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import { GeneSet } from "@/components/core/set" | ||
import { rummagene_icon } from "@/icons" | ||
import { MetaNode } from "@/spec/metanode" | ||
import { z } from 'zod' | ||
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const rummagene_url = 'https://rummagene.com' | ||
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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() | ||
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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() |
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{ | ||
"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" | ||
} | ||
} |
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