doc ODK update

FoodOntology · Jan 31, 2025 · d767f1d · d767f1d
1 parent 9c0e795
commit d767f1d
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/src/ontology/scripts/foodon-merged-remediation.py b/src/ontology/scripts/foodon-merged-remediation.py
@@ -18,7 +18,7 @@
 	    	content_dict[key] = val;
 
 new_content = [];
-with open('foodon-merged.ofn', 'r') as foodon_merged:
+with open('foodon-full.owl', 'r') as foodon_merged:
 	lines = foodon_merged.readlines()
 	for index, line in enumerate(lines):
 		# if index % 1000 == 0:	print (index)
@@ -31,5 +31,5 @@
 
 	print ("Processed",len(lines))
 
-with open('foodon-merged.ofn', 'w') as foodon_merged:
+with open('foodon-full.owl', 'w') as foodon_merged:
 	foodon_merged.writelines(new_content)
diff --git a/src/ontology/scripts/run_organism_parts.sh b/src/ontology/scripts/run_organism_parts.sh
@@ -34,7 +34,7 @@ if [ $MODE = 'test' ]; then
    if [ ! -d "$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
+   robot template --template $TEST_DIR/test_${MODULE}_template.tsv -i ../foodon-full.owl --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."
@@ -56,7 +56,7 @@ elif [ $MODE = 'run' ]; then
             if [ ! -d "$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
+            robot template --template $INTERMEDIATE_DIR/${MODULE}_template.tsv -i ../foodon-full.owl --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