| Previous changeset 4:9ee8db6ffba3 (2019-07-07) |
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Commit message:
"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables commit 9a008dba390aef21d4ab61240641bf455f5bb036" |
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modified:
ecv_retrieve.py essential_climate_variables.xml |
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| diff -r 9ee8db6ffba3 -r ee42b7a33dc7 ecv_retrieve.py --- a/ecv_retrieve.py Sun Jul 07 10:06:53 2019 -0400 +++ b/ecv_retrieve.py Tue Jun 08 08:58:04 2021 +0000 |
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| @@ -14,27 +14,28 @@ class ECV (): def __init__(self, archive, variable, product_type, year, month, time_aggregation, area, format, output, - verbose=False + climate_reference_period=None, verbose=False ): self.archive = archive self.variable = variable.split(',') + self.climate_reference_period = climate_reference_period if product_type == '': self.product_type = 'climatology' else: self.product_type = product_type - if year == '': - self.year = '2019' + if year != '' and year is not None: + self.year = year.split(',') else: - self.year = year.split(',') - if month == '': + self.year = None + if month == '' or month is None: self.month = '01' else: self.month = month.split(',') if time_aggregation == '': - self.time_aggregation = '1_month' + self.time_aggregation = '1_month_mean' else: self.time_aggregation = time_aggregation - if area == '': + if area == '' or area is None: self.area = 'global' else: self.area = area @@ -47,6 +48,7 @@ self.outputfile = "donwload." + self.format else: self.outputfile = output + self.verbose = verbose if verbose: print("archive: ", self.archive) print("variable: ", self.variable) @@ -56,17 +58,58 @@ def retrieve(self): - self.cdsapi.retrieve( - self.archive, { - 'variable': self.variable, - 'year': self.year, - 'month': self.month, - 'origin': 'era5', - 'area': self.area, - 'format': self.format, - 'product_type': self.product_type, - 'time_aggregation': self.time_aggregation, - }, + if self.verbose: + print(self.archive) + print('variable', self.variable) + print('year', self.year) + print('month', self.month) + print('origin', 'era5') + print('area', self.area) + print('format', self.format) + print('product_type', self.product_type) + print('time_aggregation', self.time_aggregation) + print('climate_reference_period', + self.climate_reference_period) + print(self.outputfile) + if self.climate_reference_period is None: + self.cdsapi.retrieve( + self.archive, { + 'variable': self.variable, + 'year': self.year, + 'month': self.month, + 'origin': 'era5', + 'area': self.area, + 'format': self.format, + 'product_type': self.product_type, + 'time_aggregation': self.time_aggregation, + }, + self.outputfile) + elif self.year is None: + self.cdsapi.retrieve( + self.archive, { + 'variable': self.variable, + 'climate_reference_period': + self.climate_reference_period, + 'month': self.month, + 'origin': 'era5', + 'format': self.format, + 'product_type': self.product_type, + 'time_aggregation': self.time_aggregation, + }, + self.outputfile) + else: + self.cdsapi.retrieve( + self.archive, { + 'variable': self.variable, + 'climate_reference_period': + self.climate_reference_period, + 'year': self.year, + 'month': self.month, + 'origin': 'era5', + 'format': self.format, + 'product_type': self.product_type, + 'time_aggregation': self.time_aggregation, + }, self.outputfile) def checktar(self): @@ -92,10 +135,10 @@ current_pwd = os.environ['HOME'] if 'GALAXY_COPERNICUS_CDSAPIRC_KEY' in os.environ and \ not os.path.isfile('.cdsapirc'): + print('GALAXY_COPERNICUS_CDSAPIRC_KEY ') 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']) + apikey.write("key: " + os.environ['GALAXY_COPERNICUS_CDSAPIRC_KEY']) remove_apikey = True parser.add_argument( @@ -127,6 +170,10 @@ help='Desired sub-area to extract (North/West/South/East)' ) parser.add_argument( + '--climate_reference_period', + help='Climate reference period (default is 1981-2010)' + ) + parser.add_argument( '--format', help='Output file format (GRIB or netCDF or tgz)' ) @@ -142,7 +189,7 @@ p = ECV(args.archive, args.variable, args.product_type, args.year, args.month, args.time_aggregation, args.area, - args.format, args.output, args.verbose) + args.format, args.output, args.climate_reference_period, args.verbose) p.retrieve() p.checktar() # remove api key file if it was created |
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| diff -r 9ee8db6ffba3 -r ee42b7a33dc7 essential_climate_variables.xml --- a/essential_climate_variables.xml Sun Jul 07 10:06:53 2019 -0400 +++ b/essential_climate_variables.xml Tue Jun 08 08:58:04 2021 +0000 |
| [ |
| @@ -1,25 +1,33 @@ -<tool id="cds_essential_variability" name="Copernicus Essential Climate Variables" version="0.1.4"> +<tool id="cds_essential_variability" name="Copernicus Essential Climate Variables" version="0.2.0" profile="20.05"> <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> + <requirement type="package" version="0.5.1">cdsapi</requirement> + <requirement type="package" version="1.9.10">cdo</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - HOME=`pwd` && - cp \$COPERNICUS_CDSAPIRC_KEY_FILE .cdsapirc | true && + export HOME=`pwd` && + #set $cdsapirc_file = os.environ.get('COPERNICUS_CDSAPIRC_KEY_FILE', '') + #if os.path.isfile(str($cdsapirc_file)) + echo "xx $cdsapirc_file xx" && + cp $cdsapirc_file .cdsapirc && + #else + echo 'use tool cdsapirc file' && + cp '$__tool_directory__/cdsapirc.cfg' .cdsapirc && + #end if python3 '$__tool_directory__/ecv_retrieve.py' 'ecv-for-climate-change' '$variable' --month '$month' #if str($product_type.product) == 'monthly_mean' --year '$product_type.year' - --time_aggregation '1_month' + --time_aggregation '1_month_mean' #else if str($product_type.product) == 'anomaly' + --climate_reference_period $product_type.climate_reference_period --time_aggregation '$product_type.selector' --year '$product_type.year' #else - --year '2018' - --time_aggregation '1_month' + --climate_reference_period $product_type.climate_reference_period + --time_aggregation '1_month_mean' #end if --product_type '$product_type.product' --format 'tgz' --output 'tmp.tgz' @@ -43,6 +51,12 @@ <option value="climatology">Climatology</option> <option value="anomaly">Anomaly</option> </param> + <when value="climatology"> + <param name="climate_reference_period" type="select" multiple="false" label="Select Climate reference period"> + <option value="1981_2010" selected="true">1981-2010</option> + <option value="1991_2020">1991-2020</option> + </param> + </when> <when value="monthly_mean"> <param name="year" type="select" multiple="true" label="Select year(s)"> <option value="1979">1979</option> @@ -85,10 +99,15 @@ <option value="2016">2016</option> <option value="2017">2017</option> <option value="2018">2018</option> - <option value="2019" selected="true">2019</option> + <option value="2019">2019</option> + <option value="2020" selected="true">2020</option> </param> </when> <when value="anomaly"> + <param name="climate_reference_period" type="select" multiple="false" label="Select Climate reference period"> + <option value="1981_2010" selected="true">1981-2010</option> + <option value="1991_2020">1991-2020</option> + </param> <param name="year" type="select" multiple="true" label="Select year(s)"> <option value="1979">1979</option> <option value="1980">1980</option> @@ -129,11 +148,13 @@ <option value="2015">2015</option> <option value="2016">2016</option> <option value="2017">2017</option> - <option value="2018" selected="true">2018</option> + <option value="2018">2018</option> + <option value="2019">2019</option> + <option value="2020" selected="true">2020</option> </param> <param name="selector" type="select" label="Time aggregation"> - <option value="12_month" selected="true">yearly</option> - <option value="1_month">monthly</option> + <option value="12_month_running_mean" selected="true">yearly</option> + <option value="1_month_mean">monthly</option> </param> </when> </conditional> @@ -205,7 +226,7 @@ the corresponding anomalies. -- ECV Factsheets: https://gcos.wmo.int/en/essential-climate-variables/ecv-factsheets +- ECV: https://gcos.wmo.int/en/essential-climate-variables - Copernicus Climate Data Store documentation on Essential Climate Variables: https://cds.climate.copernicus.eu/cdsapp#!/dataset/ecv-for-climate-change?tab=overview @@ -229,4 +250,13 @@ <citation type="doi">10.1002/qj.828</citation> <citation type="doi">10.1002/qj.2949</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> |