dendro: adjustments for better code and correction in Snakefile

Snakefile

@@ -161,10 +161,10 @@ rule quicklook:
     output: touch("{path}/{station_key}-quicklook")
     shell: "python {pythonflags} -m plotting.do_plot_current_level1_soilnet --fail --station {wildcards.station_key} --ndays 15"
 
-rule calculateStorage:
-    input: "{path}/{station_key}-{soilnet_key}-level2"
-    output: touch("{path}/{station_key}-{soilnet_key}-aggregate")
-    shell: "python {pythonflags} -m level2.do_dendro_calculation --station HH --device BC1 BC2 BC3 T5 --doall"
+rule calculateDendro:
+    input: "{path}/{station_key}-{meteo_key}-level2"
+    output: touch("{path}/{station_key}-derived-dendro")
+    shell: "python {pythonflags} -m level1.do_dendro_calculation --station HH --device BC1 BC2 BC3 T5 --doall"
 
 
 # NOTE: will be obsolete when HH is moved

level1/do_dendro_calculation.py

@@ -25,7 +25,7 @@ def filter(data, flags):
     return data[data.columns[data.columns.str.match(".*dendro(?!.*r)")]]
 
 
-def grouper(df, n, fillvalue=None):
+def grouper(df, n=3, fillvalue=None):
     """
     This grouper function splits a pd.DataFrame into pd.DataFrames with `n` columns.
 
@@ -39,7 +39,7 @@ def grouper(df, n, fillvalue=None):
 
 
 def fillNa(df):
-    for bhd_value, bhd_manu, flag in grouper(df, n=3):
+    for bhd_value, bhd_manu, flag in grouper(df):
         # setting 91 flag on all values, where calculated value is nan
         df.loc[df[bhd_value].isna(), flag] = 91
         df[bhd_value] = df[bhd_value].fillna(df[bhd_manu])
@@ -182,7 +182,7 @@ def main(station, device, start_date, end_date, debug):
 
         # corrections in index Order and not setted flags
         final = final.sort_index()
-        for a, b, c in grouper(final, n=3):
+        for a, b, c in grouper(final):
             final = final.fillna({a: NODATA, b: NODATA, c: 92})
 
         writeData(final, device)

[David Schäfer]

As none of BC1, BC2, BC3 and T5 are currently processed at the VM we need to integrate a caching job here:

    input: 
        "{path}/{station_key}-{meteo_key}-level2",
        "{path}/HH-BC1-cache",
        "{path}/HH-BC1-cache",
        "{path}/HH-BC2-cache",
        "{path}/HH-BC3-cache",
        "{path}/HH-T5-cache",
    output: touch("{path}/{station_key}-derived-dendro")
    shell: "python {pythonflags} -m level1.do_dendro_calculation --station HH --device BC1 BC2 BC3 T5 --doall"