Merge branch 'dev-sql-tables' into dev-frontend

Author: michaelwenk

cmd/mb3dbtool/main.go

@@ -83,7 +83,7 @@ func main() {
 	}
 	count, err = db.Count()
 
-	println("Database update was succesful. ", count, " records in database.")
+	println("Database update was successful. ", count, " records in database.")
 }
 
 func readDirectoryData(dir string) ([]*massbank.MassBank2, *massbank.MbMetaData, error) {

cmd/mb3server/src/api_default_service.go

@@ -74,8 +74,6 @@ func (s *DefaultApiService) GetRecord(ctx context.Context, accession string) (Im
 
 	record, err := GetRecord(accession)
 	return Response(200, record), err
-
-	return Response(http.StatusNotImplemented, nil), errors.New("GetRecord method not implemented")
 }
 
 // GetRecords - Get a list of records

compose/docker-compose.yaml

@@ -0,0 +1,81 @@
+services:
+
+  postgres:
+    image: docker.io/postgres:latest
+    restart: always
+    ports:
+      - '${DB_PORT}:${DB_PORT}'
+    environment:
+      POSTGRES_PASSWORD: ${DB_PASSWORD}
+      POSTGRES_USER: ${DB_USER}
+      POSTGRES_DB: ${DB_NAME}
+    healthcheck:
+      test: ["CMD-SHELL", "pg_isready", "-d", "$$POSTGRES_DB","-U", "$$POSTGRES_USER"]
+      interval: 30s
+      timeout: 60s
+      retries: 5
+      start_period: 40s
+
+  mb3server:
+    build: ../
+    restart: always
+    ports:
+      - "${MB3_API_PORT}:${MB3_SERVER_PORT}"
+    depends_on:
+      postgres:
+        condition: service_healthy
+    environment:
+      - DB_TYPE
+      - DB_PORT
+      - DB_PASSWORD
+      - DB_HOST
+      - DB_NAME
+      - DB_CONN_STRING
+      - MB3_SERVER_PORT
+      - CDKDEPICT_URL
+
+  similarity-service-cosine:
+    build: ../similarity-service-cosine
+    restart: always
+    ports:
+      - "${SIMILARITY_SERVICE_COSINE_PORT}:8080"
+    depends_on:
+      mb3tool:
+        condition: service_completed_successfully
+    environment:
+      - DB_PORT
+      - DB_USER
+      - DB_PASSWORD
+      - DB_HOST
+      - DB_NAME
+
+  mb3frontend:
+    build:
+      context: ..
+      dockerfile: Dockerfile-frontend
+      args:
+        MB3_API_URL: "http://${MB3_API_HOST}:${MB3_API_PORT}"
+        MB3_FRONTEND_BASE_URL: "${MB3_FRONTEND_BASE_URL}"
+    restart: always
+    ports:
+      - "${MB3_FRONTEND_PORT}:3000"
+
+  mb3tool:
+    build:
+      context: ..
+      dockerfile: Dockerfile-dbtool
+    depends_on:
+      postgres:
+        condition: service_healthy
+    environment:
+      - DB_TYPE
+      - DB_PORT
+      - DB_USER
+      - DB_PASSWORD
+      - DB_HOST
+      - DB_NAME
+      - DB_CONN_STRING
+      - MB_GIT_REPO
+      - MB_GIT_BRANCH
+      - MB_DATA_DIRECTORY
+      - MB_DROP_ALL

compose/env.dist

@@ -0,0 +1,79 @@
+############################
+# Massbank 3 configuration #
+############################
+
+# --------------------
+# Server configuration
+# --------------------
+
+# The port where the API is exposed for frontend and application usage
+MB3_API_PORT=8081
+
+# The host where the frontend is running
+MB3_API_HOST=localhost
+
+# The port used internally by the server
+MB3_SERVER_PORT=8080
+
+
+# ----------------------
+# Frontend configuration
+# ----------------------
+
+# The Port where the frontend ist exposed
+MB3_FRONTEND_PORT=8080
+
+# The base URL
+MB3_FRONTEND_BASE_URL=/massbank3/
+
+# ----------------------
+# Database configuration
+# ----------------------
+
+# The database type: "mongodb" or "postgres"
+DB_TYPE=postgres
+
+# The port of the database
+DB_PORT=5432
+
+# The database user name
+DB_USER=massbank3
+
+# The database password
+DB_PASSWORD=massbank3password
+
+# The database host name
+DB_HOST=localhost
+
+# The name of the database
+DB_NAME=massbank3
+
+# A connection string to connect with the database. If set to non empty string other "DB_..." environment variables will be ignored
+DB_CONN_STRING=""
+
+# ------------------------------
+# Similarity microservice cosine
+# ------------------------------
+
+# The port where the similarity service is exposed
+SIMILARITY_SERVICE_COSINE_PORT=8082
+
+# The host where the similarity service is running
+SIMILARITY_SERVICE_COSINE_HOST=localhost
+
+# ---------------------------
+# Massbank-data configuration
+# ---------------------------
+
+# The repo where to load massbank data from
+MB_GIT_REPO="https://github.com/MassBank/MassBank-data"
+
+# The git branch of the massbank data repo
+MB_GIT_BRANCH=main
+
+# A directory where the massbank data is stored. If set, this will tried first before getting data from git.
+MB_DATA_DIRECTORY=""
+
+# Set to true to clear the database before filling with new data, otherwise data is upserted.
+MB_DROP_ALL=true
+

docker/docker-compose-database-only.yaml

@@ -31,10 +31,10 @@ MB3_FRONTEND_BASE_URL=/massbank3/
 # ----------------------
 
 # The database type: "mongodb" or "postgres"
-DB_TYPE=mongodb
+DB_TYPE=postgres
 
 # The port of the database
-DB_PORT=27017
+DB_PORT=5432
 
 # The database user name
 DB_USER=massbank3
@@ -43,7 +43,7 @@ DB_USER=massbank3
 DB_PASSWORD=massbank3password
 
 # The database host name
-DB_HOST=mongodb
+DB_HOST=postgres
 
 # The name of the database
 DB_NAME=massbank3

docker/env.dist

@@ -3,10 +3,11 @@ package config
 import (
 	"errors"
 	"flag"
-	"github.com/MassBank/MassBank3/pkg/database"
 	"log"
 	"os"
 	"strconv"
+
+	"github.com/MassBank/MassBank3/pkg/database"
 )
 
 type ToolConfig struct {
@@ -63,6 +64,10 @@ func GetToolConfig() ToolConfig {
 	flag.Parse()
 	if len(toolConfig.GitRepo) > 0 && len(toolConfig.DataDir) > 0 {
 		println("Git repo and data directory are set. Using data directory as default and git repo as fallback.")
+	} else if(len(toolConfig.GitRepo) > 0) {
+		println("Git repo is set. Using git repo as data source.")
+	} else if(len(toolConfig.DataDir) > 0) {
+		println("Data directory is set. Using data directory as data source.")
 	}
 	return *toolConfig
 }

pkg/config/config.go

@@ -1,10 +1,11 @@
 package database
 
 import (
-	"github.com/Code-Hex/dd"
-	"github.com/MassBank/MassBank3/pkg/massbank"
 	"log"
 	"math"
+
+	"github.com/Code-Hex/dd"
+	"github.com/MassBank/MassBank3/pkg/massbank"
 )
 
 // Filters is the abstract description of filters used to find MassBank records

pkg/database/db_interface.go

@@ -3,16 +3,17 @@ package database
 import (
 	"context"
 	"errors"
+	"log"
+	"reflect"
+	"strconv"
+	"time"
+
 	"github.com/MassBank/MassBank3/pkg/massbank"
 	"go.mongodb.org/mongo-driver/bson"
 	"go.mongodb.org/mongo-driver/bson/primitive"
 	"go.mongodb.org/mongo-driver/mongo"
 	"go.mongodb.org/mongo-driver/mongo/options"
 	bson2 "gopkg.in/mgo.v2/bson"
-	"log"
-	"reflect"
-	"strconv"
-	"time"
 )
 
 // Mb3MongoDB represents a mongodb connection and should implement [MB3Database]