Adds ability to upload tsv to db

frontend/app/(dashboard)/data/features/[featureId]/page.tsx

@@ -11,7 +11,7 @@ export default async function FeatureId({ params }: { params: { featureId: strin
 	const headers = lines[0].split("\t");
 
 	for (let i = 1; i < lines.length; i++) {
-		const obj = {} as { featureid: String, species: String };
+		const obj = {} as { featureid: string, species: string };
 		const currentline = lines[i].split("\t");
 
 		for (let j = 0; j < headers.length; j++) {
@@ -21,7 +21,7 @@ export default async function FeatureId({ params }: { params: { featureId: strin
 
     	result.push(obj);
  	}
-	const feature = result.find((f) => f.featureid === params.featureId) as { featureid: String, species: String };
+	const feature = result.find((f) => f.featureid === params.featureId) as { featureid: string, species: string };
 	//const records = parse(content, { bom: true, columns: true });
 	//console.log(records)
 

frontend/app/(dashboard)/data/page.tsx

@@ -1,6 +1,6 @@
+import AsvUpload from "@/components/AsvUpload";
 import ProjectCatalogue from "@/components/ProjectCatalogue";
 import Search from "@/components/Search";
-import { getRemoteUrl } from "@/helpers/utils";
 import dynamic from "next/dynamic";
 const Map = dynamic(() => import("@/components/Map"), {
 	ssr: false,
@@ -18,6 +18,7 @@ export default async function Dashboard() {
 
 	return (
 		<main className="flex flex-col z-40 m-5 gap-5">
+			<AsvUpload></AsvUpload>
 			<Search placeholder="Search"></Search>
 			<div className="flex-grow">
 				<Map></Map>

frontend/app/(dashboard)/data/taxonomies/[taxonomy]/page.tsx

@@ -11,7 +11,7 @@ export default async function FeatureId({ params }: { params: { taxonomy: string
 	const headers = lines[0].split("\t");
 
 	for (let i = 1; i < lines.length; i++) {
-		const obj = {} as { featureid: String, species: String };
+		const obj = {} as { featureid: string, species: string };
 		const currentline = lines[i].split("\t");
 
 		for (let j = 0; j < headers.length; j++) {

frontend/components/AsvUpload.tsx

@@ -0,0 +1,66 @@
+import { prisma } from "@/helpers/prisma";
+
+export default function AsvUpload() {
+	async function asvUpload(formData: FormData) {
+		"use server"
+
+		const content = await (formData.get("asvFile") as File).text();
+		const lines = content.split("\n");
+		const entriesByTaxa = {} as { [key: string]: [{}] }; //object where values are arrays of objects
+		const headers = lines[0].split("\t");
+		const taxonomies = new Set();
+
+		for (let i = 1; i < lines.length; i++) {
+			const obj = {} as { featureid: string, species: string, taxonomy: string };
+			const currentline = lines[i].split("\t");
+
+			for (let j = 0; j < headers.length; j++) {
+				//@ts-ignore
+				obj[headers[j]] = currentline[j];
+			}
+
+			const taxa = obj.taxonomy as keyof typeof entriesByTaxa;
+			if (entriesByTaxa[taxa]) {
+				entriesByTaxa[taxa].push(obj);
+			} else {
+				entriesByTaxa[taxa] = [obj];
+			}
+			taxonomies.add(obj.taxonomy);
+		}
+
+		//console.log(entriesByTaxa[[...taxonomies][0] as string])
+		for (const taxa in entriesByTaxa) {
+			console.log(taxa)
+			await prisma.taxonomy.upsert({
+				where: {
+					stringIdentifier: taxa
+				},
+				update: {
+					Feature: {
+						createMany: {
+							data: entriesByTaxa[taxa].map((obj: any) => ({ featureId: obj.featureid, sequence: obj.sequence })),
+							skipDuplicates: true
+						}
+					}
+				},
+				create: {
+					stringIdentifier: taxa,
+					Feature: {
+						createMany: {
+							data: entriesByTaxa[taxa].map((obj: any) => ({ featureId: obj.featureid, sequence: obj.sequence })),
+							skipDuplicates: true
+						}
+					}
+				}
+			});
+		}
+		console.log("success")
+	}
+
+	return (
+		<form action={asvUpload}>
+			<input type="file" name="asvFile" className="file-input file-input-bordered w-full max-w-xs" />
+			<button className="btn">Submit</button>
+		</form>
+	);
+}

frontend/helpers/utils.ts

@@ -5,10 +5,10 @@ export async function fetcher(url: string) {
 }
 
 export function getBaseUrl() {
-	// if (process.env.NODE_ENV === "development") {
+	 if (process.env.NODE_ENV === "development") {
 		return "http://localhost:3000";
-	// }
-	// return "https://opal-ochre.vercel.app";
+	 }
+	 return "https://opaldb.vercel.app/";
 }
 
 export function getRemoteUrl() {

frontend/prisma/dbml/OpalERD.dbml

@@ -167,7 +167,7 @@ Table Feature {
   Assignments Assignment [not null]
   consensusTaxonomyId String
   consensusTaxonomy Taxonomy
-  featureId String [not null]
+  featureId String [unique, not null]
   sequence String [not null]
 }
 

frontend/prisma/migrations/20241016194957_feature_unique/migration.sql

@@ -0,0 +1,147 @@
+/*
+  Warnings:
+
+  - You are about to drop the column `step1Id` on the `Step2_16S` table. All the data in the column will be lost.
+  - You are about to drop the column `step1Id` on the `Step2_18S` table. All the data in the column will be lost.
+  - You are about to drop the `Step1` table. If the table is not empty, all the data it contains will be lost.
+  - You are about to drop the `Step1_Metadata` table. If the table is not empty, all the data it contains will be lost.
+  - A unique constraint covering the columns `[featureId]` on the table `Feature` will be added. If there are existing duplicate values, this will fail.
+  - Added the required column `sampleId` to the `Occurrence` table without a default value. This is not possible if the table is not empty.
+  - Added the required column `dateModified` to the `Run` table without a default value. This is not possible if the table is not empty.
+  - Added the required column `uploadedBy` to the `Run` table without a default value. This is not possible if the table is not empty.
+  - Added the required column `SampleId` to the `Step2_16S` table without a default value. This is not possible if the table is not empty.
+  - Added the required column `SampleId` to the `Step2_18S` table without a default value. This is not possible if the table is not empty.
+
+*/
+-- DropForeignKey
+ALTER TABLE "Step1" DROP CONSTRAINT "Step1_projectId_fkey";
+
+-- DropForeignKey
+ALTER TABLE "Step1" DROP CONSTRAINT "Step1_step1_MetadataId_fkey";
+
+-- DropForeignKey
+ALTER TABLE "Step2_16S" DROP CONSTRAINT "Step2_16S_step1Id_fkey";
+
+-- DropForeignKey
+ALTER TABLE "Step2_18S" DROP CONSTRAINT "Step2_18S_step1Id_fkey";
+
+-- AlterTable
+ALTER TABLE "Occurrence" ADD COLUMN     "sampleId" TEXT NOT NULL;
+
+-- AlterTable
+ALTER TABLE "Run" ADD COLUMN     "dateModified" TEXT NOT NULL,
+ADD COLUMN     "uploadedBy" TEXT NOT NULL;
+
+-- AlterTable
+ALTER TABLE "Step2_16S" DROP COLUMN "step1Id",
+ADD COLUMN     "SampleId" TEXT NOT NULL;
+
+-- AlterTable
+ALTER TABLE "Step2_18S" DROP COLUMN "step1Id",
+ADD COLUMN     "SampleId" TEXT NOT NULL;
+
+-- DropTable
+DROP TABLE "Step1";
+
+-- DropTable
+DROP TABLE "Step1_Metadata";
+
+-- CreateTable
+CREATE TABLE "Sample_Metadata" (
+    "id" TEXT NOT NULL,
+    "nucl_acid_ext" TEXT,
+    "nucl_acid_ext_kit" TEXT,
+    "nucl_acid_ext_modify" TEXT,
+    "precip_method_ext" TEXT,
+    "dna_cleanup_0_1" TEXT,
+    "dna_cleanup_method" TEXT,
+    "concentration_method" TEXT,
+    "seq_kit" TEXT,
+    "lib_layout" TEXT NOT NULL,
+    "adapter_forward" TEXT,
+    "adapter_reverse" TEXT,
+    "seq_facility" TEXT,
+    "lib_screen" TEXT,
+    "platform" TEXT NOT NULL,
+    "instrument_model" TEXT NOT NULL,
+    "seq_meth" TEXT,
+    "seq_method_additional" TEXT,
+
+    CONSTRAINT "Sample_Metadata_pkey" PRIMARY KEY ("id")
+);
+
+-- CreateTable
+CREATE TABLE "Sample" (
+    "id" TEXT NOT NULL,
+    "projectId" TEXT NOT NULL,
+    "sample_name" TEXT NOT NULL,
+    "sample_name_original" TEXT NOT NULL,
+    "sample_type" "sample_type",
+    "serial_number" TEXT,
+    "cruise_id" TEXT,
+    "line_id" TEXT,
+    "station" TEXT,
+    "locationID" TEXT,
+    "habitat_natural_artificial_0_1" TEXT,
+    "ctd_bottle_no" TEXT,
+    "sample_replicate" TEXT,
+    "source_material_id" TEXT,
+    "biological_replicates" TEXT,
+    "notes_sampling" TEXT,
+    "verbatimEventDate" TEXT,
+    "eventDate" TEXT NOT NULL,
+    "minimumDepthInMeters" DOUBLE PRECISION,
+    "maximumDepthInMeters" DOUBLE PRECISION,
+    "env_broad_scale" TEXT NOT NULL,
+    "env_local_scale" TEXT NOT NULL,
+    "env_medium" TEXT NOT NULL,
+    "geo_loc_name" TEXT NOT NULL,
+    "waterBody" TEXT,
+    "country" TEXT,
+    "decimalLatitude" DOUBLE PRECISION,
+    "decimalLongitude" DOUBLE PRECISION,
+    "collection_method" TEXT,
+    "samp_collect_device" TEXT,
+    "samp_size" DOUBLE PRECISION,
+    "samp_size_unit" TEXT,
+    "extract_number" TEXT,
+    "samp_mat_process" TEXT,
+    "filter_passive_active_0_1" TEXT,
+    "filter_onsite_dur" TEXT,
+    "size_frac" TEXT,
+    "samp_vol_we_dna_ext" TEXT,
+    "samp_vol_ext_unit" DOUBLE PRECISION,
+    "sample_title" TEXT,
+    "bioproject_accession" TEXT,
+    "biosample_accession" TEXT,
+    "organism" TEXT NOT NULL,
+    "description" TEXT,
+    "amplicon_sequenced" TEXT,
+    "metagenome_sequenced" TEXT,
+    "sterilise_method" TEXT,
+    "samp_store_dur" TEXT,
+    "samp_store_loc" TEXT,
+    "samp_store_temp" DOUBLE PRECISION,
+    "samp_store_sol" TEXT,
+    "sample_MetadataId" TEXT,
+
+    CONSTRAINT "Sample_pkey" PRIMARY KEY ("id")
+);
+
+-- CreateIndex
+CREATE UNIQUE INDEX "Feature_featureId_key" ON "Feature"("featureId");
+
+-- AddForeignKey
+ALTER TABLE "Sample" ADD CONSTRAINT "Sample_projectId_fkey" FOREIGN KEY ("projectId") REFERENCES "Project"("id") ON DELETE RESTRICT ON UPDATE CASCADE;
+
+-- AddForeignKey
+ALTER TABLE "Sample" ADD CONSTRAINT "Sample_sample_MetadataId_fkey" FOREIGN KEY ("sample_MetadataId") REFERENCES "Sample_Metadata"("id") ON DELETE SET NULL ON UPDATE CASCADE;
+
+-- AddForeignKey
+ALTER TABLE "Step2_16S" ADD CONSTRAINT "Step2_16S_SampleId_fkey" FOREIGN KEY ("SampleId") REFERENCES "Sample"("id") ON DELETE RESTRICT ON UPDATE CASCADE;
+
+-- AddForeignKey
+ALTER TABLE "Step2_18S" ADD CONSTRAINT "Step2_18S_SampleId_fkey" FOREIGN KEY ("SampleId") REFERENCES "Sample"("id") ON DELETE RESTRICT ON UPDATE CASCADE;
+
+-- AddForeignKey
+ALTER TABLE "Occurrence" ADD CONSTRAINT "Occurrence_sampleId_fkey" FOREIGN KEY ("sampleId") REFERENCES "Sample"("id") ON DELETE RESTRICT ON UPDATE CASCADE;

frontend/prisma/schema.prisma

@@ -454,7 +454,7 @@ model Feature {
     consensusTaxonomyId String?
     consensusTaxonomy   Taxonomy?    @relation(fields: [consensusTaxonomyId], references: [id])
 
-    featureId String
+    featureId String @unique
     sequence  String
 }