Merge branch '50-new-persistence-model-classes-need-more-annotations'…

… into 'master' Resolve "new persistence model classes need more annotations" Closes #50 See merge request bright-giant/sirius/sirius-libs!23
sirius-ms · Nov 16, 2023 · ed2cea9 · ed2cea9
2 parents 7b11aa2 + 13257dd
commit ed2cea9
Show file tree

Hide file tree

Showing 11 changed files with 42 additions and 19 deletions.
diff --git a/chemistry_base/src/main/java/de/unijena/bioinf/ChemistryBase/ms/IsolationWindow.java b/chemistry_base/src/main/java/de/unijena/bioinf/ChemistryBase/ms/IsolationWindow.java
@@ -20,6 +20,7 @@
 
 package de.unijena.bioinf.ChemistryBase.ms;
 
+import com.fasterxml.jackson.annotation.JsonProperty;
 import com.google.common.collect.Range;
 
 import java.util.Locale;
@@ -30,7 +31,7 @@ public class IsolationWindow {
     protected final double windowWidth;
 
 
-    public IsolationWindow(double windowOffset, double windowWidth) {
+    public IsolationWindow(@JsonProperty("windowOffset") double windowOffset, @JsonProperty("windowWidth") double windowWidth) {
         this.windowOffset = windowOffset;
         this.windowWidth = windowWidth;
     }

diff --git a/...nce_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/AbstractScan.java b/...nce_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/AbstractScan.java
@@ -21,7 +21,6 @@
 package de.unijena.bioinf.ms.persistence.model.core;
 
 import de.unijena.bioinf.ChemistryBase.ms.utils.SimpleSpectrum;
-import jakarta.persistence.Id;
 import lombok.*;
 
 /**
@@ -31,6 +30,7 @@
 @Setter
 @AllArgsConstructor
 @NoArgsConstructor
+@ToString
 public class AbstractScan {
     /**
      * Database ID of the Run this Scan belongs to
@@ -55,5 +55,6 @@ public class AbstractScan {
     /**
      * The actual spectrum that has been measured (masses and intensities)
      */
+    @ToString.Exclude
     protected SimpleSpectrum peaks;
 }
diff --git a/..._model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/AlignedFeatures.java b/..._model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/AlignedFeatures.java
@@ -48,6 +48,7 @@
 @AllArgsConstructor
 @Builder
 @JsonAutoDetect(fieldVisibility = ANY, getterVisibility = NONE, setterVisibility = NONE, isGetterVisibility = NONE)
+@ToString
 public class AlignedFeatures {
     @Id
     private long alignedFeatureId;
@@ -61,6 +62,7 @@ public class AlignedFeatures {
 
     protected double mergedIonMass;
     protected RetentionTime mergedRT;
+    @ToString.Exclude
     protected LongList correlationPairIds;
 
     protected CompoundAnnotation topAnnotation;
@@ -77,6 +79,7 @@ public Optional<List<MSMSScan>> getMsms() {
     }
 
     @JsonIgnore
+    @ToString.Exclude
     protected List<Feature> features;
 
     public Optional<List<Feature>> getFeatures() {

diff --git a/...istence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/Compound.java b/...istence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/Compound.java
@@ -37,6 +37,7 @@
 @Builder
 @AllArgsConstructor
 @NoArgsConstructor
+@ToString
 public class Compound {
     @Id
     private long compoundId;
@@ -48,17 +49,20 @@ public class Compound {
      * Group of edges between pairs of feature alignments that correlate among each other. Connected components
      * from the whole graph of correlated pairs (whole dataset)
      */
+    @ToString.Exclude
     LongList correlatedIonPairIds; //todo denormalize instead?
 
     //foreign fields
     @JsonIgnore
+    @ToString.Exclude
     List<AlignedFeatures> adductFeatures;
 
     public Optional<List<AlignedFeatures>> getAdductFeatures() {
         return Optional.ofNullable(adductFeatures);
     }
 
     @JsonIgnore
+    @ToString.Exclude
     List<CorrelatedIonPair> correlatedIonPairs;
 
     public Optional<List<CorrelatedIonPair>> getCorrelatedIonPairs() {

diff --git a/...odel_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/CorrelatedIonPair.java b/...odel_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/CorrelatedIonPair.java
@@ -21,19 +21,20 @@
 package de.unijena.bioinf.ms.persistence.model.core;
 
 import jakarta.persistence.Id;
-import lombok.Getter;
-import lombok.NoArgsConstructor;
-import lombok.Setter;
+import lombok.*;
 import org.jetbrains.annotations.NotNull;
 
 /**
  * Edge between two {@link AlignedFeatures}s
  */
 @Getter
 @Setter
+@Builder
+@AllArgsConstructor
 @NoArgsConstructor
+@ToString
 public class CorrelatedIonPair {
-    enum Type {ADDUCT, INSOURCE, MULTIMERE, ISOMERE}
+    public enum Type {ADDUCT, INSOURCE, MULTIMERE, ISOMERE}
 
     @Id
     private long ionPairId;

diff --git a/...sistence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/Feature.java b/...sistence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/Feature.java
@@ -36,6 +36,7 @@
 @NoArgsConstructor
 @AllArgsConstructor
 @Builder
+@ToString
 public class Feature {
 
 
@@ -63,6 +64,7 @@ public class Feature {
      * Foreign Field by apexScanId
      */
     @JsonIgnore
+    @ToString.Exclude
     protected Scan apexScan;
 
     public Optional<Scan> getApexScan() {
@@ -76,13 +78,15 @@ protected SimpleSpectrum getApexSpectrum() {
     /**
      * Extracted isotope pattern of this feature
      */
+    @ToString.Exclude
     protected SimpleSpectrum isotopePattern; //artificial spectrum -> no scan
 
     /**
      * MS/MS spectra belonging to this feature, referenced by the feature id
      * Foreign Field by featureId
      */
     @JsonIgnore
+    @ToString.Exclude
     protected List<MSMSScan> msms;
 
     public Optional<List<MSMSScan>> getMsms() {
@@ -99,5 +103,6 @@ public Stream<MutableMs2Spectrum> getMSMSSpectra(){
      * Traces of this feature (mono-isotopic + isotope peaks)
      * Optional Field
      */
+    @ToString.Exclude
     protected List<Trace> traces;
 }
diff --git a/...istence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/MSMSScan.java b/...istence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/MSMSScan.java
@@ -24,17 +24,15 @@
 import de.unijena.bioinf.ChemistryBase.ms.IsolationWindow;
 import de.unijena.bioinf.ChemistryBase.ms.utils.SimpleSpectrum;
 import jakarta.persistence.Id;
-import lombok.Builder;
-import lombok.Getter;
-import lombok.NoArgsConstructor;
-import lombok.Setter;
+import lombok.*;
 
 /**
  * A measured MS/MS Spectrum (usually MS2) with metadata.
  */
 @Getter
 @Setter
 @NoArgsConstructor
+@ToString(callSuper = true)
 public class MSMSScan extends AbstractScan {
     @Builder
     public MSMSScan(long scanId, Long runId, String scanNumber, Double scanTime, Double ccs, SimpleSpectrum peaks, Long precursorScanId, byte msLevel, IsolationWindow isolationWindow, CollisionEnergy collisionEnergy, Double mzOfInterest) {

diff --git a/..._persistence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/Run.java b/..._persistence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/Run.java
@@ -22,18 +22,21 @@
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import jakarta.persistence.Id;
-import lombok.Getter;
-import lombok.NoArgsConstructor;
-import lombok.Setter;
+import lombok.*;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 
+import java.util.List;
+
 @Getter
 @Setter
+@Builder
+@AllArgsConstructor
 @NoArgsConstructor
+@ToString
 public class Run {
     //todo are there other types like validation or calibration???
-    enum Type {
+    public enum Type {
         SAMPLE,
         BLANK
     }
@@ -57,7 +60,7 @@ enum Type {
     private ChromatographyType chromatography;
     private IonizationType ionization;
     private FragmentationType fragmentation;
-    private MassAnalyzerType massAnalyzer;
+    private List<MassAnalyzerType> massAnalyzers;
 
 
     /**
@@ -72,6 +75,7 @@ enum Type {
      */
     @Nullable
     @JsonIgnore
+    @ToString.Exclude
     private SourceFile sourceFile;
     //endregion
 

diff --git a/...persistence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/Scan.java b/...persistence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/Scan.java
@@ -30,6 +30,7 @@
 @Getter
 @Setter
 @NoArgsConstructor
+@ToString(callSuper = true)
 public class Scan extends AbstractScan{
     @Builder
     public Scan(long scanId, Long runId, String scanNumber, Double scanTime, Double ccs, SimpleSpectrum peaks) {

diff --git a/...tence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/SourceFile.java b/...tence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/SourceFile.java
@@ -21,15 +21,16 @@
 package de.unijena.bioinf.ms.persistence.model.core;
 
 import jakarta.persistence.Id;
-import lombok.Getter;
-import lombok.NoArgsConstructor;
-import lombok.Setter;
+import lombok.*;
 
 @Getter
 @Setter
+@Builder
+@AllArgsConstructor
 @NoArgsConstructor
+@ToString
 public class SourceFile {
-    enum Format {
+    public enum Format {
         //todo do we need more info here?
         MZML("Open MzML format"), MZXML("Open MzXML format (Deprecated)"), OTHER("Unknown or unspecified format");
 
@@ -59,5 +60,6 @@ enum Format {
     /**
      * File contents stored as gzipped byte stream
      */
+    @ToString.Exclude
     private byte[] data;
 }
diff --git a/...ersistence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/Trace.java b/...ersistence_model_oss/src/main/java/de/unijena/bioinf/ms/persistence/model/core/Trace.java
@@ -29,16 +29,19 @@
 @NoArgsConstructor
 @AllArgsConstructor
 @Builder
+@ToString(onlyExplicitlyIncluded = true)
 public class Trace {
     /**
      * ID of the Run this trace belongs to
      */
+    @ToString.Include
     long runId;
 
     /**
      * Ids of the scans this trace is build from
      * should be sorted by RT
      */
+    @ToString.Include
     LongList scanIds;
 
     /**