Initialize reference spectra data only once

ipb-halle · Oct 28, 2024 · d1623d0 · d1623d0
1 parent 3f7ee62
commit d1623d0
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Showing 2 changed files with 101 additions and 82 deletions.
diff --git a/...le/metfraglib/scoreinitialisation/OfflineIndividualMoNASpectralSimilarityInitialiser.java b/...le/metfraglib/scoreinitialisation/OfflineIndividualMoNASpectralSimilarityInitialiser.java
@@ -21,6 +21,9 @@
 public class OfflineIndividualMoNASpectralSimilarityInitialiser implements IScoreInitialiser {
 	private Logger logger = Logger.getLogger(OfflineIndividualMoNASpectralSimilarityInitialiser.class);
 
+	private static volatile SpectralPeakListCollection spectralPeakLists = null;
+	private static final Object lock = new Object();
+
 	@Override
 	public void initScoreParameters(Settings settings) throws Exception {
 		logger.setLevel(Level.toLevel("info"));
@@ -30,44 +33,51 @@ public void initScoreParameters(Settings settings) throws Exception {
 			return;
 		}
 
-		MultipleTandemMassPeakListReader multiplePeakListReader = new MultipleTandemMassPeakListReader(settings);
-		SpectralPeakListCollection spectralPeakLists = null;
-		Path offlineSpectralFilePath = null;
+		if (spectralPeakLists == null) {
+			synchronized (lock) {
+				if (spectralPeakLists == null) {
+					MultipleTandemMassPeakListReader multiplePeakListReader = new MultipleTandemMassPeakListReader(settings);
+					Path offlineSpectralFilePath = null;
 
-		if (settings.containsKey(VariableNames.OFFLINE_SPECTRAL_DATABASE_FILE_NAME) &&
-				settings.get(VariableNames.OFFLINE_SPECTRAL_DATABASE_FILE_NAME) != null) {
-			offlineSpectralFilePath = Paths.get((String) settings.get(VariableNames.OFFLINE_SPECTRAL_DATABASE_FILE_NAME));
-		} else {
-			logger.info("Load reference data from default resource \"MoNA-export-LC-MS.mb\".");
-			URI uri = Objects.requireNonNull(getClass().getClassLoader().getResource("/MoNA-export-LC-MS.mb")).toURI();
-			if ("jar".equals(uri.getScheme())) {
-				try {
-					FileSystems.getFileSystem(uri);
-				} catch (FileSystemNotFoundException e) {
-					FileSystems.newFileSystem(uri, Collections.emptyMap());
-				}
-			}
-			offlineSpectralFilePath = Paths.get(uri);
-		}
+					if (settings.containsKey(VariableNames.OFFLINE_SPECTRAL_DATABASE_FILE_NAME) &&
+							settings.get(VariableNames.OFFLINE_SPECTRAL_DATABASE_FILE_NAME) != null) {
+						offlineSpectralFilePath = Paths.get((String) settings.get(VariableNames.OFFLINE_SPECTRAL_DATABASE_FILE_NAME));
+					} else {
+						logger.info("Load reference data from default resource \"MoNA-export-LC-MS.mb\".");
+						URI uri = Objects.requireNonNull(getClass().getClassLoader().getResource("/MoNA-export-LC-MS.mb")).toURI();
+						if ("jar".equals(uri.getScheme())) {
+							try {
+								FileSystems.getFileSystem(uri);
+							} catch (FileSystemNotFoundException e) {
+								FileSystems.newFileSystem(uri, Collections.emptyMap());
+							}
+						}
+						offlineSpectralFilePath = Paths.get(uri);
+					}
 
-		if (Files.isRegularFile(offlineSpectralFilePath)) {
-			logger.info("Load reference data from file: " + offlineSpectralFilePath);
-			try (InputStream inStream = Files.newInputStream(offlineSpectralFilePath)) {
-				spectralPeakLists = multiplePeakListReader.readMultiple(inStream);
+					if (Files.isRegularFile(offlineSpectralFilePath)) {
+						logger.info("Load reference data from file: " + offlineSpectralFilePath);
+						try (InputStream inStream = Files.newInputStream(offlineSpectralFilePath)) {
+							spectralPeakLists = multiplePeakListReader.readMultiple(inStream);
+						}
+					} else if (Files.isDirectory(offlineSpectralFilePath)) {
+						logger.info("Load reference data from directory: " + offlineSpectralFilePath);
+						List<Path> libFiles = Files.walk(offlineSpectralFilePath)
+								.filter(Files::isRegularFile)
+								.filter(p -> p.getFileName().toString().endsWith(".mb"))
+								.collect(Collectors.toList());
+						logger.info("Reference data files found: " + libFiles);
+						spectralPeakLists = multiplePeakListReader.readMultiple(libFiles);
+					}
+
+					if (spectralPeakLists != null) {
+						//check whether MoNA InChIKeys are given as resource
+						spectralPeakLists.calculateSimilarities((SortedTandemMassPeakList) settings.get(VariableNames.PEAK_LIST_NAME));
+					}
+				}
 			}
-		} else if (Files.isDirectory(offlineSpectralFilePath)) {
-			logger.info("Load reference data from directory: " + offlineSpectralFilePath);
-			List<Path> libFiles = Files.walk(offlineSpectralFilePath)
-					.filter(Files::isRegularFile)
-					.filter(p -> p.getFileName().toString().endsWith(".mb"))
-					.collect(Collectors.toList());
-			logger.info("Reference data files found: " + libFiles);
-			spectralPeakLists = multiplePeakListReader.readMultiple(libFiles);
 		}
-
 		if (spectralPeakLists != null) {
-			//check whether MoNA InChIKeys are given as resource
-			spectralPeakLists.calculateSimilarities((SortedTandemMassPeakList) settings.get(VariableNames.PEAK_LIST_NAME));
 			settings.set(VariableNames.OFFLINE_METFUSION_MONA_SPECTRAL_SIMILARITY_PEAK_LIST_COLLECTION_NAME, spectralPeakLists);
 		}
 	}

diff --git a/...le/metfraglib/scoreinitialisation/OfflineMetFusionSpectralSimilarityScoreInitialiser.java b/...le/metfraglib/scoreinitialisation/OfflineMetFusionSpectralSimilarityScoreInitialiser.java
@@ -19,62 +19,71 @@
 import de.ipbhalle.metfraglib.settings.Settings;
 
 public class OfflineMetFusionSpectralSimilarityScoreInitialiser implements IScoreInitialiser {
-	private Logger logger = Logger.getLogger(OfflineMetFusionSpectralSimilarityScoreInitialiser.class);
+    private Logger logger = Logger.getLogger(OfflineMetFusionSpectralSimilarityScoreInitialiser.class);
 
+    private static volatile SpectralPeakListCollection spectralPeakLists = null;
+    private static final Object lock = new Object();
 
-	@Override
-	public void initScoreParameters(Settings settings) throws Exception {
-		logger.setLevel(Level.toLevel("info"));
+    @Override
+    public void initScoreParameters(Settings settings) throws Exception {
+        logger.setLevel(Level.toLevel("info"));
 
-		if (settings.containsKey(VariableNames.OFFLINE_METFUSION_MONA_SPECTRAL_SIMILARITY_PEAK_LIST_COLLECTION_NAME) &&
-				settings.get(VariableNames.OFFLINE_METFUSION_MONA_SPECTRAL_SIMILARITY_PEAK_LIST_COLLECTION_NAME) != null) {
-			return;
-		}
+        if (settings.containsKey(VariableNames.OFFLINE_METFUSION_MONA_SPECTRAL_SIMILARITY_PEAK_LIST_COLLECTION_NAME) &&
+                settings.get(VariableNames.OFFLINE_METFUSION_MONA_SPECTRAL_SIMILARITY_PEAK_LIST_COLLECTION_NAME) != null) {
+            return;
+        }
 
-		MultipleTandemMassPeakListReader multiplePeakListReader = new MultipleTandemMassPeakListReader(settings);
-		SpectralPeakListCollection spectralPeakLists = null;
-		Path offlineSpectralFilePath = null;
+        if (spectralPeakLists == null) {
+            synchronized (lock) {
+                if (spectralPeakLists == null) {
+                    MultipleTandemMassPeakListReader multiplePeakListReader = new MultipleTandemMassPeakListReader(settings);
+                    Path offlineSpectralFilePath = null;
 
-		if (settings.containsKey(VariableNames.OFFLINE_SPECTRAL_DATABASE_FILE_NAME) &&
-            settings.get(VariableNames.OFFLINE_SPECTRAL_DATABASE_FILE_NAME) != null) {
-            offlineSpectralFilePath = Paths.get((String) settings.get(VariableNames.OFFLINE_SPECTRAL_DATABASE_FILE_NAME));
-        } else {
-			logger.info("Load reference data from default resource \"MoNA-export-LC-MS.mb\".");
-			URI uri = Objects.requireNonNull(getClass().getClassLoader().getResource("/MoNA-export-LC-MS.mb")).toURI();
-			if ("jar".equals(uri.getScheme())) {
-				try {
-					FileSystems.getFileSystem(uri);
-				} catch (FileSystemNotFoundException e) {
-					FileSystems.newFileSystem(uri, Collections.emptyMap());
-				}
-			}
-			offlineSpectralFilePath = Paths.get(uri);
-		}
+                    if (settings.containsKey(VariableNames.OFFLINE_SPECTRAL_DATABASE_FILE_NAME) &&
+                            settings.get(VariableNames.OFFLINE_SPECTRAL_DATABASE_FILE_NAME) != null) {
+                        offlineSpectralFilePath = Paths.get((String) settings.get(VariableNames.OFFLINE_SPECTRAL_DATABASE_FILE_NAME));
+                    } else {
+                        logger.info("Load reference data from default resource \"MoNA-export-LC-MS.mb\".");
+                        URI uri = Objects.requireNonNull(getClass().getClassLoader().getResource("/MoNA-export-LC-MS.mb")).toURI();
+                        if ("jar".equals(uri.getScheme())) {
+                            try {
+                                FileSystems.getFileSystem(uri);
+                            } catch (FileSystemNotFoundException e) {
+                                FileSystems.newFileSystem(uri, Collections.emptyMap());
+                            }
+                        }
+                        offlineSpectralFilePath = Paths.get(uri);
+                    }
 
-		if (Files.isRegularFile(offlineSpectralFilePath)) {
-			logger.info("Load reference data from file: " + offlineSpectralFilePath);
-			try (InputStream inStream = Files.newInputStream(offlineSpectralFilePath)) {
-				spectralPeakLists = multiplePeakListReader.readMultiple(inStream);
-			}
-		} else if (Files.isDirectory(offlineSpectralFilePath)) {
-			logger.info("Load reference data from directory: " + offlineSpectralFilePath);
-			List<Path> libFiles = Files.walk(offlineSpectralFilePath)
-					.filter(Files::isRegularFile)
-					.filter(p -> p.getFileName().toString().endsWith(".mb"))
-					.collect(Collectors.toList());
-			logger.info("Reference data files found: " + libFiles);
-			spectralPeakLists = multiplePeakListReader.readMultiple(libFiles);
-		}
+                    if (Files.isRegularFile(offlineSpectralFilePath)) {
+                        logger.info("Load reference data from file: " + offlineSpectralFilePath);
+                        try (InputStream inStream = Files.newInputStream(offlineSpectralFilePath)) {
+                            spectralPeakLists = multiplePeakListReader.readMultiple(inStream);
+                        }
+                    } else if (Files.isDirectory(offlineSpectralFilePath)) {
+                        logger.info("Load reference data from directory: " + offlineSpectralFilePath);
+                        List<Path> libFiles = Files.walk(offlineSpectralFilePath)
+                                .filter(Files::isRegularFile)
+                                .filter(p -> p.getFileName().toString().endsWith(".mb"))
+                                .collect(Collectors.toList());
+                        logger.info("Reference data files found: " + libFiles);
+                        spectralPeakLists = multiplePeakListReader.readMultiple(libFiles);
+                    }
 
-		if (spectralPeakLists != null) {
-			//check whether MoNA InChIKeys are given as resource
-            spectralPeakLists.calculateSimilarities((SortedTandemMassPeakList) settings.get(VariableNames.PEAK_LIST_NAME));
-            settings.set(VariableNames.OFFLINE_METFUSION_MONA_SPECTRAL_SIMILARITY_PEAK_LIST_COLLECTION_NAME, spectralPeakLists);
+                    if (spectralPeakLists != null) {
+                        //check whether MoNA InChIKeys are given as resource
+                        spectralPeakLists.calculateSimilarities((SortedTandemMassPeakList) settings.get(VariableNames.PEAK_LIST_NAME));
+                    }
+                }
+            }
         }
-	}
+		if (spectralPeakLists != null) {
+			settings.set(VariableNames.OFFLINE_METFUSION_MONA_SPECTRAL_SIMILARITY_PEAK_LIST_COLLECTION_NAME, spectralPeakLists);
+		}
+    }
+
+    public void postProcessScoreParameters(Settings settings) {
+        return;
+    }
 
-	public void postProcessScoreParameters(Settings settings) {
-		return;
-	}
-
 }