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comparison cads_retrieve.py @ 0:b768e517a7d0 draft default tip

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"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"
author climate
date Sat, 19 Jun 2021 18:35:50 +0000
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-1:000000000000 0:b768e517a7d0
1 import argparse
2 import ast
3 from os import environ, path
4
5 import cdsapi
6
7 parser = argparse.ArgumentParser()
8 parser.add_argument("-i", "--request", type=str, help="input API request")
9 parser.add_argument("-o", "--output", type=str, help="output API request")
10 args = parser.parse_args()
11
12 mapped_chars = {
13 '>': '__gt__',
14 '<': '__lt__',
15 "'": '__sq__',
16 '"': '__dq__',
17 '[': '__ob__',
18 ']': '__cb__',
19 '{': '__oc__',
20 '}': '__cc__',
21 '@': '__at__',
22 '#': '__pd__',
23 "": '__cn__'
24 }
25
26 with open(args.request) as f:
27 req = f.read()
28
29 # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
30 for key, value in mapped_chars.items():
31 req = req.replace(value, key)
32
33 print("req = ", req)
34 c3s_type = req.split('c.retrieve')[1].split('(')[1].split(',')[0].strip(' "\'\t\r\n')
35
36 c3s_req = '{' + req.split('{', 1)[1].rsplit('}', 1)[0].replace('\n', '') + '}'
37 c3s_req_dict = ast.literal_eval(c3s_req)
38
39 c3s_output = req.rsplit('}', 1)[1].split(',')[1].split(')')[0].strip(' "\'\t\r\n')
40
41 with open(args.output, "w") as f:
42 f.write(f'dataset to retrieve: {c3s_type}\nrequest: {c3s_req}\noutput filename: {c3s_output}')
43
44 print("start retrieving data...")
45
46 cdapi_file = path.join(environ.get('HOME'), '.cdsapirc')
47
48 if path.isfile(cdapi_file):
49 c = cdsapi.Client()
50
51 c.retrieve(
52 c3s_type,
53 c3s_req_dict,
54 c3s_output)
55
56 print("data retrieval successful")