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Accomodate the updates to semantic search #1026

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Merged
merged 4 commits into from
Dec 16, 2021
Merged

Accomodate the updates to semantic search #1026

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5771228
- semantic search endpoint /search
jvwong Jun 18, 2021
811173b
Merge branch 'unstable' into iss990_semantic-search-api
jvwong Dec 14, 2021
041920f
Use a development version of semantic search now.
jvwong Dec 16, 2021
4a0d0d9
Accommodate the new schema for semantic search.
jvwong Dec 16, 2021
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2 changes: 1 addition & 1 deletion src/config.js
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Expand Up @@ -65,7 +65,7 @@ export const NCBI_EUTILS_BASE_URL = env('NCBI_EUTILS_BASE_URL', 'https://eutils.
export const NCBI_EUTILS_API_KEY = env('NCBI_EUTILS_API_KEY', 'b99e10ebe0f90d815a7a99f18403aab08008');
export const INDRA_DB_BASE_URL = env('INDRA_DB_BASE_URL', 'https://db.indra.bio/latest/');
export const INDRA_ENGLISH_ASSEMBLER_URL = env('INDRA_ENGLISH_ASSEMBLER_URL', 'http://api.indra.bio:8000/assemblers/english');
export const SEMANTIC_SEARCH_BASE_URL = env('SEMANTIC_SEARCH_BASE_URL', 'https://semanticsearch.baderlab.org/');
export const SEMANTIC_SEARCH_BASE_URL = env('SEMANTIC_SEARCH_BASE_URL', 'https://main.semanticsearch.baderlab.org/');

// Links
export const UNIPROT_LINK_BASE_URL = env('UNIPROT_LINK_BASE_URL', 'http://www.uniprot.org/uniprot/');
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5 changes: 4 additions & 1 deletion src/server/routes/api/document/index.js
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Expand Up @@ -2339,7 +2339,10 @@ const getRelPprsForDoc = async doc => {
const documents = elink2UidList( elinkResponse );
let uids;
try {
let rankedDocs = await indra.semanticSearch({ query: pmid, documents });
let rankedDocs = await indra.semanticSearch({
query: { uid: pmid },
documents: documents.map( uid => ({ uid }) )
});
uids = rankedDocs.map( getUid );

} catch ( err ) {
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5 changes: 3 additions & 2 deletions src/server/routes/api/document/indra.js
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Expand Up @@ -64,9 +64,10 @@ const fetchRetryUrl = ( url, opts ) => {


const semanticSearch = params => {
return fetch( SEMANTIC_SEARCH_BASE_URL, {
const opts = _.defaults( params, { top_k: SEMANTIC_SEARCH_LIMIT } );
return fetch( `${SEMANTIC_SEARCH_BASE_URL}search`, {
method: 'POST',
body: JSON.stringify( params ),
body: JSON.stringify( opts ),
headers: { 'Content-Type': 'application/json' }
})
.then( res => res.json() );
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