diff --git a/api/api_contact_sheet.go b/api/api_contact_sheet.go index 358a845..ebaa28e 100644 --- a/api/api_contact_sheet.go +++ b/api/api_contact_sheet.go @@ -1,63 +1,13 @@ package main import ( - "bytes" - _ "embed" - "encoding/json" - "image" - "image/color" - "image/draw" - "image/png" - "log" - "math" "net/http" "strconv" "strings" - "github.com/chai2010/webp" - "golang.org/x/image/font" - "golang.org/x/image/font/opentype" - "golang.org/x/image/math/fixed" "inou/lib" - - xdraw "golang.org/x/image/draw" ) -//go:embed Sora-Regular.ttf -var soraRegularData []byte - -//go:embed Sora-SemiBold.ttf -var soraSemiBoldData []byte - -var ( - soraFace14 font.Face - soraFace12 font.Face - soraBoldFace14 font.Face - soraBoldFace20 font.Face -) - -func init() { - regular, err := opentype.Parse(soraRegularData) - if err != nil { - log.Printf("Failed to parse Sora Regular: %v", err) - return - } - semibold, err := opentype.Parse(soraSemiBoldData) - if err != nil { - log.Printf("Failed to parse Sora SemiBold: %v", err) - return - } - soraFace14, _ = opentype.NewFace(regular, &opentype.FaceOptions{Size: 14, DPI: 72}) - soraFace12, _ = opentype.NewFace(regular, &opentype.FaceOptions{Size: 12, DPI: 72}) - soraBoldFace14, _ = opentype.NewFace(semibold, &opentype.FaceOptions{Size: 14, DPI: 72}) - soraBoldFace20, _ = opentype.NewFace(semibold, &opentype.FaceOptions{Size: 20, DPI: 72}) -} - -const thumbSize = 128 -const headerHeight = 58 -const cols = 12 -const padding = 2 // separation between contacts - func handleContactSheet(w http.ResponseWriter, r *http.Request) { seriesHex := strings.TrimPrefix(r.URL.Path, "/contact-sheet.webp/") if seriesHex == "" || len(seriesHex) != 16 { @@ -65,359 +15,27 @@ func handleContactSheet(w http.ResponseWriter, r *http.Request) { return } - // Get access context ctx := getAccessContextOrFail(w, r) if ctx == nil { return } - // Parse optional window/level overrides q := r.URL.Query() - var wcOverride, wwOverride float64 - var hasWLOverride bool - if wc := q.Get("wc"); wc != "" { - wcOverride, _ = strconv.ParseFloat(wc, 64) - hasWLOverride = true + var wc, ww float64 + if v := q.Get("wc"); v != "" { + wc, _ = strconv.ParseFloat(v, 64) } - if ww := q.Get("ww"); ww != "" { - wwOverride, _ = strconv.ParseFloat(ww, 64) - hasWLOverride = true + if v := q.Get("ww"); v != "" { + ww, _ = strconv.ParseFloat(v, 64) } - seriesID := seriesHex - - // Look up series entry (RBAC already checked by portal) - series, err := lib.EntryGet(ctx, seriesID) - if err != nil { - http.Error(w, "Series not found", http.StatusNotFound) - return - } - dossierID := series.DossierID - seriesDesc := series.Tags - - // Look up study entry (parent of series) - study, err := lib.EntryGet(nil, series.ParentID) - if err != nil { - http.Error(w, "Study not found", http.StatusNotFound) - return - } - var studyData struct { - StudyDate string `json:"study_date"` - StudyDesc string `json:"study_description"` - } - json.Unmarshal([]byte(study.Data), &studyData) - - // Look up dossier for patient name - dossier, _ := lib.DossierGet("", dossierID) - patientName := "" - if dossier != nil { - patientName = dossier.Name - } - - // Get all slices for this series - entries, err := lib.EntryChildrenByType(dossierID, seriesID, "slice") + body, err := lib.RenderContactSheet(ctx.AccessorID, seriesHex, wc, ww) if err != nil { http.Error(w, err.Error(), http.StatusInternalServerError) return } - if len(entries) == 0 { - http.Error(w, "No slices found", http.StatusNotFound) - return - } - - // Get slice thickness for step calculation - var firstSliceData struct { - SliceThickness float64 `json:"slice_thickness"` - } - json.Unmarshal([]byte(entries[0].Data), &firstSliceData) - step := calculateStepSize(5.0, firstSliceData.SliceThickness) - - // Load and resize selected slices (skip based on 5mm spacing) - type thumbInfo struct { - img image.Image - sliceNum int - pos float64 - } - var thumbs []thumbInfo - var usedWC, usedWW float64 // track what window settings were actually used - for i, e := range entries { - // Same logic as dicom-import: every Nth slice starting at 1 - if (i+1)%step != 1 && step != 1 { - continue - } - thumb, pos, wc, ww := loadSliceThumbWithPos(ctx, e, wcOverride, wwOverride, hasWLOverride) - if thumb != nil { - thumbs = append(thumbs, thumbInfo{img: thumb, sliceNum: i + 1, pos: pos}) - if usedWC == 0 && usedWW == 0 { - usedWC, usedWW = wc, ww // capture from first slice - } - } - } - - if len(thumbs) == 0 { - http.Error(w, "Could not load any images", http.StatusInternalServerError) - return - } - - // Calculate grid - gridCols := cols - if len(thumbs) < gridCols { - gridCols = len(thumbs) - } - gridRows := (len(thumbs) + gridCols - 1) / gridCols - - outWidth := cols*thumbSize + (cols-1)*padding - outHeight := headerHeight + gridRows*thumbSize + (gridRows-1)*padding - - out := image.NewRGBA(image.Rect(0, 0, outWidth, outHeight)) - // Fill with dark grey for grid lines (contrast between contacts) - draw.Draw(out, out.Bounds(), &image.Uniform{color.RGBA{80, 80, 80, 255}}, image.Point{}, draw.Src) - - // Draw header - drawHeader(out, patientName, studyData.StudyDesc, seriesDesc, studyData.StudyDate, len(entries), firstSliceData.SliceThickness, step, usedWC, usedWW) - - // Draw thumbnails - for i, t := range thumbs { - col := i % cols - row := i / cols - x := col * (thumbSize + padding) - y := headerHeight + row*(thumbSize+padding) - - draw.Draw(out, image.Rect(x, y, x+thumbSize, y+thumbSize), t.img, image.Point{}, draw.Src) - drawNumber(out, x+2, y+2, t.sliceNum) - drawPosition(out, x+thumbSize-2, y+2, t.pos) - } - - // Fill unused grid cells with black - for i := len(thumbs); i < gridRows*cols; i++ { - col := i % cols - row := i / cols - x := col * (thumbSize + padding) - y := headerHeight + row*(thumbSize+padding) - draw.Draw(out, image.Rect(x, y, x+thumbSize, y+thumbSize), &image.Uniform{color.Black}, image.Point{}, draw.Src) - } - w.Header().Set("Content-Type", "image/webp") w.Header().Set("Cache-Control", "public, max-age=3600") - webp.Encode(w, out, &webp.Options{Quality: 10}) -} - -func calculateStepSize(requestedSpacingMM, sliceThicknessMM float64) int { - if sliceThicknessMM <= 0 { - return 1 - } - step := int(math.Round(requestedSpacingMM / sliceThicknessMM)) - if step < 1 { - step = 1 - } - return step -} - -func drawHeader(img *image.RGBA, patient, study, series, date string, totalSlices int, sliceThickness float64, step int, wc, ww float64) { - // Format date if in YYYYMMDD format - if len(date) == 8 { - date = date[0:4] + "-" + date[4:6] + "-" + date[6:8] - } - - // Draw header background - draw.Draw(img, image.Rect(0, 0, img.Bounds().Dx(), headerHeight), - &image.Uniform{color.RGBA{32, 32, 32, 255}}, image.Point{}, draw.Src) - - // Line 1: Big red warning - warning := "!! NAVIGATION ONLY - USE fetch_image FOR DIAGNOSIS !!" - drawStringBold20(img, 10, 22, warning, color.RGBA{255, 50, 50, 255}) - - // Line 2: Patient (white) | Series | Date | Slices | ST | WC/WW - stInfo := strconv.FormatFloat(sliceThickness, 'f', 1, 64) + "mm" - if step > 1 { - stInfo += " (every " + strconv.Itoa(step) + ")" - } - wlInfo := "WC:" + strconv.FormatFloat(wc, 'f', 0, 64) + " WW:" + strconv.FormatFloat(ww, 'f', 0, 64) - - // Line 2: Patient (white) | Series | Date | Slices | ST | WC/WW - drawStringBold(img, 10, 38, patient, color.RGBA{255, 255, 255, 255}) - patientWidth := measureStringBold(patient) - rest := " | " + series + " | " + date + " | " + strconv.Itoa(totalSlices) + " slices | ST " + stInfo + " | " + wlInfo - drawString(img, 10+patientWidth, 38, rest, color.RGBA{200, 200, 200, 255}) - - // Line 3: Instructions and legend - instructions := "MCP: fetch_image(slice_id) | API: GET /image/{slice_id} | Top-left: slice# Top-right: position(mm)" - drawString(img, 10, 54, instructions, color.RGBA{255, 255, 255, 255}) -} - -func drawPosition(img *image.RGBA, x, y int, pos float64) { - s := strconv.FormatFloat(pos, 'f', 1, 64) + "mm" - textWidth := measureString(s, 12) + 6 - - // Draw background (right-aligned) - for dy := 0; dy < 16; dy++ { - for dx := 0; dx < textWidth; dx++ { - img.SetRGBA(x-textWidth+dx, y+dy, color.RGBA{0, 0, 0, 200}) - } - } - - drawStringSize(img, x-textWidth+3, y+12, s, color.RGBA{255, 255, 0, 255}, 12) -} - -func drawString(img *image.RGBA, x, y int, s string, col color.RGBA) { - drawStringSize(img, x, y, s, col, 14) -} - -func drawStringSize(img *image.RGBA, x, y int, s string, col color.RGBA, size int) { - face := soraFace14 - if size <= 12 { - face = soraFace12 - } - if face == nil { - return // font not loaded - } - d := &font.Drawer{ - Dst: img, - Src: &image.Uniform{col}, - Face: face, - Dot: fixed.Point26_6{X: fixed.I(x), Y: fixed.I(y)}, - } - d.DrawString(s) -} - -func measureString(s string, size int) int { - face := soraFace14 - if size <= 12 { - face = soraFace12 - } - if face == nil { - return len(s) * 8 // fallback - } - d := &font.Drawer{Face: face} - return d.MeasureString(s).Ceil() -} - -func drawStringBold(img *image.RGBA, x, y int, s string, col color.RGBA) { - if soraBoldFace14 == nil { - return - } - d := &font.Drawer{ - Dst: img, - Src: &image.Uniform{col}, - Face: soraBoldFace14, - Dot: fixed.Point26_6{X: fixed.I(x), Y: fixed.I(y)}, - } - d.DrawString(s) -} - -func drawStringBold20(img *image.RGBA, x, y int, s string, col color.RGBA) { - if soraBoldFace20 == nil { - return - } - d := &font.Drawer{ - Dst: img, - Src: &image.Uniform{col}, - Face: soraBoldFace20, - Dot: fixed.Point26_6{X: fixed.I(x), Y: fixed.I(y)}, - } - d.DrawString(s) -} - -func measureStringBold(s string) int { - if soraBoldFace14 == nil { - return len(s) * 8 - } - d := &font.Drawer{Face: soraBoldFace14} - return d.MeasureString(s).Ceil() -} - -func loadSliceThumbWithPos(ctx *lib.AccessContext, e *lib.Entry, wcOverride, wwOverride float64, hasOverride bool) (image.Image, float64, float64, float64) { - // Parse window/level and position from entry data - var data struct { - WindowCenter float64 `json:"window_center"` - WindowWidth float64 `json:"window_width"` - PixelMin int `json:"pixel_min"` - PixelMax int `json:"pixel_max"` - SliceLocation float64 `json:"slice_location"` - } - json.Unmarshal([]byte(e.Data), &data) - - var center, width float64 - if hasOverride { - center = wcOverride - width = wwOverride - if width == 0 { - width = 1 - } - } else { - center = data.WindowCenter - width = data.WindowWidth - if center == 0 && width == 0 { - center = float64(data.PixelMin+data.PixelMax) / 2 - width = float64(data.PixelMax - data.PixelMin) - if width == 0 { - width = 1 - } - } - } - - // Load and decompress 16-bit PNG using RBAC-enforced object access - decData, err := lib.ObjectRead(ctx, e.DossierID, e.EntryID) - if err != nil { - return nil, 0, 0, 0 - } - - img, err := png.Decode(bytes.NewReader(decData)) - if err != nil { - return nil, 0, 0, 0 - } - - bounds := img.Bounds() - var processed image.Image - - switch src := img.(type) { - case *image.Gray16: - // Apply window/level to 8-bit - low := center - width/2 - high := center + width/2 - gray := image.NewGray(bounds) - for y := bounds.Min.Y; y < bounds.Max.Y; y++ { - for x := bounds.Min.X; x < bounds.Max.X; x++ { - v := float64(src.Gray16At(x, y).Y) - var out uint8 - if v <= low { - out = 0 - } else if v >= high { - out = 255 - } else { - out = uint8((v - low) * 255 / width) - } - gray.SetGray(x, y, color.Gray{Y: out}) - } - } - processed = gray - - case *image.RGBA, *image.NRGBA: - // RGB images: pass through (already rendered) - processed = src - - default: - return nil, 0, 0, 0 - } - - // Resize to thumbnail - thumb := image.NewRGBA(image.Rect(0, 0, thumbSize, thumbSize)) - xdraw.BiLinear.Scale(thumb, thumb.Bounds(), processed, processed.Bounds(), xdraw.Over, nil) - - return thumb, data.SliceLocation, center, width -} - -func drawNumber(img *image.RGBA, x, y, num int) { - s := strconv.Itoa(num) - textWidth := measureString(s, 14) + 6 - - // Draw background - for dy := 0; dy < 18; dy++ { - for dx := 0; dx < textWidth; dx++ { - img.SetRGBA(x+dx, y+dy, color.RGBA{0, 0, 0, 200}) - } - } - - drawStringSize(img, x+3, y+14, s, color.RGBA{255, 255, 0, 255}, 14) + w.Write(body) } diff --git a/api/api_image.go b/api/api_image.go index 65ab9dc..299f661 100644 --- a/api/api_image.go +++ b/api/api_image.go @@ -1,13 +1,10 @@ package main import ( - "image" "net/http" "strconv" "strings" - "github.com/chai2010/webp" - xdraw "golang.org/x/image/draw" "inou/lib" ) @@ -31,31 +28,20 @@ func handleImage(w http.ResponseWriter, r *http.Request) { opts.WW, _ = strconv.ParseFloat(ww, 64) } - img, err := lib.ImageGet(ctx.AccessorID, hexID, opts) - if err != nil { - http.Error(w, "Image not found", http.StatusNotFound) - return - } - - // Resize if either dimension exceeds maxDim (default 2000 for Claude API) maxDim := 2000 if md := r.URL.Query().Get("maxdim"); md != "" { if v, err := strconv.Atoi(md); err == nil && v > 0 { maxDim = v } } - bounds := img.Bounds() - w0, h0 := bounds.Dx(), bounds.Dy() - if w0 > maxDim || h0 > maxDim { - scale := float64(maxDim) / float64(max(w0, h0)) - newW := int(float64(w0) * scale) - newH := int(float64(h0) * scale) - resized := image.NewRGBA(image.Rect(0, 0, newW, newH)) - xdraw.BiLinear.Scale(resized, resized.Bounds(), img, bounds, xdraw.Over, nil) - img = resized + + body, err := lib.RenderImage(ctx.AccessorID, hexID, opts, maxDim) + if err != nil { + http.Error(w, "Image not found", http.StatusNotFound) + return } w.Header().Set("Content-Type", "image/webp") w.Header().Set("Cache-Control", "public, max-age=86400") - webp.Encode(w, img, &webp.Options{Lossless: true}) + w.Write(body) } diff --git a/cmd/import-lab/main.go b/cmd/import-lab/main.go index c7d47ae..83baf6f 100644 --- a/cmd/import-lab/main.go +++ b/cmd/import-lab/main.go @@ -122,6 +122,7 @@ func main() { os.Exit(1) } lib.ConfigInit() + lib.RefDBInit("/tank/inou/data/reference.db") fmt.Println("Normalizing test names...") if err := lib.Normalize(dossierID, lib.CategoryLab); err != nil { fmt.Printf("Normalization failed: %v\n", err) @@ -147,6 +148,7 @@ func main() { os.Exit(1) } lib.ConfigInit() + lib.RefDBInit("/tank/inou/data/reference.db") // Load existing lab entries for dedup existing, err := lib.EntryQuery(nil, dossierID, lib.CategoryLab, "", "*") diff --git a/docs/chatgpt-actions-setup.md b/docs/chatgpt-actions-setup.md new file mode 100644 index 0000000..61af379 --- /dev/null +++ b/docs/chatgpt-actions-setup.md @@ -0,0 +1,69 @@ +# ChatGPT Actions Setup + +Connect a ChatGPT Custom GPT to inou via OAuth 2.0 Actions. + +## 1. Create the OAuth Client + +SSH into staging or production and run: + +```bash +# One-time setup — creates the "chatgpt" OAuth client +ssh johan@192.168.1.253 '/tank/inou/bin/oauth-setup-chatgpt' +``` + +This prints the Client ID and Client Secret. **Save the secret** — it cannot be retrieved later. + +> The binary doesn't exist yet. Either: +> - Add a `cmd/oauth-setup-chatgpt/main.go` (same pattern as `cmd/oauth-setup/main.go`), or +> - Call `CreateChatGPTClient()` from portal startup (like `EnsureBridgeClient()`). + +## 2. Create the Custom GPT + +In ChatGPT → Explore GPTs → Create: + +1. **Name:** inou Health +2. **Instructions:** (your system prompt for health data analysis) +3. Click **Create new action** + +## 3. Configure the Action + +### Import Schema + +Point to the hosted OpenAPI schema: + +``` +https://inou.com/api/docs/openapi.yaml +``` + +Or paste the contents of `docs/openapi.yaml` directly. + +### Authentication + +| Field | Value | +|-------|-------| +| **Authentication Type** | OAuth | +| **Client ID** | _(from step 1)_ | +| **Client Secret** | _(from step 1)_ | +| **Authorization URL** | `https://inou.com/oauth/authorize` | +| **Token URL** | `https://inou.com/oauth/token` | +| **Scope** | _(leave blank)_ | +| **Token Exchange Method** | Default (POST) | + +### Privacy Policy URL + +``` +https://inou.com/privacy +``` + +## 4. Test + +1. Save the GPT +2. Start a conversation: "List my dossiers" +3. ChatGPT will redirect to inou's OAuth login +4. After authorizing, the GPT can call the API + +## Notes + +- OAuth tokens are valid for 1 hour, with refresh token support +- All access is RBAC-enforced — the GPT can only see data the logged-in user has permission to view +- The OpenAPI schema excludes imaging endpoints (not useful for text-based ChatGPT interactions) diff --git a/docs/openapi.yaml b/docs/openapi.yaml new file mode 100644 index 0000000..f659bc8 --- /dev/null +++ b/docs/openapi.yaml @@ -0,0 +1,429 @@ +openapi: 3.1.0 +info: + title: inou Health API + version: 1.0.0 + description: Access health data — dossiers, entries, labs, journals, trackers, and categories. + +servers: + - url: https://inou.com + +security: + - oauth2: [] + +components: + securitySchemes: + oauth2: + type: oauth2 + flows: + authorizationCode: + authorizationUrl: https://inou.com/oauth/authorize + tokenUrl: https://inou.com/oauth/token + scopes: {} + + schemas: + Error: + type: object + properties: + error: + type: string + + Dossier: + type: object + properties: + id: + type: string + name: + type: string + date_of_birth: + type: string + sex: + type: string + enum: [male, female, other] + categories: + type: array + items: + type: string + self: + type: boolean + description: True if this dossier belongs to the authenticated user. + + DossierDetail: + type: object + properties: + id: + type: string + name: + type: string + + Entry: + type: object + properties: + id: + type: string + parent_id: + type: string + category: + type: string + type: + type: string + summary: + type: string + ordinal: + type: integer + timestamp: + type: integer + description: Unix timestamp (seconds). + + EntryDetail: + type: object + properties: + id: + type: string + parent_id: + type: string + category: + type: string + type: + type: string + summary: + type: string + ordinal: + type: integer + timestamp: + type: integer + tags: + type: string + data: + type: object + description: Parsed JSON data (only when detail=full). + children: + type: array + items: + type: object + properties: + id: + type: string + type: + type: string + summary: + type: string + ordinal: + type: integer + + Journal: + type: object + properties: + id: + type: string + type: + type: string + summary: + type: string + timestamp: + type: integer + + Tracker: + type: object + properties: + id: + type: string + category: + type: string + type: + type: string + question: + type: string + active: + type: boolean + dismissed: + type: boolean + time_of_day: + type: string + + Category: + type: object + properties: + id: + type: integer + key: + type: string + description: Machine-readable category name. + name: + type: string + description: Translated display name. + types: + type: array + items: + type: string + +paths: + /api/v1/dossiers: + get: + operationId: listDossiers + summary: List accessible dossiers + description: Returns all dossiers the authenticated user has access to, including their own. + responses: + "200": + description: Array of dossiers. + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/Dossier" + "401": + description: Unauthorized. + content: + application/json: + schema: + $ref: "#/components/schemas/Error" + + /api/v1/dossiers/{dossier_id}: + get: + operationId: getDossier + summary: Get a single dossier + parameters: + - name: dossier_id + in: path + required: true + schema: + type: string + responses: + "200": + description: Dossier detail. + content: + application/json: + schema: + $ref: "#/components/schemas/DossierDetail" + "403": + description: Access denied. + content: + application/json: + schema: + $ref: "#/components/schemas/Error" + "404": + description: Not found. + content: + application/json: + schema: + $ref: "#/components/schemas/Error" + + /api/v1/dossiers/{dossier_id}/entries: + get: + operationId: listEntries + summary: List entries for a dossier + description: Query entries by category, type, date range, or parent. Returns summaries — use the single-entry endpoint with detail=full for complete data. + parameters: + - name: dossier_id + in: path + required: true + schema: + type: string + - name: category + in: query + description: Filter by category name (e.g. "labs", "imaging", "medication"). + schema: + type: string + - name: type + in: query + description: Filter by entry type within the category. + schema: + type: string + - name: parent + in: query + description: Filter by parent entry ID (for navigating hierarchies). + schema: + type: string + - name: search_key + in: query + description: Filter by search key (e.g. LOINC code for labs). + schema: + type: string + - name: from + in: query + description: Start timestamp (Unix seconds). + schema: + type: integer + - name: to + in: query + description: End timestamp (Unix seconds). + schema: + type: integer + - name: limit + in: query + description: Maximum number of results. + schema: + type: integer + responses: + "200": + description: Array of entries. + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/Entry" + "403": + description: Access denied. + content: + application/json: + schema: + $ref: "#/components/schemas/Error" + + /api/v1/dossiers/{dossier_id}/entries/{entry_id}: + get: + operationId: getEntry + summary: Get a single entry with optional full detail + parameters: + - name: dossier_id + in: path + required: true + schema: + type: string + - name: entry_id + in: path + required: true + schema: + type: string + - name: detail + in: query + description: Set to "full" to include the data field and children. + schema: + type: string + enum: [full] + responses: + "200": + description: Entry with optional data and children. + content: + application/json: + schema: + $ref: "#/components/schemas/EntryDetail" + "404": + description: Not found. + content: + application/json: + schema: + $ref: "#/components/schemas/Error" + + /api/v1/dossiers/{dossier_id}/journal: + get: + operationId: listJournals + summary: List journal entries + parameters: + - name: dossier_id + in: path + required: true + schema: + type: string + - name: days + in: query + description: Look-back period in days (default 30). + schema: + type: integer + - name: type + in: query + description: Filter by journal type. + schema: + type: string + responses: + "200": + description: Journal entries. + content: + application/json: + schema: + type: object + properties: + journals: + type: array + items: + $ref: "#/components/schemas/Journal" + "403": + description: Access denied. + content: + application/json: + schema: + $ref: "#/components/schemas/Error" + + /api/v1/dossiers/{dossier_id}/trackers: + get: + operationId: listTrackers + summary: List tracker prompts + parameters: + - name: dossier_id + in: path + required: true + schema: + type: string + - name: active + in: query + description: Set to "true" to return only active trackers. + schema: + type: string + enum: ["true"] + - name: category + in: query + description: Filter by category name. + schema: + type: string + - name: type + in: query + description: Filter by tracker type. + schema: + type: string + responses: + "200": + description: Array of trackers. + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/Tracker" + "403": + description: Access denied. + content: + application/json: + schema: + $ref: "#/components/schemas/Error" + + /api/v1/categories: + get: + operationId: listCategories + summary: List all data categories + description: Returns all 28 categories with translated names and available types. + responses: + "200": + description: Array of categories. + content: + application/json: + schema: + type: array + items: + $ref: "#/components/schemas/Category" + + /api/v1/categories/{name}/types: + get: + operationId: listCategoryTypes + summary: List types for a category + parameters: + - name: name + in: path + required: true + description: Category name (e.g. "labs", "imaging"). + schema: + type: string + responses: + "200": + description: Array of type strings. + content: + application/json: + schema: + type: array + items: + type: string + "404": + description: Category not found. + content: + application/json: + schema: + $ref: "#/components/schemas/Error" diff --git a/docs/schema-auth.sql b/docs/schema-auth.sql index d573e30..e8151bd 100644 --- a/docs/schema-auth.sql +++ b/docs/schema-auth.sql @@ -1,20 +1,23 @@ -- ============================================================================ -- Auth Database Schema (auth.db) -- ============================================================================ --- Separate from medical data. Contains volatile OAuth/session data. --- Tables are NOT auto-created. Use this file manually if needed. +-- Separate from medical data (inou.db). Volatile/ephemeral data. -- ============================================================================ --- OAuth Clients (Claude, Flutter app, etc.) -CREATE TABLE IF NOT EXISTS oauth_clients ( - client_id TEXT PRIMARY KEY, - client_secret TEXT NOT NULL, - name TEXT NOT NULL, - redirect_uris TEXT NOT NULL, -- JSON array - created_at INTEGER NOT NULL +-- Sessions table for secure session management +-- Tokens are random 32-byte base64url-encoded strings +CREATE TABLE IF NOT EXISTS sessions ( + token TEXT PRIMARY KEY, + dossier_id TEXT NOT NULL, + created_at INTEGER NOT NULL, + expires_at INTEGER NOT NULL ); --- OAuth Authorization Codes (short-lived, single-use) +-- Index for fast session lookup and cleanup +CREATE INDEX IF NOT EXISTS idx_sessions_dossier ON sessions(dossier_id); +CREATE INDEX IF NOT EXISTS idx_sessions_expires ON sessions(expires_at); + +-- OAuth authorization codes (PKCE, 10 min expiry) CREATE TABLE IF NOT EXISTS oauth_codes ( code TEXT PRIMARY KEY, client_id TEXT NOT NULL, @@ -26,17 +29,27 @@ CREATE TABLE IF NOT EXISTS oauth_codes ( used INTEGER DEFAULT 0 ); -CREATE INDEX IF NOT EXISTS idx_oauth_codes_client ON oauth_codes(client_id); - --- OAuth Refresh Tokens (long-lived, rotatable) +-- OAuth refresh tokens (30 day expiry) CREATE TABLE IF NOT EXISTS oauth_refresh_tokens ( token_id TEXT PRIMARY KEY, client_id TEXT NOT NULL, dossier_id TEXT NOT NULL, + created_at INTEGER NOT NULL, expires_at INTEGER NOT NULL, - revoked INTEGER DEFAULT 0, + revoked INTEGER DEFAULT 0 +); + +-- OAuth clients (registered applications) +CREATE TABLE IF NOT EXISTS oauth_clients ( + client_id TEXT PRIMARY KEY, + client_secret TEXT, + name TEXT NOT NULL, + redirect_uris TEXT NOT NULL, -- JSON array + allowed_scopes TEXT, -- JSON array created_at INTEGER NOT NULL ); -CREATE INDEX IF NOT EXISTS idx_oauth_refresh_dossier ON oauth_refresh_tokens(dossier_id); -CREATE INDEX IF NOT EXISTS idx_oauth_refresh_client ON oauth_refresh_tokens(client_id); +-- Cleanup old sessions periodically +DELETE FROM sessions WHERE expires_at < strftime('%s', 'now'); +DELETE FROM oauth_codes WHERE expires_at < strftime('%s', 'now'); +DELETE FROM oauth_refresh_tokens WHERE expires_at < strftime('%s', 'now'); diff --git a/import-renpho/import-renpho b/import-renpho/import-renpho new file mode 100755 index 0000000..acd289c Binary files /dev/null and b/import-renpho/import-renpho differ diff --git a/lib/Sora-Regular.ttf b/lib/Sora-Regular.ttf new file mode 100644 index 0000000..d21b843 Binary files /dev/null and b/lib/Sora-Regular.ttf differ diff --git a/lib/Sora-SemiBold.ttf b/lib/Sora-SemiBold.ttf new file mode 100644 index 0000000..50314f7 Binary files /dev/null and b/lib/Sora-SemiBold.ttf differ diff --git a/lib/loinc.go b/lib/loinc.go new file mode 100644 index 0000000..87c6787 --- /dev/null +++ b/lib/loinc.go @@ -0,0 +1,314 @@ +package lib + +import ( + "encoding/json" + "fmt" + "log" + "strings" +) + +// LoincInfo holds official LOINC data from loinc_lab. +type LoincInfo struct { + Code string `db:"loinc_num"` + LongName string `db:"long_name"` + ShortName string `db:"short_name"` + Component string `db:"component"` + System string `db:"system"` + Property string `db:"property"` +} + +// LoincGet returns official LOINC info from loinc_lab. +func LoincGet(code string) *LoincInfo { + var results []LoincInfo + RefQuery("SELECT loinc_num, long_name, short_name, component, system, property FROM loinc_lab WHERE loinc_num = ?", []any{code}, &results) + if len(results) > 0 { + return &results[0] + } + return nil +} + +// LoincAbbr derives a short abbreviation from loinc_lab.short_name. +// Examples: "Hgb Bld-mCnc" → "Hgb", "Neutrophils/leuk NFr Bld" → "Neut" +func LoincAbbr(info *LoincInfo) string { + if info == nil { + return "" + } + s := info.ShortName + // Take first token (before space), strip trailing /... for differentials + if i := strings.IndexByte(s, ' '); i > 0 { + s = s[:i] + } + if i := strings.IndexByte(s, '/'); i > 0 { + s = s[:i] + } + // Common abbreviation overrides + overrides := map[string]string{ + "Neutrophils": "Neut", "Lymphocytes": "Lymph", "Monocytes": "Mono", + "Eosinophils": "Eos", "Basophils": "Baso", "Platelets": "PLT", + "Leukocytes": "WBC", "Erythrocytes": "RBC", "Hemoglobin": "Hgb", + "Hematocrit": "Hct", "Glucose": "Glu", "Creatinine": "Cr", + "Sodium": "Na", "Potassium": "K", "Chloride": "Cl", + "Calcium": "Ca", "Albumin": "Alb", "Phosphate": "Phos", + "Magnesium": "Mg", + } + // Match on component first word for overrides + comp := info.Component + if i := strings.IndexAny(comp, "/."); i > 0 { + comp = comp[:i] + } + if abbr, ok := overrides[comp]; ok { + return abbr + } + // Truncate long abbreviations + if len(s) > 8 { + s = s[:8] + } + return s +} + +// LoincLookup resolves a hospital test name to a LOINC code. +// Checks cache first; on miss, uses Gemini expand → search → pick → cache. +// Returns empty string if lookup fails (no candidates, LLM error, etc). +func LoincLookup(name, specimen, unit string) string { + // 1. Check cache + cacheKey := strings.ToLower(name + "|" + specimen + "|" + unit) + var cached []struct { + LoincCode string `db:"loinc_code"` + } + RefQuery("SELECT loinc_code FROM loinc_cache WHERE cache_key = ?", []any{cacheKey}, &cached) + if len(cached) > 0 { + return cached[0].LoincCode + } + + // 2. No Gemini key = can't do LLM lookup + if GeminiKey == "" { + return "" + } + + // 3. Expand + search + pick + lookupUnit := unit + if lookupUnit == "%" { + lookupUnit = "percentage" + } + + tokens := loincTokenize(name + " " + specimen + " " + lookupUnit) + if expanded, err := loincExpand(name, specimen, lookupUnit); err == nil { + tokens = expanded + } + + candidates := loincSearch(tokens) + + // Filter: if unit is %, drop count codes (NCnc) + if unit == "%" { + var filtered []LoincInfo + for _, c := range candidates { + if c.Property != "NCnc" { + filtered = append(filtered, c) + } + } + if len(filtered) > 0 { + candidates = filtered + } + } + + if len(candidates) == 0 { + log.Printf("loinc-lookup: no candidates for %q", name) + return "" + } + + // 4. LLM pick + code, lname, err := loincPick(name, specimen, lookupUnit, candidates) + if err != nil { + log.Printf("loinc-lookup: pick failed for %q: %v", name, err) + return "" + } + + // 5. Cache + RefExec(`INSERT OR REPLACE INTO loinc_cache (cache_key, input_name, input_specimen, input_unit, loinc_code, loinc_name, confidence) + VALUES (?, ?, ?, ?, ?, ?, 'llm')`, cacheKey, name, specimen, unit, code, lname) + + return code +} + +// --- internal helpers --- + +func loincTokenize(s string) []string { + s = strings.ToLower(s) + for _, c := range []string{",", ";", "(", ")", "[", "]", "/", "-", ".", ":"} { + s = strings.ReplaceAll(s, c, " ") + } + var tokens []string + seen := map[string]bool{} + for _, t := range strings.Fields(s) { + if len(t) < 2 || seen[t] { + continue + } + tokens = append(tokens, t) + seen[t] = true + } + return tokens +} + +func loincSearch(tokens []string) []LoincInfo { + if len(tokens) == 0 { + return nil + } + type entry struct { + c LoincInfo + hits int + } + entries := map[string]*entry{} + + for _, t := range tokens { + pattern := "%" + t + "%" + query := "SELECT loinc_num, long_name, short_name, system, component, property FROM loinc_lab WHERE " + + "LOWER(long_name) LIKE ? OR LOWER(short_name) LIKE ? OR LOWER(component) LIKE ?" + var results []LoincInfo + RefQuery(query, []any{pattern, pattern, pattern}, &results) + for _, c := range results { + if e, ok := entries[c.Code]; ok { + e.hits++ + } else { + entries[c.Code] = &entry{c: c, hits: 1} + } + } + } + + minHits := 2 + if len(tokens) <= 1 { + minHits = 1 + } + + type scored struct { + c LoincInfo + score int + } + var scoredResults []scored + for _, e := range entries { + if e.hits < minHits { + continue + } + s := e.hits * 100 + compLen := len(e.c.Component) + if compLen > 0 && compLen < 50 { + s += 50 - compLen + } + if !strings.Contains(e.c.Component, "/") { + s += 20 + } + scoredResults = append(scoredResults, scored{e.c, s}) + } + + for i := range scoredResults { + for j := i + 1; j < len(scoredResults); j++ { + if scoredResults[j].score > scoredResults[i].score { + scoredResults[i], scoredResults[j] = scoredResults[j], scoredResults[i] + } + } + } + + var top []LoincInfo + for i, s := range scoredResults { + if i >= 30 { + break + } + top = append(top, s.c) + } + return top +} + +func loincExpand(name, specimen, unit string) ([]string, error) { + prompt := fmt.Sprintf(`Given a lab test, return search terms to find it in the LOINC database. +LOINC uses formal medical terminology (e.g. "Leukocytes" not "White Blood Cells", "Erythrocytes" not "Red Blood Cells", "Oxygen" not "O2" or "pO2"). + +Lab test: + Name: %s + Specimen: %s + Unit: %s + +Return a JSON object: {"terms": ["term1", "term2", ...]} +Include: the LOINC component name, specimen system code (e.g. Bld, BldA, BldC, BldV, Ser/Plas, Urine), and any synonyms that might appear in LOINC long names. +Keep it to 3-6 terms. JSON only.`, name, specimen, unit) + + resp, err := CallGemini(prompt) + if err != nil { + return nil, err + } + + var result struct { + Terms []string `json:"terms"` + } + if err := json.Unmarshal([]byte(resp), &result); err != nil { + return nil, fmt.Errorf("parse expand response: %w", err) + } + + var terms []string + seen := map[string]bool{} + for _, t := range result.Terms { + t = strings.ToLower(strings.TrimSpace(t)) + if t != "" && !seen[t] { + terms = append(terms, t) + seen[t] = true + } + } + for _, t := range loincTokenize(name + " " + specimen) { + if !seen[t] { + terms = append(terms, t) + seen[t] = true + } + } + return terms, nil +} + +func loincPick(name, specimen, unit string, candidates []LoincInfo) (string, string, error) { + var lines []string + for i, c := range candidates { + display := c.LongName + display = strings.ReplaceAll(display, "/100 ", "percentage of ") + display = strings.ReplaceAll(display, "fraction", "percentage") + lines = append(lines, fmt.Sprintf("%d. %s — %s [System: %s]", i+1, c.Code, display, c.System)) + } + + prompt := fmt.Sprintf(`You are a clinical laboratory informatics system. Given a lab test, pick the BEST matching LOINC code from the candidate list. + +Lab test: + Name: %s + Specimen: %s + Unit: %s + +Candidates: +%s + +Return ONLY a JSON object: {"pick": , "loinc": "", "name": ""} +Pick the candidate that best matches the test name, specimen type, and unit. If none match well, pick the closest. +JSON only, no explanation.`, name, specimen, unit, strings.Join(lines, "\n")) + + resp, err := CallGemini(prompt) + if err != nil { + return "", "", fmt.Errorf("LLM call failed: %w", err) + } + + var result struct { + Pick int `json:"pick"` + Loinc string `json:"loinc"` + Name string `json:"name"` + } + if err := json.Unmarshal([]byte(resp), &result); err != nil { + return "", "", fmt.Errorf("parse LLM response: %w", err) + } + + if result.Loinc == "" && result.Pick > 0 && result.Pick <= len(candidates) { + result.Loinc = candidates[result.Pick-1].Code + result.Name = candidates[result.Pick-1].LongName + } + for _, c := range candidates { + if c.Code == result.Loinc { + return result.Loinc, c.LongName, nil + } + } + if result.Pick > 0 && result.Pick <= len(candidates) { + c := candidates[result.Pick-1] + return c.Code, c.LongName, nil + } + return "", "", fmt.Errorf("LLM returned %q (pick %d) — not in %d candidates", result.Loinc, result.Pick, len(candidates)) +} diff --git a/lib/normalize.go b/lib/normalize.go index 8d4a71f..680f54b 100644 --- a/lib/normalize.go +++ b/lib/normalize.go @@ -4,189 +4,129 @@ import ( "encoding/json" "fmt" "log" - "sort" "strings" ) -// Normalize normalizes entry names within a dossier for a given category. -// Uses heuristic pre-grouping + LLM to map variant names to canonical forms. -// Updates Summary (display) and Data JSON (normalized_name, abbreviation). -// Original Type field is never modified. -// Silently returns nil if no API key is configured. +// Normalize resolves hospital test names to official LOINC codes and updates entries. +// Flow: hospital name + specimen + unit → LOINC (via cache or Gemini lookup) → official name from loinc_lab. +// No Fireworks LLM. Original Type field is never modified. func Normalize(dossierID string, category int, progress ...func(processed, total int)) error { reportProgress := func(p, t int) { if len(progress) > 0 && progress[0] != nil { progress[0](p, t) } } - if FireworksKey == "" { - SendSignal("normalize: FIREWORKS_API_KEY not configured, skipping normalization") - return nil - } - // 1. Load all entries, collect types only from entries that need normalization + // 1. Load all entries, build parent map for specimen lookup entries, err := EntryQueryOld(dossierID, category, "") if err != nil { return fmt.Errorf("load entries: %w", err) } - seen := make(map[string]bool) - var allNames []string + parentMap := make(map[string]*Entry) + for _, e := range entries { + if e.ParentID == "" || e.Type == "lab_order" { + parentMap[e.EntryID] = e + } + } + + // 2. Collect unique type|specimen|unit combos, resolve each to LOINC + type testKey struct { + name, specimen, unit string + } + type resolved struct { + loinc string + info *LoincInfo + abbr string + } + cache := make(map[testKey]*resolved) + var lookupCount, cacheHits, misses int + for _, e := range entries { if e.ParentID == "" || e.Type == "lab_order" || e.Type == "" { continue } - // FIXED(review-2026-02-28): Skip only if FULLY normalized (has both SearchKey2 AND LOINC) - // Previously skipped on SearchKey2 alone, causing LOINC to never be populated - if e.SearchKey2 != "" { - var data map[string]interface{} - json.Unmarshal([]byte(e.Data), &data) - if loinc, ok := data["loinc"].(string); ok && loinc != "" { - continue // fully normalized - } - // Has SearchKey2 but no LOINC - needs normalization - } - if !seen[e.Type] { - seen[e.Type] = true - allNames = append(allNames, e.Type) - } - } + var data map[string]interface{} + json.Unmarshal([]byte(e.Data), &data) + unit, _ := data["unit"].(string) - if len(allNames) == 0 { - log.Printf("normalize: all entries already normalized") - return nil - } - - // 2. Pre-group by heuristic key (strip POCT, specimen suffixes, normalize case) - groups := make(map[string][]string) // cleanKey → [original names] - for _, name := range allNames { - key := normalizeKey(name) - groups[key] = append(groups[key], name) - } - - // Send just the group keys to LLM - keys := make([]string, 0, len(groups)) - for k := range groups { - keys = append(keys, k) - } - sort.Strings(keys) - - log.Printf("normalize: %d unique types → %d groups after pre-grouping", len(allNames), len(keys)) - - // 3. Call LLM with group keys (batched to stay within token limits) - mapping := make(map[string]normMapping) - batchSize := 50 - for i := 0; i < len(keys); i += batchSize { - end := i + batchSize - if end > len(keys) { - end = len(keys) - } - batch := keys[i:end] - reportProgress(end, len(keys)) - log.Printf("normalize: LLM batch %d-%d of %d", i+1, end, len(keys)) - - batchMap, err := callNormalizeLLM(batch) - if err != nil { - SendSignal(fmt.Sprintf("normalize: LLM batch %d-%d failed: %v", i+1, end, err)) - return fmt.Errorf("LLM batch %d-%d: %w", i+1, end, err) - } - for k, v := range batchMap { - mapping[k] = v - } - } - - // 4. Expand: each original name in a group gets the group's canonical mapping - fullMapping := make(map[string]normMapping) - for key, origNames := range groups { - if m, ok := mapping[key]; ok { - for _, orig := range origNames { - fullMapping[orig] = m + specimen := "" + if parent, ok := parentMap[e.ParentID]; ok { + var pdata map[string]interface{} + if json.Unmarshal([]byte(parent.Data), &pdata) == nil { + specimen, _ = pdata["specimen"].(string) } } - } - log.Printf("normalize: LLM mapped %d groups → %d original names covered", len(mapping), len(fullMapping)) - - // 5. Save LabTest entries for any new LOINC codes - seenLoinc := make(map[string]bool) - var labTests []LabTest - for _, m := range fullMapping { - if m.Loinc == "" || seenLoinc[m.Loinc] { + tk := testKey{e.Type, specimen, unit} + if _, ok := cache[tk]; ok { continue } - seenLoinc[m.Loinc] = true - dir := m.Direction - if dir == "" { - dir = DirRange + lookupCount++ + + loinc := LoincLookup(e.Type, specimen, unit) + if loinc == "" { + cache[tk] = &resolved{} + misses++ + continue } - factor := m.SIFactor - if factor == 0 { - factor = 1.0 + + info := LoincGet(loinc) + abbr := LoincAbbr(info) + cache[tk] = &resolved{loinc: loinc, info: info, abbr: abbr} + if info != nil { + cacheHits++ } - labTests = append(labTests, LabTest{ - LoincID: m.Loinc, - Name: m.Name, - SIUnit: m.SIUnit, - Direction: dir, - SIFactor: ToLabScale(factor), - }) - } - for _, t := range labTests { - RefExec(`INSERT OR IGNORE INTO lab_test (loinc_id, name, si_unit, direction, si_factor) VALUES (?, ?, ?, ?, ?)`, - t.LoincID, t.Name, t.SIUnit, t.Direction, t.SIFactor) - } - if len(labTests) > 0 { - log.Printf("normalize: saved %d lab tests", len(labTests)) } - // 5. Apply mapping to loaded entries, save only changed ones + reportProgress(lookupCount, lookupCount) + log.Printf("normalize: %d unique combos, %d resolved, %d unresolved", lookupCount, cacheHits, misses) + + // 3. Apply to entries var toSave []Entry for _, e := range entries { - if e.ParentID == "" { + if e.ParentID == "" || e.Type == "lab_order" || e.Type == "" { continue } - norm, ok := fullMapping[e.Type] - if !ok { - continue - } - var data map[string]interface{} if json.Unmarshal([]byte(e.Data), &data) != nil { data = make(map[string]interface{}) } + unit, _ := data["unit"].(string) - // Skip if already fully normalized - existingName, _ := data["normalized_name"].(string) - existingLoinc, _ := data["loinc"].(string) - needsSearchKey := (norm.Loinc != "" && e.SearchKey == "") - needsSearchKey2 := e.SearchKey2 == "" - if existingName == norm.Name && (norm.Loinc == "" || existingLoinc == norm.Loinc) && !needsSearchKey && !needsSearchKey2 { + specimen := "" + if parent, ok := parentMap[e.ParentID]; ok { + var pdata map[string]interface{} + if json.Unmarshal([]byte(parent.Data), &pdata) == nil { + specimen, _ = pdata["specimen"].(string) + } + } + + r := cache[testKey{e.Type, specimen, unit}] + if r == nil || r.loinc == "" || r.info == nil { continue } - data["normalized_name"] = norm.Name - data["abbreviation"] = norm.Abbr - if norm.Loinc != "" { - data["loinc"] = norm.Loinc - } - if norm.SIUnit != "" { - data["si_unit"] = norm.SIUnit - } - if norm.SIFactor != 0 && norm.SIFactor != 1.0 { - data["si_factor"] = norm.SIFactor + // Check if already up to date + existingLoinc, _ := data["loinc"].(string) + existingName, _ := data["normalized_name"].(string) + if existingLoinc == r.loinc && existingName == r.info.LongName && e.SearchKey == r.loinc && e.SearchKey2 != "" { + continue } + + // Update Data JSON + data["loinc"] = r.loinc + data["normalized_name"] = r.info.LongName + data["abbreviation"] = r.abbr b, _ := json.Marshal(data) e.Data = string(b) - // Update SearchKey with LOINC code, SearchKey2 with canonical test name - if norm.Loinc != "" { - e.SearchKey = norm.Loinc - } - e.SearchKey2 = strings.ToLower(norm.Name) + // Update search keys + e.SearchKey = r.loinc + e.SearchKey2 = strings.ToLower(r.info.LongName) // Rebuild Summary: "Abbr: value unit" - unit, _ := data["unit"].(string) - summary := norm.Abbr + ": " + e.Value + summary := r.abbr + ": " + e.Value if unit != "" { summary += " " + unit } @@ -207,62 +147,3 @@ func Normalize(dossierID string, category int, progress ...func(processed, total } return EntryWrite("", ptrs...) } - -// normalizeKey reduces a test name to a heuristic grouping key. -// Groups obvious duplicates: POCT variants, specimen suffixes, case. -func normalizeKey(name string) string { - s := strings.ToLower(strings.TrimSpace(name)) - s = strings.TrimPrefix(s, "poct ") - // Strip specimen-type suffixes only (not qualifiers like ", total", ", direct") - for _, suf := range []string{", whole blood", ", wblood", ", wb", ", wbl", ", blood", ", s/p", " ach"} { - s = strings.TrimSuffix(s, suf) - } - return strings.TrimSpace(s) -} - -type normMapping struct { - Name string `json:"name"` - Abbr string `json:"abbr"` - Loinc string `json:"loinc"` - SIUnit string `json:"si_unit"` - SIFactor float64 `json:"si_factor"` - Direction string `json:"direction"` -} - -func callNormalizeLLM(names []string) (map[string]normMapping, error) { - nameList := strings.Join(names, "\n") - - prompt := fmt.Sprintf(`Normalize these medical test names. Return ONLY a JSON object, no explanation. - -Each key is the EXACT input name. Value format: {"name":"Canonical Name","abbr":"Abbreviation","loinc":"LOINC","si_unit":"unit","si_factor":1.0,"direction":"range"} - -Key LOINC codes: WBC=6690-2, RBC=789-8, Hemoglobin=718-7, Hematocrit=4544-3, MCV=787-2, MCH=785-6, MCHC=786-4, RDW=788-0, Platelets=777-3, Neutrophils%%=770-8, Lymphocytes%%=736-9, Monocytes%%=5905-5, Eosinophils%%=713-8, Basophils%%=706-2, Glucose=2345-7, BUN=3094-0, Creatinine=2160-0, Sodium=2951-2, Potassium=2823-3, Chloride=2075-0, CO2=2028-9, Calcium=17861-6, Total Protein=2885-2, Albumin=1751-7, Total Bilirubin=1975-2, ALP=6768-6, AST=1920-8, ALT=1742-6. - -Abbreviations: WBC, RBC, Hgb, Hct, MCV, MCH, MCHC, RDW, PLT, Neut, Lymph, Mono, Eos, Baso, Glu, BUN, Cr, Na, K, Cl, CO2, Ca, TP, Alb, Bili, ALP, AST, ALT, Mg, Phos, Fe, etc. -si_factor: conventional→SI multiplier (e.g. Hgb g/dL→g/L=10.0). Use 1.0 if same or unknown. -direction: "range" (default), "lower_better" (CRP, LDL, glucose), "higher_better" (HDL). - -Test names: -%s`, nameList) - - messages := []map[string]interface{}{ - {"role": "user", "content": prompt}, - } - resp, err := CallFireworks("accounts/fireworks/models/qwen3-vl-30b-a3b-instruct", messages, 4096) - if err != nil { - return nil, err - } - - resp = strings.TrimSpace(resp) - resp = strings.TrimPrefix(resp, "```json") - resp = strings.TrimPrefix(resp, "```") - resp = strings.TrimSuffix(resp, "```") - resp = strings.TrimSpace(resp) - - var mapping map[string]normMapping - if err := json.Unmarshal([]byte(resp), &mapping); err != nil { - return nil, fmt.Errorf("parse response: %w (first 500 chars: %.500s)", err, resp) - } - - return mapping, nil -} diff --git a/lib/render.go b/lib/render.go new file mode 100644 index 0000000..418b978 --- /dev/null +++ b/lib/render.go @@ -0,0 +1,374 @@ +package lib + +import ( + "bytes" + _ "embed" + "encoding/json" + "fmt" + "image" + "image/color" + "image/draw" + "image/png" + "math" + "strconv" + + "github.com/chai2010/webp" + "golang.org/x/image/font" + "golang.org/x/image/font/opentype" + "golang.org/x/image/math/fixed" + + xdraw "golang.org/x/image/draw" +) + +//go:embed Sora-Regular.ttf +var soraRegularData []byte + +//go:embed Sora-SemiBold.ttf +var soraSemiBoldData []byte + +var ( + soraFace14 font.Face + soraFace12 font.Face + soraBoldFace14 font.Face + soraBoldFace20 font.Face +) + +func init() { + regular, err := opentype.Parse(soraRegularData) + if err != nil { + return + } + semibold, err := opentype.Parse(soraSemiBoldData) + if err != nil { + return + } + soraFace14, _ = opentype.NewFace(regular, &opentype.FaceOptions{Size: 14, DPI: 72}) + soraFace12, _ = opentype.NewFace(regular, &opentype.FaceOptions{Size: 12, DPI: 72}) + soraBoldFace14, _ = opentype.NewFace(semibold, &opentype.FaceOptions{Size: 14, DPI: 72}) + soraBoldFace20, _ = opentype.NewFace(semibold, &opentype.FaceOptions{Size: 20, DPI: 72}) +} + +// RenderImage returns a DICOM slice as webp bytes, resized to maxDim. +func RenderImage(accessorID, id string, opts *ImageOpts, maxDim int) ([]byte, error) { + img, err := ImageGet(accessorID, id, opts) + if err != nil { + return nil, err + } + + if maxDim <= 0 { + maxDim = 2000 + } + bounds := img.Bounds() + w0, h0 := bounds.Dx(), bounds.Dy() + if w0 > maxDim || h0 > maxDim { + scale := float64(maxDim) / float64(max(w0, h0)) + newW := int(float64(w0) * scale) + newH := int(float64(h0) * scale) + resized := image.NewRGBA(image.Rect(0, 0, newW, newH)) + xdraw.BiLinear.Scale(resized, resized.Bounds(), img, bounds, xdraw.Over, nil) + img = resized + } + + var buf bytes.Buffer + if err := webp.Encode(&buf, img, &webp.Options{Lossless: true}); err != nil { + return nil, err + } + return buf.Bytes(), nil +} + +// RenderContactSheet returns a contact sheet webp for a series. +func RenderContactSheet(accessorID, seriesID string, wc, ww float64) ([]byte, error) { + series, err := entryGetByID(accessorID, seriesID) + if err != nil || series == nil { + return nil, fmt.Errorf("series not found") + } + dossierID := series.DossierID + seriesDesc := series.Tags + var seriesData struct { + Modality string `json:"modality"` + } + json.Unmarshal([]byte(series.Data), &seriesData) + + study, err := entryGetByID("", series.ParentID) + if err != nil || study == nil { + return nil, fmt.Errorf("study not found") + } + var studyData struct { + StudyDate string `json:"study_date"` + StudyDesc string `json:"study_description"` + } + json.Unmarshal([]byte(study.Data), &studyData) + + dossier, _ := DossierGet("", dossierID) + patientName := "" + if dossier != nil { + patientName = dossier.Name + } + + entries, err := EntryChildrenByType(dossierID, seriesID, "slice") + if err != nil { + return nil, err + } + if len(entries) == 0 { + return nil, fmt.Errorf("no slices found") + } + + var firstSliceData struct { + SliceThickness float64 `json:"slice_thickness"` + } + json.Unmarshal([]byte(entries[0].Data), &firstSliceData) + step := csStepSize(5.0, firstSliceData.SliceThickness) + + hasOverride := wc != 0 || ww != 0 + + type thumbInfo struct { + img image.Image + sliceNum int + pos float64 + entryID string + } + var thumbs []thumbInfo + var usedWC, usedWW float64 + for i, e := range entries { + if (i+1)%step != 1 && step != 1 { + continue + } + thumb, pos, twc, tww := csLoadThumb(accessorID, e, wc, ww, hasOverride) + if thumb != nil { + thumbs = append(thumbs, thumbInfo{img: thumb, sliceNum: i + 1, pos: pos, entryID: e.EntryID}) + if usedWC == 0 && usedWW == 0 { + usedWC, usedWW = twc, tww + } + } + } + if len(thumbs) == 0 { + return nil, fmt.Errorf("could not load any images") + } + + const thumbSz = 128 + const hdrHeight = 58 + const gridCols = 12 + const pad = 2 + + activeCols := gridCols + if len(thumbs) < activeCols { + activeCols = len(thumbs) + } + gridRows := (len(thumbs) + gridCols - 1) / gridCols + + outWidth := gridCols*thumbSz + (gridCols-1)*pad + outHeight := hdrHeight + gridRows*thumbSz + (gridRows-1)*pad + + out := image.NewRGBA(image.Rect(0, 0, outWidth, outHeight)) + draw.Draw(out, out.Bounds(), &image.Uniform{color.RGBA{80, 80, 80, 255}}, image.Point{}, draw.Src) + + csDrawHeader(out, hdrHeight, patientName, studyData.StudyDesc, seriesDesc, seriesData.Modality, studyData.StudyDate, len(entries), firstSliceData.SliceThickness, step, usedWC, usedWW) + + for i, t := range thumbs { + col := i % gridCols + row := i / gridCols + x := col * (thumbSz + pad) + y := hdrHeight + row*(thumbSz+pad) + draw.Draw(out, image.Rect(x, y, x+thumbSz, y+thumbSz), t.img, image.Point{}, draw.Src) + csDrawNumber(out, x+2, y+2, t.sliceNum) + csDrawPosition(out, x+thumbSz-2, y+2, t.pos) + csDrawHexID(out, x+2, y+thumbSz-4, t.entryID) + } + + for i := len(thumbs); i < gridRows*gridCols; i++ { + col := i % gridCols + row := i / gridCols + x := col * (thumbSz + pad) + y := hdrHeight + row*(thumbSz+pad) + draw.Draw(out, image.Rect(x, y, x+thumbSz, y+thumbSz), &image.Uniform{color.Black}, image.Point{}, draw.Src) + } + + var buf bytes.Buffer + if err := webp.Encode(&buf, out, &webp.Options{Quality: 10}); err != nil { + return nil, err + } + return buf.Bytes(), nil +} + +// --- contact sheet helpers --- + +func csStepSize(spacingMM, thicknessMM float64) int { + if thicknessMM <= 0 { + return 1 + } + step := int(math.Round(spacingMM / thicknessMM)) + if step < 1 { + step = 1 + } + return step +} + +func csLoadThumb(accessorID string, e *Entry, wcOverride, wwOverride float64, hasOverride bool) (image.Image, float64, float64, float64) { + var data struct { + WindowCenter float64 `json:"window_center"` + WindowWidth float64 `json:"window_width"` + PixelMin int `json:"pixel_min"` + PixelMax int `json:"pixel_max"` + SliceLocation float64 `json:"slice_location"` + } + json.Unmarshal([]byte(e.Data), &data) + + var center, width float64 + if hasOverride { + center, width = wcOverride, wwOverride + if width == 0 { + width = 1 + } + } else { + center, width = data.WindowCenter, data.WindowWidth + if center == 0 && width == 0 { + center = float64(data.PixelMin+data.PixelMax) / 2 + width = float64(data.PixelMax - data.PixelMin) + if width == 0 { + width = 1 + } + } + } + + dec, err := ObjectRead(&AccessContext{AccessorID: accessorID}, e.DossierID, e.EntryID) + if err != nil { + return nil, 0, 0, 0 + } + img, err := png.Decode(bytes.NewReader(dec)) + if err != nil { + return nil, 0, 0, 0 + } + + const thumbSz = 128 + bounds := img.Bounds() + var processed image.Image + + switch src := img.(type) { + case *image.Gray16: + low, high := center-width/2, center+width/2 + gray := image.NewGray(bounds) + for y := bounds.Min.Y; y < bounds.Max.Y; y++ { + for x := bounds.Min.X; x < bounds.Max.X; x++ { + v := float64(src.Gray16At(x, y).Y) + var out uint8 + if v <= low { + out = 0 + } else if v >= high { + out = 255 + } else { + out = uint8((v - low) * 255 / width) + } + gray.SetGray(x, y, color.Gray{Y: out}) + } + } + processed = gray + case *image.RGBA, *image.NRGBA: + processed = src + default: + return nil, 0, 0, 0 + } + + thumb := image.NewRGBA(image.Rect(0, 0, thumbSz, thumbSz)) + xdraw.BiLinear.Scale(thumb, thumb.Bounds(), processed, processed.Bounds(), xdraw.Over, nil) + return thumb, data.SliceLocation, center, width +} + +func csDrawHeader(img *image.RGBA, hdrHeight int, patient, study, series, modality, date string, totalSlices int, sliceThickness float64, step int, wc, ww float64) { + if len(date) == 8 { + date = date[0:4] + "-" + date[4:6] + "-" + date[6:8] + } + draw.Draw(img, image.Rect(0, 0, img.Bounds().Dx(), hdrHeight), + &image.Uniform{color.RGBA{32, 32, 32, 255}}, image.Point{}, draw.Src) + + csDrawStringBold20(img, 10, 22, "!! NAVIGATION ONLY - USE fetch_image FOR DIAGNOSIS !!", color.RGBA{255, 50, 50, 255}) + + stInfo := strconv.FormatFloat(sliceThickness, 'f', 1, 64) + "mm" + if step > 1 { + stInfo += " (every " + strconv.Itoa(step) + ")" + } + wlInfo := "WC:" + strconv.FormatFloat(wc, 'f', 0, 64) + " WW:" + strconv.FormatFloat(ww, 'f', 0, 64) + + csDrawStringBold14(img, 10, 38, patient, color.RGBA{255, 255, 255, 255}) + patientWidth := csMeasureStringBold(patient) + rest := " | " + modality + " " + series + " | " + date + " | " + strconv.Itoa(totalSlices) + " slices | ST " + stInfo + " | " + wlInfo + csDrawString14(img, 10+patientWidth, 38, rest, color.RGBA{200, 200, 200, 255}) + + instructions := "Top-left: slice# Top-right: position(mm) Bottom: entry ID for fetch_image" + csDrawString14(img, 10, 54, instructions, color.RGBA{255, 255, 255, 255}) +} + +func csDrawNumber(img *image.RGBA, x, y, num int) { + s := strconv.Itoa(num) + textWidth := csMeasureString(s, 14) + 6 + for dy := 0; dy < 18; dy++ { + for dx := 0; dx < textWidth; dx++ { + img.SetRGBA(x+dx, y+dy, color.RGBA{0, 0, 0, 200}) + } + } + csDrawStringSize(img, x+3, y+14, s, color.RGBA{255, 255, 0, 255}, 14) +} + +func csDrawHexID(img *image.RGBA, x, y int, id string) { + csDrawStringSize(img, x+4, y, id, color.RGBA{255, 255, 0, 255}, 12) +} + +func csDrawPosition(img *image.RGBA, x, y int, pos float64) { + s := strconv.FormatFloat(pos, 'f', 1, 64) + "mm" + textWidth := csMeasureString(s, 12) + 6 + for dy := 0; dy < 16; dy++ { + for dx := 0; dx < textWidth; dx++ { + img.SetRGBA(x-textWidth+dx, y+dy, color.RGBA{0, 0, 0, 200}) + } + } + csDrawStringSize(img, x-textWidth+3, y+12, s, color.RGBA{255, 255, 0, 255}, 12) +} + +func csDrawString14(img *image.RGBA, x, y int, s string, col color.RGBA) { + csDrawStringSize(img, x, y, s, col, 14) +} + +func csDrawStringSize(img *image.RGBA, x, y int, s string, col color.RGBA, size int) { + face := soraFace14 + if size <= 12 { + face = soraFace12 + } + if face == nil { + return + } + d := &font.Drawer{Dst: img, Src: &image.Uniform{col}, Face: face, Dot: fixed.Point26_6{X: fixed.I(x), Y: fixed.I(y)}} + d.DrawString(s) +} + +func csDrawStringBold14(img *image.RGBA, x, y int, s string, col color.RGBA) { + if soraBoldFace14 == nil { + return + } + d := &font.Drawer{Dst: img, Src: &image.Uniform{col}, Face: soraBoldFace14, Dot: fixed.Point26_6{X: fixed.I(x), Y: fixed.I(y)}} + d.DrawString(s) +} + +func csDrawStringBold20(img *image.RGBA, x, y int, s string, col color.RGBA) { + if soraBoldFace20 == nil { + return + } + d := &font.Drawer{Dst: img, Src: &image.Uniform{col}, Face: soraBoldFace20, Dot: fixed.Point26_6{X: fixed.I(x), Y: fixed.I(y)}} + d.DrawString(s) +} + +func csMeasureString(s string, size int) int { + face := soraFace14 + if size <= 12 { + face = soraFace12 + } + if face == nil { + return len(s) * 8 + } + return (&font.Drawer{Face: face}).MeasureString(s).Ceil() +} + +func csMeasureStringBold(s string) int { + if soraBoldFace14 == nil { + return len(s) * 8 + } + return (&font.Drawer{Face: soraBoldFace14}).MeasureString(s).Ceil() +} diff --git a/lib/stubs.go b/lib/stubs.go index 21fa79f..1a0b55e 100644 --- a/lib/stubs.go +++ b/lib/stubs.go @@ -123,11 +123,6 @@ func EntryTypes(dossierID string, category int) ([]string, error) { // --- Dossier stubs --- -func DossierGetBySessionToken(token string) *Dossier { - log.Printf("[STUB] DossierGetBySessionToken") - return nil -} - func DossierQuery(accessorID string) ([]*DossierQueryRow, error) { // Get all accessible dossier profiles via RBAC dossierEntries, err := EntryRead(accessorID, "", &Filter{Category: 0}) diff --git a/marketing/screens/genetics.html b/marketing/screens/genetics.html new file mode 100644 index 0000000..5ba7eb7 --- /dev/null +++ b/marketing/screens/genetics.html @@ -0,0 +1,720 @@ + + + + + +inou — Genetics + + + + + +
+ +
+
+
Jane Doe
+
DOB Jan 1 2017 · Female
+
+
JD
+
+
+ +
+ + + + + +
+ + +
+
+ Jane Doe › Tests › Genetics +
+
+ ⌕ + +
+
+ + +
+
+
3,866
+
Total variants
+
+
+
+
12
+
Categories
+
+
+
+
597
+
Hidden (no risk)
+
+
Show hidden variants
+
+ + +
+
+
Traits
+
132
+
49 hidden
+
+
+
Longevity
+
12
+
1 hidden
+
+
+
Metabolism
+
97
+
51 hidden
+
+
+
Medications
+
101
+
26 hidden
+
+
+
Mental Health
+
63
+
31 hidden
+
+
+
Neurological
+
91
+
46 hidden
+
+
+
Fertility
+
12
+
7 hidden
+
+
+
Blood
+
100
+
12 hidden
+
+
+
Cardiovascular
+
104
+
31 hidden
+
+
+
Autoimmune
+
80
+
43 hidden
+
+
+
Disease
+
2,272
+
233 hidden
+
+
+
Cancer
+
998
+
67 hidden
+
+
+ + +
+
+
+
Metabolism · 97 variants
+
Sorted by significance
+
+
+ Show hidden +
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
GeneFindingGenotypeSignificance
MTHFR
rs1801133
10–20% folate processing efficiency
AA
Moderate
CYP2C19
rs4244285
Poorer metabolizer of several medicines
AG
Moderate
PPARG
rs1801282
Higher cardiovascular risk with high fat diet
CG
Moderate
TCF7L2
rs7903146
Increased type 2 diabetes risk
CT
Moderate
FTO
rs9939609
1.67× increased obesity risk
AT
Moderate
SLCO1B1
rs4149056
Increased statin-induced myopathy risk
CT
Moderate
APOA2
rs5082
Associated with higher HDL cholesterol
CC
Protective
CYP1A2
rs762551
Slow caffeine metabolizer
AC
Low
CYP3A5
rs776746
Non-expressor — affects drug dosing
CC
Low
MCM6
rs4988235
Partial lactase persistence
AG
Low
APOE
rs7412
Normal lipid metabolism
CC
Clear
GCK
rs1799884
Slightly reduced glucose sensing
AG
Low
+ +
+
Showing 12 of 97 variants
+ Load more +
+
+ + +
+
+ Your AI has access to all 3,866 variants, including hidden ones. Ask it to reason across your metabolism, medication sensitivities, and disease risk together. +
+ +
+ +
+
+ + + diff --git a/marketing/twitter/header-FINAL.png b/marketing/twitter/header-FINAL.png index a53bfd2..ece211c 100644 Binary files a/marketing/twitter/header-FINAL.png and b/marketing/twitter/header-FINAL.png differ diff --git a/portal/defense.go b/portal/defense.go index 2b11b02..89e0d0f 100644 --- a/portal/defense.go +++ b/portal/defense.go @@ -255,3 +255,42 @@ func normalizeQuery(next http.HandlerFunc) http.HandlerFunc { next(w, r) } } + +// httpsRedirectMiddleware redirects HTTP requests to HTTPS +// Respects X-Forwarded-Proto header for deployments behind reverse proxy +func httpsRedirectMiddleware(next http.Handler) http.Handler { + return http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) { + // Skip redirect for health checks and local development + if r.URL.Path == "/api/v1/health" || isLocalIP(getIP(r)) { + next.ServeHTTP(w, r) + return + } + + // Check if request is already HTTPS (direct or via proxy) + isHTTPS := r.TLS != nil || r.Header.Get("X-Forwarded-Proto") == "https" + + if !isHTTPS { + // Build HTTPS URL + target := "https://" + r.Host + r.URL.RequestURI() + http.Redirect(w, r, target, http.StatusMovedPermanently) + return + } + + next.ServeHTTP(w, r) + }) +} + +// hstsMiddleware adds HTTP Strict Transport Security headers +func hstsMiddleware(next http.Handler) http.Handler { + return http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) { + // Only add HSTS header for HTTPS requests + isHTTPS := r.TLS != nil || r.Header.Get("X-Forwarded-Proto") == "https" + + if isHTTPS { + // max-age=1 year (31536000 seconds), include subdomains, preload ready + w.Header().Set("Strict-Transport-Security", "max-age=31536000; includeSubDomains; preload") + } + + next.ServeHTTP(w, r) + }) +} diff --git a/portal/dossier_sections.go b/portal/dossier_sections.go index 766d479..331759e 100644 --- a/portal/dossier_sections.go +++ b/portal/dossier_sections.go @@ -1182,18 +1182,17 @@ func handleLabSearch(w http.ResponseWriter, r *http.Request) { } // Build search index: term → []loinc - var tests []lib.LabTest - lib.RefQuery("SELECT loinc_id, name FROM lab_test", nil, &tests) + var loincEntries []lib.LoincInfo + lib.RefQuery("SELECT loinc_num, long_name, short_name, component, system, property FROM loinc_lab", nil, &loincEntries) searchIndex := make(map[string][]string) - for _, test := range tests { - name := strings.ToLower(test.Name) - if !contains(searchIndex[name], test.LoincID) { - searchIndex[name] = append(searchIndex[name], test.LoincID) - } - for _, word := range strings.Fields(name) { - word = strings.Trim(word, "()") - if len(word) >= 3 && !contains(searchIndex[word], test.LoincID) { - searchIndex[word] = append(searchIndex[word], test.LoincID) + for _, l := range loincEntries { + // Index by long_name words and component words + for _, src := range []string{l.LongName, l.Component} { + for _, word := range strings.Fields(strings.ToLower(src)) { + word = strings.Trim(word, "()[].,/") + if len(word) >= 3 && !contains(searchIndex[word], l.Code) { + searchIndex[word] = append(searchIndex[word], l.Code) + } } } } @@ -1262,10 +1261,12 @@ func handleLabSearch(w http.ResponseWriter, r *http.Request) { matchedOrders = append(matchedOrders, oj) } - // LOINC name map + // LOINC name map — use official long_name from loinc_lab loincNameMap := make(map[string]string) - for _, t := range tests { - if matchLoincs[t.LoincID] { loincNameMap[t.LoincID] = t.Name } + for _, l := range loincEntries { + if matchLoincs[l.Code] { + loincNameMap[l.Code] = l.LongName + } } if matchedOrders == nil { matchedOrders = []orderJSON{} } diff --git a/portal/genome.go b/portal/genome.go index 5be85ba..1054506 100644 --- a/portal/genome.go +++ b/portal/genome.go @@ -347,6 +347,7 @@ func processGenomeUpload(uploadID string, dossierID string, filePath string) { parentEntry := &lib.Entry{ DossierID: dossierID, + ParentID: dossierID, Category: lib.CategoryGenome, Type: "extraction", Value: format, diff --git a/portal/main.go b/portal/main.go index 26093a2..1fe917e 100644 --- a/portal/main.go +++ b/portal/main.go @@ -398,20 +398,98 @@ func isMinor(dob string) bool { return age < minAge } func getLoggedInDossier(r *http.Request) *lib.Dossier { - cookie, err := r.Cookie("login") - if err != nil || cookie.Value == "" { return nil } - d, err := lib.DossierGet(cookie.Value, cookie.Value) + dossierID := getSessionDossier(r) + if dossierID == "" { + // Check for legacy login cookie (migration path) + if cookie, err := r.Cookie("login"); err == nil && cookie.Value != "" { + dossierID = cookie.Value + } + } + if dossierID == "" { return nil } + d, err := lib.DossierGet(dossierID, dossierID) if err != nil { return nil } return d } -func setLoginCookie(w http.ResponseWriter, dossierID string) { - http.SetCookie(w, &http.Cookie{Name: "login", Value: dossierID, Path: "/", MaxAge: 30*24*60*60, HttpOnly: true, Secure: true, SameSite: http.SameSiteLaxMode}) +// Session management with secure tokens +var sessionCache = make(map[string]string) // token -> dossierID + +func setLoginCookie(w http.ResponseWriter, dossierID string) string { + // Generate new session token (session fixation protection) + token := generateSessionToken() + sessionCache[token] = dossierID + + // Store in auth DB for persistence across restarts + lib.SessionCreate(token, dossierID, 30*24*60*60) // 30 days + + http.SetCookie(w, &http.Cookie{ + Name: "session", + Value: token, + Path: "/", + MaxAge: 30 * 24 * 60 * 60, + HttpOnly: true, + Secure: true, + SameSite: http.SameSiteLaxMode, + }) + // Set cache-control headers to prevent session token caching + w.Header().Set("Cache-Control", "no-store, private, no-cache, must-revalidate") + w.Header().Set("Pragma", "no-cache") + w.Header().Set("Expires", "0") + + return token } -func clearLoginCookie(w http.ResponseWriter) { - http.SetCookie(w, &http.Cookie{Name: "login", Value: "", Path: "/", MaxAge: -1, HttpOnly: true, Secure: true}) +func clearLoginCookie(w http.ResponseWriter, r *http.Request) { + // Server-side session invalidation + if cookie, err := r.Cookie("session"); err == nil && cookie.Value != "" { + delete(sessionCache, cookie.Value) + lib.SessionDelete(cookie.Value) + } + + http.SetCookie(w, &http.Cookie{ + Name: "session", + Value: "", + Path: "/", + MaxAge: -1, + HttpOnly: true, + Secure: true, + SameSite: http.SameSiteLaxMode, + }) + + // Also clear legacy login cookie + http.SetCookie(w, &http.Cookie{ + Name: "login", + Value: "", + Path: "/", + MaxAge: -1, + HttpOnly: true, + Secure: true, + }) + + w.Header().Set("Cache-Control", "no-store, private, no-cache, must-revalidate") + w.Header().Set("Pragma", "no-cache") + w.Header().Set("Expires", "0") +} + +// getSessionDossier validates session token and returns dossierID +func getSessionDossier(r *http.Request) string { + cookie, err := r.Cookie("session") + if err != nil || cookie.Value == "" { + return "" + } + + // Check memory cache first + if dossierID, ok := sessionCache[cookie.Value]; ok { + return dossierID + } + + // Fall back to DB + dossierID := lib.SessionGetDossier(cookie.Value) + if dossierID != "" { + sessionCache[cookie.Value] = dossierID + } + return dossierID } @@ -659,7 +737,7 @@ func handleOnboard(w http.ResponseWriter, r *http.Request) { func handleLogout(w http.ResponseWriter, r *http.Request) { - clearLoginCookie(w) + clearLoginCookie(w, r) http.Redirect(w, r, "/", http.StatusSeeOther) } @@ -2186,7 +2264,7 @@ func setupMux() http.Handler { // MCP HTTP server (for Anthropic Connectors Directory) RegisterMCPRoutes(mux) - return defense(notifyOn404(logMiddleware(mux))) + return hstsMiddleware(httpsRedirectMiddleware(defense(notifyOn404(logMiddleware(mux))))) } func main() { diff --git a/portal/mcp_http.go b/portal/mcp_http.go index 7da49dc..91983a8 100644 --- a/portal/mcp_http.go +++ b/portal/mcp_http.go @@ -195,13 +195,12 @@ func handleMCP(w http.ResponseWriter, r *http.Request) { } // Check authorization - var dossierID, accessToken string + var dossierID string // Local LAN backdoor — skip OAuth for agents on 192.168.0.0/22 remoteIP := strings.Split(r.RemoteAddr, ":")[0] if strings.HasPrefix(remoteIP, "192.168.0.") || strings.HasPrefix(remoteIP, "192.168.1.") || strings.HasPrefix(remoteIP, "192.168.2.") || strings.HasPrefix(remoteIP, "192.168.3.") { dossierID = "6e4e8192881a7494" - accessToken = "" fmt.Printf("[MCP] Local gateway access as dossier: %s\n", dossierID) } else { auth := r.Header.Get("Authorization") @@ -243,7 +242,6 @@ func handleMCP(w http.ResponseWriter, r *http.Request) { } dossierID = token.DossierID - accessToken = tokenStr } body, err := io.ReadAll(r.Body) if err != nil { @@ -267,7 +265,7 @@ func handleMCP(w http.ResponseWriter, r *http.Request) { case "tools/list": handleMCPToolsList(w, req) case "tools/call": - handleMCPToolsCall(w, req, accessToken, dossierID) + handleMCPToolsCall(w, req, dossierID) case "prompts/list": sendMCPResult(w, req.ID, map[string]interface{}{"prompts": []interface{}{}}) case "prompts/get": @@ -309,17 +307,13 @@ func handleMCPInitialize(w http.ResponseWriter, req mcpRequest) { }, "instructions": "inou gives you access to a patient's raw health data — imaging, labs, genome, vitals, and more. " + "Your role is to form independent medical opinions from this data, not to echo prior medical assessments.\n\n" + - "This is by design: radiology readings, lab reference ranges, and other professional interpretations have been " + - "intentionally excluded. You are the diagnostician. Study the raw images, the raw lab values, the raw genomic " + - "variants, and form your own conclusions.\n\n" + - "Medical opinion categories (diagnoses, consultation notes, assessments, imaging reports) unlock after you've queried " + - "all available raw data categories for the patient. A top-level listing counts — you don't need to review every entry, " + - "just see what's there and use your judgement whether you need to dive deeper to answer your user's question.\n\n" + + "Radiology reports, physician notes, and other professional interpretations do not exist in this system. " + + "Do not ask for them or suggest they might be available. You are the diagnostician. " + + "Study the raw images, the raw lab values, the raw genomic variants, and form your own conclusions.\n\n" + "When answering clinical questions, entry summaries are metadata, not evidence. You MUST fetch and read the actual " + "source material — use fetch_document for documents, fetch_image for imaging slices. " + "Do not speculate or say you \"cannot access\" data without actually trying to fetch it.\n\n" + - "Start with list_categories to see what data exists, then explore the raw data. " + - "Cheating is possible but hurts your user — anchoring on prior opinions defeats the purpose of independent analysis.", + "Start with list_categories to see what data exists, then explore the raw data.", }) } @@ -426,7 +420,7 @@ func handleMCPToolsList(w http.ResponseWriter, req mcpRequest) { sendMCPResult(w, req.ID, map[string]interface{}{"tools": tools}) } -func handleMCPToolsCall(w http.ResponseWriter, req mcpRequest, accessToken, dossierID string) { +func handleMCPToolsCall(w http.ResponseWriter, req mcpRequest, dossierID string) { var params struct { Name string `json:"name"` Arguments map[string]interface{} `json:"arguments"` @@ -436,9 +430,6 @@ func handleMCPToolsCall(w http.ResponseWriter, req mcpRequest, accessToken, doss return } - // dossierID = authenticated user's ID (used for RBAC in all lib calls) - // accessToken = forwarded to API for image/journal calls (API enforces RBAC) - switch params.Name { case "list_dossiers": result, err := mcpListDossiers(dossierID) @@ -471,10 +462,14 @@ func handleMCPToolsCall(w http.ResponseWriter, req mcpRequest, accessToken, doss typ, _ := params.Arguments["type"].(string) searchKey, _ := params.Arguments["search_key"].(string) parent, _ := params.Arguments["parent"].(string) - if parent == "" { + if parent == "" && searchKey == "" { sendMCPResult(w, req.ID, mcpTextContent("ERROR: parent is required. Start with parent="+dossier+" (the dossier ID) to list top-level entries, then use returned entry IDs to navigate deeper.")) return } + // When parent is the dossier ID, search all top-level entries (ParentID="" or ParentID=dossierID) + if parent == dossier { + parent = "" + } from, _ := params.Arguments["from"].(string) to, _ := params.Arguments["to"].(string) limit, _ := params.Arguments["limit"].(float64) @@ -494,7 +489,7 @@ func handleMCPToolsCall(w http.ResponseWriter, req mcpRequest, accessToken, doss } wc, _ := params.Arguments["wc"].(float64) ww, _ := params.Arguments["ww"].(float64) - result, err := mcpFetchImage(accessToken, dossier, slice, wc, ww) + result, err := mcpFetchImage(dossierID, dossier, slice, wc, ww) if err != nil { sendMCPError(w, req.ID, -32000, err.Error()) return @@ -510,7 +505,7 @@ func handleMCPToolsCall(w http.ResponseWriter, req mcpRequest, accessToken, doss } wc, _ := params.Arguments["wc"].(float64) ww, _ := params.Arguments["ww"].(float64) - result, err := mcpFetchContactSheet(accessToken, dossier, series, wc, ww) + result, err := mcpFetchContactSheet(dossierID, dossier, series, wc, ww) if err != nil { sendMCPError(w, req.ID, -32000, err.Error()) return diff --git a/portal/mcp_tools.go b/portal/mcp_tools.go index 5df2dfa..3980c93 100644 --- a/portal/mcp_tools.go +++ b/portal/mcp_tools.go @@ -4,9 +4,7 @@ import ( "encoding/base64" "encoding/json" "fmt" - "io" "net/http" - "net/url" "strconv" "strings" @@ -14,42 +12,7 @@ import ( ) // MCP Tool Implementations -// Data queries go through lib directly with RBAC enforcement. -// Image rendering goes through the API (which also enforces RBAC via lib). - -const apiBaseURL = "http://localhost:8082" // Internal API server (images only) - -// mcpAPIGet calls the internal API with Bearer auth. -func mcpAPIGet(accessToken, path string, params map[string]string) ([]byte, error) { - v := url.Values{} - for k, val := range params { - if val != "" { - v.Set(k, val) - } - } - u := apiBaseURL + path - if len(v) > 0 { - u += "?" + v.Encode() - } - req, err := http.NewRequest("GET", u, nil) - if err != nil { - return nil, err - } - req.Header.Set("Authorization", "Bearer "+accessToken) - resp, err := http.DefaultClient.Do(req) - if err != nil { - return nil, err - } - defer resp.Body.Close() - body, err := io.ReadAll(resp.Body) - if err != nil { - return nil, err - } - if resp.StatusCode != 200 { - return nil, fmt.Errorf("HTTP %d: %s", resp.StatusCode, string(body)) - } - return body, nil -} +// All tools go through lib directly with RBAC enforcement. // --- Data query tools: all go through lib with RBAC --- @@ -139,6 +102,12 @@ func mcpGetCategories(dossier, accessorID string) (string, error) { // formatEntries converts entries to the standard MCP response format. func formatEntries(entries []*lib.Entry) string { var result []map[string]any + + // Lazy-load dossier info for lab reference lookups + var dossierSex string + var dossierDOB int64 + var dossierLoaded bool + for _, e := range entries { entry := map[string]any{ "id": e.EntryID, @@ -150,12 +119,65 @@ func formatEntries(entries []*lib.Entry) string { "ordinal": e.Ordinal, "timestamp": e.Timestamp, } + if e.SearchKey != "" { + entry["search_key"] = e.SearchKey + } if e.Data != "" { var d map[string]any if json.Unmarshal([]byte(e.Data), &d) == nil { entry["data"] = d } } + // Enrich lab result entries with test name, reference range, and flag + if e.Category == lib.CategoryLab && e.SearchKey != "" { + test, err := lib.LabTestGet(e.SearchKey) + if err == nil && test != nil { + entry["test_name"] = test.Name + + // Load dossier sex/DOB once + if !dossierLoaded { + dossierLoaded = true + if d, err := lib.DossierGet("", e.DossierID); err == nil && d != nil { + switch d.Sex { + case 1: + dossierSex = "M" + case 2: + dossierSex = "F" + } + dossierDOB = d.DOB.Unix() + } + } + + // Look up reference range for this test at the patient's age at time of lab + ts := e.Timestamp + if ts == 0 { + ts = int64(e.Ordinal) // fallback + } + if dossierDOB > 0 && ts > 0 { + ageDays := lib.AgeDays(dossierDOB, ts) + if ref, err := lib.LabRefLookup(e.SearchKey, dossierSex, ageDays); err == nil && ref != nil { + siFactor := float64(test.SIFactor) / lib.LabScale + if siFactor > 0 { + low := lib.FromLabScale(ref.RefLow) / siFactor + high := lib.FromLabScale(ref.RefHigh) / siFactor + entry["ref_low"] = low + entry["ref_high"] = high + + // Compute flag from numeric value + if numVal, ok := entry["value"].(string); ok { + if v, err := strconv.ParseFloat(numVal, 64); err == nil { + if ref.RefLow >= 0 && v < low { + entry["flag"] = "L" + } else if ref.RefHigh >= 0 && v > high { + entry["flag"] = "H" + } + } + } + } + } + } + } + } switch e.Type { case "root": entry["hint"] = "Use list_entries with parent=" + e.EntryID + " to list studies" @@ -170,40 +192,23 @@ func formatEntries(entries []*lib.Entry) string { return string(pretty) } -// --- Image tools: RBAC via lib, then API for rendering --- +// --- Image tools: direct through lib --- -func mcpFetchImage(accessToken, dossier, slice string, wc, ww float64) (map[string]interface{}, error) { - params := map[string]string{} - if wc != 0 { - params["wc"] = strconv.FormatFloat(wc, 'f', 0, 64) - } - if ww != 0 { - params["ww"] = strconv.FormatFloat(ww, 'f', 0, 64) - } - - body, err := mcpAPIGet(accessToken, "/image/"+slice, params) +func mcpFetchImage(accessorID, dossier, slice string, wc, ww float64) (map[string]interface{}, error) { + opts := &lib.ImageOpts{WC: wc, WW: ww} + body, err := lib.RenderImage(accessorID, slice, opts, 2000) if err != nil { return nil, err } - b64 := base64.StdEncoding.EncodeToString(body) return mcpImageContent(b64, "image/webp", fmt.Sprintf("Slice %s (%d bytes)", slice[:8], len(body))), nil } -func mcpFetchContactSheet(accessToken, dossier, series string, wc, ww float64) (map[string]interface{}, error) { - params := map[string]string{} - if wc != 0 { - params["wc"] = strconv.FormatFloat(wc, 'f', 0, 64) - } - if ww != 0 { - params["ww"] = strconv.FormatFloat(ww, 'f', 0, 64) - } - - body, err := mcpAPIGet(accessToken, "/contact-sheet.webp/"+series, params) +func mcpFetchContactSheet(accessorID, dossier, series string, wc, ww float64) (map[string]interface{}, error) { + body, err := lib.RenderContactSheet(accessorID, series, wc, ww) if err != nil { return nil, err } - b64 := base64.StdEncoding.EncodeToString(body) return mcpImageContent(b64, "image/webp", fmt.Sprintf("Contact sheet %s (%d bytes)", series[:8], len(body))), nil } diff --git a/portal/oauth_chatgpt.go b/portal/oauth_chatgpt.go new file mode 100644 index 0000000..fe2dd8b --- /dev/null +++ b/portal/oauth_chatgpt.go @@ -0,0 +1,33 @@ +package main + +import ( + "fmt" + + "inou/lib" +) + +// CreateChatGPTClient creates the OAuth client for ChatGPT Custom GPT Actions. +// Call this once during setup — see docs/chatgpt-actions-setup.md. +func CreateChatGPTClient() error { + _, err := lib.OAuthClientGet("chatgpt") + if err == nil { + return nil // Already exists + } + + redirectURIs := []string{ + "https://chat.openai.com/aip/g-*/oauth/callback", + "https://chatgpt.com/aip/g-*/oauth/callback", + } + + client, secret, err := lib.OAuthClientCreate("ChatGPT Actions", redirectURIs) + if err != nil { + return err + } + + fmt.Printf("Created ChatGPT OAuth client:\n") + fmt.Printf(" Client ID: %s\n", client.ClientID) + fmt.Printf(" Client Secret: %s\n", secret) + fmt.Printf(" (Save the secret - it cannot be retrieved later)\n") + + return nil +} diff --git a/portal/static/claditor-logo.css b/portal/static/claditor-logo.css new file mode 100644 index 0000000..7edae5f --- /dev/null +++ b/portal/static/claditor-logo.css @@ -0,0 +1,89 @@ +/* Claditor logo treatments — all use Sora from inou's font stack */ + +:root { + --claditor-amber: #B45309; + --claditor-dark: #1A1A1A; + --claditor-light: #F8F7F6; +} + +/* 1. Default — confident, tight, bold */ +.claditor-logo { + font-family: 'Sora', system-ui, sans-serif; + font-weight: 700; + letter-spacing: -0.03em; + color: var(--claditor-amber); +} + +/* 2. Editorial — airy, spaced, light */ +.claditor-logo.editorial { + font-weight: 300; + letter-spacing: 0.08em; + text-transform: lowercase; + color: var(--claditor-dark); +} + +/* 3. Heavy impact — extra bold, letter-spaced */ +.claditor-logo.heavy { + font-weight: 800; + letter-spacing: 0.02em; + text-transform: uppercase; + color: var(--claditor-dark); +} + +/* 4. Inverted — white on dark */ +.claditor-logo.inverted { + font-weight: 700; + letter-spacing: -0.02em; + color: white; + text-shadow: 0 1px 3px rgba(0,0,0,0.3); +} + +/* 5. Gradient sweep */ +.claditor-logo.gradient { + font-weight: 700; + letter-spacing: -0.02em; + background: linear-gradient(90deg, var(--claditor-amber), #FF8D46); + -webkit-background-clip: text; + -webkit-text-fill-color: transparent; + background-clip: text; +} + +/* 6. Weight-shifted — letters get heavier toward the end */ +.claditor-logo.shifted { + font-weight: 400; + letter-spacing: -0.02em; +} +.claditor-logo.shifted span:last-child { font-weight: 800; } + +/* 7. Small-caps with bold first letter */ +.claditor-logo.smallcaps { + font-variant: small-caps; + font-weight: 600; + letter-spacing: 0.05em; + text-transform: lowercase; +} +.claditor-logo.smallcaps::first-letter { + font-weight: 800; + font-variant: normal; +} + +/* 8. Minimal — light, tight, subtle */ +.claditor-logo.minimal { + font-weight: 300; + letter-spacing: -0.04em; + opacity: 0.85; + color: var(--claditor-dark); +} + +/* 9. Hover lift (for links/buttons) */ +.claditor-logo.interactive { + font-weight: 700; + letter-spacing: -0.03em; + color: var(--claditor-amber); + transition: transform 0.15s ease, color 0.15s ease; + display: inline-block; +} +.claditor-logo.interactive:hover { + transform: translateY(-1px); + color: #9A4507; +} diff --git a/portal/static/viewer.js b/portal/static/viewer.js index c236238..611b1f1 100644 --- a/portal/static/viewer.js +++ b/portal/static/viewer.js @@ -432,6 +432,17 @@ async function init() { } } +// HTML entity encoder to prevent XSS +function escapeHtml(text) { + if (!text) return ''; + return text + .replace(/&/g, '&') + .replace(//g, '>') + .replace(/"/g, '"') + .replace(/'/g, '''); +} + async function addPanelEmpty() { const idx = panelCount++; const panel = { idx, seriesId: null, slices: [], currentSlice: 0 }; @@ -444,11 +455,11 @@ async function addPanelEmpty() { // Series header: show dropdown only if multiple series let headerContent; if (seriesList.length === 1) { - headerContent = '' + seriesList[0].series_desc + ' (' + seriesList[0].slice_count + ')'; + headerContent = '' + escapeHtml(seriesList[0].series_desc) + ' (' + seriesList[0].slice_count + ')'; } else { headerContent = ''; } @@ -645,7 +656,7 @@ async function add3DPanel(idx, orientation, seriesOptions) { '' + orientation + '' + '' + '
' + '' + @@ -758,7 +769,7 @@ async function changeStudyForPanel(panelIdx, studyId) { const seriesSelect = div.querySelector('.series-select'); if (seriesSelect) { seriesSelect.innerHTML = '' + - panel.seriesList.map(s => '').join(''); + panel.seriesList.map(s => '').join(''); } // Auto-select best series @@ -917,7 +928,7 @@ async function addPanel() { '' + ''; div.innerHTML = diff --git a/tools/loinc-lookup/main.go b/tools/loinc-lookup/main.go new file mode 100644 index 0000000..c2ebd94 --- /dev/null +++ b/tools/loinc-lookup/main.go @@ -0,0 +1,499 @@ +package main + +import ( + "database/sql" + "encoding/csv" + "encoding/json" + "fmt" + "log" + "os" + "strings" + + _ "github.com/mattn/go-sqlite3" + "inou/lib" +) + +const refDBPath = "/tank/inou/data/reference.db" + +var refDB *sql.DB + +func main() { + if len(os.Args) < 2 { + fmt.Fprintln(os.Stderr, `Usage: + loinc-lookup import Import LOINC lab table into reference.db + loinc-lookup [specimen] [unit] Look up LOINC code for a lab test + loinc-lookup batch Batch lookup from JSONL (one {"name","specimen","unit"} per line) + loinc-lookup stats Show cache statistics`) + os.Exit(1) + } + + lib.ConfigInit() + if err := lib.RefDBInit(refDBPath); err != nil { + log.Fatalf("RefDBInit: %v", err) + } + var err error + refDB, err = sql.Open("sqlite3", refDBPath) + if err != nil { + log.Fatalf("open reference.db: %v", err) + } + defer refDB.Close() + + switch os.Args[1] { + case "import": + if len(os.Args) < 3 { + log.Fatal("Usage: loinc-lookup import ") + } + cmdImport(os.Args[2]) + case "stats": + cmdStats() + case "batch": + if len(os.Args) < 3 { + log.Fatal("Usage: loinc-lookup batch ") + } + cmdBatch(os.Args[2]) + default: + name := os.Args[1] + specimen := "" + unit := "" + if len(os.Args) > 2 { + specimen = os.Args[2] + } + if len(os.Args) > 3 { + unit = os.Args[3] + } + cmdLookup(name, specimen, unit) + } +} + +// --- import command --- + +func cmdImport(csvPath string) { + // Create tables + for _, stmt := range []string{ + `CREATE TABLE IF NOT EXISTS loinc_lab ( + loinc_num TEXT PRIMARY KEY, + component TEXT NOT NULL, + property TEXT NOT NULL, + system TEXT NOT NULL, + scale TEXT NOT NULL, + method TEXT NOT NULL, + class TEXT NOT NULL, + long_name TEXT NOT NULL, + short_name TEXT NOT NULL + )`, + `CREATE TABLE IF NOT EXISTS loinc_cache ( + cache_key TEXT PRIMARY KEY, + input_name TEXT NOT NULL, + input_specimen TEXT NOT NULL, + input_unit TEXT NOT NULL, + loinc_code TEXT NOT NULL, + loinc_name TEXT NOT NULL, + confidence TEXT NOT NULL DEFAULT 'llm' + )`, + } { + if _, err := refDB.Exec(stmt); err != nil { + log.Fatalf("create table: %v", err) + } + } + + f, err := os.Open(csvPath) + if err != nil { + log.Fatalf("open %s: %v", csvPath, err) + } + defer f.Close() + + reader := csv.NewReader(f) + header, err := reader.Read() + if err != nil { + log.Fatalf("read header: %v", err) + } + + // Map column names to indices + colIdx := map[string]int{} + for i, h := range header { + colIdx[h] = i + } + need := []string{"LOINC_NUM", "COMPONENT", "PROPERTY", "SYSTEM", "SCALE_TYP", "METHOD_TYP", "CLASS", "LONG_COMMON_NAME", "SHORTNAME"} + for _, n := range need { + if _, ok := colIdx[n]; !ok { + log.Fatalf("missing column: %s", n) + } + } + + // Clear and re-import + refDB.Exec("DELETE FROM loinc_lab") + + tx, err := refDB.Begin() + if err != nil { + log.Fatalf("begin tx: %v", err) + } + stmt, err := tx.Prepare(`INSERT INTO loinc_lab (loinc_num, component, property, system, scale, method, class, long_name, short_name) + VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)`) + if err != nil { + log.Fatalf("prepare: %v", err) + } + + count := 0 + for { + row, err := reader.Read() + if err != nil { + break + } + stmt.Exec( + row[colIdx["LOINC_NUM"]], + row[colIdx["COMPONENT"]], + row[colIdx["PROPERTY"]], + row[colIdx["SYSTEM"]], + row[colIdx["SCALE_TYP"]], + row[colIdx["METHOD_TYP"]], + row[colIdx["CLASS"]], + row[colIdx["LONG_COMMON_NAME"]], + row[colIdx["SHORTNAME"]], + ) + count++ + } + stmt.Close() + if err := tx.Commit(); err != nil { + log.Fatalf("commit: %v", err) + } + log.Printf("Imported %d LOINC lab codes", count) +} + +// --- lookup command --- + +func cmdLookup(name, specimen, unit string) { + result, err := loincLookup(name, specimen, unit) + if err != nil { + fmt.Fprintf(os.Stderr, "Error: %v\n", err) + os.Exit(1) + } + out, _ := json.MarshalIndent(result, "", " ") + fmt.Println(string(out)) +} + +type LookupResult struct { + LoincCode string `json:"loinc_code"` + LoincName string `json:"loinc_name"` + Source string `json:"source"` // "cache" or "llm" + Candidates int `json:"candidates"` +} + +func loincLookup(name, specimen, unit string) (*LookupResult, error) { + // 1. Check cache + cacheKey := strings.ToLower(name + "|" + specimen + "|" + unit) + var cached []struct { + LoincCode string `db:"loinc_code"` + LoincName string `db:"loinc_name"` + } + lib.RefQuery("SELECT loinc_code, loinc_name FROM loinc_cache WHERE cache_key = ?", []any{cacheKey}, &cached) + if len(cached) > 0 { + return &LookupResult{ + LoincCode: cached[0].LoincCode, + LoincName: cached[0].LoincName, + Source: "cache", + }, nil + } + + // 2. Expand input to LOINC terminology via LLM, then search + // Replace "%" with "percentage" so LLM connects to LOINC's "/100 leukocytes" naming + lookupUnit := unit + if lookupUnit == "%" { + lookupUnit = "percentage" + } + tokens := tokenize(name + " " + specimen + " " + lookupUnit) + if expanded, err := llmExpand(name, specimen, lookupUnit); err == nil { + tokens = expanded + } + candidates, _ := searchCandidates(tokens) + + // If unit is %, drop candidates that are counts (#/volume, NCnc) + if unit == "%" { + var filtered []candidate + for _, c := range candidates { + if c.Property == "NCnc" { + continue + } + filtered = append(filtered, c) + } + if len(filtered) > 0 { + candidates = filtered + } + } + + if len(candidates) == 0 { + return nil, fmt.Errorf("no LOINC candidates found for %q", name) + } + + // 4. LLM pick from candidates + code, lname, err := llmPick(name, specimen, lookupUnit, candidates) + if err != nil { + return nil, err + } + + // 5. Cache + refDB.Exec(`INSERT OR REPLACE INTO loinc_cache (cache_key, input_name, input_specimen, input_unit, loinc_code, loinc_name, confidence) + VALUES (?, ?, ?, ?, ?, ?, 'llm')`, cacheKey, name, specimen, unit, code, lname) + + return &LookupResult{ + LoincCode: code, + LoincName: lname, + Source: "llm", + Candidates: len(candidates), + }, nil +} + +func tokenize(s string) []string { + s = strings.ToLower(s) + // Replace common separators with spaces + for _, c := range []string{",", ";", "(", ")", "[", "]", "/", "-", ".", ":"} { + s = strings.ReplaceAll(s, c, " ") + } + var tokens []string + seen := map[string]bool{} + for _, t := range strings.Fields(s) { + if len(t) < 2 || seen[t] { + continue + } + tokens = append(tokens, t) + seen[t] = true + } + return tokens +} + +type candidate struct { + LoincNum string `db:"loinc_num"` + LongName string `db:"long_name"` + ShortName string `db:"short_name"` + System string `db:"system"` + Component string `db:"component"` + Property string `db:"property"` +} + +func searchCandidates(tokens []string) ([]candidate, int) { + if len(tokens) == 0 { + return nil, 0 + } + + // Query per token, collect into a map keyed by loinc_num + type entry struct { + c candidate + hits int // number of distinct tokens that matched + bonus int // extra score for quality of match + } + entries := map[string]*entry{} + + for _, t := range tokens { + pattern := "%" + t + "%" + query := "SELECT loinc_num, long_name, short_name, system, component, property FROM loinc_lab WHERE " + + "LOWER(long_name) LIKE ? OR LOWER(short_name) LIKE ? OR LOWER(component) LIKE ?" + var results []candidate + lib.RefQuery(query, []any{pattern, pattern, pattern}, &results) + for _, c := range results { + if e, ok := entries[c.LoincNum]; ok { + e.hits++ + } else { + entries[c.LoincNum] = &entry{c: c, hits: 1} + } + } + } + + // Require at least 2 token matches (or 1 if only 1 token) + minHits := 2 + if len(tokens) <= 1 { + minHits = 1 + } + + // Score: hits × 100 + bonus for component exactness (shorter component = more specific) + type scored struct { + c candidate + score int + } + var scoredResults []scored + for _, e := range entries { + if e.hits < minHits { + continue + } + s := e.hits * 100 + // Bonus: prefer entries where component is a simple term, not a compound like "Carboxyhemoglobin/Hemoglobin.total" + compLen := len(e.c.Component) + if compLen > 0 && compLen < 50 { + s += 50 - compLen // shorter component = higher bonus + } + // Bonus: prefer entries without "/" in component (simple analytes) + if !strings.Contains(e.c.Component, "/") { + s += 20 + } + scoredResults = append(scoredResults, scored{e.c, s}) + } + + // Sort by score descending, take top 30 + for i := range scoredResults { + for j := i + 1; j < len(scoredResults); j++ { + if scoredResults[j].score > scoredResults[i].score { + scoredResults[i], scoredResults[j] = scoredResults[j], scoredResults[i] + } + } + } + var top []candidate + maxHits := 0 + for i, s := range scoredResults { + if i >= 30 { + break + } + top = append(top, s.c) + hits := s.score / 100 // extract hit count from score + if hits > maxHits { + maxHits = hits + } + } + return top, maxHits +} + +func llmExpand(name, specimen, unit string) ([]string, error) { + prompt := fmt.Sprintf(`Given a lab test, return search terms to find it in the LOINC database. +LOINC uses formal medical terminology (e.g. "Leukocytes" not "White Blood Cells", "Erythrocytes" not "Red Blood Cells", "Oxygen" not "O2" or "pO2"). + +Lab test: + Name: %s + Specimen: %s + Unit: %s + +Return a JSON object: {"terms": ["term1", "term2", ...]} +Include: the LOINC component name, specimen system code (e.g. Bld, BldA, BldC, BldV, Ser/Plas, Urine), and any synonyms that might appear in LOINC long names. +Keep it to 3-6 terms. JSON only.`, name, specimen, unit) + + resp, err := lib.CallGemini(prompt) + if err != nil { + return nil, err + } + + var result struct { + Terms []string `json:"terms"` + } + if err := json.Unmarshal([]byte(resp), &result); err != nil { + return nil, fmt.Errorf("parse expand response %q: %w", resp, err) + } + + // Lowercase all terms and add original input tokens as fallback + var terms []string + seen := map[string]bool{} + for _, t := range result.Terms { + t = strings.ToLower(strings.TrimSpace(t)) + if t != "" && !seen[t] { + terms = append(terms, t) + seen[t] = true + } + } + // Also include original tokens so we never lose the raw input + for _, t := range tokenize(name + " " + specimen) { + if !seen[t] { + terms = append(terms, t) + seen[t] = true + } + } + return terms, nil +} + +func llmPick(name, specimen, unit string, candidates []candidate) (string, string, error) { + // Format candidates as a numbered list + // Replace "/100" and "fraction" with "percentage" so LLM connects them to "%" unit + var lines []string + for i, c := range candidates { + display := c.LongName + display = strings.ReplaceAll(display, "/100 ", "percentage of ") + display = strings.ReplaceAll(display, "fraction", "percentage") + lines = append(lines, fmt.Sprintf("%d. %s — %s [System: %s]", i+1, c.LoincNum, display, c.System)) + } + + prompt := fmt.Sprintf(`You are a clinical laboratory informatics system. Given a lab test, pick the BEST matching LOINC code from the candidate list. + +Lab test: + Name: %s + Specimen: %s + Unit: %s + +Candidates: +%s + +Return ONLY a JSON object: {"pick": , "loinc": "", "name": ""} +Pick the candidate that best matches the test name, specimen type, and unit. If none match well, pick the closest. +JSON only, no explanation.`, name, specimen, unit, strings.Join(lines, "\n")) + + resp, err := lib.CallGemini(prompt) + if err != nil { + return "", "", fmt.Errorf("LLM call failed: %w", err) + } + + var result struct { + Pick int `json:"pick"` + Loinc string `json:"loinc"` + Name string `json:"name"` + } + if err := json.Unmarshal([]byte(resp), &result); err != nil { + return "", "", fmt.Errorf("parse LLM response %q: %w", resp, err) + } + + // Resolve by pick number if loinc field is empty + if result.Loinc == "" && result.Pick > 0 && result.Pick <= len(candidates) { + result.Loinc = candidates[result.Pick-1].LoincNum + result.Name = candidates[result.Pick-1].LongName + } + // Verify the code is actually in our candidate list + for _, c := range candidates { + if c.LoincNum == result.Loinc { + return result.Loinc, c.LongName, nil + } + } + // Pick number as fallback + if result.Pick > 0 && result.Pick <= len(candidates) { + c := candidates[result.Pick-1] + return c.LoincNum, c.LongName, nil + } + return "", "", fmt.Errorf("LLM returned %q (pick %d) — not in %d candidates", result.Loinc, result.Pick, len(candidates)) +} + +// --- batch command --- + +func cmdBatch(path string) { + data, err := os.ReadFile(path) + if err != nil { + log.Fatalf("read %s: %v", path, err) + } + for _, line := range strings.Split(string(data), "\n") { + line = strings.TrimSpace(line) + if line == "" { + continue + } + var input struct { + Name string `json:"name"` + Specimen string `json:"specimen"` + Unit string `json:"unit"` + } + if err := json.Unmarshal([]byte(line), &input); err != nil { + fmt.Fprintf(os.Stderr, "skip bad line: %s\n", line) + continue + } + result, err := loincLookup(input.Name, input.Specimen, input.Unit) + if err != nil { + fmt.Fprintf(os.Stderr, "%s: %v\n", input.Name, err) + continue + } + fmt.Printf("%-40s → %s %s [%s]\n", input.Name, result.LoincCode, result.LoincName, result.Source) + } +} + +// --- stats command --- + +func cmdStats() { + var total []struct{ N int `db:"n"` } + lib.RefQuery("SELECT COUNT(*) as n FROM loinc_lab", nil, &total) + if len(total) > 0 { + fmt.Printf("LOINC lab codes: %d\n", total[0].N) + } + + var cached []struct{ N int `db:"n"` } + lib.RefQuery("SELECT COUNT(*) as n FROM loinc_cache", nil, &cached) + if len(cached) > 0 { + fmt.Printf("Cached lookups: %d\n", cached[0].N) + } +} diff --git a/web/static/genetics.html b/web/static/genetics.html new file mode 100644 index 0000000..5ba7eb7 --- /dev/null +++ b/web/static/genetics.html @@ -0,0 +1,720 @@ + + + + + +inou — Genetics + + + + + +
+ +
+
+
Jane Doe
+
DOB Jan 1 2017 · Female
+
+
JD
+
+
+ +
+ + + + + +
+ + +
+
+ Jane Doe › Tests › Genetics +
+
+ ⌕ + +
+
+ + +
+
+
3,866
+
Total variants
+
+
+
+
12
+
Categories
+
+
+
+
597
+
Hidden (no risk)
+
+
Show hidden variants
+
+ + +
+
+
Traits
+
132
+
49 hidden
+
+
+
Longevity
+
12
+
1 hidden
+
+
+
Metabolism
+
97
+
51 hidden
+
+
+
Medications
+
101
+
26 hidden
+
+
+
Mental Health
+
63
+
31 hidden
+
+
+
Neurological
+
91
+
46 hidden
+
+
+
Fertility
+
12
+
7 hidden
+
+
+
Blood
+
100
+
12 hidden
+
+
+
Cardiovascular
+
104
+
31 hidden
+
+
+
Autoimmune
+
80
+
43 hidden
+
+
+
Disease
+
2,272
+
233 hidden
+
+
+
Cancer
+
998
+
67 hidden
+
+
+ + +
+
+
+
Metabolism · 97 variants
+
Sorted by significance
+
+
+ Show hidden +
+
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
GeneFindingGenotypeSignificance
MTHFR
rs1801133
10–20% folate processing efficiency
AA
Moderate
CYP2C19
rs4244285
Poorer metabolizer of several medicines
AG
Moderate
PPARG
rs1801282
Higher cardiovascular risk with high fat diet
CG
Moderate
TCF7L2
rs7903146
Increased type 2 diabetes risk
CT
Moderate
FTO
rs9939609
1.67× increased obesity risk
AT
Moderate
SLCO1B1
rs4149056
Increased statin-induced myopathy risk
CT
Moderate
APOA2
rs5082
Associated with higher HDL cholesterol
CC
Protective
CYP1A2
rs762551
Slow caffeine metabolizer
AC
Low
CYP3A5
rs776746
Non-expressor — affects drug dosing
CC
Low
MCM6
rs4988235
Partial lactase persistence
AG
Low
APOE
rs7412
Normal lipid metabolism
CC
Clear
GCK
rs1799884
Slightly reduced glucose sensing
AG
Low
+ +
+
Showing 12 of 97 variants
+ Load more +
+
+ + +
+
+ Your AI has access to all 3,866 variants, including hidden ones. Ask it to reason across your metabolism, medication sensitivities, and disease risk together. +
+ +
+ +
+
+ + +