feat(server-go): 分子检测扩展(qPCR Ct 判读/SERS 光谱上传/光谱库,#19)

This commit is contained in:
weijuesen
2026-08-12 19:33:05 +08:00
parent afb1df6f10
commit 7bb87dd89c
7 changed files with 323 additions and 0 deletions
+1
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@@ -35,6 +35,7 @@ func Init(cfg *config.Config) error {
&model.LampTest{}, &model.LampTestStep{},
&model.Consumable{},
&model.Consultation{},
&model.SpectrumEntry{},
); err != nil {
slog.Warn("自动迁移有警告(可忽略)", "err", err)
}
@@ -65,6 +65,17 @@ func buildImageKey(filename string) (string, string, error) {
return buildObjectKey("knowledge", filename)
}
// buildDataKey 生成 <prefix>/<日期>/<随机><ext>(不校验扩展名,由调用方校验)
func buildDataKey(prefix, filename string) (string, string, error) {
ext := strings.ToLower(filepath.Ext(filename))
buf := make([]byte, 8)
if _, err := rand.Read(buf); err != nil {
return "", "", err
}
date := time.Now().Format("20060102")
return fmt.Sprintf("%s/%s/%s%s", prefix, date, hex.EncodeToString(buf), ext), ext, nil
}
// uploadKnowledgeImage 上传知识库图片(multipart 字段名 file
func uploadKnowledgeImage(s3 *service.S3Service, bucket string) gin.HandlerFunc {
return func(c *gin.Context) {
@@ -77,3 +77,16 @@ func TestBuildObjectKeyPrefix(t *testing.T) {
t.Errorf("key/ext 应以 .jpg 结尾: %s / %s", key, ext)
}
}
func TestBuildDataKey(t *testing.T) {
key, ext, err := buildDataKey("spectrum", "a.CSV")
if err != nil {
t.Fatalf("buildDataKey 失败: %v", err)
}
if !strings.HasPrefix(key, "spectrum/") || !strings.HasSuffix(key, ".csv") {
t.Errorf("key 不正确: %s", key)
}
if ext != ".csv" {
t.Errorf("ext = %s, want .csv", ext)
}
}
+190
View File
@@ -28,6 +28,12 @@ func RegisterLampRoutes(rg *gin.RouterGroup, db *gorm.DB, s3 *service.S3Service,
rg.PATCH("/lamp-tests/:id/steps/:stepNo", write, updateLampTestStep(db))
rg.POST("/lamp-tests/:id/result-image", write, uploadLampResultImage(db, s3, imageBucket))
rg.GET("/lamp-tests/:id/cross-validation", read, getLampCrossValidation(db))
rg.POST("/lamp-tests/:id/judge-qpcr", write, judgeQPCR(db))
rg.POST("/lamp-tests/:id/spectrum", write, uploadLampSpectrum(db, s3, imageBucket))
rg.GET("/spectrum-entries", read, listSpectrumEntries(db))
rg.POST("/spectrum-entries", write, createSpectrumEntry(db))
rg.POST("/spectrum-entries/upload", write, uploadSpectrumEntryFile(s3, imageBucket))
rg.DELETE("/spectrum-entries/:id", write, deleteSpectrumEntry(db))
}
// listLampTests 检测任务单列表(roomId/batchId/status 过滤)
@@ -58,6 +64,13 @@ func createLampTest(db *gorm.DB) gin.HandlerFunc {
return
}
t.ID = ""
if t.Method == "" {
t.Method = "lamp"
}
if !model.ValidDetectionMethod(t.Method) {
c.JSON(http.StatusBadRequest, gin.H{"error": "method 仅支持 lamp/qpcr/sers/hyperspectral"})
return
}
if t.RoomID != nil && !isUUID(*t.RoomID) {
c.JSON(http.StatusBadRequest, gin.H{"error": "roomId 不是合法的 UUID"})
return
@@ -85,6 +98,183 @@ func createLampTest(db *gorm.DB) gin.HandlerFunc {
}
}
// judgeQPCR qPCR Ct 值录入并自动判读(#19)
func judgeQPCR(db *gorm.DB) gin.HandlerFunc {
return func(c *gin.Context) {
id := c.Param("id")
var t model.LampTest
if db.Where("id = ?", id).First(&t).Error != nil {
c.JSON(http.StatusNotFound, gin.H{"error": "lamp test not found"})
return
}
var body struct {
CtValues []float64 `json:"ctValues"`
Threshold float64 `json:"threshold"`
}
if err := c.ShouldBindJSON(&body); err != nil {
c.JSON(http.StatusBadRequest, gin.H{"error": err.Error()})
return
}
result, reason := model.JudgeQPCR(body.CtValues, body.Threshold)
extra := map[string]interface{}{}
if len(t.ExtraData) > 0 {
_ = json.Unmarshal(t.ExtraData, &extra)
}
extra["ctValues"] = body.CtValues
extra["judgeReason"] = reason
raw, _ := json.Marshal(extra)
now := time.Now()
db.Model(&model.LampTest{}).Where("id = ?", id).Updates(map[string]interface{}{
"extra_data": raw, "result": result, "status": "resulted", "resulted_at": now,
})
_ = runCrossValidation(db, id, result)
db.Where("id = ?", id).First(&t)
c.JSON(http.StatusOK, t)
}
}
// uploadLampSpectrum SERS 光谱数据上传(S3 spectrum/ 前缀)
func uploadLampSpectrum(db *gorm.DB, s3 *service.S3Service, bucket string) gin.HandlerFunc {
return func(c *gin.Context) {
id := c.Param("id")
var t model.LampTest
if db.Where("id = ?", id).First(&t).Error != nil {
c.JSON(http.StatusNotFound, gin.H{"error": "lamp test not found"})
return
}
file, header, err := c.Request.FormFile("file")
if err != nil {
c.JSON(http.StatusBadRequest, gin.H{"error": "请选择光谱文件(字段名 file"})
return
}
defer file.Close()
if err := model.ValidateSpectrumFile(header.Filename, header.Size); err != nil {
c.JSON(http.StatusBadRequest, gin.H{"error": err.Error()})
return
}
data, err := io.ReadAll(file)
if err != nil {
c.JSON(http.StatusInternalServerError, gin.H{"error": "读取文件失败"})
return
}
key, ext, err := buildDataKey("spectrum", header.Filename)
if err != nil {
c.JSON(http.StatusBadRequest, gin.H{"error": err.Error()})
return
}
if err := s3.EnsureBucket(bucket); err != nil {
c.JSON(http.StatusInternalServerError, gin.H{"error": "存储不可用: " + err.Error()})
return
}
if err := s3.UploadImage(bucket, key, bytes.NewReader(data), spectrumContentType(ext)); err != nil {
c.JSON(http.StatusInternalServerError, gin.H{"error": "上传失败: " + err.Error()})
return
}
url := s3.Endpoint() + "/" + bucket + "/" + key
extra := map[string]interface{}{}
if len(t.ExtraData) > 0 {
_ = json.Unmarshal(t.ExtraData, &extra)
}
extra["spectrumUrl"] = url
raw, _ := json.Marshal(extra)
db.Model(&model.LampTest{}).Where("id = ?", id).Update("extra_data", raw)
c.JSON(http.StatusOK, gin.H{"url": url})
}
}
// spectrumContentType 光谱文件 Content-Type
func spectrumContentType(ext string) string {
switch ext {
case ".json":
return "application/json"
case ".csv":
return "text/csv"
default:
return "text/plain"
}
}
// ---------- 光谱库 ----------
func listSpectrumEntries(db *gorm.DB) gin.HandlerFunc {
return func(c *gin.Context) {
q := db.Model(&model.SpectrumEntry{})
if disease := c.Query("disease"); disease != "" {
q = q.Where("disease = ?", disease)
}
var list []model.SpectrumEntry
q.Order("created_at DESC").Find(&list)
c.JSON(http.StatusOK, list)
}
}
func createSpectrumEntry(db *gorm.DB) gin.HandlerFunc {
return func(c *gin.Context) {
var e model.SpectrumEntry
if err := c.ShouldBindJSON(&e); err != nil {
c.JSON(http.StatusBadRequest, gin.H{"error": err.Error()})
return
}
e.ID = ""
if e.Disease == "" {
c.JSON(http.StatusBadRequest, gin.H{"error": "病种不能为空"})
return
}
if err := db.Create(&e).Error; err != nil {
c.JSON(http.StatusBadRequest, gin.H{"error": "创建失败"})
return
}
c.JSON(http.StatusCreated, e)
}
}
func uploadSpectrumEntryFile(s3 *service.S3Service, bucket string) gin.HandlerFunc {
return func(c *gin.Context) {
file, header, err := c.Request.FormFile("file")
if err != nil {
c.JSON(http.StatusBadRequest, gin.H{"error": "请选择光谱文件(字段名 file"})
return
}
defer file.Close()
if err := model.ValidateSpectrumFile(header.Filename, header.Size); err != nil {
c.JSON(http.StatusBadRequest, gin.H{"error": err.Error()})
return
}
data, err := io.ReadAll(file)
if err != nil {
c.JSON(http.StatusInternalServerError, gin.H{"error": "读取文件失败"})
return
}
key, ext, err := buildDataKey("spectrum", header.Filename)
if err != nil {
c.JSON(http.StatusBadRequest, gin.H{"error": err.Error()})
return
}
if err := s3.EnsureBucket(bucket); err != nil {
c.JSON(http.StatusInternalServerError, gin.H{"error": "存储不可用: " + err.Error()})
return
}
if err := s3.UploadImage(bucket, key, bytes.NewReader(data), spectrumContentType(ext)); err != nil {
c.JSON(http.StatusInternalServerError, gin.H{"error": "上传失败: " + err.Error()})
return
}
c.JSON(http.StatusOK, gin.H{"url": s3.Endpoint() + "/" + bucket + "/" + key})
}
}
func deleteSpectrumEntry(db *gorm.DB) gin.HandlerFunc {
return func(c *gin.Context) {
id := c.Param("id")
var e model.SpectrumEntry
if db.Where("id = ?", id).First(&e).Error != nil {
c.JSON(http.StatusNotFound, gin.H{"error": "spectrum entry not found"})
return
}
db.Where("id = ?", id).Delete(&model.SpectrumEntry{})
c.JSON(http.StatusOK, gin.H{"id": id})
}
}
// updateLampTest 更新任务单;result 合法时自动置状态 resulted
func updateLampTest(db *gorm.DB) gin.HandlerFunc {
return func(c *gin.Context) {
+14
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@@ -8,6 +8,7 @@ import (
// LampTest LAMP 检测任务单
type LampTest struct {
ID string `gorm:"type:uuid;primaryKey;default:gen_random_uuid()" json:"id"`
Method string `gorm:"size:32;default:lamp" json:"method"` // lamp/qpcr/sers/hyperspectral
RoomID *string `gorm:"column:room_id;type:uuid;index" json:"roomId,omitempty"`
BatchID *string `gorm:"column:batch_id;type:uuid;index" json:"batchId,omitempty"`
Diseases json.RawMessage `gorm:"type:jsonb" json:"diseases,omitempty"`
@@ -19,6 +20,7 @@ type LampTest struct {
ResultedAt *time.Time `gorm:"column:resulted_at;type:timestamptz" json:"resultedAt,omitempty"`
CrossStatus string `gorm:"column:cross_status;size:16;default:pending" json:"crossStatus"` // pending/consistent/inconsistent
CrossReason *string `gorm:"column:cross_reason;type:text" json:"crossReason,omitempty"`
ExtraData json.RawMessage `gorm:"column:extra_data;type:jsonb" json:"extraData,omitempty"`
Note *string `gorm:"type:text" json:"note,omitempty"`
CreatedAt time.Time `gorm:"type:timestamptz" json:"createdAt"`
UpdatedAt time.Time `gorm:"type:timestamptz" json:"updatedAt"`
@@ -41,6 +43,18 @@ type LampTestStep struct {
func (LampTestStep) TableName() string { return "lamp_test_steps" }
// SpectrumEntry 光谱库条目
type SpectrumEntry struct {
ID string `gorm:"type:uuid;primaryKey;default:gen_random_uuid()" json:"id"`
Disease string `gorm:"size:64" json:"disease"`
Source *string `gorm:"size:128" json:"source,omitempty"`
DataURL *string `gorm:"column:data_url;size:512" json:"dataUrl,omitempty"`
Note *string `gorm:"type:text" json:"note,omitempty"`
CreatedAt time.Time `gorm:"type:timestamptz" json:"createdAt"`
}
func (SpectrumEntry) TableName() string { return "spectrum_entries" }
// DefaultLampSteps LAMP 标准 5 步流程(规格书 3.3.2.1)
func DefaultLampSteps() []string {
return []string{"采样", "DNA提取", "反应体系配制", "恒温反应", "结果判读"}
+49
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@@ -0,0 +1,49 @@
package model
import (
"errors"
"path/filepath"
"strings"
)
const maxSpectrumSize = 5 << 20 // 5MB
// ValidDetectionMethod 检测方式枚举
func ValidDetectionMethod(method string) bool {
switch method {
case "lamp", "qpcr", "sers", "hyperspectral":
return true
default:
return false
}
}
// JudgeQPCR qPCR Ct 值自动判读:任一 Ct < threshold 判阳性,无 Ct 判阴性
func JudgeQPCR(cts []float64, threshold float64) (string, string) {
if threshold <= 0 {
threshold = 35
}
if len(cts) == 0 {
return "negative", "未检出 Ct 值,判为阴性"
}
for _, ct := range cts {
if ct < threshold {
return "positive", "存在 Ct 值低于阈值,判为阳性"
}
}
return "negative", "全部 Ct 值不低于阈值,判为阴性"
}
// ValidateSpectrumFile 光谱数据文件校验(csv/txt/json,≤5MB
func ValidateSpectrumFile(filename string, size int64) error {
if size <= 0 || size > maxSpectrumSize {
return errors.New("光谱文件大小需在 1B~5MB 之间")
}
ext := strings.ToLower(filepath.Ext(filename))
switch ext {
case ".csv", ".txt", ".json":
return nil
default:
return errors.New("仅支持 csv/txt/json 光谱数据文件")
}
}
@@ -0,0 +1,45 @@
package model
import "testing"
func TestJudgeQPCR(t *testing.T) {
cases := []struct {
name string
cts []float64
threshold float64
want string
}{
{"Ct32 阳性", []float64{32}, 35, "positive"},
{"Ct38 阴性", []float64{38}, 35, "negative"},
{"无Ct 阴性", nil, 35, "negative"},
{"多个Ct含阳性", []float64{33, 37}, 35, "positive"},
{"自定义阈值40", []float64{38}, 40, "positive"},
{"阈值为0用默认35", []float64{38}, 0, "negative"},
}
for _, c := range cases {
got, reason := JudgeQPCR(c.cts, c.threshold)
if got != c.want {
t.Errorf("%s: result=%s, want %s(原因 %s", c.name, got, c.want, reason)
}
if reason == "" {
t.Errorf("%s: 缺少判读说明", c.name)
}
}
}
func TestValidateSpectrumFile(t *testing.T) {
for _, name := range []string{"a.csv", "b.txt", "c.json"} {
if err := ValidateSpectrumFile(name, 1024); err != nil {
t.Errorf("%s 应被允许: %v", name, err)
}
}
if err := ValidateSpectrumFile("a.jpg", 1024); err == nil {
t.Error("图片扩展名不应被允许")
}
if err := ValidateSpectrumFile("a.csv", 0); err == nil {
t.Error("空文件应被拒绝")
}
if err := ValidateSpectrumFile("a.csv", maxSpectrumSize+1); err == nil {
t.Error("超 5MB 应被拒绝")
}
}