Merge branch '28-add-result-annotations-to-nightsky-api' into 'master'

Resolve "add result Annotations to Nightsky API"

Closes #47 and #28

See merge request bright-giant/sirius/sirius-frontend!17

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/controller/AlignedFeaturesController.java

@@ -20,8 +20,8 @@
 package de.unijena.bioinf.ms.middleware.controller;
 
 import de.unijena.bioinf.ms.middleware.model.SearchQueryType;
+import de.unijena.bioinf.ms.middleware.model.annotations.*;
 import de.unijena.bioinf.ms.middleware.model.features.AlignedFeature;
-import de.unijena.bioinf.ms.middleware.model.features.annotations.*;
 import de.unijena.bioinf.ms.middleware.model.spectra.AnnotatedSpectrum;
 import de.unijena.bioinf.ms.middleware.service.projects.ProjectsProvider;
 import io.swagger.v3.oas.annotations.Hidden;
@@ -111,12 +111,12 @@ public void deleteAlignedFeature(@PathVariable String projectId, @PathVariable S
      * @return StructureCandidate of this feature (aligned over runs) candidate with specified optional fields.
      */
     @GetMapping(value = "/{alignedFeatureId}/structures", produces = MediaType.APPLICATION_JSON_VALUE)
-    public Page<StructureCandidateExt> getStructureCandidates(
+    public Page<StructureCandidateFormula> getStructureCandidates(
             @PathVariable String projectId, @PathVariable String alignedFeatureId,
             @ParameterObject Pageable pageable,
             @RequestParam(required = false) String searchQuery,
             @RequestParam(defaultValue = "LUCENE") SearchQueryType querySyntax,
-            @RequestParam(defaultValue = "") EnumSet<StructureCandidate.OptFields> optFields
+            @RequestParam(defaultValue = "") EnumSet<StructureCandidateScored.OptFields> optFields
     ) {
         return projectsProvider.getProjectOrThrow(projectId)
                 .findStructureCandidatesByFeatureId(alignedFeatureId, pageable, optFields);
@@ -177,12 +177,12 @@ public FormulaCandidate getFormulaCandidate(
      * @return StructureCandidate of this formula candidate with specified optional fields.
      */
     @GetMapping(value = "/{alignedFeatureId}/formulas/{formulaId}/structures", produces = MediaType.APPLICATION_JSON_VALUE)
-    public Page<StructureCandidate> getStructureCandidatesByFormula(
+    public Page<StructureCandidateScored> getStructureCandidatesByFormula(
             @PathVariable String projectId, @PathVariable String alignedFeatureId, @PathVariable String formulaId,
             @ParameterObject Pageable pageable,
             @RequestParam(required = false) String searchQuery,
             @RequestParam(defaultValue = "LUCENE") SearchQueryType querySyntax,
-            @RequestParam(defaultValue = "") EnumSet<StructureCandidate.OptFields> optFields
+            @RequestParam(defaultValue = "") EnumSet<StructureCandidateScored.OptFields> optFields
     ) {
         return projectsProvider.getProjectOrThrow(projectId)
                 .findStructureCandidatesByFeatureIdAndFormulaId(formulaId, alignedFeatureId, pageable, optFields);

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/features/annotations/BinaryFingerprint.java → sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/BinaryFingerprint.java

@@ -18,7 +18,7 @@
  *  You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
  */
 
-package de.unijena.bioinf.ms.middleware.model.features.annotations;
+package de.unijena.bioinf.ms.middleware.model.annotations;
 
 import de.unijena.bioinf.ChemistryBase.fp.Fingerprint;
 import lombok.Getter;

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/features/annotations/CanopusLevels.java → sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/CanopusLevels.java

@@ -18,7 +18,7 @@
  *  You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
  */
 
-package de.unijena.bioinf.ms.middleware.model.features.annotations;
+package de.unijena.bioinf.ms.middleware.model.annotations;
 
 import de.unijena.bioinf.ChemistryBase.fp.NPCFingerprintVersion;
 

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/features/annotations/CanopusPrediction.java → sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/CanopusPrediction.java

@@ -18,7 +18,7 @@
  *  You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
  */
 
-package de.unijena.bioinf.ms.middleware.model.features.annotations;
+package de.unijena.bioinf.ms.middleware.model.annotations;
 
 import de.unijena.bioinf.ChemistryBase.fp.ClassyfireProperty;
 import de.unijena.bioinf.ChemistryBase.fp.FPIter;

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/features/annotations/CompoundClass.java → sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/CompoundClass.java

@@ -3,7 +3,7 @@
  *  This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  *  Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- *  Chair of Bioinformatics, Friedrich-Schilller University.
+ *  Chair of Bioinformatics, Friedrich-Schiller University.
  *
  *  This library is free software; you can redistribute it and/or
  *  modify it under the terms of the GNU Lesser General Public
@@ -18,7 +18,7 @@
  *  You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
  */
 
-package de.unijena.bioinf.ms.middleware.model.features.annotations;
+package de.unijena.bioinf.ms.middleware.model.annotations;
 
 import de.unijena.bioinf.ChemistryBase.fp.ClassyfireProperty;
 import de.unijena.bioinf.ChemistryBase.fp.NPCFingerprintVersion;

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/features/annotations/CompoundClasses.java → sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/CompoundClasses.java

@@ -3,7 +3,7 @@
  *  This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  *  Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- *  Chair of Bioinformatics, Friedrich-Schilller University.
+ *  Chair of Bioinformatics, Friedrich-Schiller University.
  *
  *  This library is free software; you can redistribute it and/or
  *  modify it under the terms of the GNU Lesser General Public
@@ -18,8 +18,7 @@
  *  You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
  */
 
-
-package de.unijena.bioinf.ms.middleware.model.features.annotations;
+package de.unijena.bioinf.ms.middleware.model.annotations;
 
 import de.unijena.bioinf.ChemistryBase.fp.*;
 import de.unijena.bioinf.canopus.CanopusResult;

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/ConsensusAnnotations.java

@@ -0,0 +1,50 @@
+/*
+ *
+ *  This file is part of the SIRIUS library for analyzing MS and MS/MS data
+ *
+ *  Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
+ *  Chair of Bioinformatics, Friedrich-Schilller University.
+ *
+ *  This library is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU Lesser General Public
+ *  License as published by the Free Software Foundation; either
+ *  version 3 of the License, or (at your option) any later version.
+ *
+ *  This library is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ *  Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
+ */
+
+package de.unijena.bioinf.ms.middleware.model.annotations;
+
+import lombok.Getter;
+import lombok.Setter;
+import lombok.experimental.SuperBuilder;
+
+import java.util.List;
+
+@Getter
+@Setter
+@SuperBuilder
+abstract class ConsensusAnnotations {
+
+    /**
+     * Molecular formula of the consensus annotation
+     * Might be null if no consensus formula is available.
+     */
+    protected String molecularFormula;
+
+    /**
+     * Compound classes (predicted with CANOPUS) corresponding to the molecularFormula
+     * Might be null if no fingerprints or compound classes are available.
+     */
+    protected CompoundClasses compoundClasses;
+
+    /**
+     * FeatureIds where the topAnnotation supports this annotation.
+     */
+    protected List<String> supportingFeatureIds;
+}

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/ConsensusAnnotationsCSI.java

@@ -0,0 +1,64 @@
+/*
+ *
+ *  This file is part of the SIRIUS library for analyzing MS and MS/MS data
+ *
+ *  Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
+ *  Chair of Bioinformatics, Friedrich-Schilller University.
+ *
+ *  This library is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU Lesser General Public
+ *  License as published by the Free Software Foundation; either
+ *  version 3 of the License, or (at your option) any later version.
+ *
+ *  This library is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ *  Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
+ */
+
+package de.unijena.bioinf.ms.middleware.model.annotations;
+
+import lombok.Getter;
+import lombok.Setter;
+import lombok.experimental.SuperBuilder;
+
+@Getter
+@Setter
+@SuperBuilder
+public class ConsensusAnnotationsCSI extends ConsensusAnnotations {
+    public enum Criterion {
+        MAJORITY_STRUCTURE,
+        CONFIDENCE_STRUCTURE,
+        SINGLETON_STRUCTURE,
+        MAJORITY_FORMULA,
+        TOP_FORMULA,
+        SINGLETON_FORMULA
+    }
+
+
+    /**
+     * Null if this is a custom selection
+     */
+    protected Criterion selectionCriterion;
+
+    /**
+     * Database structure candidate (searched with CSI:FingerID), that also defines the molecularFormula
+     * Might be null if no consensus structure is available.
+     */
+    protected StructureCandidate csiFingerIdStructure;
+
+    /**
+     * Confidence value that represents the certainty that reported consensus structure is exactly the measured one
+     * If multiple features support this consensus structure the maximum confidence is reported
+     */
+    protected Double confidenceExactMatch;
+
+    /**
+     * Confidence value that represents the certainty that the exact consensus structure or a very similar
+     * structure (e.g. measured by Maximum Common Edge Subgraph Distance) is the measured one.
+     * If multiple features support this consensus structure the maximum confidence is reported
+     */
+    protected Double confidenceApproxMatch;
+}

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/ConsensusAnnotationsDeNovo.java

@@ -0,0 +1,44 @@
+/*
+ *
+ *  This file is part of the SIRIUS library for analyzing MS and MS/MS data
+ *
+ *  Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
+ *  Chair of Bioinformatics, Friedrich-Schilller University.
+ *
+ *  This library is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU Lesser General Public
+ *  License as published by the Free Software Foundation; either
+ *  version 3 of the License, or (at your option) any later version.
+ *
+ *  This library is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ *  Lesser General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
+ */
+
+package de.unijena.bioinf.ms.middleware.model.annotations;
+
+import lombok.Getter;
+import lombok.Setter;
+import lombok.experimental.SuperBuilder;
+
+@Getter
+@Setter
+@SuperBuilder
+public class ConsensusAnnotationsDeNovo extends ConsensusAnnotations{
+    public enum Criterion {
+        MAJORITY_FORMULA,
+        TOP_FORMULA,
+        SINGLETON_FORMULA
+    }
+
+    protected Criterion selectionCriterion;
+
+//    /**
+//     * DeNovo Structure candidate (predicted with MSNovelist) corresponding to the molecularFormula
+//     * Might be null if no consensus structure is available.
+//     */
+//    protected StructureCandidate structureMsNovelist;
+}

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/features/annotations/Annotations.java → sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/FeatureAnnotations.java

@@ -17,25 +17,32 @@
  *  You should have received a copy of the GNU Affero General Public License along with SIRIUS.  If not, see <https://www.gnu.org/licenses/agpl-3.0.txt>
  */
 
-package de.unijena.bioinf.ms.middleware.model.features.annotations;
+package de.unijena.bioinf.ms.middleware.model.annotations;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import lombok.Getter;
 import lombok.Setter;
 
 /**
  * Summary of the results of a feature (aligned over runs). Can be added to a AlignedFeature.
- * It is null within a AlignedFeature if it was not requested und non-null otherwise.
  * The different annotation fields within this summary object are null if the corresponding
  * feature does not contain the represented results. If fields are non-null
  * the corresponding result has been computed but might still be empty.
  * */
 @Getter
 @Setter
 @JsonInclude(JsonInclude.Include.NON_NULL)
-public class Annotations {
-    //result previews
+public class FeatureAnnotations {
+    /**
+     * Best matching FormulaCandidate.
+     */
     protected FormulaCandidate formulaAnnotation; // SIRIUS + ZODIAC
-    protected StructureCandidate structureAnnotation; // CSI:FingerID
+    /**
+     * Best matching StructureCandidate ranked by CSI:FingerID Score over all FormulaCandidates.
+     */
+    protected StructureCandidateScored structureAnnotation; // CSI:FingerID or MSNovelist
+    /**
+     * Best matching compound classes that correspond to the formulaAnnotation
+     */
     protected CompoundClasses compoundClassAnnotation; // CANOPUS
 }

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/features/annotations/FormulaCandidate.java → sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/FormulaCandidate.java

@@ -18,24 +18,12 @@
  *  You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
  */
 
-
-package de.unijena.bioinf.ms.middleware.model.features.annotations;
+package de.unijena.bioinf.ms.middleware.model.annotations;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import de.unijena.bioinf.ChemistryBase.ms.Deviation;
-import de.unijena.bioinf.ChemistryBase.ms.ft.FTree;
-import de.unijena.bioinf.GibbsSampling.ZodiacScore;
 import de.unijena.bioinf.ms.middleware.model.spectra.AnnotatedSpectrum;
-import de.unijena.bioinf.projectspace.FormulaResult;
-import de.unijena.bioinf.projectspace.FormulaResultId;
-import de.unijena.bioinf.projectspace.FormulaScoring;
-import de.unijena.bioinf.sirius.FTreeMetricsHelper;
-import de.unijena.bioinf.sirius.scores.IsotopeScore;
-import de.unijena.bioinf.sirius.scores.SiriusScore;
-import de.unijena.bioinf.sirius.scores.TreeScore;
 import lombok.*;
-import org.jetbrains.annotations.NotNull;
-import org.jetbrains.annotations.Nullable;
 
 /**
  * Molecular formula candidate that holds a unique identifier (molecular formula + adduct).

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/features/annotations/FragmentNode.java → sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/FragmentNode.java

@@ -18,7 +18,7 @@
  *  You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
  */
 
-package de.unijena.bioinf.ms.middleware.model.features.annotations;
+package de.unijena.bioinf.ms.middleware.model.annotations;
 
 import lombok.Getter;
 import lombok.Setter;

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/features/annotations/FragmentationTree.java → sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/FragmentationTree.java

@@ -3,7 +3,7 @@
  *  This file is part of the SIRIUS library for analyzing MS and MS/MS data
  *
  *  Copyright (C) 2013-2020 Kai Dührkop, Markus Fleischauer, Marcus Ludwig, Martin A. Hoffman, Fleming Kretschmer and Sebastian Böcker,
- *  Chair of Bioinformatics, Friedrich-Schilller University.
+ *  Chair of Bioinformatics, Friedrich-Schiller University.
  *
  *  This library is free software; you can redistribute it and/or
  *  modify it under the terms of the GNU Lesser General Public
@@ -18,7 +18,7 @@
  *  You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
  */
 
-package de.unijena.bioinf.ms.middleware.model.features.annotations;
+package de.unijena.bioinf.ms.middleware.model.annotations;
 
 import de.unijena.bioinf.ChemistryBase.ms.AnnotatedPeak;
 import de.unijena.bioinf.ChemistryBase.ms.Deviation;

sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/features/annotations/LossEdge.java → sirius_rest_service/src/main/java/de/unijena/bioinf/ms/middleware/model/annotations/LossEdge.java

@@ -18,7 +18,7 @@
  *  You should have received a copy of the GNU Lesser General Public License along with SIRIUS. If not, see <https://www.gnu.org/licenses/lgpl-3.0.txt>
  */
 
-package de.unijena.bioinf.ms.middleware.model.features.annotations;
+package de.unijena.bioinf.ms.middleware.model.annotations;
 
 import lombok.Getter;
 import lombok.Setter;