From 76077ff1467621245d0bbd8c018e640347a44736 Mon Sep 17 00:00:00 2001 From: Dario Date: Thu, 15 Aug 2024 18:46:09 +0200 Subject: [PATCH] static init biggdb --- .../edu/ucsd/sbrg/ModelPolisherCLILauncher.java | 10 ++++------ .../java/edu/ucsd/sbrg/db/adb/AnnotateDB.java | 9 +++------ src/main/java/edu/ucsd/sbrg/db/bigg/BiGGDB.java | 16 +++++++--------- .../edu/ucsd/sbrg/util/ext/fbc/GPRParser.java | 2 +- .../annotation/bigg/BiGGDBContainerTest.java | 3 ++- 5 files changed, 17 insertions(+), 23 deletions(-) diff --git a/src/main/java/edu/ucsd/sbrg/ModelPolisherCLILauncher.java b/src/main/java/edu/ucsd/sbrg/ModelPolisherCLILauncher.java index 19011db..84a38a0 100644 --- 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 index bc21e03..572a51d 100644 --- 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 index b5c66e2..f9ec076 100644 --- 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 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 index acc814f..4e09445 100644 --- 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 index 520856d..286b680 100644 --- 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