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(),