#21 Add backend for SpectraList

cmd/mb3server/src/api-impl.go

@@ -76,6 +76,64 @@ func GetBrowseOptions() (*BrowseOptions, error) {
 			Count: int32(val.Count),
 		})
 	}
+	for _, val := range vals.Contributor {
+		result.Contributor = append(result.Contributor, StringCountInner{
+			Value: val.Val,
+			Count: int32(val.Count),
+		})
+	}
+	for _, val := range vals.CompoundStart {
+		result.CompoundStart = append(result.CompoundStart, StringCountInner{
+			Value: val.Val,
+			Count: int32(val.Count),
+		})
+	}
+
+	return &result, nil
+}
 
+func GetRecords(limit int32, offset int32) (*SearchResult, error) {
+	if limit <= 0 {
+		limit = 20
+	}
+	if offset <= 0 {
+		offset = 0
+	}
+	if err := initDB(); err != nil {
+		return nil, err
+	}
+	var filters = database.Filters{
+		InstrumentType:  nil,
+		Splash:          "",
+		MsType:          nil,
+		IonMode:         "",
+		CompoundName:    "",
+		Mass:            nil,
+		MassEpsilon:     nil,
+		Formula:         "",
+		Peaks:           nil,
+		PeakDifferences: nil,
+		InchiKey:        "",
+		Contributor:     "",
+		IntensityCutoff: nil,
+		Limit:           int64(limit),
+		Offset:          int64(offset),
+	}
+	records, err := db.GetRecords(filters)
+	if err != nil {
+		return nil, err
+	}
+	var result = SearchResult{}
+	for _, record := range records {
+		var val = SearchResultDataInner{
+			Data:    map[string]interface{}{},
+			Name:    record.Compound.Names[1].String,
+			Formula: record.Compound.Formula.String,
+			Mass:    record.Compound.Mass.Value,
+			Smiles:  record.Compound.Smiles.String,
+			Spectra: []SearchResultDataInnerSpectraInner{{record.RecordTitle.String, record.Accession.String}},
+		}
+		result.Data = append(result.Data, val)
+	}
 	return &result, nil
 }

cmd/mb3server/src/api_default_service.go

@@ -70,11 +70,10 @@ func (s *DefaultApiService) GetRecord(ctx context.Context, accession string) (Im
 
 // GetRecords - Get a list of records
 func (s *DefaultApiService) GetRecords(ctx context.Context, instrumentType []string, splash string, msType []string, ionMode string, compoundName string, exactMass string, massTolerance float64, formula string, peaks []string, intensity int32, peakDifferences []string, peakList []string, limit int32, page int32, intensityCutoff int32, inchiKey string, contributor string) (ImplResponse, error) {
-	// TODO - update GetRecords with the required logic for this service method.
-	// Add api_default_service.go to the .openapi-generator-ignore to avoid overwriting this service implementation when updating open api generation.
-
-	//TODO: Uncomment the next line to return response Response(200, SearchResult{}) or use other options such as http.Ok ...
-	//return Response(200, SearchResult{}), nil
+	result, err := GetRecords(limit, (page-1)*limit)
+	if err != nil {
+		return Response(http.StatusInternalServerError, nil), errors.New("Could not get results")
+	}
+	return Response(200, result), nil
 
-	return Response(http.StatusNotImplemented, nil), errors.New("GetRecords method not implemented")
 }

cmd/mb3server/src/model_string_count_inner.go

@@ -0,0 +1,33 @@
+/*
+ * MassBank3 API
+ *
+ * No description provided (generated by Openapi Generator https://github.com/openapitools/openapi-generator)
+ *
+ * API version: 3.0
+ * Generated by: OpenAPI Generator (https://openapi-generator.tech)
+ */
+
+package mb3server
+
+type StringCountInner struct {
+	Value string `json:"value,omitempty"`
+
+	Count int32 `json:"count,omitempty"`
+}
+
+// AssertStringCountInnerRequired checks if the required fields are not zero-ed
+func AssertStringCountInnerRequired(obj StringCountInner) error {
+	return nil
+}
+
+// AssertRecurseStringCountInnerRequired recursively checks if required fields are not zero-ed in a nested slice.
+// Accepts only nested slice of StringCountInner (e.g. [][]StringCountInner), otherwise ErrTypeAssertionError is thrown.
+func AssertRecurseStringCountInnerRequired(objSlice interface{}) error {
+	return AssertRecurseInterfaceRequired(objSlice, func(obj interface{}) error {
+		aStringCountInner, ok := obj.(StringCountInner)
+		if !ok {
+			return ErrTypeAssertionError
+		}
+		return AssertStringCountInnerRequired(aStringCountInner)
+	})
+}

pkg/database/db_interface.go

@@ -93,6 +93,8 @@ type MBMinMaxValues struct {
 }
 
 type MB3Values struct {
+	CompoundStart  []MBCountValues
+	Contributor    []MBCountValues
 	InstrumentType []MBCountValues
 	MSType         []MBCountValues
 	IonMode        []MBCountValues
@@ -101,6 +103,15 @@ type MB3Values struct {
 	Peak           MBMinMaxValues
 }
 
+type MB3MetaData struct {
+	Version       string
+	TimeStamp     string
+	GitCommit     string
+	SpectraCount  int
+	CompoundCount int
+	IsomerCount   int
+}
+
 // MB3Database This is the Interface which has to be implemented for databases using MassBank3
 //
 // Any database can be used as in the backend as long as it defines the interface.
@@ -133,6 +144,8 @@ type MB3Database interface {
 	// GetUniqueValues is used to get the values for filter frontend
 	GetUniqueValues(filters Filters) (MB3Values, error)
 
+	GetMetaData() (*MB3MetaData, error)
+
 	// UpdateMetadata updates the metadata describing the MassBank version.
 	// Provides the database id of an existing entry if it is already in the
 	// database.

pkg/database/mongodb.go

@@ -27,10 +27,78 @@ type Mb3MongoDB struct {
 	dirty    bool            // if true, the database connection was changed and the database will reconnect.
 }
 
+func (db *Mb3MongoDB) GetMetaData() (*MB3MetaData, error) {
+	var query = ``
+	var bdoc interface{}
+	if err := bson2.UnmarshalJSON([]byte(query), &bdoc); err != nil {
+		return nil, err
+	}
+	cur, err := db.database.Collection(mbCollection).Aggregate(context.Background(), bdoc)
+	if err != nil {
+		return nil, err
+	}
+	var temp = make([]bson.D, 0)
+	if err = cur.All(context.Background(), &temp); err != nil {
+		return nil, err
+	}
+	result := MB3MetaData{
+		Version:       "",
+		TimeStamp:     "",
+		GitCommit:     "",
+		SpectraCount:  0,
+		CompoundCount: 0,
+		IsomerCount:   0,
+	}
+	return &result, nil
+}
+
 func (db *Mb3MongoDB) GetUniqueValues(filters Filters) (MB3Values, error) {
 	var query = `
 [
     { "$facet": {
+		"CompoundStart": [
+    { "$project": { "compound.names": 1}},
+        { "$unwind": "$compound.names" },
+    {"$group": {
+        "_id": {"$substr": [ {"$trim": { "input": {"$toUpper":"$compound.names"}, "chars": "()+-[]{}/? ,"}},0,1]},
+        "Count": {"$sum": 1}
+        }},
+    {
+        "$project": {
+            "_id": 0,
+            "Val": "$_id",
+            "Count": 1
+        }
+    },
+    {
+        "$sort": {
+            "Val": 1
+        }
+    }
+    ],
+		"Contributor": [
+    {
+        "$project": { "_id": 0, "cont": {"$arrayElemAt":[ {"$split": [ "$accession","-"]}, 1]} }
+    },
+    {
+        "$group": {
+            "_id": "$cont",
+            "Count": {"$sum": 1}
+        },
+    },
+    {
+        "$project": {
+            "_id": 0,
+            "Val": "$_id",
+            "Count": 1
+        }
+    },
+    {
+        "$sort": {
+            "Val": 1
+        }
+    }
+],
         "InstrumentType": [
             {
                 "$group": {
@@ -178,16 +246,20 @@ func (db *Mb3MongoDB) GetUniqueValues(filters Filters) (MB3Values, error) {
 		return result, err
 	}
 	type MB3ValuesTemp struct {
+		CompoundStart  []MBCountValues
 		InstrumentType []MBCountValues
 		MSType         []MBCountValues
 		IonMode        []MBCountValues
+		Contributor    []MBCountValues
 		Intensity      []MBMinMaxValues
 		Mass           []MBMinMaxValues
 		Peak           []MBMinMaxValues
 	}
 	var tempV MB3ValuesTemp
 	err = bson.Unmarshal(doc, &tempV)
 	result = MB3Values{
+		CompoundStart:  tempV.CompoundStart,
+		Contributor:    tempV.Contributor,
 		InstrumentType: tempV.InstrumentType,
 		MSType:         tempV.MSType,
 		IonMode:        tempV.IonMode,

web-frontend/src/routes/contents/+page.svelte

@@ -22,8 +22,10 @@
     {:then filters}
         <div class="card">
         <h2>Filters</h2>
-
         <h3>Contributor</h3>
+            {#each filters.contributor as t}
+                <FilterButton group="cont" val={t.value}>{t.value} ({t.count})</FilterButton>
+            {/each}
         <h3>Instrument Type</h3>
             {#each filters.instrument_type as t}
                 <FilterButton group="insttype" val={t.value}>{t.value} ({t.count})</FilterButton>
@@ -36,6 +38,10 @@
             {#each filters.ion_mode as t}
                 <FilterButton group="ionmode" val={t.value}>{t.value} ({t.count})</FilterButton>
             {/each}
+        <h3>Compound Start</h3>
+            {#each filters.compound_start as t}
+                <FilterButton group="compoundstart" val={t.value}>{t.value} ({t.count})</FilterButton>
+            {/each}
         </div>
 
     {/await}