new test cases for mzid 1.2

julianu · Jul 12, 2024 · 20dd8d3 · 20dd8d3
1 parent a568536
commit 20dd8d3
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Showing 3 changed files with 13,016 additions and 45 deletions.
diff --git a/src/test/java/de/mpc/pia/intermediate/IntermediateJAXBTest.java b/src/test/java/de/mpc/pia/intermediate/IntermediateJAXBTest.java
@@ -5,59 +5,33 @@
 import java.io.File;
 import java.io.IOException;
 
-import org.apache.log4j.Logger;
-import org.junit.BeforeClass;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.junit.Test;
 
 import de.mpc.pia.intermediate.xmlhandler.PIAIntermediateJAXBHandler;
-import de.mpc.pia.modeller.PIAModellerTest;
 
 public class IntermediateJAXBTest {
 
     /** logger for this class */
-    private static final Logger LOGGER = Logger.getLogger(IntermediateJAXBTest.class);
-
-    private static File piaFile;
-
-
-    @BeforeClass
-    public static void setUpBeforeClass() {
-        piaFile = new File(PIAModellerTest.class.getResource("/55merge_mascot_tandem.pia.xml").getPath());
-    }
-
+    private static final Logger LOGGER = LogManager.getLogger();
 
     @Test
-    public void testIntermediateJAXB() {
+    public void testIntermediateJAXB() throws IOException{
         PIAIntermediateJAXBHandler intermediateHandler;
         intermediateHandler = new PIAIntermediateJAXBHandler();
 
-        Runtime runtime = Runtime.getRuntime();
-        double mb = 1024*1024;
-        final long startTime = System.nanoTime();
-        final long endTime;
-
-        try {
-            intermediateHandler.parse(piaFile.getAbsolutePath(), null);
-        } catch (IOException e) {
-            LOGGER.error(e);
-        }
-
-        endTime = System.nanoTime();
-
-        assertEquals(2, intermediateHandler.getFiles().size());
-        assertEquals(2, intermediateHandler.getSpectraData().size());
-        assertEquals(2, intermediateHandler.getSearchDatabase().size());
-        assertEquals(2, intermediateHandler.getAnalysisSoftware().size());
-        assertEquals(1941, intermediateHandler.getGroups().size());
-        assertEquals(2131, intermediateHandler.getAccessions().size());
-        assertEquals(2113, intermediateHandler.getPeptides().size());
-        assertEquals(2478, intermediateHandler.getPSMs().size());
-        assertEquals(1856, intermediateHandler.getNrTrees());
-
-        LOGGER.info("Total Memory: " + runtime.totalMemory() / mb + " MB");
-        LOGGER.info("Used Memory: " + (runtime.totalMemory() - runtime.freeMemory()) / mb + " MB");
-        LOGGER.info("Free Memory: " + runtime.freeMemory() / mb + " MB");
-        LOGGER.info("Max Memory: " + runtime.maxMemory() / mb + " MB");
-        LOGGER.info("Execution time: " + ((endTime - startTime) / 1000000000.0) + " s");
+        File piaFile = new File(IntermediateJAXBTest.class.getResource("/55merge_mascot_tandem.pia.xml").getPath());
+        intermediateHandler.parse(piaFile.getAbsolutePath(), null);
+
+        assertEquals("Number of Files differ", 2, intermediateHandler.getFiles().size());
+        assertEquals("Number of SpectraData differ", 2, intermediateHandler.getSpectraData().size());
+        assertEquals("Number of SearchDatabases differ", 2, intermediateHandler.getSearchDatabase().size());
+        assertEquals("Number of AnalysisSoftware differ", 2, intermediateHandler.getAnalysisSoftware().size());
+        assertEquals("Number of Groups differ", 1941, intermediateHandler.getGroups().size());
+        assertEquals("Number of Accessions differ", 2131, intermediateHandler.getAccessions().size());
+        assertEquals("Number of Peptides differ", 2113, intermediateHandler.getPeptides().size());
+        assertEquals("Number of PSMs differ", 2478, intermediateHandler.getPSMs().size());
+        assertEquals("Number of NrTrees differ", 1856, intermediateHandler.getNrTrees());
     }
 }
diff --git a/src/test/java/de/mpc/pia/modeller/exporter/MzIdentMLExportAndImportTest.java b/src/test/java/de/mpc/pia/modeller/exporter/MzIdentMLExportAndImportTest.java
@@ -12,7 +12,6 @@
 import org.junit.Test;
 
 import de.mpc.pia.intermediate.compiler.PIACompiler;
-import de.mpc.pia.intermediate.compiler.PIACompilerTest;
 import de.mpc.pia.intermediate.compiler.PIASimpleCompiler;
 import de.mpc.pia.modeller.PIAModeller;
 import de.mpc.pia.modeller.protein.inference.SpectrumExtractorInference;
@@ -28,6 +27,7 @@ public class MzIdentMLExportAndImportTest {
 
     private File tandemIdXMLResults;
     private File tandemMzidResults;
+    private File cometMzid12Results;
     private String piaIntermediateFileName;
     /** logger for this class */
     private static final Logger LOGGER = Logger.getLogger(PIACompiler.class);
@@ -36,8 +36,9 @@ public class MzIdentMLExportAndImportTest {
     public void setUp() {
         piaIntermediateFileName = "PIACompilerTest.pia.xml";
 
-        tandemIdXMLResults = new File(PIACompilerTest.class.getResource("/merge1-tandem-fdr_filtered-015.idXML").getPath());
-        tandemMzidResults = new File(PIACompilerTest.class.getResource("/55merge_tandem.mzid").getPath());
+        tandemIdXMLResults = new File(MzIdentMLExportAndImportTest.class.getResource("/merge1-tandem-fdr_filtered-015.idXML").getPath());
+        tandemMzidResults = new File(MzIdentMLExportAndImportTest.class.getResource("/55merge_tandem.mzid").getPath());
+        cometMzid12Results = new File(MzIdentMLExportAndImportTest.class.getResource("/comet_mzid12.mzid").getPath());
     }
 
 
@@ -57,6 +58,22 @@ public void testMzIdentMLv1_1_0Import() throws IOException {
     }
 
 
+    @Test
+    public void testMzIdentMLv1_2_0Import() {
+        PIACompiler piaCompiler = new PIASimpleCompiler();
+
+        assertTrue(piaCompiler.getDataFromFile("mzid", cometMzid12Results.getAbsolutePath(), null, null));
+
+        piaCompiler.buildClusterList();
+        piaCompiler.buildIntermediateStructure();
+
+        piaCompiler.setName("testFile");
+
+        assertEquals("Wrong number of imported peptides", 600, piaCompiler.getNrPeptides());
+        assertEquals("Wrong number of imported PSMs", 610, piaCompiler.getNrPeptideSpectrumMatches());
+    }
+
+
     @Test
     public void testMzIdentMLExportAndImport() throws IOException {
         PIACompiler piaCompiler = new PIASimpleCompiler();