Feature/add dataset metadata finder

DHIS2/metadata_manipulation/dataset_metadata_finder.py

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+#!/usr/bin/env python3
+
+"""
+Get a csv with all the dhis2 data elements and its category combo options in the given dataset
+"""
+
+from argparse import ArgumentParser, ArgumentDefaultsHelpFormatter as fmt
+
+import json
+import dhis2 as d2
+dataset_query = "dataSets/%s?fields=name,dataSetElements[dataElement[*]]"
+default_category_combo = "Xr12mI7VPn3"
+
+def main():
+    args = get_args()
+    d2.USER = args.user
+    d2.URLBASE = args.urlbase
+    rows = list()
+    for dataset_uid in args.dataset:
+        dataset = d2.get(dataset_query % dataset_uid)
+        for data_set_element in dataset["dataSetElements"]:
+            row = dict()
+            data_element = data_set_element["dataElement"]
+            row["name"] = data_element["name"]
+            row["dataset"] = dataset["name"]
+            if "code" in data_element.keys():
+                row["code"] = data_element["code"]
+            else:
+                row["code"] = "no code"
+            row["id"] = data_element["id"]
+            category_combo = d2.get_object(data_element["categoryCombo"]["id"])
+            row["topic"] = category_combo["name"]
+            row["category_combo_options"] = list()
+            for category_option_combo_id in category_combo["categoryOptionCombos"]:
+                category_option_combo = d2.get_object(category_option_combo_id["id"])
+                row["category_combo_options"].append({"name": category_option_combo["name"], "id": category_option_combo["id"]})
+            rows.append(row)
+
+
+    with open(args.output, mode='w') as file:
+        csv_final_file = create_csv(file)
+        for row in rows:
+            for category_option_combo in row["category_combo_options"]:
+                print([row["dataset"], row["name"], row["id"], row["code"], row["topic"],
+                       category_option_combo["name"], category_option_combo["id"],default_category_combo, ""])
+                csv_final_file.writerow([row["dataset"], row["name"], row["id"], row["code"], row["topic"],
+                                         category_option_combo["name"], category_option_combo["id"],
+                                         default_category_combo, ""])
+
+
+def create_csv(file):
+    import csv
+    csv_final_file = csv.writer(file, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL)
+    csv_final_file.writerow(['Module','Element','delid','code','Topic','Catcombo','catid','attid','Codes_version'])
+    return csv_final_file
+
+def get_args():
+    parser = ArgumentParser(description=__doc__, formatter_class=fmt)
+    add = parser.add_argument  # shortcut
+    add('-o', '--output', help='output file')
+    add('-d', '--dataset', nargs='*', help='dataset id')
+    add('-u', '--user', metavar='USER:PASSWORD', required=True,
+        help='username and password for server authentication')
+    add('--urlbase', default='https://extranet-uat.who.int/dhis2',
+        help='base url of the dhis server')
+
+    return parser.parse_args()
+
+if __name__ == '__main__':
+    main()