From 05fd980bd4ba533ed4d844685baa576822e69813 Mon Sep 17 00:00:00 2001
From: kaiiam <kblumberg@email.arizona.edu>
Date: Mon, 12 Feb 2024 16:04:25 +0100
Subject: [PATCH] Add bash script to run organisms parts modules

---
 src/ontology/scripts/run_organism_parts.sh | 79 ++++++++++++++++++++++
 1 file changed, 79 insertions(+)
 create mode 100755 src/ontology/scripts/run_organism_parts.sh

diff --git a/src/ontology/scripts/run_organism_parts.sh b/src/ontology/scripts/run_organism_parts.sh
new file mode 100755
index 00000000..e454b0e7
--- /dev/null
+++ b/src/ontology/scripts/run_organism_parts.sh
@@ -0,0 +1,79 @@
+#!/bin/bash
+
+# Author: Kai Blumberg https://orcid.org/0000-0002-3410-4655
+
+set -e
+
+for ARGUMENT in "$@"
+do
+   KEY=$(echo $ARGUMENT | cut -f1 -d=)
+
+   KEY_LENGTH=${#KEY}
+   VALUE="${ARGUMENT:$KEY_LENGTH+1}"
+
+   export "$KEY"="$VALUE"
+done
+
+
+MODULE_DIR=../imports/$MODULE
+RESOURCES_DIR=$MODULE_DIR/resources
+
+
+if [ $TERM_CONTRIBUTOR_STR ]; then TC="-c $TERM_CONTRIBUTOR_STR"; else TC=''; fi
+
+
+if [ $MODE = 'test' ]; then
+   
+   TEST_DIR=$MODULE_DIR/TEST_RUN_RESULTS
+   if [ ! -d "$TEST_DIR" ] ; then mkdir "$TEST_DIR" ; fi
+   cp $RESOURCES_DIR/id_integer.txt $TEST_DIR/id_integer.txt
+   python3 organism_parts.py -t $MODULE_DIR/${MODULE}_parts.tsv -i $RESOURCES_DIR/species_list.tsv -o $TEST_DIR/test_${MODULE}_template.tsv -m $RESOURCES_DIR/id_mapping_table.tsv -n $TEST_DIR/mapping_table_output.tsv -org $MODULE -id $TEST_DIR/id_integer.txt $TC
+   robot template --template $TEST_DIR/test_${MODULE}_template.tsv -i ../foodon-merged.ofn --ontology-iri "http://purl.obolibrary.org/test_${MODULE}_template.owl" -o $TEST_DIR/test_${MODULE}_module.ofn
+   echo ""
+   echo "Test $MODULE module run successful!"
+   echo "Check the files in '$TEST_DIR' to make sure everything is as expected."
+   echo "See '$TEST_DIR/mapping_table_output.tsv' file summarizing the new terms that will be added (once fully run)."
+   echo "It is safe to run the $MODULE module in test mode as many times as needed."
+   echo "When ready run the full version of the $MODULE module."
+   echo "Please do not commit the files in '$TEST_DIR' directory, they can be deleted once you are ready to move on to running the full module."
+
+
+elif [ $MODE = 'run' ]; then
+   while true; do
+    read -p "Have you already run the script in test mode?" yesno
+    case $yesno in
+        [Yy]* ) 
+            echo ""
+            echo "Preliminary test confirmed, running $MODULE module!"
+            # run steps here e.g. echo "run case."
+            INTERMEDIATE_DIR=$MODULE_DIR/intermediate
+            if [ ! -d "$INTERMEDIATE_DIR" ] ; then mkdir "$INTERMEDIATE_DIR" ; fi
+            python3 organism_parts.py -t $MODULE_DIR/${MODULE}_parts.tsv -i $RESOURCES_DIR/species_list.tsv -o $INTERMEDIATE_DIR/${MODULE}_template.tsv -m $RESOURCES_DIR/id_mapping_table.tsv -n $INTERMEDIATE_DIR/mapping_table_output.tsv -org $MODULE -id $RESOURCES_DIR/id_integer.txt $TC
+            echo "Success running organism_parts.py with $MODULE module!"
+            robot template --template $INTERMEDIATE_DIR/${MODULE}_template.tsv -i ../foodon-merged.ofn --ontology-iri "http://purl.obolibrary.org/obo/foodon/imports/${MODULE}/${MODULE}_parts.owl" -o $MODULE_DIR/${MODULE}_parts.ofn
+            echo "Success running generated $MODULE robot template!"
+            
+            if [ -f $INTERMEDIATE_DIR/mapping_table_output.tsv ] ; then cat $INTERMEDIATE_DIR/mapping_table_output.tsv >> $RESOURCES_DIR/id_mapping_table.tsv ; fi
+            rm -r $INTERMEDIATE_DIR
+
+            echo "You may now commit your changes to the following files:"
+            echo "'$MODULE_DIR/${MODULE}_parts.tsv'"
+            echo "'$MODULE_DIR/${MODULE}_parts.ofn'"
+            echo "'$RESOURCES_DIR/id_integer.txt'"
+            echo "'$RESOURCES_DIR/id_mapping_table.tsv'"
+            echo "As well as any changes you might have have made to the 'id_mapping_table.tsv' and or 'species_list.tsv' file(s) in '$RESOURCES_DIR'."
+            exit
+
+        ;;
+        [Nn]* ) 
+            echo "You answered no, please make sure to run the script in test mode first."
+            exit
+        ;;
+        * ) echo "Please answer either yes or no.";;
+    esac
+   done
+
+
+else
+   echo "MODE must be 'run' or 'test'."
+fi