diff cads_retrieve.py @ 0:b768e517a7d0 draft default tip

"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/cads commit 778688ee8d14e22b00b648858ad9bd1c2f46b1e0"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cads_retrieve.py	Sat Jun 19 18:35:50 2021 +0000
@@ -0,0 +1,56 @@
+import argparse
+import ast
+from os import environ, path
+
+import cdsapi
+
+parser = argparse.ArgumentParser()
+parser.add_argument("-i", "--request", type=str, help="input API request")
+parser.add_argument("-o", "--output", type=str, help="output API request")
+args = parser.parse_args()
+
+mapped_chars = {
+    '>': '__gt__',
+    '<': '__lt__',
+    "'": '__sq__',
+    '"': '__dq__',
+    '[': '__ob__',
+    ']': '__cb__',
+    '{': '__oc__',
+    '}': '__cc__',
+    '@': '__at__',
+    '#': '__pd__',
+    "": '__cn__'
+}
+
+with open(args.request) as f:
+    req = f.read()
+
+    # Unsanitize labels (element_identifiers are always sanitized by Galaxy)
+    for key, value in mapped_chars.items():
+        req = req.replace(value, key)
+
+print("req = ", req)
+c3s_type = req.split('c.retrieve')[1].split('(')[1].split(',')[0].strip(' "\'\t\r\n')
+
+c3s_req = '{' + req.split('{', 1)[1].rsplit('}', 1)[0].replace('\n', '') + '}'
+c3s_req_dict = ast.literal_eval(c3s_req)
+
+c3s_output = req.rsplit('}', 1)[1].split(',')[1].split(')')[0].strip(' "\'\t\r\n')
+
+with open(args.output, "w") as f:
+    f.write(f'dataset to retrieve: {c3s_type}\nrequest: {c3s_req}\noutput filename: {c3s_output}')
+
+print("start retrieving data...")
+
+cdapi_file = path.join(environ.get('HOME'), '.cdsapirc')
+
+if path.isfile(cdapi_file):
+    c = cdsapi.Client()
+
+    c.retrieve(
+        c3s_type,
+        c3s_req_dict,
+        c3s_output)
+
+    print("data retrieval successful")