From dfafe97bd9234d6105434d6f5b1b0cfc244cca8a Mon Sep 17 00:00:00 2001
From: Dario <d.eltzner@gmx.de>
Date: Thu, 15 Aug 2024 19:38:29 +0200
Subject: [PATCH] adb parameter name consistency

---
 .../java/edu/ucsd/sbrg/ModelPolisherCLILauncher.java   |  4 ++--
 .../ucsd/sbrg/parameters/ADBAnnotationParameters.java  | 10 +++++-----
 .../edu/ucsd/sbrg/parameters/ParametersParserTest.java |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/main/java/edu/ucsd/sbrg/ModelPolisherCLILauncher.java b/src/main/java/edu/ucsd/sbrg/ModelPolisherCLILauncher.java
index 84a38a0..dbf6620 100644
--- a/src/main/java/edu/ucsd/sbrg/ModelPolisherCLILauncher.java
+++ b/src/main/java/edu/ucsd/sbrg/ModelPolisherCLILauncher.java
@@ -126,7 +126,7 @@ public void commandLineMode(AppConf appConf) {
         BiGGDB.init(parameters.annotationParameters().biggAnnotationParameters().dbParameters());
       }
 
-      if (parameters.annotationParameters().adbAnnotationParameters().addADBAnnotations()) {
+      if (parameters.annotationParameters().adbAnnotationParameters().annotateWithAdb()) {
         AnnotateDB.init(parameters.annotationParameters().adbAnnotationParameters().dbParameters());
       }
 
@@ -230,7 +230,7 @@ private void processFile(File input, File output) throws ModelReaderException, M
               registry, annotationObservers).annotate(doc);
     }
 
-    if (parameters.annotationParameters().adbAnnotationParameters().addADBAnnotations()) {
+    if (parameters.annotationParameters().adbAnnotationParameters().annotateWithAdb()) {
       new ADBSBMLAnnotator(new AnnotateDB(), parameters.annotationParameters().adbAnnotationParameters()).annotate(doc);
     }
 
diff --git a/src/main/java/edu/ucsd/sbrg/parameters/ADBAnnotationParameters.java b/src/main/java/edu/ucsd/sbrg/parameters/ADBAnnotationParameters.java
index 9a99f8a..15f0660 100644
--- a/src/main/java/edu/ucsd/sbrg/parameters/ADBAnnotationParameters.java
+++ b/src/main/java/edu/ucsd/sbrg/parameters/ADBAnnotationParameters.java
@@ -6,8 +6,8 @@
 
 public class ADBAnnotationParameters {
 
-    @JsonProperty("add-adb-annotations")
-    protected boolean addADBAnnotations = ModelPolisherOptions.ADD_ADB_ANNOTATIONS.getDefaultValue();
+    @JsonProperty("annotate-with-adb")
+    protected boolean annotateWithAdb = ModelPolisherOptions.ADD_ADB_ANNOTATIONS.getDefaultValue();
     @JsonProperty("db-config")
     protected DBParameters dbParameters = new DBParameters(
             AnnotateDBOptions.DBNAME.getDefaultValue(),
@@ -21,7 +21,7 @@ public ADBAnnotationParameters() {
     }
 
     public ADBAnnotationParameters(SBProperties args) {
-        addADBAnnotations = args.getBooleanProperty(ModelPolisherOptions.ADD_ADB_ANNOTATIONS);
+        annotateWithAdb = args.getBooleanProperty(ModelPolisherOptions.ADD_ADB_ANNOTATIONS);
         dbParameters = new DBParameters(
                 args.getProperty(AnnotateDBOptions.DBNAME),
                 args.getProperty(AnnotateDBOptions.HOST),
@@ -30,8 +30,8 @@ public ADBAnnotationParameters(SBProperties args) {
                 args.getProperty(AnnotateDBOptions.USER));
     }
 
-    public boolean addADBAnnotations() {
-        return addADBAnnotations;
+    public boolean annotateWithAdb() {
+        return annotateWithAdb;
     }
 
     public DBParameters dbParameters() {
diff --git a/src/test/java/edu/ucsd/sbrg/parameters/ParametersParserTest.java b/src/test/java/edu/ucsd/sbrg/parameters/ParametersParserTest.java
index 648784a..1a13028 100644
--- a/src/test/java/edu/ucsd/sbrg/parameters/ParametersParserTest.java
+++ b/src/test/java/edu/ucsd/sbrg/parameters/ParametersParserTest.java
@@ -29,7 +29,7 @@ void defaults() throws IOException {
                 parameters.polishing().fluxObjectivesPolishingParameters().fluxCoefficients());
 
         assertEquals(ModelPolisherOptions.ADD_ADB_ANNOTATIONS.getDefaultValue(),
-                parameters.annotation().adbAnnotationParameters().addADBAnnotations());
+                parameters.annotation().adbAnnotationParameters().annotateWithAdb());
         assertEquals(AnnotateDBOptions.DBNAME.getDefaultValue(),
                 parameters.annotation().adbAnnotationParameters().dbParameters().dbName());
         assertEquals(AnnotateDBOptions.HOST.getDefaultValue(),