| Next changeset 1:8b30be2cef81 (2019-05-07) |
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planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables commit 49926d09bb7d28f07b24050d25c40f2ae875d6f7 |
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README.md ecv_retrieve.py essential_climate_variables.xml test-data/prep_seaice.nc test-data/soil_moisture.nc |
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| diff -r 000000000000 -r 5c0ab9932311 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Fri May 03 15:11:01 2019 -0400 |
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| @@ -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). |
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| diff -r 000000000000 -r 5c0ab9932311 ecv_retrieve.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ecv_retrieve.py Fri May 03 15:11:01 2019 -0400 |
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| @@ -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')) |
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| diff -r 000000000000 -r 5c0ab9932311 essential_climate_variables.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/essential_climate_variables.xml Fri May 03 15:11:01 2019 -0400 |
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| b'@@ -0,0 +1,167 @@\n+<tool id="cds_essential_variability" name="Copernicus Essential Climate Variables" version="0.1.4">\n+ <description>for assessing climate variability</description>\n+ <requirements>\n+ <requirement type="package" version="3">python</requirement>\n+ <requirement type="package" version="0.1.4">cdsapi</requirement>\n+ <requirement type="package" version="1.9.6">cdo</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ HOME=`pwd` &&\n+ python3 \'$__tool_directory__/ecv_retrieve.py\'\n+ \'ecv-for-climate-change\' \'$variable\'\n+ --year \'$year\'\n+ #if str($time_aggregation.selector) == \'1_month\'\n+ --month \'$time_aggregation.month\'\n+ #else\n+ --month \'01\'\n+ #end if\n+ --time_aggregation \'$time_aggregation.selector\'\n+ --product_type \'$product_type\'\n+ --format \'tgz\' --output \'tmp.tgz\'\n+ --verbose &&\n+ tar zxvf tmp.tgz &&\n+ cat *.grib > tmp.grib &&\n+ cdo -f nc -t ecmwf copy tmp.grib tmp.nc\n+ ]]></command>\n+ <inputs>\n+ <param name="variable" type="select" multiple="true" label="Variable(s)">\n+ <option value="surface_air_temperature" selected="true">Surface air temperature</option>\n+ <option value="surface_air_relative_humidity" selected="true">Surface air relative humidity</option>\n+ <option value="0_7cm_volumetric_soil_moisture" selected="true">0-7cm volumetric soil moisture</option>\n+ <option value="precipitation" selected="true">Precipitation</option>\n+ <option value="sea_ice" selected="true">Sea-ice</option>\n+ </param>\n+ <param name="product_type" type="select" label="Select type of data">\n+ <option value="climatology" selected="true">Climatology</option>\n+ <option value="anomaly">Anomaly</option>\n+ </param>\n+ <conditional name="time_aggregation">\n+ <param name="selector" type="select" label="Time aggregation">\n+ <option value="12_month" selected="true">yearly</option>\n+ <option value="1_month">monthly</option>\n+ </param>\n+ <when value="1_month">\n+ <param name="month" type="select" multiple="true" label="Select month(s)">\n+ <option value="01" selected="true">January</option>\n+ <option value="02" selected="true">February</option>\n+ <option value="03" selected="true">March</option>\n+ <option value="04" selected="true">April</option>\n+ <option value="05" selected="true">May</option>\n+ <option value="06" selected="true">June</option>\n+ <option value="07" selected="true">July</option>\n+ <option value="08" selected="true">August</option>\n+ <option value="09" selected="true">September</option>\n+ <option value="10" selected="true">October</option>\n+ <option value="11" selected="true">November</option>\n+ <option value="12" selected="true">December</option>\n+ </param>\n+ </when>\n+ </conditional>\n+\n+ <param name="year" type="select" multiple="true" label="Select year(s)">\n+ <option value="1979">1979</option>\n+ <option value="1980">1980</option>\n+ <option value="1981">1981</option>\n+ <option value="1982">1982</option>\n+ <option value="1983">1983</option>\n+ <option value="1984">1984</option>\n+ <option value="1985">1985</option>\n+ <option value="1986">1986</option>\n+ <option value="1987">1987</option>\n+ <option value="1988">1988</option>\n+ <option value="1989">1989</option'..b'n>\n+ <option value="2003">2003</option>\n+ <option value="2004">2004</option>\n+ <option value="2005">2005</option>\n+ <option value="2006">2006</option>\n+ <option value="2007">2007</option>\n+ <option value="2008">2008</option>\n+ <option value="2009">2009</option>\n+ <option value="2010">2010</option>\n+ <option value="2011">2011</option>\n+ <option value="2012">2012</option>\n+ <option value="2013">2013</option>\n+ <option value="2014">2014</option>\n+ <option value="2015">2015</option>\n+ <option value="2016">2016</option>\n+ <option value="2017">2017</option>\n+ <option value="2018">2018</option>\n+ <option value="2019" selected="true">2019</option>\n+ </param>\n+ </inputs>\n+ <outputs>\n+ <data name="ofilename" format="netcdf" from_work_dir="tmp.nc"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="variable" value="0_7cm_volumetric_soil_moisture"/>\n+ <param name="product_type" value="climatology"/>\n+ <param name="time_aggregation" value="1_month"/>\n+ <param name="month" value="12"/>\n+ <param name="year" value="2018"/>\n+ <output name="ofilename" ftype="netcdf" file="soil_moisture.nc" compare="sim_size" delta="100"/>\n+ </test>\n+ <test>\n+ <param name="variable" value="precipitation,sea_ice"/>\n+ <param name="product_type" value="anomaly"/>\n+ <param name="time_aggregation" value="12_month"/>\n+ <param name="year" value="2017"/>\n+ <output name="ofilename" ftype="netcdf" file="prep_seaice.nc" compare="sim_size" delta="100"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+**Copernicus Essential climate variables for assessment of climate variability from 1979 to present**\n+=======================================================================================================\n+\n+This tool is a wrapper to retrieve Copernicus Essential Climate Variables.\n+It corresponds to the European Contribution to the Monitoring of Essential Climate Variables from Space.\n+An Essential Climate Variable is a physical, chemical or biological variable or a group of linked variables\n+that critically contributes to the characterization of Earth\xe2\x80\x99 s climate.\n+\n+The Essential Climate Variables for assessment of climate variability from 1979 to present dataset contains\n+a selection of climatologies and monthly anomalies of Essential Climate Variables (ECVs) suitable for\n+monitoring and assessment of climate variability and change. Selection criteria are based on accuracy\n+and temporal consistency on monthly to decadal time scales. The ECV data products in this set have been\n+estimated from multiple sources and, depending on the source, may have been adjusted to account for biases\n+and other known deficiencies. Data sources and adjustment methods used are described in the Product User\n+Guide, as are various particulars such as the baseline periods used to calculate monthly climatologies and\n+the corresponding anomalies.\n+\n+\n+- ECV Factsheets: https://gcos.wmo.int/en/essential-climate-variables/ecv-factsheets\n+- Copernicus Climate Data Store documentation on Essential Climate Variables:\n+ https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview\n+\n+ See climatedata.wmo.int/ for more information on Essential Climate Variables.\n+\n+.. class:: infomark\n+\n+ It allows to retrieve estimates of Essential Climate Variables (ECVs)\n+ derived from Earth observations.\n+\n+License:\n+~~~~~~~~\n+ Copernicus License V1.1\n+\n+ Generated using Copernicus Climate Change Service information [2019].\n+ Neither the European Commission nor ECMWF is responsible for any use \n+ that may be made of the Copernicus information or data it contains.\n+\n+ ]]></help>\n+ <citations>\n+ </citations>\n+</tool>\n' |
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