Fixing tests that were broken when running in maven

josemduarte · josemduarte · commit 08eec04e6ca1 · 2018-03-10T21:37:09.000-08:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/AtomCache.java
@@ -1046,15 +1046,17 @@ else if (useMmCif) {
 	 * @throws IOException error reading from Web or file system
 	 */
 	private Structure loadStructureFromMmtfByPdbId(String pdbId) throws IOException {
-			MMTFFileReader reader = new MMTFFileReader();
-			reader.setFetchBehavior(fetchBehavior);
-			reader.setObsoleteBehavior(obsoleteBehavior);
-			Structure structure = reader.getStructureById(pdbId.toLowerCase());
-			return structure;
+		logger.debug("Loading structure {} from mmtf file.", pdbId);
+		MMTFFileReader reader = new MMTFFileReader();
+		reader.setFetchBehavior(fetchBehavior);
+		reader.setObsoleteBehavior(obsoleteBehavior);
+		Structure structure = reader.getStructureById(pdbId.toLowerCase());
+		return structure;
 	}
 
 	protected Structure loadStructureFromCifByPdbId(String pdbId) throws IOException, StructureException {
 
+		logger.debug("Loading structure {} from mmCIF file {}.", pdbId, path);
 		Structure s;
 		flagLoading(pdbId);
 		try {
@@ -1073,6 +1075,7 @@ protected Structure loadStructureFromCifByPdbId(String pdbId) throws IOException
 
 	protected Structure loadStructureFromPdbByPdbId(String pdbId) throws IOException, StructureException {
 
+		logger.debug("Loading structure {} from PDB file {}.", pdbId, path);
 		Structure s;
 		flagLoading(pdbId);
 		try {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/BondMaker.java
@@ -102,6 +102,7 @@ public BondMaker(Structure structure, FileParsingParameters params) {
 	 * </li>
 	 */
 	public void makeBonds() {
+		logger.debug("Going to start making bonds");
 		formPeptideBonds();
 		formNucleotideBonds();
 		formIntraResidueBonds();
@@ -208,12 +209,16 @@ private void formIntraResidueBonds() {
 					for(Group group : totList){
 
 						ChemComp aminoChemComp = ChemCompGroupFactory.getChemComp(group.getPDBName());
+						logger.debug("chemcomp for residue {}-{} has {} atoms and {} bonds", 
+								group.getPDBName(), group.getResidueNumber(), aminoChemComp.getAtoms().size(), aminoChemComp.getBonds().size());
 
 						for (ChemCompBond chemCompBond : aminoChemComp.getBonds()) {
 							Atom a = getAtom(chemCompBond.getAtom_id_1(), group);
 							Atom b = getAtom(chemCompBond.getAtom_id_2(), group);
 							if ( a != null && b != null){
 								int bondOrder = chemCompBond.getNumericalBondOrder();
+								logger.debug("Forming bond between atoms {}-{} and {}-{} with bond order {}", 
+										a.getPDBserial(), a.getName(), b.getPDBserial(), b.getName(), bondOrder);
 								new BondImpl(a, b, bondOrder);
 							} 
 							else{
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestBond.java
@@ -26,19 +26,30 @@
 
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.FileParsingParameters;
+import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
+import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
 import org.junit.BeforeClass;
 import org.junit.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import static org.junit.Assert.*;
 
 
 public class TestBond {
+	
+	private static final Logger logger = LoggerFactory.getLogger(TestBond.class);
 
 
 	private static AtomCache cache;
 
 	@BeforeClass
 	public static void setUp() {
+		
+		// important: without this the tests can fail when running in maven (but not in IDE)
+		// that's because it depends on the order on how tests were run - JD 2018-03-10
+		ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider()); 
+		
 		cache = new AtomCache();
 
 		cache.setUseMmCif(true);
@@ -221,6 +232,7 @@ private int countAtomsWithoutBonds(String pdbId) throws IOException, StructureEx
 					// Check they all have bonds
 					for(Atom a: atomsList){
 						if(a.getBonds()==null){
+							logger.debug("Atom {}-{} has no bonds", a.getPDBserial(), a.getName());
 							nonBondedCounter++;
 						}
 					}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/asa/TestAsaCalc.java
@@ -24,6 +24,8 @@
 import org.biojava.nbio.structure.Structure;
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.StructureIO;
+import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
+import org.biojava.nbio.structure.io.mmcif.DownloadChemCompProvider;
 
 import java.io.IOException;
 
@@ -39,6 +41,10 @@ public class TestAsaCalc extends TestCase {
 
 	public void testAsa3PIU() throws StructureException, IOException {
 
+		// important: without this the tests can fail when running in maven (but not in IDE)
+		// that's because it depends on the order on how tests were run - JD 2018-03-10
+		ChemCompGroupFactory.setChemCompProvider(new DownloadChemCompProvider()); 
+		
 		Structure structure = StructureIO.getStructure("3PIU");
 
 
diff --git a/biojava-structure/src/test/resources/log4j2.xml b/biojava-structure/src/test/resources/log4j2.xml
@@ -9,5 +9,13 @@
 		<root level="warn">
 			<appender-ref ref="Console"/>
 		</root>
+		<!--  
+		<Logger name="org.biojava.nbio.structure.io.BondMaker" level="debug" additivity="false">
+            <appender-ref ref="Console"/>
+        </Logger>
+        <Logger name="org.biojava.nbio.structure.align.util.AtomCache" level="debug" additivity="false">
+            <appender-ref ref="Console"/>
+        </Logger>
+        -->
 	</loggers>
 </configuration>
