Mercurial > repos > climate > c3s

annotate c3s_retrieve.py @ 0:7fa6bc1fb588 draft

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"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
author climate
date Tue, 13 Apr 2021 18:32:15 +0000
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7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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1 import argparse
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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2 import ast
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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3 from os import environ, path
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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5 import cdsapi
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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7 parser = argparse.ArgumentParser()
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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8 parser.add_argument("-i", "--request", type=str, help="input API request")
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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9 parser.add_argument("-o", "--output", type=str, help="output API request")
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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10 args = parser.parse_args()
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7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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12 if path.isfile(args.request):
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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13 f = open(args.request, "r")
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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14 req = f.read()
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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15 f.close()
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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16 mapped_chars = {
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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17 '>': '__gt__',
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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18 '<': '__lt__',
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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19 "'": '__sq__',
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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20 '"': '__dq__',
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21 '[': '__ob__',
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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22 ']': '__cb__',
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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23 '{': '__oc__',
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24 '}': '__cc__',
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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25 '@': '__at__',
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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26 '#': '__pd__',
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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27 "": '__cn__'
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28 }
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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30 # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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31 for key, value in mapped_chars.items():
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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32 req = req.replace(value, key)
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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34 print("req = ", req)
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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35 c3s_type = req.split('c.retrieve')[1].split('(')[1].split(',')[0].strip(' "\'\t\r\n')
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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37 c3s_req = '{' + req.split('{')[1].split('}')[0].replace('\n', '') + '}'
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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38 c3s_req_dict = ast.literal_eval(c3s_req)
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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40 c3s_output = req.split('}')[1].split(',')[1].split(')')[0].strip(' "\'\t\r\n')
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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42 f = open(args.output, "w")
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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43 f.write("dataset to retrieve: " + c3s_type + "\n")
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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44 f.write("request: " + c3s_req + "\n")
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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45 f.write("output filename: " + c3s_output)
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46 f.close()
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48 print("start retrieving data...")
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50 cdapi_file = path.join(environ.get('HOME'), '.cdsapirc')
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52 if path.isfile(cdapi_file):
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53 c = cdsapi.Client()
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55 c.retrieve(
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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56 c3s_type,
7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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57 c3s_req_dict,
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58 c3s_output)
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7fa6bc1fb588 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"
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60 print("data retrieval successful")