Add rummagene enrichment analysis

components/index.ts

@@ -263,6 +263,10 @@ import * as service_regulatoryElementInfo from "./service/regulatoryElementInfo"
 import service_regulatoryElementInfo_packageJson from "./service/regulatoryElementInfo/package.json"
 metanodes.push(...MetaNodesFromExports(service_regulatoryElementInfo, service_regulatoryElementInfo_packageJson))
 components.push("service/regulatoryElementInfo")
+import * as service_rummagene from "./service/rummagene"
+import service_rummagene_packageJson from "./service/rummagene/package.json"
+metanodes.push(...MetaNodesFromExports(service_rummagene, service_rummagene_packageJson))
+components.push("service/rummagene")
 import * as service_sigcom_lincs from "./service/sigcom-lincs"
 import service_sigcom_lincs_packageJson from "./service/sigcom-lincs/package.json"
 metanodes.push(...MetaNodesFromExports(service_sigcom_lincs, service_sigcom_lincs_packageJson))

components/service/rummagene/index.tsx

@@ -0,0 +1,51 @@
+import { GeneSet } from "@/components/core/set"
+import { rummagene_icon } from "@/icons"
+import { MetaNode } from "@/spec/metanode"
+import { z } from 'zod'
+
+const rummagene_url = 'https://rummagene.com'
+
+export const RummageneGeneSet = MetaNode(`RummageneGeneSet`)
+  .meta({
+    label: 'Rummagene Gene Set',
+    description: 'A gene set uploaded to rummagene',
+    icon: [rummagene_icon],
+  })
+  .codec(z.object({
+    id: z.string(),
+  }))
+  .view(props => (
+    <div className="flex-grow flex flex-row m-0" style={{ minHeight: 500 }}>
+      <iframe
+        className="flex-grow border-0"
+        src={`${rummagene_url}/enrich?dataset=${props.id}`}
+      />
+    </div>
+  ))
+  .build()
+
+export const RummageneEnrichmentAnalysis = MetaNode(`RummageneEnrichmentAnalysis`)
+  .meta({
+    label: 'Rummagene Enrichment Analysis',
+    description: 'Use Rummagene to search through gene sets in PubMedCentral supplemental material',
+  })
+  .inputs({ gene_set: GeneSet })
+  .output(RummageneGeneSet)
+  .resolve(async (props) => {
+    const req = await fetch(`${rummagene_url}/graphql`, {
+      headers: {
+        'Content-Type': 'application/json',
+        'Accept': 'application/json',
+      },
+      method: 'POST',
+      body: JSON.stringify({"operationName":"AddUserGeneSet","variables":{"description":`${props.inputs.gene_set.description ?? 'Gene set'} from pwb`,"genes":props.inputs.gene_set.set},"query":"mutation AddUserGeneSet($genes: [String], $description: String = \"\") {\n  addUserGeneSet(input: {genes: $genes, description: $description}) {\n    userGeneSet {\n      id\n      __typename\n    }\n    __typename\n  }\n}\n"}),
+    })
+    if (!req.ok) throw new Error('Failed to submit gene set to rummagene')
+    const { data: { addUserGeneSet: { userGeneSet: { id } } } } = await req.json()
+    return { id }
+  })
+  .story(props => ({
+    abstract: `Papers in Pub Med Central with gene sets significantly overlapping with ${props.inputs?.gene_set?.description ? props.inputs.gene_set.description : 'the gene set'} were identified using Rummagene\\ref{doi:10.1038/s42003-024-06177-7}.`,
+    legend: `A listing of significantly overlapping gene sets with ${props.inputs?.gene_set?.description ? props.inputs.gene_set.description : 'the gene set'} found from the supplemental material of papers using Rummagene\\ref{doi:10.1038/s42003-024-06177-7}.`,
+  }))
+  .build()

components/service/rummagene/package.json

@@ -0,0 +1,13 @@
+{
+  "name": "@playbook-partnership/rummagene",
+  "version": "1.0.0",
+  "license": "CC-BY-NC-SA-4.0",
+  "author": "Daniel J. B. Clarke <danieljbclarkemssm@gmail.com>",
+  "private": true,
+  "dependencies": {
+    "react": "^18.2.0"
+  },
+  "devDependencies": {
+    "@types/react": "^18.0.21"
+  }
+}