step7 insertat tax_id

Author: NIU1636242

curation-pipeline/src/components/steps/Step2GenomeTF.jsx

@@ -123,6 +123,11 @@ async function computeTaxonomyForAcc(acc) {
   return payload;
 }
 
+computeTaxonomyForAcc(accession).then((payload) => {
+  console.log("TAXONOMY payload", accession, payload);
+});
+
+
 export default function Step2GenomeTF() {
   const {
     tf,

curation-pipeline/src/components/steps/Step7CurationInfo.jsx

@@ -360,19 +360,55 @@ WHERE NOT EXISTS (
     }
 
     // Taxonomia + link a genome
+    // Inserta la cadena completa (ancestros + hoja)
+    // Pero la BD "indexa" hasta species: si el leaf es strain/subspecies, enlazamos el genoma a la species.
     const taxByAcc = taxonomyData?.byAccession || {};
 
+    const rankScore = (r) => {
+      const x = String(r || "no rank").toLowerCase();
+      const order = {
+        "no rank": 0,
+        superkingdom: 1,
+        kingdom: 2,
+        phylum: 3,
+        class: 4,
+        order: 5,
+        family: 6,
+        genus: 7,
+        species: 8,
+        subspecies: 9,
+        strain: 10,
+      };
+      return order[x] ?? 0;
+    };
+
     for (const acc of accessions) {
       const tInfo = taxByAcc?.[acc];
-      const chain = Array.isArray(tInfo?.chain) ? tInfo.chain : [];
-      if (!chain.length) continue;
+      const chainRaw = Array.isArray(tInfo?.chain) ? tInfo.chain : [];
+      if (!chainRaw.length) continue;
+
+      // Aseguramos orden de general -> específico.
+      // Si viene al revés, invertimos (p.ej. empieza en strain y termina en phylum).
+      const chainOrdered = [...chainRaw];
+      if (chainOrdered.length >= 2) {
+        const first = rankScore(chainOrdered[0]?.rank);
+        const last = rankScore(chainOrdered[chainOrdered.length - 1]?.rank);
+        if (first > last) chainOrdered.reverse();
+      }
+
+      // Si NCBI devuelve strain/subspecies, recortamos la cadena para enlazar el genoma a species.
+      let chain = chainOrdered;
+      const idxSpecies = chainOrdered.findIndex((n) => String(n?.rank || "").toLowerCase() === "species");
+      if (idxSpecies >= 0) chain = chainOrdered.slice(0, idxSpecies + 1);
 
+      // Insert/Update de cada nodo y su parent_id (FK a core_taxonomy.id)
       for (let i = 0; i < chain.length; i++) {
         const node = chain[i];
         const taxid = String(node.taxonomy_id || "").trim();
+        if (!taxid) continue;
+
         const name = String(node.name || "").trim();
         const rank = String(node.rank || "no rank").trim();
-        if (!taxid) continue;
 
         const parentTaxid = i > 0 ? String(chain[i - 1].taxonomy_id || "").trim() : "";
         const parentIdExpr = parentTaxid
@@ -401,6 +437,7 @@ WHERE taxonomy_id='${esc(taxid)}';
     `.trim());
       }
 
+      // Enlazamos el genoma al leaf elegido (species si existe; si no, el último del chain)
       const leafTaxid = String(chain[chain.length - 1]?.taxonomy_id || "").trim();
       if (leafTaxid) {
         sql.push(`