fix: use value 0 for missing relative intensity values

Author: michaelwenk

.openapi-generator/VERSION

@@ -1 +1 @@
-7.12.0
+7.13.0

api/schemas/MBRecord.yaml

@@ -244,14 +244,16 @@ properties:
                   description: "m/z of the peak"
                   type: number
                   format: double
+                  minimum: 0
                 intensity:
                   description: "intensity of the peak"
                   type: number
                   format: double
+                  minimum: 0
                 rel:
                   description: "Relative intensity of the peak"
                   type: integer
-                  minimum: 1
+                  minimum: 0
                   maximum: 999
       neutral_loss:
         description: "Neutral Losses"
@@ -265,11 +267,12 @@ properties:
               type: number
               format: double
               minimum: 0
-            peak1_id:
-              description: "Peak identifier of the first peak"
-              type: integer
-              minimum: 1
-            peak2_id:
-              description: "Peak identifier of the second peak"
+            peak_id:
+              description: "Peak identifier of the peak in spectrum"
               type: integer
               minimum: 1
+            precursor_mass:
+              description: "Precursor mass"
+              type: number
+              format: double
+              minimum: 0

pkg/massbank/model.go

@@ -118,8 +118,8 @@ type PkPeak struct {
 
 type PkNeutralLoss struct {
 	Difference      []float64 `json:"difference"`
-	Peak1Id         []int32   `json:"peak1_id"`
-	Peak2Id         []int32   `json:"peak2_id"`
+	PeakId          []int32   `json:"peak_id"`
+	PrecursorMass   []float64 `json:"precursor_mass"`
 	MinRelIntensity []int32   `json:"min_rel_intensity"`
 }
 

pkg/mb3server/convert.go

@@ -147,20 +147,20 @@ func ConvertMb2RecordToMb3Record(record *massbank.MassBank2) (*MbRecord, error)
 
 		var diffs []float64
 		diffs = append(diffs, record.Peak.NeutralLoss.Difference...)
-		var peak1_ids []int32
-		peak1_ids = append(peak1_ids, record.Peak.NeutralLoss.Peak1Id...)
-		var peak2_ids []int32
-		peak2_ids = append(peak2_ids, record.Peak.NeutralLoss.Peak2Id...)
+		var peak_ids []int32
+		peak_ids = append(peak_ids, record.Peak.NeutralLoss.PeakId...)
+		var precursor_masses []float64
+		precursor_masses = append(precursor_masses, record.Peak.NeutralLoss.PrecursorMass...)
 		// var min_rel_intensities []int32
 		// for _, min_rel_intensity := range *&record.Peak.NeutralLoss.MinRelIntensity {
 		// 	min_rel_intensities = append(min_rel_intensities, min_rel_intensity)
 		// }
 
-		for i := 0; i < len(diffs); i++ {
+		for i := range diffs {
 			result.Peak.NeutralLoss = append(result.Peak.NeutralLoss, MbRecordPeakNeutralLossInner{
-				Difference: diffs[i],
-				Peak1Id:    peak1_ids[i],
-				Peak2Id:    peak2_ids[i],
+				Difference:    diffs[i],
+				PeakId:        peak_ids[i],
+				PrecursorMass: precursor_masses[i],
 				// MinRelIntensity: min_rel_intensities[i],
 			})
 		}