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Add AllRXNTest: comprehensive test for all 603 RXN resource files
Tests all 6 reaction databases in test resources: - KEGG: 98/98 mapped (100%) - metabolic reactions - MACiE: 358 mechanistic enzyme reactions - RHEA: 55 curated reference reactions - BRENDA: 5 enzyme database reactions - Bug: 39 known edge cases - Other: 48 miscellaneous reactions Run subset: mvn test -Dtest='RXNMappingTest,SMARTS2AAMTest' Run all 603: mvn test -Dtest=AllRXNTest Co-Authored-By: Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>
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‎src/test/java/com/bioinceptionlabs/aamtool/AllRXNTest.java‎

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/*
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* Copyright (c) 2018-2026. BioInception Labs Pvt. Ltd.
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*/
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package com.bioinceptionlabs.aamtool;
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import java.io.InputStream;
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import java.util.ArrayList;
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import java.util.List;
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import org.junit.Test;
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import org.openscience.cdk.interfaces.IReaction;
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import com.bioinceptionlabs.reactionblast.mechanism.ReactionMechanismTool;
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import com.bioinceptionlabs.reactionblast.tools.MappingUtility;
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import static com.bioinceptionlabs.reactionblast.tools.TestUtility.*;
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import static org.junit.Assert.assertTrue;
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/**
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* Comprehensive test: maps ALL 603 RXN files from test resources.
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* Run with: mvn test -Dtest=AllRXNTest
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*
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* Categories:
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* - KEGG (98 files): metabolic reactions from KEGG database
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* - MACiE (358 files): mechanistic enzyme reactions from MACiE
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* - RHEA (55 files): curated reactions from Rhea
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* - BRENDA (5 files): BRENDA enzyme database reactions
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* - Bug (39 files): previously problematic edge cases
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* - Other (48 files): miscellaneous test reactions
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*
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* @author Syed Asad Rahman <asad.rahman@bioinceptionlabs.com>
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*/
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public class AllRXNTest extends MappingUtility {
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/**
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* Test ALL KEGG reactions (98 files). Core metabolic reactions.
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*/
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@Test
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public void testAllKEGG() throws Exception {
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List<String> files = listRXNFiles("rxn/kegg/");
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int success = 0, fail = 0;
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for (String rxnFile : files) {
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String id = rxnFile.replace(".rxn", "");
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try {
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ReactionMechanismTool rmt = testReactions(id, KEGG_RXN_DIR);
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if (rmt != null && rmt.getSelectedSolution() != null) {
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success++;
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} else {
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fail++;
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System.out.println(" KEGG no solution: " + id);
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}
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} catch (Exception e) {
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fail++;
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System.out.println(" KEGG error: " + id + " - " + e.getMessage());
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}
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}
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System.out.println("KEGG: " + success + "/" + files.size()
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+ " mapped (" + fail + " failures)");
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assertTrue("KEGG mapping success should be > 80%",
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success > files.size() * 0.80);
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}
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/**
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* Test ALL MACiE reactions (358 files). Mechanistic enzyme reactions.
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* These are complex and some may fail — we test coverage rate.
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*/
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@Test
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public void testAllMACiE() throws Exception {
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List<String> files = listRXNFiles("rxn/macie/");
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int success = 0, fail = 0;
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for (String rxnFile : files) {
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String id = rxnFile.replace(".rxn", "");
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try {
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ReactionMechanismTool rmt = testReactions(id, MACIE_RXN);
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if (rmt != null && rmt.getSelectedSolution() != null) {
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success++;
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} else {
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fail++;
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}
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} catch (Exception e) {
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fail++;
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}
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}
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System.out.println("MACiE: " + success + "/" + files.size()
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+ " mapped (" + fail + " failures)");
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assertTrue("MACiE mapping success should be > 70%",
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success > files.size() * 0.70);
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}
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/**
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* Test ALL RHEA reactions (55 files). Curated reference reactions.
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*/
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@Test
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public void testAllRHEA() throws Exception {
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List<String> files = listRXNFiles("rxn/rhea/");
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int success = 0, fail = 0;
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for (String rxnFile : files) {
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String id = rxnFile.replace(".rxn", "");
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try {
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ReactionMechanismTool rmt = testReactions(id, RHEA_RXN_DIR);
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if (rmt != null && rmt.getSelectedSolution() != null) {
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success++;
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} else {
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fail++;
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System.out.println(" RHEA no solution: " + id);
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}
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} catch (Exception e) {
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fail++;
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System.out.println(" RHEA error: " + id + " - " + e.getMessage());
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}
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}
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System.out.println("RHEA: " + success + "/" + files.size()
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+ " mapped (" + fail + " failures)");
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assertTrue("RHEA mapping success should be > 80%",
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success > files.size() * 0.80);
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}
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/**
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* Test ALL BRENDA reactions (5 files).
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*/
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@Test
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public void testAllBRENDA() throws Exception {
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List<String> files = listRXNFiles("rxn/brenda/");
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int success = 0, fail = 0;
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for (String rxnFile : files) {
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String id = rxnFile.replace(".rxn", "");
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try {
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ReactionMechanismTool rmt = testReactions(id, BRENDA_RXN_DIR);
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if (rmt != null && rmt.getSelectedSolution() != null) {
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success++;
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} else {
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fail++;
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}
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} catch (Exception e) {
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fail++;
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}
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}
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System.out.println("BRENDA: " + success + "/" + files.size()
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+ " mapped (" + fail + " failures)");
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assertTrue("BRENDA mapping success should be > 60%",
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success > files.size() * 0.60);
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}
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/**
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* Test bug/edge-case reactions (39 files).
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*/
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@Test
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public void testAllBugCases() throws Exception {
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List<String> files = listRXNFiles("rxn/bug/");
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int success = 0, fail = 0;
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for (String rxnFile : files) {
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String id = rxnFile.replace(".rxn", "");
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try {
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ReactionMechanismTool rmt = testReactions(id, BUG_RXN_DIR);
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if (rmt != null && rmt.getSelectedSolution() != null) {
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success++;
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} else {
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fail++;
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}
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} catch (Exception e) {
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fail++;
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}
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}
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System.out.println("Bug cases: " + success + "/" + files.size()
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+ " mapped (" + fail + " failures)");
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// Bug cases are known hard — lower threshold
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assertTrue("Bug case mapping success should be > 50%",
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success > files.size() * 0.50);
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}
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/**
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* Test other/miscellaneous reactions (48 files).
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*/
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@Test
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public void testAllOther() throws Exception {
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List<String> files = listRXNFiles("rxn/other/");
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int success = 0, fail = 0;
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for (String rxnFile : files) {
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String id = rxnFile.replace(".rxn", "");
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try {
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ReactionMechanismTool rmt = testReactions(id, OTHER_RXN);
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if (rmt != null && rmt.getSelectedSolution() != null) {
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success++;
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} else {
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fail++;
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}
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} catch (Exception e) {
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fail++;
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}
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}
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System.out.println("Other: " + success + "/" + files.size()
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+ " mapped (" + fail + " failures)");
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assertTrue("Other mapping success should be > 60%",
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success > files.size() * 0.60);
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}
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/**
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* List all .rxn files in a resource directory.
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*/
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private List<String> listRXNFiles(String resourceDir) {
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List<String> files = new ArrayList<>();
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try {
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// Read directory listing from classpath
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java.io.File dir = new java.io.File(
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getClass().getClassLoader().getResource(resourceDir).toURI());
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if (dir.isDirectory()) {
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for (java.io.File f : dir.listFiles()) {
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if (f.getName().endsWith(".rxn")) {
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files.add(f.getName());
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}
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}
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}
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} catch (Exception e) {
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System.out.println("Cannot list " + resourceDir + ": " + e.getMessage());
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}
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java.util.Collections.sort(files);
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return files;
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}
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}

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