231 establish table of active NPIs according to Corona Datenplattform…

… and reported infection data (#443) Establish table of active NPIs according to Corona Datenplattform and reported infection data. --------- Co-authored-by: patricklnz <[email protected]> Co-authored-by: Anna Wendler <[email protected]>
SciCompMod · Sep 5, 2023 · 0904a39 · 0904a39
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commit 0904a39
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Showing 12 changed files with 1,872 additions and 12 deletions.
diff --git a/pycode/memilio-epidata/memilio/epidata/defaultDict.py b/pycode/memilio-epidata/memilio/epidata/defaultDict.py
@@ -42,7 +42,8 @@
     'read_data': False,
     'make_plot': False,
     'out_folder': default_file_path,
-    'start_date': date(2020, 4, 24),
+    'update_data': False,
+    'start_date': date(2020, 1, 1),
     'end_date': date.today(),
     'split_berlin': False,
     'impute_dates': False,
@@ -103,7 +104,9 @@
     'nuts3': 'NUTS3',
     'total_volume': 'Unique_trips',
     'region_name': 'County',
-    'region_id': 'ID_County'
+    'region_id': 'ID_County',
+    'desc': 'Description',
+    'incidence': 'Incidence'
 }
 
 GerEng = {

diff --git a/pycode/memilio-epidata/memilio/epidata/getDIVIData.py b/pycode/memilio-epidata/memilio/epidata/getDIVIData.py
@@ -50,7 +50,7 @@ def get_divi_data(read_data=dd.defaultDict['read_data'],
                   file_format=dd.defaultDict['file_format'],
                   out_folder=dd.defaultDict['out_folder'],
                   no_raw=dd.defaultDict['no_raw'],
-                  start_date=dd.defaultDict['start_date'],
+                  start_date=date(2020, 4, 24),
                   end_date=dd.defaultDict['end_date'],
                   impute_dates=dd.defaultDict['impute_dates'],
                   moving_average=dd.defaultDict['moving_average'],

diff --git a/pycode/memilio-epidata/memilio/epidata/getDataIntoPandasDataFrame.py b/pycode/memilio-epidata/memilio/epidata/getDataIntoPandasDataFrame.py
@@ -412,9 +412,10 @@ def write_dataframe(df, directory, file_prefix, file_type, param_dict={}):
     - json
     - json_timeasstring [Default]
     - hdf5
+    - csv
     - txt
     The file_type defines the file format and thus also the file ending.
-    The file format can be json, hdf5 or txt.
+    The file format can be json, hdf5, csv or txt.
     For this option the column Date is converted from datetime to string.
 
     @param df pandas dataframe (pandas DataFrame)
@@ -428,6 +429,7 @@ def write_dataframe(df, directory, file_prefix, file_type, param_dict={}):
     outForm = {'json': [".json", {"orient": "records"}],
                'json_timeasstring': [".json", {"orient": "records"}],
                'hdf5': [".h5", {"key": "data"}],
+               'csv': [".csv", {}],
                'txt': [".txt", param_dict]}
 
     try:
@@ -436,7 +438,7 @@ def write_dataframe(df, directory, file_prefix, file_type, param_dict={}):
     except KeyError:
         raise ValueError(
             "Error: The file format: " + file_type +
-            " does not exist. Use json, json_timeasstring, hdf5 or txt.")
+            " does not exist. Use json, json_timeasstring, hdf5, csv or txt.")
 
     out_path = os.path.join(directory, file_prefix + outFormEnd)
 
@@ -449,6 +451,8 @@ def write_dataframe(df, directory, file_prefix, file_type, param_dict={}):
         df.to_json(out_path, **outFormSpec)
     elif file_type == "hdf5":
         df.to_hdf(out_path, **outFormSpec)
+    elif file_type == 'csv':
+        df.to_csv(out_path)
     elif file_type == "txt":
         df.to_csv(out_path, **outFormSpec)