diff ecv_retrieve.py @ 0:5c0ab9932311 draft

planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/essential_climate_variables commit 49926d09bb7d28f07b24050d25c40f2ae875d6f7

--- /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'))