v0.25.0

README.md

@@ -51,10 +51,8 @@ General:
 CRON:
 
 - `CRON_SCHEDULE` : second (optional), minute, hour, day of month, month, day of week
-- `DOCUMENT_CRON_UPDATE_PERIOD_DAYS` : The minimum time between successive Document cron update calls
-- `DOCUMENT_CRON_CREATED_AGE_DAYS` : Only Documents created fewer than this many days will be selecte for update. When undefined (default), ignores filtering on creation date.
-- `DOCUMENT_CRON_REFRESH_ENABLED` : Flag to enable existing Document metadata to be refreshed (e.g. PubMed UID) (default true).
-- `DOCUMENT_CRON_UNEDITED_DAYS` : Number of days since Documemt was last edited; criteria for trashing
+- `DOCUMENT_CRON_UPDATE_PERIOD` : Milliseconds between successive Document cron update calls
+- `DOCUMENT_CRON_STALE_PERIOD` : Milliseconds since Documemt was last edited; criteria for trashing
 - `GRAPHDB_CRON_REFRESH_PERIOD_MINUTES` : Minimum time (minutes) between refreshes of graph DB data
 
 Database:
@@ -88,6 +86,7 @@ Services:
 - `ORCID_BASE_URL` : url for [ORCID](https://orcid.org/) website
 - `ORCID_PUBLIC_API_BASE_URL` : url for version of [ORCID](https://orcid.org/) public API
 - `NO_ABSTRACT_HANDLING` : labels directing how to sort documents missing query text. 'text' (default): autogenerate text from templates; 'date': sort by date and ignore text.
+- `CROSSREF_API_BASE_URL` : url for [Crossref Unified Resource API](https://api.crossref.org/)
 
 Links:
 

package.json

@@ -137,5 +137,5 @@
   "engines": {
     "node": ">=16.19.0"
   },
-  "version": "0.24.0"
+  "version": "0.25.0"
 }

src/client/components/document-management-components.js

@@ -507,7 +507,20 @@ class DocumentManagementDocumentComponent extends React.Component {
             checked: _.get( DOCUMENT_STATUS_FIELDS, typeVal ) === doc.status(),
             onChange: e => {
               let newlySelectedStatus = _.get( DOCUMENT_STATUS_FIELDS, e.target.value );
-              doc.status( newlySelectedStatus );
+              switch ( newlySelectedStatus ) {
+                case DOCUMENT_STATUS_FIELDS.INITIATED:
+                  doc.initiate();
+                  break;
+                case DOCUMENT_STATUS_FIELDS.SUBMITTED:
+                  doc.submit();
+                  break;
+                case DOCUMENT_STATUS_FIELDS.PUBLIC:
+                  doc.makePublic();
+                  break;
+                case DOCUMENT_STATUS_FIELDS.TRASHED:
+                  doc.trash();
+                  break;
+              }
             }
           }),
           h('label', {

src/client/components/editor/cy/layout.js

@@ -1,4 +1,4 @@
-import on from './on-key';
+// import on from './on-key';
 import * as defs from './defs';
 import _ from 'lodash';
 import { isInteractionNode, getCyLayoutOpts } from '../../../../util';
@@ -31,6 +31,6 @@ export default function( { bus, cy, document } ){
     lastLayout.run();
   };
 
-  on('r', layout);
+  // on('r', layout);
   bus.on('layout', layout);
 }

src/client/components/editor/info-panel.js

@@ -72,13 +72,14 @@ export class InfoPanel extends Component {
     const retractedPubType = _.find( citation.pubTypes, ['UI', 'D016441'] );
     const retractFlag = retractedPubType ? h('span.editor-info-flag.super-salient-button.danger', retractedPubType.value) : null;
 
-    const hasPubmedMetadata = pmid != null;
+    const hasArticleId = pmid != null || doi != null;
+    const hasRelatedPapers = !_.isEmpty( document.relatedPapers() );
 
     return h('div.editor-info-panel', [
       h('div.editor-info-flags', [ retractFlag ]),
-      
+
       h('div.editor-info-title', title),
-      
+
       h('div.editor-info-authors', _.flatten(authorProfiles.map((a, i) => {
         let orcid = findOrcidIdentifier( a.orcid ); // Backwards compatible with URI
         if ( orcid ) {
@@ -94,27 +95,26 @@ export class InfoPanel extends Component {
           i !== authorProfiles.length - 1 ? h('span.editor-info-author-spacer', ', ') : null
         ];
       }))),
-
-      h(Credits, { controller, bus, document }),
 
-      hasPubmedMetadata ? h('div.editor-info-links', [
-        h( doi ? 'a.editor-info-link.plain-link': 'div.editor-info-link', doi ? { target: '_blank', href: `${DOI_LINK_BASE_URL}${doi}` }: {}, reference),
-        h('a.editor-info-link.plain-link', { target: '_blank', href: `${PUBMED_LINK_BASE_URL}${pmid}` }, 'PubMed'),
-        h('a.editor-info-link.plain-link', { target: '_blank', href: `${GOOGLE_SCHOLAR_BASE_URL}${ doi ?  doi : ( "\u0022" + title + "\u0022") }` }, 'Google Scholar')
-      ]) : null,
+      h(Credits, { controller, bus, document }),
 
-      abstract ? h('div.editor-info-main-sections', [
-        h('div.editor-info-abstract-section.editor-info-main-section', [
+      h('div.editor-info-links', [
+        reference ? h( doi ? 'a.editor-info-link.plain-link': 'div.editor-info-link', doi ? { target: '_blank', href: `${DOI_LINK_BASE_URL}${doi}` }: {}, reference) : null,
+        pmid ? h('a.editor-info-link.plain-link', { target: '_blank', href: `${PUBMED_LINK_BASE_URL}${pmid}` }, 'PubMed') : null,
+        h('a.editor-info-link.plain-link', { target: '_blank', href: `${GOOGLE_SCHOLAR_BASE_URL}${( "\u0022" + title + "\u0022") }`}, 'Google Scholar')
+      ]),
+      h('div.editor-info-main-sections', [
+        abstract ? h('div.editor-info-abstract-section.editor-info-main-section', [
           h('div.editor-info-section-title', abstract ? 'Abstract': 'Summary'),
           h('div.editor-info-abstract-content', abstract ? abstract : document.toText() )
-        ]),
-        h('div.editor-info-related-papers-section.editor-info-main-section', [
+        ]) : null,
+        hasRelatedPapers ? h('div.editor-info-related-papers-section.editor-info-main-section', [
           h('div.editor-info-section-title', 'Recommended articles'),
           h('div.editor-info-related-papers', [ h(RelatedPapers, { document, source: document }) ])
-        ])
-      ]) : null,
+        ]) : null
+      ]),
 
-      !hasPubmedMetadata && !document.editable() ? h('div.editor-coming-soon-placeholder', `Biofactoid is looking for more information about this article from PubMed and pathway databases.  This information will appear here as soon as it is available.`) : null
+      !hasArticleId && !document.editable() ? h('div.editor-coming-soon-placeholder', `Biofactoid is looking for more information about this article from PubMed and pathway databases.  This information will appear here as soon as it is available.`) : null
     ]);
   }
 }

src/client/components/home.js

@@ -1,7 +1,6 @@
 import h from 'react-hyperscript';
 import { Component } from 'react';
 import Popover from './popover/popover';
-import RequestForm from './request-form';
 import { makeClassList } from '../dom';
 import EventEmitter from 'eventemitter3';
 import { Carousel, CAROUSEL_CONTENT } from './carousel';
@@ -277,24 +276,7 @@ class Home extends Component {
   }
 
   render(){
-    const CTAPopover = props => {
-      return h(Popover, {
-        tippy: {
-          html: h(RequestForm, {
-            bus: this.bus,
-            submitBtnText: 'Create my article profile'
-          }),
-          onHidden: () => this.bus.emit('closecta'),
-          placement: props.placement || 'top'
-        }
-      }, props.children || []);
-    };
-
-    // const CTA = () => {
-    //   return h(CTAPopover, [
-    //     h('button.home-cta-button.salient-button', 'Get started')
-    //   ]);
-    // };
+    const CTA = h('a', { href: 'document/new', target: '_blank' },[ h('button.home-intro-cta', 'Add my article') ]);
 
     const ContactPopover = (props) => {
       return h(Popover, {
@@ -412,11 +394,7 @@ class Home extends Component {
             ]),
             ` supported by their results, letting researchers explore a firsthand account of an article’s findings and connect to related articles and knowledge. `
           ]),
-          h(CTAPopover, {
-            placement: 'bottom'
-          }, [
-            h('button.home-intro-cta', 'Add my article')
-          ])
+          CTA
         ]),
         h('div.home-intro-figure'),
         h('div.home-explore#home-explore', [
@@ -426,11 +404,7 @@ class Home extends Component {
       ]),
       h('div.home-section.home-fluid-section.home-intro-figure-sm-alt-section', [
         h('div.home-intro-figure-sm-alt'),
-        h(CTAPopover, {
-          placement: 'bottom'
-        }, [
-          h('button.home-intro-cta', 'Add my article')
-        ])
+        CTA
       ]),
       h('div.home-section.home-fluid-section', [
         h('div.home-fluid-section-copy', [
@@ -470,11 +444,7 @@ class Home extends Component {
           h('h3', `Don’t let your research get left behind`),
           h('p', `Research is increasingly online, interactive, and interconnected. Biofactoid helps you connect your research to the world.`),
           h('p.home-cta-p', [
-            h(CTAPopover, {
-              placement: 'bottom'
-            }, [
-              h('button.home-cta-alt-button', 'Add my article')
-            ]),
+            CTA,
             h('a', {
               target: '_blank',
               href: `/document/${SAMPLE_DOC_ID}`
@@ -498,11 +468,7 @@ class Home extends Component {
             ])
           ]),
           h('p.home-cta-p', [
-            h(CTAPopover, {
-              placement: 'bottom'
-            }, [
-              h('button.home-cta-alt-button', 'Add my article')
-            ]),
+            CTA,
             h('a', {
               target: '_blank',
               href: `/document/${SAMPLE_DOC_ID}`
@@ -522,11 +488,7 @@ class Home extends Component {
           h('h3', `Easy sharing `),
           h('p', `Want your colleagues to know about an interesting report? Share an interactive graphical abstract via social media or email with just a click.`),
           h('p.home-cta-p', [
-            h(CTAPopover, {
-              placement: 'bottom'
-            }, [
-              h('button.home-cta-alt-button', 'Add my article')
-            ]),
+            CTA,
             h('a', {
               target: '_blank',
               href: `/document/${SAMPLE_DOC_ID}`
@@ -540,11 +502,7 @@ class Home extends Component {
             h('div.home-fluid-section-phone-aoi')
           ]),
           h('p.home-cta-p', [
-            h(CTAPopover, {
-              placement: 'bottom'
-            }, [
-              h('button.home-cta-alt-button', 'Add my article')
-            ]),
+            CTA,
             h('a', {
               target: '_blank',
               href: `/document/${SAMPLE_DOC_ID}`

src/client/components/request-form.js

@@ -40,10 +40,10 @@ class RequestForm extends Component {
 
       if(titleEl){
         focusDomElement(titleEl);
-      } 
+      }
     }, 50);
 
-    this.onCloseCTA = () => this.reset();
+    this.onCloseCTA = () => {};
     this.onOpenCTA = () => this.focusTitle();
   }
 

src/config.js

@@ -40,10 +40,8 @@ export const APPSIGNAL_APP_ENV = env('APPSIGNAL_APP_ENV', 'development');
 
 // CRON jobs
 export const CRON_SCHEDULE = env('CRON_SCHEDULE', '0 * * * *');
-export const DOCUMENT_CRON_UPDATE_PERIOD_DAYS = env('DOCUMENT_CRON_UPDATE_PERIOD_DAYS', 7);
-export const DOCUMENT_CRON_CREATED_AGE_DAYS = env('DOCUMENT_CRON_CREATED_AGE_DAYS', undefined);
-export const DOCUMENT_CRON_REFRESH_ENABLED = env('DOCUMENT_CRON_REFRESH_ENABLED', true);
-export const DOCUMENT_CRON_UNEDITED_DAYS = env('DOCUMENT_CRON_UNEDITED_DAYS', 30);
+export const DOCUMENT_CRON_UPDATE_PERIOD = env('DOCUMENT_CRON_UPDATE_PERIOD', 7 * 24 * 60 * 60 * 1000);
+export const DOCUMENT_CRON_STALE_PERIOD = env('DOCUMENT_CRON_STALE_PERIOD', 30 * 24 * 60 * 60 * 1000);
 export const GRAPHDB_CRON_REFRESH_PERIOD_MINUTES = env('GRAPHDB_CRON_REFRESH_PERIOD_MINUTES', 1440);
 
 // Connect to localhost
@@ -75,6 +73,7 @@ export const INDRA_ENGLISH_ASSEMBLER_URL = env('INDRA_ENGLISH_ASSEMBLER_URL', 'h
 export const SEMANTIC_SEARCH_BASE_URL = env('SEMANTIC_SEARCH_BASE_URL', 'https://main.semanticsearch.baderlab.org/');
 export const ORCID_BASE_URL = env('ORCID_BASE_URL', 'https://orcid.org/');
 export const ORCID_PUBLIC_API_BASE_URL = env('ORCID_PUBLIC_API_BASE_URL', 'https://pub.orcid.org/v3.0/');
+export const CROSSREF_API_BASE_URL = env('CROSSREF_API_BASE_URL', 'https://api.crossref.org/');
 
 // Links
 export const UNIPROT_LINK_BASE_URL = env('UNIPROT_LINK_BASE_URL', 'http://www.uniprot.org/uniprot/');

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

@@ -0,0 +1,85 @@
+import _ from 'lodash';
+import queryString from 'query-string';
+import fetch from 'node-fetch';
+
+import { CROSSREF_API_BASE_URL, EMAIL_ADDRESS_INFO, BASE_URL } from '../../../../../config.js';
+import { checkHTTPStatus } from '../../../../../util/index.js';
+
+const WORKS_URL = CROSSREF_API_BASE_URL + 'works';
+
+const toJson = response => response.json();
+const checkResultStatus = json => {
+  const status = _.get( json, ['status'] );
+  const isOK = status === 'ok';
+  if( isOK ){
+    return json;
+  } else {
+    const message = _.get( json, ['message'] );
+    throw new Error(`${message}`);
+  }
+};
+
+/**
+ * search
+ *
+ * Query the CrossRef web service API for matching Work.
+ * [See docs]{@link https://api.crossref.org/swagger-ui/index.html#/Works/get_works}
+ *
+ * @param { String } q The query term
+ * @param { Object } opts Search options
+ * @returns { Object } result The search results
+ * @returns { Array } result.searchHits A list of matching records
+ * @returns { Number } result.count The number of searchHits
+ */
+const search = (q, opts) => {
+  const DEFAULT_WORKS_PARAMS = {
+    'query.bibliographic': undefined, //query field for: citation look up, includes titles, authors, ISSNs and publication years
+    'rows': 5
+  };
+  const formatSearchHits = json => {
+    const searchHits =  _.get( json, ['message', 'items'] );
+    const count = searchHits.length;
+    return { searchHits, count };
+  };
+  const params = _.assign( {}, DEFAULT_WORKS_PARAMS, { 'query.bibliographic': q }, opts );
+  const url = WORKS_URL + '?' + queryString.stringify( params );
+  const userAgent = `${process.env.npm_package_name}/${process.env.npm_package_version} (${BASE_URL}; mailto:${EMAIL_ADDRESS_INFO})`;
+  return fetch( url, {
+    method: 'GET',
+    headers: {
+      'User-Agent': userAgent
+    }
+  })
+  .then( checkHTTPStatus )
+  .then( toJson )
+  .then( checkResultStatus )
+  .then( formatSearchHits );
+};
+
+
+/**
+ * get
+ *
+ * Retrieve Work from CrossRef web service API.
+ * [See docs]{@link https://api.crossref.org/swagger-ui/index.html#/Works/get_works__doi_}
+ *
+ * @param { String } doi The object DOI
+ * @returns { Object } The matching record
+ */
+const get = doi => {
+  const formatGetResponse = json => _.get( json, ['message'] );
+  const url = WORKS_URL + `/${doi}`;
+  const userAgent = `${process.env.npm_package_name}/${process.env.npm_package_version} (${BASE_URL}; mailto:${EMAIL_ADDRESS_INFO})`;
+  return fetch( url, {
+    method: 'GET',
+    headers: {
+      'User-Agent': userAgent
+    }
+  })
+  .then( checkHTTPStatus )
+  .then( toJson )
+  .then( checkResultStatus )
+  .then( formatGetResponse );
+};
+
+export { search, get };

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

@@ -0,0 +1,3 @@
+export * from './map.js';
+export * from './works.js';
+export * from './api.js';