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