="2007">2007</option> + <option value="2008">2008</option> + <option value="2009">2009</option> + <option value="2010">2010</option> + <option value="2011">2011</option> + <option value="2012">2012</option> + <option value="2013">2013</option> + <option value="2014">2014</option> + <option value="2015">2015</option> + <option value="2016">2016</option> + <option value="2017">2017</option> + <option value="2018">2018</option> + <option value="2019" selected="true">2019</option> + </param> + </inputs> + <outputs> + <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/> + </outputs> + <tests> + <test> + <param name="variable" value="0_7cm_volumetric_soil_moisture"/> + <param name="product_type" value="climatology"/> + <param name="time_aggregation" value="1_month"/> + <param name="month" value="12"/> + <param name="year" value="2018"/> + <output name="ofilename" ftype="netcdf" file="soil_moisture.nc" compare="sim_size" delta="100"/> + </test> + <test> + <param name="variable" value="precipitation,sea_ice"/> + <param name="product_type" value="anomaly"/> + <param name="time_aggregation" value="12_month"/> + <param name="year" value="2017"/> + <output name="ofilename" ftype="netcdf" file="prep_seaice.nc" compare="sim_size" delta="100"/> + </test> + </tests> + <help><![CDATA[ + +**Copernicus Essential climate variables for assessment of climate variability from 1979 to present** +======================================================================================================= + +This tool is a wrapper to retrieve Copernicus Essential Climate Variables. +It corresponds to the European Contribution to the Monitoring of Essential Climate Variables from Space. +An Essential Climate Variable is a physical, chemical or biological variable or a group of linked variables +that critically contributes to the characterization of Earth’ s climate. + +The Essential Climate Variables for assessment of climate variability from 1979 to present dataset contains +a selection of climatologies and monthly anomalies of Essential Climate Variables (ECVs) suitable for +monitoring and assessment of climate variability and change. Selection criteria are based on accuracy +and temporal consistency on monthly to decadal time scales. The ECV data products in this set have been +estimated from multiple sources and, depending on the source, may have been adjusted to account for biases +and other known deficiencies. Data sources and adjustment methods used are described in the Product User +Guide, as are various particulars such as the baseline periods used to calculate monthly climatologies and +the corresponding anomalies. + + +- ECV Factsheets: https://gcos.wmo.int/en/essential-climate-variables/ecv-factsheets +- Copernicus Climate Data Store documentation on Essential Climate Variables: + https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview + + See climatedata.wmo.int/ for more information on Essential Climate Variables. + +.. class:: infomark + + It allows to retrieve estimates of Essential Climate Variables (ECVs) + derived from Earth observations. + +License: +~~~~~~~~ + Copernicus License V1.1 + + Generated using Copernicus Climate Change Service information [2019]. + Neither the European Commission nor ECMWF is responsible for any use + that may be made of the Copernicus information or data it contains. + + ]]></help> + <citations> + </citations> +</tool>