feat: sunburst plot (ChemOnt)

Author: michaelwenk

Dockerfile-server

@@ -16,4 +16,4 @@ COPY api/schemas ./swagger-ui/schemas
 COPY entrypoint-mb3server.sh ./entrypoint-mb3server.sh
 
 EXPOSE 8080
-ENTRYPOINT sh entrypoint-mb3server.sh "${MB3_API_URL}"
+ENTRYPOINT ["sh", "entrypoint-mb3server.sh", "${MB3_API_URL}"]

api/openapi.yaml

@@ -138,7 +138,7 @@ paths:
 
   /metadata:
     get:
-      summary: Get the metadata of the database and the current dataset in use. It includes the version, timestamp, git commit hash, unique spectra count (SPLASH), unique compound count (InChI) and all compound classes with counts.
+      summary: Get the metadata of the database and the current dataset in use. It includes the version, timestamp, git commit hash, unique spectra count (SPLASH), unique compound count (InChI) and compound classes (free text/ChemOnt) with counts.
       operationId: getMetadata
       responses:
         "200":

api/schemas/FilterOptions.yaml

@@ -86,3 +86,13 @@ components:
               count:
                 type: integer
                 minimum: 1
+        compound_class_chemont:
+          type: array
+          items:
+            type: object
+            properties:
+              name:
+                type: string
+              count:
+                type: integer
+                minimum: 1

pkg/database/postgres.go

@@ -287,7 +287,7 @@ func (p *PostgresSQLDB) GetMetadata() (*massbank.MbMetaData, error) {
 	result.SpectraCount = spectraCount
 	result.CompoundCount = compoundCount
 
-	// compound classes
+	// compound classes (free text)
 	query = "SELECT class, COUNT(class) as count FROM compound_class GROUP BY class ORDER BY class;"
 	stmt, err = p.database.Prepare(query)
 	if err != nil {
@@ -314,6 +314,33 @@ func (p *PostgresSQLDB) GetMetadata() (*massbank.MbMetaData, error) {
 		}
 	}
 
+	// compound classes (ClassyFire)
+	query = "SELECT identifier, COUNT(identifier) as count FROM compound_link WHERE database = 'ChemOnt' GROUP BY identifier ORDER BY count DESC;"
+	stmt, err = p.database.Prepare(query)
+	if err != nil {
+		return nil, err
+	}
+	rows, err = stmt.Query()
+	stmt.Close()
+	if err == nil {
+		result.CompoundClassChemOnt = []string{}
+		result.CompoundClassCountChemOnt = []uint{}
+		for rows.Next() {
+			var class string
+			var count uint
+			if err := rows.Scan(&class, &count); err != nil {
+				return nil, err
+			}
+			result.CompoundClassChemOnt = append(result.CompoundClassChemOnt, class)
+			result.CompoundClassCountChemOnt = append(result.CompoundClassCountChemOnt, count)
+		}
+		rows.Close()
+	} else {
+		if err != sql.ErrNoRows {
+			return nil, err
+		}
+	}
+
 	return result, nil
 }
 

pkg/massbank/model.go

@@ -5,15 +5,17 @@ import (
 )
 
 type MbMetaData struct {
-	GitCommit          string   `json:"git_commit"`
-	Version            string   `json:"Version"`
-	Timestamp          string   `json:"timestamp"`
-	SpectraCount       uint     `json:"spectra_count"`
-	CompoundCount      uint     `json:"compound_count"`
-	CompoundName       []string `json:"compound_name"`
-	CompoundNameCount  []uint   `json:"compound_name_count"`
-	CompoundClass      []string `json:"compound_class"`
-	CompoundClassCount []uint   `json:"compound_class_count"`
+	GitCommit                 string   `json:"git_commit"`
+	Version                   string   `json:"Version"`
+	Timestamp                 string   `json:"timestamp"`
+	SpectraCount              uint     `json:"spectra_count"`
+	CompoundCount             uint     `json:"compound_count"`
+	CompoundName              []string `json:"compound_name"`
+	CompoundNameCount         []uint   `json:"compound_name_count"`
+	CompoundClass             []string `json:"compound_class"`
+	CompoundClassCount        []uint   `json:"compound_class_count"`
+	CompoundClassChemOnt      []string `json:"compound_class_chemont"`
+	CompoundClassCountChemOnt []uint   `json:"compound_class_count_chemont"`
 }
 
 type SubtagProperty struct {

pkg/mb3server/api-impl.go

@@ -618,12 +618,13 @@ func GetMetadata() (*Metadata, error) {
 	}
 
 	result := Metadata{
-		Version:       metadata.Version,
-		Timestamp:     metadata.Timestamp,
-		GitCommit:     metadata.GitCommit,
-		SpectraCount:  int32(metadata.SpectraCount),
-		CompoundCount: int32(metadata.CompoundCount),
-		CompoundClass: []MetadataCompoundClassInner{},
+		Version:              metadata.Version,
+		Timestamp:            metadata.Timestamp,
+		GitCommit:            metadata.GitCommit,
+		SpectraCount:         int32(metadata.SpectraCount),
+		CompoundCount:        int32(metadata.CompoundCount),
+		CompoundClass:        []MetadataCompoundClassInner{},
+		CompoundClassChemont: []MetadataCompoundClassInner{},
 	}
 
 	for i, compoundClass := range metadata.CompoundClass {
@@ -632,6 +633,12 @@ func GetMetadata() (*Metadata, error) {
 			Count: int32(metadata.CompoundClassCount[i]),
 		})
 	}
+	for i, compoundClassChemOnt := range metadata.CompoundClassChemOnt {
+		result.CompoundClassChemont = append(result.CompoundClassChemont, MetadataCompoundClassInner{
+			Name:  compoundClassChemOnt,
+			Count: int32(metadata.CompoundClassCountChemOnt[i]),
+		})
+	}
 
 	return &result, nil
 }