Biomarker-KG

.env.example

@@ -2,7 +2,6 @@ NEXT_PUBLIC_PREFIX=
 NEXT_PUBLIC_NEO4J_DEV_URL=bolt://localhost:7687
 NEXT_PUBLIC_NEO4J_URL=bolt://neo4j:7687
 NEO4J_DEV_URL=bolt://localhost:7687
-NEXT_PUBLIC_NEO4J_V5_URL=bolt://neo4j-v5:7687
 
 NEXT_PUBLIC_NEO4J_USER=neo4j
 NEXT_PUBLIC_NEO4J_NAME=kg

BiomarkerKGDemo-1.code-workspace

@@ -0,0 +1,12 @@
+{
+	"folders": [
+		{
+			"name": "BiomarkerKGDemo-1",
+			"path": "../../BiomarkerKGDemo-1"
+		},
+		{
+			"path": "."
+		}
+	],
+	"settings": {}
+}

app/ThemeRegistry.tsx

@@ -8,10 +8,12 @@ import CssBaseline from '@mui/material/CssBaseline';
 import { cfde_theme } from '@/themes/cfde';
 import { enrichr_kg_theme } from '@/themes/enrichr-kg';
 import { lncRNAlyzr } from '@/themes/lncRNAlyzr';
+import { biomarker_kg_theme } from '@/themes/biomarker-kg';
 const themes = {
     cfde_theme: cfde_theme,
     enrichr_kg_theme: enrichr_kg_theme,
-    lncRNAlyzr: lncRNAlyzr
+    lncRNAlyzr: lncRNAlyzr,
+    biomarker_kg_theme: biomarker_kg_theme,
 }
 
 // This implementation is from emotion-js

app/api/biomarker/breastcancerdiagnosis/route.ts

@@ -0,0 +1,110 @@
+import { resolve_results } from "../../knowledge_graph/helper";
+import { NextResponse } from "next/server";
+import type { NextRequest } from "next/server";
+import { z } from 'zod';
+import { initialize } from "../../initialize/helper";
+async function process_query({
+    term,
+    limit,
+    aggr_scores,
+    colors,
+    field,
+    type}: {
+        term: string,
+        limit: number,
+        aggr_scores?: {[key:string]: {max: number, min: number}},
+        colors?: {[key: string]: {color?: string, field?: string, aggr_type?: string}},
+        field: string,
+        type: string,
+    }) {
+
+    const query = `MATCH p = (c:Condition {label: 'breast cancer'})<-[:diagnostic_for]-(b:Biomarker)-[:diagnostic_for]->(a:Condition)
+    RETURN p, nodes(p) AS n, relationships(p) AS r LIMIT TOINTEGER($limit)
+
+    `
+    const query_params = { term, limit }
+    return resolve_results({query, query_params, terms: [term],  aggr_scores, colors, fields: [field]})
+}
+
+const InputSchema = z.object({
+    start: z.string(),
+    start_term: z.string(),
+    limit: z.number().optional(),
+    start_field: z.string().optional(),
+})
+/**
+ * @swagger
+ * /api/distillery/disease2exrna:
+ *   get:
+ *     description: Performs liquid biopsy of condition
+ *     tags:
+ *       - distillery apps
+ *     parameters:
+ *       - name: filter
+ *         in: query
+ *         required: true
+ *         content:
+ *            application/json:
+ *              schema: 			
+ *                type: object
+ *                required:
+ *                  - start
+ *                  - start_term
+ *                properties:
+ *                  start:
+ *                    type: string
+ *                  start_field:
+ *                    type: string
+ *                  start_term:
+ *                    type: string
+ *                  limit:
+ *                    type: integer
+ *                    default: 5
+ *     responses:
+ *       200:
+ *         description: Subnetwork
+ *         content:
+ *           application/json:
+ *             schema:
+ *               type: object
+ *               properties:
+ *                 nodes:
+ *                   type: array
+ *                   items:
+ *                     type: object
+ *                     properties:
+ *                       data:
+ *                         type: object
+ *                 edges:
+ *                   type: array
+ *                   items:
+ *                     type: object
+ *                     properties:
+ *                       data:
+ *                         type: object
+ */
+export async function GET(req: NextRequest) {
+    try {
+        const filter = req.nextUrl.searchParams.get("filter")
+        if (!filter) return NextResponse.json({error: "No filter inputted"}, {status: 400})
+        const f = JSON.parse(filter)
+        if (f.limit && !isNaN(f.limit) && typeof f.limit === 'string') f.limit = parseInt(f.limit)
+        const { start, start_term, limit=10, start_field="label" } = InputSchema.parse(f)
+
+        const {aggr_scores, colors} = await initialize()
+
+        if (start_term === undefined) return NextResponse.json({error: "No term inputted"}, {status: 400})
+        else { 
+            try {
+                const results = await process_query({type:start, term:start_term, limit, aggr_scores, colors, field:start_field })
+                fetch(`${process.env.NEXT_PUBLIC_HOST}${process.env.NEXT_PUBLIC_PREFIX ? process.env.NEXT_PUBLIC_PREFIX: ''}/api/counter/update`)
+                return NextResponse.json(results, {status: 200})
+            } catch (e) {
+                return NextResponse.json(e, {status: 400})
+            }
+        }
+    } catch (e) {
+        return NextResponse.json(e, {status: 400})
+    }
+  }
+

app/api/biomarker/thyroidandskinmelanoma/route.ts

@@ -0,0 +1,110 @@
+import { resolve_results } from "../../knowledge_graph/helper";
+import { NextResponse } from "next/server";
+import type { NextRequest } from "next/server";
+import { z } from 'zod';
+import { initialize } from "../../initialize/helper";
+async function process_query({
+    term,
+    limit,
+    aggr_scores,
+    colors,
+    field,
+    type}: {
+        term: string,
+        limit: number,
+        aggr_scores?: {[key:string]: {max: number, min: number}},
+        colors?: {[key: string]: {color?: string, field?: string, aggr_type?: string}},
+        field: string,
+        type: string,
+    }) {
+
+    const query = `MATCH p = (c:Condition {label: 'thyroid cancer'})<-[:indicates_risk_of_developing]-(b:Biomarker)-[:indicates_risk_of_developing]->(a:Condition {label: 'Skin Squamous Cell Carcinoma'})
+    RETURN p, nodes(p) AS n, relationships(p) AS r LIMIT TOINTEGER($limit)
+
+    `
+    const query_params = { term, limit }
+    return resolve_results({query, query_params, terms: [term],  aggr_scores, colors, fields: [field]})
+}
+
+const InputSchema = z.object({
+    start: z.string(),
+    start_term: z.string(),
+    limit: z.number().optional(),
+    start_field: z.string().optional(),
+})
+/**
+ * @swagger
+ * /api/distillery/disease2exrna:
+ *   get:
+ *     description: Performs liquid biopsy of condition
+ *     tags:
+ *       - distillery apps
+ *     parameters:
+ *       - name: filter
+ *         in: query
+ *         required: true
+ *         content:
+ *            application/json:
+ *              schema: 			
+ *                type: object
+ *                required:
+ *                  - start
+ *                  - start_term
+ *                properties:
+ *                  start:
+ *                    type: string
+ *                  start_field:
+ *                    type: string
+ *                  start_term:
+ *                    type: string
+ *                  limit:
+ *                    type: integer
+ *                    default: 5
+ *     responses:
+ *       200:
+ *         description: Subnetwork
+ *         content:
+ *           application/json:
+ *             schema:
+ *               type: object
+ *               properties:
+ *                 nodes:
+ *                   type: array
+ *                   items:
+ *                     type: object
+ *                     properties:
+ *                       data:
+ *                         type: object
+ *                 edges:
+ *                   type: array
+ *                   items:
+ *                     type: object
+ *                     properties:
+ *                       data:
+ *                         type: object
+ */
+export async function GET(req: NextRequest) {
+    try {
+        const filter = req.nextUrl.searchParams.get("filter")
+        if (!filter) return NextResponse.json({error: "No filter inputted"}, {status: 400})
+        const f = JSON.parse(filter)
+        if (f.limit && !isNaN(f.limit) && typeof f.limit === 'string') f.limit = parseInt(f.limit)
+        const { start, start_term, limit=10, start_field="label" } = InputSchema.parse(f)
+
+        const {aggr_scores, colors} = await initialize()
+
+        if (start_term === undefined) return NextResponse.json({error: "No term inputted"}, {status: 400})
+        else { 
+            try {
+                const results = await process_query({type:start, term:start_term, limit, aggr_scores, colors, field:start_field })
+                fetch(`${process.env.NEXT_PUBLIC_HOST}${process.env.NEXT_PUBLIC_PREFIX ? process.env.NEXT_PUBLIC_PREFIX: ''}/api/counter/update`)
+                return NextResponse.json(results, {status: 200})
+            } catch (e) {
+                return NextResponse.json(e, {status: 400})
+            }
+        }
+    } catch (e) {
+        return NextResponse.json(e, {status: 400})
+    }
+  }
+

app/api/counter/route.ts

@@ -32,4 +32,6 @@ export async function GET() {
         console.log(error)
         return NextResponse.error()
     }
-}
+}
+
+export const revalidate = 0;

app/api/counter/update/route.ts

@@ -40,4 +40,6 @@ export async function GET() {
         console.log(error)
         return NextResponse.error()
     }
-}
+}
+
+export const revalidate = 0;

app/api/knowledge_graph/node_search/route.ts

@@ -45,7 +45,7 @@ const query_schema = z.object({
  */
 export async function GET(req: NextRequest) {
     try {
-        const node_properties = await (await fetch(`${process.env.NEXT_PUBLIC_HOST}${process.env.NEXT_PUBLIC_PREFIX ? process.env.NEXT_PUBLIC_PREFIX: ''}/api/knowledge_graph/search_properties`)).json()
+        const node_properties = await (await fetch(`${process.env.NODE_ENV==="development" ? process.env.NEXT_PUBLIC_HOST_DEV : process.env.NEXT_PUBLIC_HOST}${process.env.NEXT_PUBLIC_PREFIX ? process.env.NEXT_PUBLIC_PREFIX: ''}/api/knowledge_graph/search_properties`)).json()
         const {type, field="label", term, limit=100, filter={}} = query_schema.parse(convert_query(req))
         const session = neo4jDriver.session({
             defaultAccessMode: neo4j.session.READ

app/api/knowledge_graph/route.ts

@@ -681,16 +681,13 @@ export async function GET(req: NextRequest) {
                     if (start && end && start_term && end_term) {
                         if(augment)  return NextResponse.json({error: "You can only augment on single search"}, {status: 400})
                         const results = await resolve_two_terms({edges, start, start_field, start_term, end, end_field, end_term, relation, limit, path_length, aggr_scores, colors, remove: remove ?  remove: [], expand: expand ? expand : [], gene_links, additional_link_tags})
-                        fetch(`${process.env.NEXT_PUBLIC_HOST}${process.env.NEXT_PUBLIC_PREFIX ? process.env.NEXT_PUBLIC_PREFIX: ''}/api/counter/update`)
                         return NextResponse.json(results, {status: 200})
                     } else if (start && end && start_term ) {
                         if(augment)  return NextResponse.json({error: "You can only augment on single search"}, {status: 400})
                         const results = await resolve_term_and_end_type({edges, start_term, start_field, start, end, relation, limit, path_length, aggr_scores, colors, remove, expand: expand, gene_links, additional_link_tags})
-                        fetch(`${process.env.NEXT_PUBLIC_HOST}${process.env.NEXT_PUBLIC_PREFIX ? process.env.NEXT_PUBLIC_PREFIX: ''}/api/counter/update`)
                         return NextResponse.json(results, {status: 200})
                     } else if (start) {
                         const results = await resolve_one_term({edges, start, field: start_field, term: start_term, relation, limit, path_length, aggr_scores, colors, remove, expand, gene_links, additional_link_tags, augment, augment_limit })
-                        fetch(`${process.env.NEXT_PUBLIC_HOST}${process.env.NEXT_PUBLIC_PREFIX ? process.env.NEXT_PUBLIC_PREFIX: ''}/api/counter/update`)
                         return NextResponse.json(results, {status: 200})
                     } else {
                         return NextResponse.json({error: "Invalid Input"}, {status: 400})
@@ -708,4 +705,4 @@ export async function GET(req: NextRequest) {
         } catch (error) {
             return NextResponse.json(error, {status: 400})
         }
-}
+}

app/page.tsx

@@ -38,11 +38,9 @@ export default async function Home({searchParams}: {
           <main className="mt-8 pb-8 pl-10 pr-10">
             <Grid container spacing={2}>
               <Grid item xs={12}>
-                <Suspense>
-                  <QueryTranslator>
-                    <Component searchParams={searchParams} {...root_tab}/>
-                  </QueryTranslator>
-                </Suspense>
+                <QueryTranslator>
+                  <Component searchParams={searchParams} {...root_tab}/>
+                </QueryTranslator>
               </Grid>
             </Grid>
           </main>

components/APIDoc/react-swagger.tsx

@@ -13,7 +13,7 @@ function ReactSwagger({ spec }: Props) {
   const [specs, setSpecs] = useState(null)
   useEffect(()=>{
     const resolve_specs = async () => {
-      const specs = await (await fetch(`${process.env.NEXT_PUBLIC_HOST}/api/docs`)).json()
+      const specs = await (await fetch(`${process.env.NODE_ENV==="development" ? process.env.NEXT_PUBLIC_HOST_DEV : process.env.NEXT_PUBLIC_HOST}/api/docs`)).json()
       setSpecs(specs)
     }
     resolve_specs()

components/Counter.tsx

@@ -1,32 +1,17 @@
 'use client'
-import {useState, useEffect} from 'react'
-import { delay } from '@/utils/helper';
 import { Stack, Typography } from '@mui/material';
-export const Counter = ({ui_theme}: {ui_theme?: string}) => {
-    const [count, setCount] = useState(0)
-    const [timer, setTimer] = useState(0)
-    const query_counter = async (delay_time=5000) => {
-        try {
-            await delay(delay_time)
-            const {count} = await ( await fetch(`${process.env.NEXT_PUBLIC_HOST}${process.env.NEXT_PUBLIC_PREFIX ? process.env.NEXT_PUBLIC_PREFIX: ''}/api/counter`)).json()
-            setCount(count)
-            setTimer(timer + 1)
-        } catch (error) {
-            console.log(error)
-            console.error(error)
-        }
-    }
+import useSWR from 'swr';
+const fetcher = (url) => fetch(url).then(r => r.json())
+export const Counter = ({ui_theme}: {ui_theme?: string}) => {  
+
+    const { data } = useSWR('/api/counter', fetcher, { refreshInterval: 5000 })
 
-    useEffect(()=>{
-        if (timer === 0) query_counter(0)
-        else query_counter()
-    }, [timer])
     return (
         <Stack direction={"row"} spacing={1}>
             <Typography variant="nav">Queries Submitted: </Typography> 
             {ui_theme === undefined || ui_theme === 'cfde_theme' ?
-            <Typography><b>{count}</b></Typography>:
-            <Typography variant={'nav'}><b>{count}</b></Typography>
+            <Typography><b>{(data || {}).count}</b></Typography>:
+            <Typography variant={'nav'}><b>{(data || {}).count}</b></Typography>
             }
         </Stack>
     )