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Revert 'fix: add legacy genome data format support to API' - investigating actual issue

This commit is contained in:
James 2026-02-09 14:04:50 -05:00
parent 0ac8f0f42d
commit c88c50bc12
1 changed files with 3 additions and 73 deletions
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76
lib/v2.go
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@ -1028,34 +1028,16 @@ func AccessRevokeEntry(dossierID, granteeID, entryID string) error {
// API handlers, the API should perform its own RBAC check first.
// GenomeGetExtraction returns the extraction entry for genome data
// Supports both new hierarchical format (extraction -> tier -> variant) and legacy flat format
func GenomeGetExtraction(ctx *AccessContext, dossierID string) (*Entry, error) {
// Try new format first (type="extraction")
entries, err := EntryList(accessorIDFromContext(ctx), "", CategoryGenome, &EntryFilter{
DossierID: dossierID,
Type: "extraction",
Limit: 1,
})
if err == nil && len(entries) > 0 {
return entries[0], nil
}
// Fallback: check if there are ANY category 4 entries (legacy format)
legacyEntries, err := EntryList(accessorIDFromContext(ctx), "", CategoryGenome, &EntryFilter{
DossierID: dossierID,
Limit: 1,
})
if err != nil || len(legacyEntries) == 0 {
if err != nil || len(entries) == 0 {
return nil, fmt.Errorf("no genome data")
}
// Return a synthetic extraction entry for legacy data
return &Entry{
EntryID: "legacy-extraction",
DossierID: dossierID,
Category: CategoryGenome,
Type: "extraction-legacy",
}, nil
return entries[0], nil
}
// GenomeTier represents a genome category tier
@ -1065,18 +1047,7 @@ type GenomeTier struct {
}
// GenomeGetTiers returns all tier entries for a genome extraction
// Supports both new hierarchical format and legacy flat format
func GenomeGetTiers(ctx *AccessContext, dossierID, extractionID string) ([]GenomeTier, error) {
// Check if this is legacy format
if extractionID == "legacy-extraction" {
// For legacy format, return a single synthetic "all" tier
return []GenomeTier{{
TierID: "legacy-all",
Category: "all",
}}, nil
}
// New format: get actual tier entries
entries, err := EntryList(accessorIDFromContext(ctx), extractionID, CategoryGenome, &EntryFilter{
DossierID: dossierID,
Type: "tier",
@ -1126,53 +1097,12 @@ type GenomeVariant struct {
}
// GenomeGetVariants returns variants for specified tier IDs
// Supports both new hierarchical format and legacy flat format
func GenomeGetVariants(ctx *AccessContext, dossierID string, tierIDs []string) ([]GenomeVariant, error) {
if len(tierIDs) == 0 {
return nil, nil
}
// Check if this is legacy format
if len(tierIDs) == 1 && tierIDs[0] == "legacy-all" {
// Legacy format: get all top-level category 4 entries
entries, err := EntryList(accessorIDFromContext(ctx), "", CategoryGenome, &EntryFilter{
DossierID: dossierID,
})
if err != nil {
return nil, err
}
var variants []GenomeVariant
for _, e := range entries {
// Skip non-rsid types (like "extraction", "tier", etc.)
if !strings.HasPrefix(e.Type, "rs") {
continue
}
var data struct {
Mag float64 `json:"mag"`
Rep string `json:"rep"`
Sum string `json:"sum"`
Sub string `json:"sub"`
}
json.Unmarshal([]byte(e.Data), &data)
variants = append(variants, GenomeVariant{
EntryID: e.EntryID,
RSID: e.Type,
Genotype: e.Value,
Gene: e.Tags,
Magnitude: data.Mag,
Repute: data.Rep,
Summary: data.Sum,
Subcategory: data.Sub,
TierID: "legacy-all",
})
}
return variants, nil
}
// New format: query entries for each tier and deduplicate by type (rsid)
// Query entries for each tier and deduplicate by type (rsid)
seen := make(map[string]bool)
var variants []GenomeVariant