new config options for fixer

draeger-lab · Aug 18, 2024 · 546261e · 546261e
1 parent f7775cd
commit 546261e
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Showing 6 changed files with 92 additions and 25 deletions.
diff --git a/build.gradle b/build.gradle
@@ -107,17 +107,26 @@ dependencies {
     implementation("org.sbml.jsbml:jsbml:1.6.1") {
         exclude group: "org.apache.logging.log4j", module: "log4j-core"
         exclude group: "org.apache.logging.log4j", module: "log4j-api"
-        exclude group: "org.apache.logging.log4j", module: "log4j-1.2-api   "
+        exclude group: "org.apache.logging.log4j", module: "log4j-1.2-api"
         exclude group: "org.apache.logging.log4j", module: "log4j-slf4j-impl"
         exclude group: "org.apache.commons", module: "logging"
     }
     // ontology support within BioJava
-    implementation "org.biojava:biojava-ontology:7.1.1"
+    implementation("org.biojava:biojava-ontology:7.1.1") {
+	exclude group: "org.apache.logging.log4j", module: "log4j-core"
+	exclude group: "org.apache.logging.log4j", module: "log4j-slf4j-impl"
+    }
     // handle Combine Archives (packages of biological models)
     implementation "de.uni-rostock.sbi:CombineArchive:1.4.1"
     // interacting with MATLAB files
     implementation 'us.hebi.matlab.mat:mfl-core:0.5.15'
 
+    implementation "org.slf4j:slf4j-api:2.0.9"
+    implementation "org.slf4j:jul-to-slf4j:2.0.9"
+    implementation "org.slf4j:jcl-over-slf4j:2.0.9"
+    implementation "org.slf4j:log4j-over-slf4j:2.0.9"
+    implementation "org.slf4j:osgi-over-slf4j:2.0.9"
+
     // JDBC connection pool
     implementation "com.zaxxer:HikariCP:5.1.0"
     // https://mvnrepository.com/artifact/commons-io/commons-io
@@ -275,4 +284,4 @@ tasks.register('uberjar', Jar) {
  */
 application {
     mainClass.set('ModelPolisher')
-}
+}
diff --git a/src/main/java/edu/ucsd/sbrg/parameters/FixingParameters.java b/src/main/java/edu/ucsd/sbrg/parameters/FixingParameters.java
@@ -0,0 +1,38 @@
+package edu.ucsd.sbrg.parameters;
+
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import java.util.Objects;
+
+public class FixingParameters {
+
+    @JsonProperty("dont-fix")
+    private boolean dontFix = false;
+
+    public FixingParameters() {
+    }
+
+    public boolean dontFix() {
+        return dontFix;
+    }
+
+    @Override
+    public String toString() {
+        return "FixingParameters{" +
+                "dontFix=" + dontFix +
+                '}';
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        FixingParameters that = (FixingParameters) o;
+        return dontFix == that.dontFix;
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hashCode(dontFix);
+    }
+}
diff --git a/src/main/java/edu/ucsd/sbrg/parameters/Parameters.java b/src/main/java/edu/ucsd/sbrg/parameters/Parameters.java
@@ -6,6 +6,8 @@
 
 public class Parameters {
 
+    @JsonProperty("fixing")
+    private final FixingParameters fixing = new FixingParameters();
     @JsonProperty("polishing")
     private final PolishingParameters polishing = new PolishingParameters();
     @JsonProperty("annotation")
@@ -39,27 +41,33 @@ public ModelPolisherOptions.OutputType outputType() {
         return outputType;
     }
 
-    @Override
-    public String toString() {
-        return "Parameters{" +
-                "polishing=" + polishing +
-                ", annotation=" + annotation +
-                ", sboTerms=" + sboTerms +
-                ", sbmlValidation=" + sbmlValidation +
-                ", outputType=" + outputType +
-            '}';    
+    public FixingParameters fixing() {
+        return fixing;
     }
 
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
         if (o == null || getClass() != o.getClass()) return false;
         Parameters that = (Parameters) o;
-        return sbmlValidation == that.sbmlValidation && Objects.equals(polishing, that.polishing) && Objects.equals(annotation, that.annotation) && Objects.equals(sboTerms, that.sboTerms) && outputType == that.outputType;
+        return sbmlValidation == that.sbmlValidation && Objects.equals(fixing, that.fixing) && Objects.equals(polishing, that.polishing) && Objects.equals(annotation, that.annotation) && Objects.equals(sboTerms, that.sboTerms) && outputType == that.outputType;
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash(polishing, annotation, sboTerms, sbmlValidation, outputType);
+        return Objects.hash(fixing, polishing, annotation, sboTerms, sbmlValidation, outputType);
     }
+
+    @Override
+    public String toString() {
+        return "Parameters{" +
+                "fixing=" + fixing +
+                ", polishing=" + polishing +
+                ", annotation=" + annotation +
+                ", sboTerms=" + sboTerms +
+                ", sbmlValidation=" + sbmlValidation +
+                ", outputType=" + outputType +
+                '}';
+    }
+
 }
diff --git a/src/main/java/edu/ucsd/sbrg/parameters/PolishingParameters.java b/src/main/java/edu/ucsd/sbrg/parameters/PolishingParameters.java
@@ -7,6 +7,8 @@
 
 public class PolishingParameters {
 
+  @JsonProperty("polish-even-if-model-invalid")
+  private boolean polishEvenIfModelInvalid = false;
   @JsonProperty("reactions")
   private ReactionPolishingParameters reactionPolishingParameters = new ReactionPolishingParameters();
   @JsonProperty("flux-objectives")
@@ -15,9 +17,11 @@ public class PolishingParameters {
   public PolishingParameters() {  }
 
   public PolishingParameters(ReactionPolishingParameters reactionPolishingParameters,
-                             FluxObjectivesPolishingParameters fluxObjectivesPolishingParameters) {
+                             FluxObjectivesPolishingParameters fluxObjectivesPolishingParameters,
+                             boolean polishEvenIfModelInvalid) {
     this.reactionPolishingParameters = reactionPolishingParameters;
     this.fluxObjectivesPolishingParameters = fluxObjectivesPolishingParameters;
+    this.polishEvenIfModelInvalid = polishEvenIfModelInvalid;
   }
 
   public PolishingParameters(SBProperties args) throws IllegalArgumentException {
@@ -33,24 +37,30 @@ public FluxObjectivesPolishingParameters fluxObjectivesPolishingParameters() {
     return fluxObjectivesPolishingParameters;
   }
 
-  @Override
-  public String toString() {
-    return "PolishingParameters{" +
-            "reactionPolishingParameters=" + reactionPolishingParameters +
-            ", fluxObjectivesPolishingParameters=" + fluxObjectivesPolishingParameters +
-            '}';
+  public boolean polishEvenIfModelInvalid() {
+    return polishEvenIfModelInvalid;
   }
 
   @Override
   public boolean equals(Object o) {
     if (this == o) return true;
     if (o == null || getClass() != o.getClass()) return false;
     PolishingParameters that = (PolishingParameters) o;
-    return Objects.equals(reactionPolishingParameters, that.reactionPolishingParameters) && Objects.equals(fluxObjectivesPolishingParameters, that.fluxObjectivesPolishingParameters);
+    return polishEvenIfModelInvalid == that.polishEvenIfModelInvalid && Objects.equals(reactionPolishingParameters, that.reactionPolishingParameters) && Objects.equals(fluxObjectivesPolishingParameters, that.fluxObjectivesPolishingParameters);
   }
 
   @Override
   public int hashCode() {
-    return Objects.hash(reactionPolishingParameters, fluxObjectivesPolishingParameters);
+    return Objects.hash(polishEvenIfModelInvalid, reactionPolishingParameters, fluxObjectivesPolishingParameters);
   }
+
+  @Override
+  public String toString() {
+    return "PolishingParameters{" +
+            "polishEvenIfModelInvalid=" + polishEvenIfModelInvalid +
+            ", reactionPolishingParameters=" + reactionPolishingParameters +
+            ", fluxObjectivesPolishingParameters=" + fluxObjectivesPolishingParameters +
+            '}';
+  }
+
 }
diff --git a/src/test/java/edu/ucsd/sbrg/fixing/fbc/ListOfObjectivesFixerTest.java b/src/test/java/edu/ucsd/sbrg/fixing/fbc/ListOfObjectivesFixerTest.java
@@ -43,7 +43,8 @@ public void argumentsAreUsedToInferFluxObjectives() {
                 null,
                 new FluxObjectivesPolishingParameters(
                         null,
-                        List.of("objective_reaction1", "objective_reaction2")));
+                        List.of("objective_reaction1", "objective_reaction2")),
+                false);
 
         new ListOfObjectivesFixer(parameters, fbcPlugin).fix(fbcPlugin.getListOfObjectives(), 0);
 

diff --git a/src/test/java/edu/ucsd/sbrg/polishing/fbc/ObjectivesPolisherTest.java b/src/test/java/edu/ucsd/sbrg/polishing/fbc/ObjectivesPolisherTest.java
@@ -34,7 +34,8 @@ public void activeObjectiveRemainsUnchangedIfItHasFluxObjective() {
                 null,
                 new FluxObjectivesPolishingParameters(
                         null,
-                        List.of(" objective_reaction1 ")));
+                        List.of(" objective_reaction1 ")),
+                false);
 
         m.createReaction("objective_reaction1");
         m.createReaction("yadda_Biomass_yadda");