static init biggdb

draeger-lab · Aug 15, 2024 · 76077ff · 76077ff
1 parent 7d57fdd
commit 76077ff
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Showing 5 changed files with 17 additions and 23 deletions.
diff --git a/src/main/java/edu/ucsd/sbrg/ModelPolisherCLILauncher.java b/src/main/java/edu/ucsd/sbrg/ModelPolisherCLILauncher.java
@@ -76,8 +76,6 @@ public class ModelPolisherCLILauncher extends Launcher {
 
   private CommandLineParameters parameters;
   private Registry registry;
-  private BiGGDB bigg;
-  private AnnotateDB adb;
 
   /**
    * Entry point
@@ -125,11 +123,11 @@ public void commandLineMode(AppConf appConf) {
       validateIOParameters();
 
       if (parameters.annotationParameters().biggAnnotationParameters().annotateWithBiGG()) {
-        this.bigg = new BiGGDB(parameters.annotationParameters().biggAnnotationParameters().dbParameters());
+        BiGGDB.init(parameters.annotationParameters().biggAnnotationParameters().dbParameters());
       }
 
       if (parameters.annotationParameters().adbAnnotationParameters().addADBAnnotations()) {
-        this.adb = new AnnotateDB(parameters.annotationParameters().adbAnnotationParameters().dbParameters());
+        AnnotateDB.init(parameters.annotationParameters().adbAnnotationParameters().dbParameters());
       }
 
       var inputFiles = FileUtils.listFiles(parameters.input(), new String[]{"xml", "sbml", "json", "mat"}, true);
@@ -228,12 +226,12 @@ private void processFile(File input, File output) throws ModelReaderException, M
     }
 
     if (parameters.annotationParameters().biggAnnotationParameters().annotateWithBiGG()) {
-      new BiGGSBMLAnnotator(bigg, parameters.annotationParameters().biggAnnotationParameters(), parameters.sboParameters(),
+      new BiGGSBMLAnnotator(new BiGGDB(), parameters.annotationParameters().biggAnnotationParameters(), parameters.sboParameters(),
               registry, annotationObservers).annotate(doc);
     }
 
     if (parameters.annotationParameters().adbAnnotationParameters().addADBAnnotations()) {
-      new ADBSBMLAnnotator(adb, parameters.annotationParameters().adbAnnotationParameters()).annotate(doc);
+      new ADBSBMLAnnotator(new AnnotateDB(), parameters.annotationParameters().adbAnnotationParameters()).annotate(doc);
     }
 
     for (var o : annotationObservers) {

diff --git a/src/main/java/edu/ucsd/sbrg/db/adb/AnnotateDB.java b/src/main/java/edu/ucsd/sbrg/db/adb/AnnotateDB.java
@@ -33,7 +33,9 @@ public class AnnotateDB {
   private static final Logger logger = LoggerFactory.getLogger(AnnotateDB.class);
   private static PostgresConnectionPool connectionPool;
 
-  public AnnotateDB (DBParameters parameters) {
+  public AnnotateDB () {}
+
+  public static void init(DBParameters parameters) {
     String dbName = parameters.dbName();
     String host = parameters.host();
     String passwd = parameters.passwd();
@@ -52,11 +54,6 @@ private static boolean iStrNotNullOrEmpty(String string) {
     return !(string == null || string.isEmpty());
   }
 
-  public AnnotateDB(String host, Integer port, String user, String passwd, String dbName)
-  {
-    init(host, port, user, passwd, dbName);
-  }
-
   public static void init(String host, Integer port, String user, String passwd, String dbName) {
     if (null == connectionPool) {
       logger.debug("Initialize AnnotateDB");

diff --git a/src/main/java/edu/ucsd/sbrg/db/bigg/BiGGDB.java b/src/main/java/edu/ucsd/sbrg/db/bigg/BiGGDB.java
@@ -54,7 +54,13 @@ public class BiGGDB {
   private static Set<String> BiGGDBReactions = new HashSet<>();
 
 
-  public BiGGDB (DBParameters parameters) {
+  public BiGGDB () {}
+
+  private static boolean iStrNotNullOrEmpty(String string) {
+    return !(string == null || string.isEmpty());
+  }
+
+  public static void init(DBParameters parameters) {
     String dbName = parameters.dbName();
     String host = parameters.host();
     String passwd = parameters.passwd();
@@ -69,14 +75,6 @@ public BiGGDB (DBParameters parameters) {
     }
   }
 
-  private static boolean iStrNotNullOrEmpty(String string) {
-    return !(string == null || string.isEmpty());
-  }
-
-  public BiGGDB(String host, Integer port, String user, String passwd, String dbName) {
-    init(host, port, user, passwd, dbName);
-  }
-
   public static void init(String host, Integer port, String user, String passwd, String dbName) {
 
     if (null == connectionPool) {

diff --git a/src/main/java/edu/ucsd/sbrg/util/ext/fbc/GPRParser.java b/src/main/java/edu/ucsd/sbrg/util/ext/fbc/GPRParser.java
@@ -100,7 +100,7 @@ private static GeneProductRef createGPR(String astString, Model model) {
 
     // Normalize the identifier to include "G_" prefix if missing.
     String oldId = astString.startsWith("G_") ? astString : "G_" + astString;
-    boolean containsOldId = !model.containsUniqueNamedSBase(oldId);
+    boolean containsOldId = model.containsUniqueNamedSBase(oldId);
 
     // Attempt to create or find the GeneProduct using a standardized identifier.
     var id = BiGGId.createGeneId(astString).toBiGGId();

diff --git a/src/test/java/edu/ucsd/sbrg/annotation/bigg/BiGGDBContainerTest.java b/src/test/java/edu/ucsd/sbrg/annotation/bigg/BiGGDBContainerTest.java
@@ -24,12 +24,13 @@ public abstract class BiGGDBContainerTest {
 
     static {
         biggContainer.start();
-        bigg = new BiGGDB(
+        BiGGDB.init(
                 biggContainer.getHost(),
                 biggContainer.getFirstMappedPort(),
                 "postgres",
                 "postgres",
                 "bigg");
+        bigg = new BiGGDB();
     }
 
     @AfterClass