Updated data and fixed bug in line remove script

run_analysis_gurobi.sh

@@ -1,19 +1,34 @@
-MODEL_RUN_NAME=TEMBA_09_08_Ref
-DATA_FOLDER=output_data
+#!/bin/bash
+if [ "$1" != "" ]; then
+    echo "Running model workflow for $1"
+    MODEL_RUN_NAME=$1
+    DATA_FOLDER=output_data
 
-INPUT_FILE=$MODEL_RUN_NAME.xlsx
+    INPUT_FILE=$MODEL_RUN_NAME.xlsx
 
-MODEL_FILE=model/Temba_0406_modex.txt
+    # This should be replaced by a model file downloaded from the OSeMOSYS repository (or a branch of the repository)
+    MODEL_FILE=model/Temba_0406_modex.txt
 
-DATA_FILE=$DATA_FOLDER/$MODEL_RUN_NAME.txt
-LP_FILE=$DATA_FOLDER/$MODEL_RUN_NAME.lp.gz
-GUROBI_FILE=$DATA_FOLDER/$MODEL_RUN_NAME
+    DATA_FILE=$DATA_FOLDER/$MODEL_RUN_NAME.txt
+    LP_FILE=$DATA_FOLDER/$MODEL_RUN_NAME.lp.gz
+    GUROBI_FILE=$DATA_FOLDER/$MODEL_RUN_NAME
 
-python scripts/excel_to_osemosys.py input_data $INPUT_FILE $DATA_FILE
-python scripts/CBC_results_AS_MODEX.py $DATA_FILE
+    python scripts/excel_to_osemosys.py input_data $INPUT_FILE $DATA_FILE
+    python scripts/CBC_results_AS_MODEX.py $DATA_FILE
 
-glpsol -m $MODEL_FILE -d $DATA_FILE --wlp $LP_FILE --check
+    glpsol -m $MODEL_FILE -d $DATA_FILE --wlp $LP_FILE --check
 
-# Solve with Gurobi
-gurobi_cl NumericFocus=1 ResultFile=$GUROBI_FILE.sol LogFile=$GUROBI_FILE.log $LP_FILE
-sed '/ * 0/d' $GUROBI_FILE.sol >> results/$GUROBI_FILE.sol # Remove zero value items
+    # Solve with Gurobi
+    gurobi_cl NumericFocus=1 ResultFile=$GUROBI_FILE.sol ResultFile=$GUROBI_FILE.ilp LogFile=$GUROBI_FILE.log $LP_FILE
+    sed '/ * 0$/d' $GUROBI_FILE.sol > results/$MODEL_RUN_NAME.sol # Remove zero value items
+
+    # Create a folder in which to place the csv files computed by the generate_pickle script
+    mkdir -p results/$MODEL_RUN_NAME
+
+    # Generate the processed results files including csv files of computed results and a pickle file for the viewer
+    python scripts/generate_pickle.py  output_data/$MODEL_RUN_NAME.txt results/$MODEL_RUN_NAME.sol gurobi results/$MODEL_RUN_NAME.pickle results/$MODEL_RUN_NAME
+
+else
+    echo "usage: bash $0 <model run name>"
+    exit 1
+fi