diff c3s_retrieve.py @ 0:250554670f72 draft

"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/c3s commit 04069ef63198279caf3d97de5a58fb32df12c811"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/c3s_retrieve.py	Tue Apr 13 18:32:45 2021 +0000
@@ -0,0 +1,60 @@
+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()
+
+if path.isfile(args.request):
+    f = open(args.request, "r")
+    req = f.read()
+    f.close()
+    mapped_chars = {
+        '>': '__gt__',
+        '<': '__lt__',
+        "'": '__sq__',
+        '"': '__dq__',
+        '[': '__ob__',
+        ']': '__cb__',
+        '{': '__oc__',
+        '}': '__cc__',
+        '@': '__at__',
+        '#': '__pd__',
+        "": '__cn__'
+    }
+
+    # 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].split('}')[0].replace('\n', '') + '}'
+c3s_req_dict = ast.literal_eval(c3s_req)
+
+c3s_output = req.split('}')[1].split(',')[1].split(')')[0].strip(' "\'\t\r\n')
+
+f = open(args.output, "w")
+f.write("dataset to retrieve: " + c3s_type + "\n")
+f.write("request: " + c3s_req + "\n")
+f.write("output filename: " + c3s_output)
+f.close()
+
+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")