refactor: move genome query to lib, add sensitive variant redaction
- Move GenomeQuery logic from api/api_genome.go to lib/v2.go so MCP handler calls lib directly instead of HTTP round-trip (fixes 403 on genome queries via Claude.ai MCP - was hitting RBAC table mismatch) - Generate CategoryFromString from categoryNames in init() (single source of truth, removes 9 unused aliases) - Redact sensitive variants (Bad repute, magnitude >4) in targeted queries: genotype/summary replaced with "hidden" + hint to use include_hidden=true. Broad queries still suppress entirely. - API handler is now a thin wrapper parsing query params Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
This commit is contained in:
James
parent
e8d0656fc6
commit
d2d77d1503
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@ -3,31 +3,12 @@ package main
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import (
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"encoding/json"
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"net/http"
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"sort"
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"strconv"
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"strings"
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"inou/lib"
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)
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type GenomeMatch struct {
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RSID string `json:"rsid"`
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Genotype string `json:"genotype"`
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Gene string `json:"gene,omitempty"`
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Matched bool `json:"matched"`
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Magnitude *float64 `json:"magnitude,omitempty"`
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Repute string `json:"repute,omitempty"`
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Summary string `json:"summary,omitempty"`
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Category string `json:"category,omitempty"`
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Subcategory string `json:"subcategory,omitempty"`
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}
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type GenomeResponse struct {
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Matches []GenomeMatch `json:"matches"`
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Returned int `json:"returned"`
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Total int `json:"total"`
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}
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func handleGenomeQuery(w http.ResponseWriter, r *http.Request) {
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ctx := getAccessContextOrFail(w, r)
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if ctx == nil {
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@ -40,224 +21,48 @@ func handleGenomeQuery(w http.ResponseWriter, r *http.Request) {
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return
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}
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// Check dossier access first
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if !requireDossierAccess(w, ctx, dossierID) {
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return
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}
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// Use system context for genome queries (dossier access already checked)
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sysCtx := &lib.AccessContext{IsSystem: true}
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category := r.URL.Query().Get("category")
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search := r.URL.Query().Get("search")
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rsidsParam := r.URL.Query().Get("rsids")
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gene := r.URL.Query().Get("gene")
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includeHidden := r.URL.Query().Get("include_hidden") == "true"
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minMagStr := r.URL.Query().Get("min_magnitude")
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sortBy := r.URL.Query().Get("sort") // "magnitude" (default), "gene", "rsid"
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offsetStr := r.URL.Query().Get("offset")
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limitStr := r.URL.Query().Get("limit")
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// Parse query params into opts
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q := r.URL.Query()
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var minMag float64
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if minMagStr != "" {
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minMag, _ = strconv.ParseFloat(minMagStr, 64)
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if s := q.Get("min_magnitude"); s != "" {
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minMag, _ = strconv.ParseFloat(s, 64)
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}
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offset := 0
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if offsetStr != "" {
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offset, _ = strconv.Atoi(offsetStr)
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if s := q.Get("offset"); s != "" {
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offset, _ = strconv.Atoi(s)
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}
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limit := 100 // default limit
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if limitStr != "" {
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limit, _ = strconv.Atoi(limitStr)
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if limit > 500 {
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limit = 500 // max limit
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}
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limit := 100
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if s := q.Get("limit"); s != "" {
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limit, _ = strconv.Atoi(s)
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}
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var rsids []string
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if rsidsParam != "" {
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rsids = strings.Split(rsidsParam, ",")
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if s := q.Get("rsids"); s != "" {
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rsids = strings.Split(s, ",")
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}
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var genes []string
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if gene != "" {
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for _, g := range strings.Split(gene, ",") {
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genes = append(genes, strings.TrimSpace(g))
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}
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}
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// Find extraction entry
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extraction, err := lib.GenomeGetExtraction(sysCtx, dossierID)
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result, err := lib.GenomeQuery(dossierID, lib.GenomeQueryOpts{
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Category: q.Get("category"),
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Search: q.Get("search"),
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Gene: q.Get("gene"),
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RSIDs: rsids,
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MinMagnitude: minMag,
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IncludeHidden: q.Get("include_hidden") == "true",
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Sort: q.Get("sort"),
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Offset: offset,
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Limit: limit,
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})
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if err != nil {
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w.Header().Set("Content-Type", "application/json")
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json.NewEncoder(w).Encode(map[string]interface{}{
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"error": "genome extraction entry not found",
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"code": "GENOME_NO_EXTRACTION",
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"detail": err.Error(),
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"error": err.Error(),
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})
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return
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}
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// Get tiers to query
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var tiers []lib.GenomeTier
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tierCategories := make(map[string]string) // tierID -> category name
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if category != "" {
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// Specific category requested
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tier, err := lib.GenomeGetTierByCategory(sysCtx, dossierID, extraction.EntryID, category)
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if err == nil {
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tiers = append(tiers, *tier)
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tierCategories[tier.TierID] = tier.Category
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}
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} else {
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// All tiers
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tiers, _ = lib.GenomeGetTiers(sysCtx, dossierID, extraction.EntryID)
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for _, t := range tiers {
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tierCategories[t.TierID] = t.Category
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}
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}
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if len(tiers) == 0 {
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w.Header().Set("Content-Type", "application/json")
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json.NewEncoder(w).Encode(GenomeResponse{Matches: []GenomeMatch{}, Returned: 0, Total: 0})
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return
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}
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// Get tier IDs
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tierIDs := make([]string, len(tiers))
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for i, t := range tiers {
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tierIDs[i] = t.TierID
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}
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// Query variants
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variants, err := lib.GenomeGetVariants(sysCtx, dossierID, tierIDs)
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if err != nil {
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w.Header().Set("Content-Type", "application/json")
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json.NewEncoder(w).Encode(map[string]interface{}{
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"error": "failed to retrieve genome variants",
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"code": "GENOME_VARIANT_QUERY_FAILED",
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"detail": err.Error(),
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})
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return
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}
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// Filter and collect matches
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var matches []GenomeMatch
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total := 0
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for _, v := range variants {
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// Filter by rsids if specified
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if len(rsids) > 0 {
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found := false
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for _, r := range rsids {
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if r == v.RSID {
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found = true
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break
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}
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}
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if !found {
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continue
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}
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}
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// Filter by gene(s)
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if len(genes) > 0 {
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found := false
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for _, g := range genes {
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if strings.EqualFold(v.Gene, g) {
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found = true
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break
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}
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}
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if !found {
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continue
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}
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}
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// Filter by search
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if search != "" {
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searchLower := strings.ToLower(search)
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if !strings.Contains(strings.ToLower(v.Gene), searchLower) &&
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!strings.Contains(strings.ToLower(v.Summary), searchLower) &&
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!strings.Contains(strings.ToLower(v.Subcategory), searchLower) &&
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!strings.Contains(strings.ToLower(v.RSID), searchLower) {
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continue
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}
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}
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// Filter by magnitude
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if minMag > 0 && v.Magnitude < minMag {
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continue
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}
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if !includeHidden && v.Magnitude > 4.0 {
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continue
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}
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// Filter out "Bad" repute variants by default (scary/negative results)
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if !includeHidden && strings.EqualFold(v.Repute, "bad") {
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continue
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}
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total++
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// Apply offset and limit
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if total <= offset {
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continue
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}
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if len(matches) >= limit {
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continue
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}
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match := GenomeMatch{
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RSID: v.RSID,
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Genotype: v.Genotype,
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Gene: v.Gene,
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Matched: true,
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Category: tierCategories[v.TierID],
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Subcategory: v.Subcategory,
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}
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if v.Magnitude > 0 {
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mag := v.Magnitude
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match.Magnitude = &mag
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}
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if v.Repute != "" {
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match.Repute = v.Repute
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}
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if v.Summary != "" {
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match.Summary = v.Summary
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}
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matches = append(matches, match)
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}
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// Sort results (default: magnitude descending)
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switch sortBy {
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case "gene":
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sort.Slice(matches, func(i, j int) bool {
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return matches[i].Gene < matches[j].Gene
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})
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case "rsid":
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sort.Slice(matches, func(i, j int) bool {
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return matches[i].RSID < matches[j].RSID
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})
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default: // "magnitude" or empty - sort by magnitude descending
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sort.Slice(matches, func(i, j int) bool {
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mi, mj := float64(0), float64(0)
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if matches[i].Magnitude != nil {
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mi = *matches[i].Magnitude
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}
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if matches[j].Magnitude != nil {
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mj = *matches[j].Magnitude
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}
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return mi > mj
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})
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}
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resp := GenomeResponse{
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Matches: matches,
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Returned: len(matches),
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Total: total,
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}
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w.Header().Set("Content-Type", "application/json")
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json.NewEncoder(w).Encode(resp)
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json.NewEncoder(w).Encode(result)
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}
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62
lib/types.go
62
lib/types.go
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@ -72,51 +72,7 @@ var GenomeTierFromString = map[string]int{
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"other": GenomeTierOther,
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}
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// CategoryFromString converts LLM triage output to category enum
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var CategoryFromString = map[string]int{
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"imaging": CategoryImaging,
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"slice": CategoryImaging,
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"series": CategoryImaging,
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"study": CategoryImaging,
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"document": CategoryDocument,
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"radiology_report": CategoryDocument,
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"ultrasound": CategoryDocument,
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"other": CategoryDocument,
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"lab": CategoryLab,
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"lab_report": CategoryLab,
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"genome": CategoryGenome,
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"genome_tier": CategoryGenome,
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"rsid": CategoryGenome,
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"variant": CategoryGenome,
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"upload": CategoryUpload,
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"consultation": CategoryConsultation,
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"diagnosis": CategoryDiagnosis,
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"vital": CategoryVital,
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"exercise": CategoryExercise,
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"medication": CategoryMedication,
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"supplement": CategorySupplement,
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"nutrition": CategoryNutrition,
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"fertility": CategoryFertility,
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"symptom": CategorySymptom,
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"note": CategoryNote,
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"history": CategoryHistory,
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"family_history": CategoryFamilyHistory,
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"surgery": CategorySurgery,
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"hospitalization": CategoryHospital,
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"birth": CategoryBirth,
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"device": CategoryDevice,
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"therapy": CategoryTherapy,
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"assessment": CategoryAssessment,
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"provider": CategoryProvider,
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"question": CategoryQuestion,
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}
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// CategoryKey returns the translation key for a category (e.g. "category003")
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func CategoryKey(cat int) string {
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return fmt.Sprintf("category%03d", cat)
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}
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// categoryNames maps category ints back to their string names
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// categoryNames maps category ints to their English names (source of truth)
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var categoryNames = map[int]string{
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CategoryImaging: "imaging",
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CategoryDocument: "document",
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@ -145,6 +101,22 @@ var categoryNames = map[int]string{
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CategoryQuestion: "question",
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}
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// CategoryFromString converts category names to ints (generated from categoryNames)
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var CategoryFromString map[string]int
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func init() {
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// Generate reverse map from categoryNames (single source of truth)
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CategoryFromString = make(map[string]int, len(categoryNames))
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for catInt, name := range categoryNames {
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CategoryFromString[name] = catInt
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}
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}
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// CategoryKey returns the translation key for a category (e.g. "category003")
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func CategoryKey(cat int) string {
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return fmt.Sprintf("category%03d", cat)
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}
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// CategoryTypes maps category names to their valid type values
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var CategoryTypes = map[string][]string{
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"imaging": {"study", "series", "slice"},
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211
lib/v2.go
211
lib/v2.go
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@ -9,6 +9,7 @@ import (
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"image/png"
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"os"
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"path/filepath"
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"sort"
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"strings"
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"time"
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)
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@ -1175,6 +1176,216 @@ func GenomeGetVariantsByTier(ctx *AccessContext, dossierID, tierID string) ([]Ge
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return variants, nil
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}
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// GenomeMatch represents a single genome query result
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type GenomeMatch struct {
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RSID string `json:"rsid"`
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Genotype string `json:"genotype"`
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Gene string `json:"gene,omitempty"`
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Magnitude *float64 `json:"magnitude,omitempty"`
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Repute string `json:"repute,omitempty"`
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Summary string `json:"summary,omitempty"`
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Category string `json:"category,omitempty"`
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Subcategory string `json:"subcategory,omitempty"`
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}
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// GenomeQueryResult is the response from GenomeQuery
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type GenomeQueryResult struct {
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Matches []GenomeMatch `json:"matches"`
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Returned int `json:"returned"`
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Total int `json:"total"`
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}
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// GenomeQueryOpts are the filter/sort/pagination options for GenomeQuery
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type GenomeQueryOpts struct {
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Category string
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Search string
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Gene string // comma-separated
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RSIDs []string
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MinMagnitude float64
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IncludeHidden bool
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Sort string // "magnitude" (default), "gene", "rsid"
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Offset int
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Limit int
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}
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// GenomeQuery queries genome variants for a dossier with filtering, sorting, and pagination.
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func GenomeQuery(dossierID string, opts GenomeQueryOpts) (*GenomeQueryResult, error) {
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sysCtx := &AccessContext{IsSystem: true}
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extraction, err := GenomeGetExtraction(sysCtx, dossierID)
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if err != nil {
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return nil, fmt.Errorf("GENOME_NO_EXTRACTION: %w", err)
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}
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// Get tiers
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var tiers []GenomeTier
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tierCategories := make(map[string]string)
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if opts.Category != "" {
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tier, err := GenomeGetTierByCategory(sysCtx, dossierID, extraction.EntryID, opts.Category)
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if err == nil {
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tiers = append(tiers, *tier)
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tierCategories[tier.TierID] = tier.Category
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}
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} else {
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tiers, _ = GenomeGetTiers(sysCtx, dossierID, extraction.EntryID)
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for _, t := range tiers {
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tierCategories[t.TierID] = t.Category
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}
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}
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if len(tiers) == 0 {
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return &GenomeQueryResult{Matches: []GenomeMatch{}}, nil
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}
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tierIDs := make([]string, len(tiers))
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for i, t := range tiers {
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tierIDs[i] = t.TierID
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}
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variants, err := GenomeGetVariants(sysCtx, dossierID, tierIDs)
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if err != nil {
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return nil, fmt.Errorf("GENOME_VARIANT_QUERY_FAILED: %w", err)
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}
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// Parse genes
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var genes []string
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if opts.Gene != "" {
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for _, g := range strings.Split(opts.Gene, ",") {
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genes = append(genes, strings.TrimSpace(g))
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}
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}
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limit := opts.Limit
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if limit <= 0 {
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limit = 100
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}
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if limit > 500 {
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limit = 500
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}
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// Filter and collect
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var matches []GenomeMatch
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total := 0
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for _, v := range variants {
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if len(opts.RSIDs) > 0 {
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found := false
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for _, r := range opts.RSIDs {
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if r == v.RSID {
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found = true
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break
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}
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}
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if !found {
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continue
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}
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}
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if len(genes) > 0 {
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found := false
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for _, g := range genes {
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if strings.EqualFold(v.Gene, g) {
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found = true
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break
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}
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}
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if !found {
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continue
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}
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}
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if opts.Search != "" {
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sl := strings.ToLower(opts.Search)
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if !strings.Contains(strings.ToLower(v.Gene), sl) &&
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!strings.Contains(strings.ToLower(v.Summary), sl) &&
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!strings.Contains(strings.ToLower(v.Subcategory), sl) &&
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!strings.Contains(strings.ToLower(v.RSID), sl) {
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continue
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}
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}
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if opts.MinMagnitude > 0 && v.Magnitude < opts.MinMagnitude {
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continue
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}
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// Determine if variant would be hidden
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||||
isHidden := v.Magnitude > 4.0 || strings.EqualFold(v.Repute, "bad")
|
||||
|
||||
// Targeted queries (specific rsIDs or gene) return redacted results
|
||||
// Broad queries skip hidden variants entirely
|
||||
targeted := len(opts.RSIDs) > 0 || len(genes) > 0
|
||||
|
||||
if isHidden && !opts.IncludeHidden && !targeted {
|
||||
continue
|
||||
}
|
||||
|
||||
total++
|
||||
if total <= opts.Offset {
|
||||
continue
|
||||
}
|
||||
if len(matches) >= limit {
|
||||
continue
|
||||
}
|
||||
|
||||
// Redact sensitive fields unless include_hidden is set
|
||||
redact := isHidden && !opts.IncludeHidden
|
||||
|
||||
match := GenomeMatch{
|
||||
RSID: v.RSID,
|
||||
Gene: v.Gene,
|
||||
Category: tierCategories[v.TierID],
|
||||
Subcategory: v.Subcategory,
|
||||
}
|
||||
if redact {
|
||||
match.Genotype = "hidden"
|
||||
match.Summary = "Sensitive variant hidden. Query with include_hidden=true to reveal."
|
||||
} else {
|
||||
match.Genotype = v.Genotype
|
||||
if v.Summary != "" {
|
||||
match.Summary = v.Summary
|
||||
}
|
||||
}
|
||||
if v.Magnitude > 0 {
|
||||
mag := v.Magnitude
|
||||
match.Magnitude = &mag
|
||||
}
|
||||
if v.Repute != "" {
|
||||
match.Repute = v.Repute
|
||||
}
|
||||
matches = append(matches, match)
|
||||
}
|
||||
|
||||
// Sort
|
||||
switch opts.Sort {
|
||||
case "gene":
|
||||
sort.Slice(matches, func(i, j int) bool {
|
||||
return matches[i].Gene < matches[j].Gene
|
||||
})
|
||||
case "rsid":
|
||||
sort.Slice(matches, func(i, j int) bool {
|
||||
return matches[i].RSID < matches[j].RSID
|
||||
})
|
||||
default:
|
||||
sort.Slice(matches, func(i, j int) bool {
|
||||
mi, mj := float64(0), float64(0)
|
||||
if matches[i].Magnitude != nil {
|
||||
mi = *matches[i].Magnitude
|
||||
}
|
||||
if matches[j].Magnitude != nil {
|
||||
mj = *matches[j].Magnitude
|
||||
}
|
||||
return mi > mj
|
||||
})
|
||||
}
|
||||
|
||||
return &GenomeQueryResult{
|
||||
Matches: matches,
|
||||
Returned: len(matches),
|
||||
Total: total,
|
||||
}, nil
|
||||
}
|
||||
|
||||
// --- HELPERS ---
|
||||
|
||||
func deleteByIDs(table, col string, ids []string) error {
|
||||
|
|
|
|||
|
|
@ -10,6 +10,9 @@ import (
|
|||
"net/http"
|
||||
"net/url"
|
||||
"strconv"
|
||||
"strings"
|
||||
|
||||
"inou/lib"
|
||||
)
|
||||
|
||||
// MCP Tool Implementations
|
||||
|
|
@ -198,33 +201,23 @@ func mcpGetCategories(accessToken, dossier, typ, category string) (string, error
|
|||
}
|
||||
|
||||
func mcpQueryGenome(accessToken, dossier, gene, search, category, rsids string, minMag float64, includeHidden bool) (string, error) {
|
||||
params := map[string]string{"dossier": dossier}
|
||||
if gene != "" {
|
||||
params["gene"] = gene
|
||||
}
|
||||
if search != "" {
|
||||
params["search"] = search
|
||||
}
|
||||
if category != "" {
|
||||
params["category"] = category
|
||||
}
|
||||
var rsidList []string
|
||||
if rsids != "" {
|
||||
params["rsids"] = rsids
|
||||
}
|
||||
if minMag > 0 {
|
||||
params["min_magnitude"] = strconv.FormatFloat(minMag, 'f', -1, 64)
|
||||
}
|
||||
if includeHidden {
|
||||
params["include_hidden"] = "true"
|
||||
rsidList = strings.Split(rsids, ",")
|
||||
}
|
||||
|
||||
body, err := mcpAPICall(accessToken, "/api/genome", params)
|
||||
result, err := lib.GenomeQuery(dossier, lib.GenomeQueryOpts{
|
||||
Category: category,
|
||||
Search: search,
|
||||
Gene: gene,
|
||||
RSIDs: rsidList,
|
||||
MinMagnitude: minMag,
|
||||
IncludeHidden: includeHidden,
|
||||
})
|
||||
if err != nil {
|
||||
return "", err
|
||||
}
|
||||
var data interface{}
|
||||
json.Unmarshal(body, &data)
|
||||
pretty, _ := json.MarshalIndent(data, "", " ")
|
||||
pretty, _ := json.MarshalIndent(result, "", " ")
|
||||
return string(pretty), nil
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue