Related papers notification

src/config.js

@@ -78,8 +78,10 @@ export const IDENTIFIERS_ORG_ID_BASE_URL = env('IDENTIFIERS_ORG_ID_BASE_URL', '
 
 // Email
 export const EMAIL_ENABLED = env('EMAIL_ENABLED', false);
+export const EMAIL_RELPPRS_CONTACT = env('EMAIL_RELPPRS_CONTACT', true);
 export const EMAIL_FROM = env('EMAIL_FROM', 'Biofactoid');
 export const EMAIL_FROM_ADDR = env('EMAIL_FROM_ADDR', 'support@biofactoid.org');
+export const EMAIL_ADMIN_ADDR = env('EMAIL_ADMIN_ADDR', 'support@biofactoid.org');
 export const SMTP_PORT = env('SMTP_PORT', 587);
 export const SMTP_HOST = env('SMTP_HOST', 'localhost');
 export const SMTP_USER = env('SMTP_USER', 'user');
@@ -89,9 +91,11 @@ export const EMAIL_VENDOR_MAILJET = env('EMAIL_VENDOR_MAILJET', 'Mailjet');
 export const MAILJET_TMPLID_INVITE = env('MAILJET_TMPLID_INVITE', '1330760');
 export const MAILJET_TMPLID_FOLLOWUP = env('MAILJET_TMPLID_FOLLOWUP', '988309');
 export const MAILJET_TMPLID_REQUEST_ISSUE = env('MAILJET_TMPLID_REQUEST_ISSUE', '1202251');
+export const MAILJET_TMPLID_REL_PPR = env('MAILJET_TMPLID_REL_PPR', '1871553');
 export const EMAIL_TYPE_INVITE = env('EMAIL_TYPE_INVITE', 'invite');
 export const EMAIL_TYPE_FOLLOWUP = env('EMAIL_TYPE_FOLLOWUP', 'followUp');
 export const EMAIL_TYPE_REQUEST_ISSUE = env('EMAIL_TYPE_REQUEST_ISSUE', 'requestIssue');
+export const EMAIL_TYPE_REL_PPR_NOTIFICATION = env('EMAIL_TYPE_REL_PPR_NOTIFICATION', 'relatedPaperNotification');
 export const EMAIL_ADDRESS_INFO = env('EMAIL_ADDRESS_INFO', 'info@biofactoid.org');
 
 // Sharing

src/model/document/document.js

@@ -436,6 +436,21 @@ class Document {
     }
   }
 
+  referencedPapers( papersData ){
+    if( papersData ){
+      let p = this.syncher.update({ 'referencedPapers': papersData });
+      this.emit( 'referencedPapers', papersData );
+      return p;
+    }
+    else if( !papersData ){
+      return this.syncher.get( 'referencedPapers' );
+    }
+  }
+
+  relatedPapersNotified(newVal){
+    return !!this.rwMeta('relatedPapersNotified', newVal);
+  }
+
   status( field ){
     if( field && _.includes( _.values( DOCUMENT_STATUS_FIELDS ), field ) ){
       let p = this.syncher.update({ 'status': field });

src/model/element/interaction.js

@@ -22,6 +22,7 @@ const makeAssociation = ( type, intn ) => {
 const DEFAULTS = Object.freeze({
   type: TYPE,
   association: INTERACTION_TYPE.INTERACTION.value,
+  novel: false,
   entries: [] // used by elementSet
 });
 
@@ -177,6 +178,21 @@ class Interaction extends Element {
     return this.participantsOf( type, (t1, t2) => t1 !== t2 );
   }
 
+  setNovel( novel ) {
+    let currVal = this.isNovel();
+    if ( currVal == novel ) {
+      return Promise.resolve();
+    }
+
+    let update = this.update({
+      novel
+    });
+
+    this.emit( 'novel', novel, currVal );
+
+    return update;
+  }
+
   associate( interactionType ){
     let type = makeAssociation( interactionType, this );
     let oldType = makeAssociation( this.syncher.get('association'), this );
@@ -221,6 +237,10 @@ class Interaction extends Element {
     return this.syncher.get('association') != null;
   }
 
+  isNovel(){
+    return this.syncher.get('novel') == true;
+  }
+
   json(){
     return _.assign( {}, super.json(), _.pick( this.syncher.get(), _.keys(DEFAULTS) ) );
   }

src/server/routes/api/document/index.js

@@ -34,15 +34,18 @@ import { BASE_URL,
   MAX_TWEET_LENGTH,
   DEMO_CAN_BE_SHARED,
   DOCUMENT_IMAGE_PADDING,
+  EMAIL_ADMIN_ADDR,
+  EMAIL_RELPPRS_CONTACT,
   EMAIL_TYPE_INVITE,
   DOCUMENT_IMAGE_CACHE_SIZE,
   EMAIL_TYPE_FOLLOWUP,
   MIN_RELATED_PAPERS,
-  SEMANTIC_SEARCH_LIMIT
+  SEMANTIC_SEARCH_LIMIT,
+  EMAIL_TYPE_REL_PPR_NOTIFICATION
  } from '../../../../config';
 
 import { ENTITY_TYPE } from '../../../../model/element/entity-type';
-import { db2pubmed } from './pubmed/linkPubmed';
+import { eLink, elink2UidList } from './pubmed/linkPubmed';
 import { fetchPubmed } from './pubmed/fetchPubmed';
 import { docs2Sitemap } from '../../../sitemap';
 const DOCUMENT_STATUS_FIELDS = Document.statusFields();
@@ -1220,6 +1223,60 @@ const checkApiKey = (apiKey) => {
   }
 };
 
+const getNovelInteractions = async doc => {
+  // n.b. will be empty if we haven't yet queried for related papers
+  return doc.interactions().filter(intn => intn.isNovel());
+};
+
+const emailRelatedPaperAuthors = async doc => {
+  if( doc.relatedPapersNotified() ){ return; } // bail out if already notified
+
+  const getContact = paper => _.get(paper, ['pubmed', 'authors', 'contacts', 0]);
+
+  const hasContact = paper => getContact(paper) != null;
+
+  const sendEmail = async (paper, novelIntns) => {
+    const contact = getContact(paper);
+    const email = EMAIL_RELPPRS_CONTACT ? contact.email[0] : EMAIL_ADMIN_ADDR;
+    const name = contact.name;
+
+    // prevent duplicate sending
+    doc.relatedPapersNotified(true);
+
+    const mailOpts =  await msgFactory(EMAIL_TYPE_REL_PPR_NOTIFICATION, doc, {
+      to: EMAIL_RELPPRS_CONTACT ? email : EMAIL_ADMIN_ADDR, //must explicitly turn off
+      name,
+      paper,
+      novelIntns
+    });
+
+    // Sending blocked by default, otherwise set EMAIL_ENABLED=true
+    await sendMail(mailOpts);
+
+    logger.info(`Related paper notification email for doc ${doc.id()} sent to ${name} at ${email} with ${novelIntns.length} novel interactions`);
+  };
+
+  // TODO RPN use semantic search score etc. in future
+  // just send to all for now, as we already have a small cutoff at 30
+  const paperIsGoodFit = async paper => true; // eslint-disable-line
+
+  const getSendablePapers = async papers => {
+    const isGoodFit = await Promise.all(papers.map(paperIsGoodFit));
+
+    return papers.filter((paper, i) => isGoodFit[i] && hasContact(paper));
+  };
+
+  const novelIntns = await getNovelInteractions(doc);
+
+  const papers = await getSendablePapers(doc.referencedPapers());
+
+  logger.info(`Sending related paper notifications for doc ${doc.id()} with ${papers.length} papers`);
+
+  await Promise.all(papers.map(async paper => sendEmail(paper, novelIntns)));
+
+  logger.info(`Related paper notifications complete for ${papers.length} emails`);
+};
+
 /**
  * @swagger
  *
@@ -1435,7 +1492,16 @@ http.patch('/:id/:secret', function( req, res, next ){
     return;
   };
 
-  const sendFollowUpNotification = async doc => await configureAndSendMail( EMAIL_TYPE_FOLLOWUP, doc.id(), doc.secret() );
+  const sendFollowUpNotification = async doc => {
+    await configureAndSendMail( EMAIL_TYPE_FOLLOWUP, doc.id(), doc.secret() );
+    await emailRelatedPaperAuthors( doc );
+  };
+
+  const onDocPublic = async doc => {
+    await updateRelatedPapers( doc );
+    await sendFollowUpNotification( doc );
+  };
+
   const tryTweetingDoc = async doc => {
     if ( !doc.hasTweet() ) {
       try {
@@ -1449,9 +1515,8 @@ http.patch('/:id/:secret', function( req, res, next ){
   const handleMakePublicRequest = async doc => {
     await tryMakePublic( doc );
     if( doc.isPublic() ) {
-      updateRelatedPapers( doc );
       await tryTweetingDoc( doc );
-      sendFollowUpNotification( doc );
+      onDocPublic( doc );
     }
   };
 
@@ -1476,6 +1541,7 @@ http.patch('/:id/:secret', function( req, res, next ){
         case 'relatedPapers':
           if( op === 'replace' ){
             await updateRelatedPapers( doc );
+            await emailRelatedPaperAuthors( doc );
           }
           break;
       }
@@ -1608,23 +1674,37 @@ const updateRelatedPapers = async doc => {
 
 const getRelPprsForDoc = async doc => {
   let papers = [];
+  let referencedPapers = [];
 
   try {
     logger.info(`Updating document-level related papers for doc ${doc.id()}`);
     const getUid = result => _.get( result, 'uid' );
     const { pmid } = doc.citation();
 
     if( pmid ){
-      const pmids = await db2pubmed({ uids: [pmid] });
-      let rankedDocs = await indra.semanticSearch({ query: pmid, documents: pmids });
+      const elinkResponse = await eLink( { id: [pmid] } );
+
+      // For .relatedPapers
+      const documents = elink2UidList( elinkResponse );
+      let rankedDocs = await indra.semanticSearch({ query: pmid, documents });
       const uids = _.take( rankedDocs, SEMANTIC_SEARCH_LIMIT ).map( getUid );
-      const { PubmedArticleSet } = await fetchPubmed({ uids });
-      papers = PubmedArticleSet
+      const relatedPapersResponse = await fetchPubmed({ uids });
+      papers = _.get( relatedPapersResponse, 'PubmedArticleSet', [] )
         .map( getPubmedCitation )
         .map( citation => ({ pmid: citation.pmid, pubmed: citation }) );
+
+      // For .referencedPapers
+      const referencedPaperUids = elink2UidList( elinkResponse, ['pubmed_pubmed_refs'], 100 );
+      if( referencedPaperUids.length ){
+        const referencedPapersResponse = await fetchPubmed({ uids: referencedPaperUids });
+        referencedPapers = _.get( referencedPapersResponse, 'PubmedArticleSet', [] )
+          .map( getPubmedCitation )
+          .map( citation => ({ pmid: citation.pmid, pubmed: citation }) );
+      }
     }
 
     doc.relatedPapers( papers );
+    doc.referencedPapers( referencedPapers );
     logger.info(`Finished updating document-level related papers`);
     return doc;
 
@@ -1652,9 +1732,16 @@ const getRelatedPapersForNetwork = async doc => {
         entities: el.isEntity() ? [ template ] : []
       };
 
-      const indraRes = await indra.searchDocuments({ templates, doc });
+      let indraRes = await indra.searchDocuments({ templates, doc });
+      indraRes = indraRes || [];
+
+      if ( el.isInteraction() ) {
+        if ( indraRes.length == 0 ) {
+          el.setNovel( true );
+        }
+      }
 
-      el.relatedPapers( indraRes || [] );
+      el.relatedPapers( indraRes );
     };
 
     await Promise.all([ ...els.map(getRelPprsForEl) ]);

src/server/routes/api/document/pubmed/linkPubmed.js

@@ -20,8 +20,17 @@ const DEFAULT_ELINK_PARAMS = {
   linkname: undefined
 };
 
-const data2UidList = ( json, maxPerLink ) => {
-  const { ids, linksetdbs = [] } =  _.get( json, ['linksets', '0'] );
+/**
+ * elink2UidList
+ * Retrieve PubMed uids from the ELINK response
+ * @param {Object} json The ELINK response
+ * @param {Object} linknames The list linknames to consider
+ * @param {number} maxPerLink Take this top number of uids for any one subset (dbfrom_db_subset)
+ * @return {Object} The array of PubMed uids
+ */
+const elink2UidList = ( json, linknames, maxPerLink = DEFAULT_MAX_PER_LINK ) => {
+  let { ids, linksetdbs = [] } =  _.get( json, ['linksets', '0'] );
+  if( linknames ) linksetdbs = linksetdbs.filter( linksetdb => _.includes( linknames, linksetdb.linkname ) );
   const links =  linksetdbs.map( linksetdb => _.take( _.get( linksetdb, ['links'] ), maxPerLink ) );
   let uids = _.flatten( links );
   uids = _.uniq( uids ); // Remove redundancy
@@ -50,20 +59,4 @@ const eLink = opts => {
   .then( response => response.json() );
 };
 
-/**
- * db2pubmed
- * Retrieve PubMed uids for one or more uids from the source database
- * @param {Object} uids Array of strings that represent PubMed uids
- * @param {string} dbfrom The database (e.g. gene, protein) from which the uids are derived
- * @param {string} reldate Restrict to uids to those with Publication Date within the last n days
- * @param {string} term Text query used to limit the set of unique identifiers (UIDs) returned, similar to the search string you would put into an Entrez database’s web interface.
- * @param {number} maxPerLink Take this top number of uids for any one subset (dbfrom_db_subset)
- * @return {Object} The array of PubMed uids
- */
-const db2pubmed = ({ uids, db, reldate, term, maxPerLink = DEFAULT_MAX_PER_LINK }) => {
-  const id = uids.join(',');
-  return  eLink( { id, dbfrom: db, reldate, term } )
-    .then( data => data2UidList( data, maxPerLink ) );
-};
-
-export { eLink, db2pubmed };
+export { eLink, elink2UidList };

src/util/email.js

@@ -1,5 +1,8 @@
+/** N.b. this can only be run on the server */
+
 import _ from 'lodash';
 import { tryPromise } from './promise';
+import logger from '../server/logger';
 
 import {
   BASE_URL,
@@ -11,10 +14,12 @@ import {
   MAILJET_TMPLID_REQUEST_ISSUE,
   EMAIL_TYPE_INVITE,
   EMAIL_TYPE_FOLLOWUP,
-  EMAIL_TYPE_REQUEST_ISSUE
+  EMAIL_TYPE_REQUEST_ISSUE,
+  EMAIL_TYPE_REL_PPR_NOTIFICATION,
+  MAILJET_TMPLID_REL_PPR
 } from '../config' ;
 
-const msgFactory = ( emailType, doc ) => {
+const msgFactory = ( emailType, doc, info = {} ) => {
   const { authorEmail } = doc.correspondence();
 
   const {
@@ -25,6 +30,7 @@ const msgFactory = ( emailType, doc ) => {
   const privateUrl = `${BASE_URL}${doc.privateUrl()}`;
   const publicUrl =  `${BASE_URL}${doc.publicUrl()}`;
   const imageUrl = `${BASE_URL}/api${doc.publicUrl()}.png`;
+  const authorsAbbreviation = _.get(doc.citation(), ['authors', 'abbreviation']);
 
   const DEFAULTS = {
     from: {
@@ -62,7 +68,19 @@ const msgFactory = ( emailType, doc ) => {
         imageUrl,
       });
       break;
-    default:
+    case EMAIL_TYPE_REL_PPR_NOTIFICATION:
+      _.set( data, ['to'], _.get(info, ['to']) );
+      _.set( data, ['template', 'id'], MAILJET_TMPLID_REL_PPR );
+      _.set( data, ['template', 'vars'], { // TODO RPN this may need to be reconfigured
+        publicUrl,
+        name: info.name, // of author of related paper
+        authorsAbbreviation, // of factoid
+        paperTitle: _.get(info.paper, ['pubmed', 'title']),
+        hasNovelInteraction: info.novelIntns.length > 0,
+        novelInteraction: info.novelIntns.length > 0 ? info.novelIntns[0].toString() : ''
+      });
+      logger.info(`Sending related papers email with template (excl. defaults)`, data); // TODO RPN remove
+      break;
   }
 
   const mailOpts = _.defaultsDeep( data, DEFAULTS );