986 reference papers

database/009-create-mention-table.sql

@@ -40,12 +40,15 @@ CREATE TABLE mention (
 	page VARCHAR(50),
 	image_url VARCHAR(500) CHECK (image_url ~ '^https?://'),
 	mention_type mention_type NOT NULL,
+	external_id VARCHAR(500),
 	source VARCHAR(50) NOT NULL,
 	version VARCHAR(100),
 	note VARCHAR(500),
 	scraped_at TIMESTAMPTZ,
+	citations_scraped_at TIMESTAMPTZ,
 	created_at TIMESTAMPTZ NOT NULL,
-	updated_at TIMESTAMPTZ NOT NULL
+	updated_at TIMESTAMPTZ NOT NULL,
+	UNIQUE(external_id, source)
 );
 
 CREATE FUNCTION sanitise_insert_mention() RETURNS TRIGGER LANGUAGE plpgsql AS
@@ -81,6 +84,20 @@ CREATE TABLE mention_for_software (
 );
 
 
+CREATE TABLE reference_paper_for_software (
+	mention UUID REFERENCES mention (id),
+	software UUID REFERENCES software (id),
+	PRIMARY KEY (mention, software)
+);
+
+
+CREATE TABLE citation_for_mention (
+	mention UUID REFERENCES mention (id),
+	citation UUID REFERENCES mention (id),
+	PRIMARY KEY (mention, citation)
+);
+
+
 CREATE FUNCTION search_mentions_for_software(software_id UUID, search_text VARCHAR) RETURNS SETOF mention STABLE LANGUAGE plpgsql AS
 $$
 BEGIN

database/020-row-level-security.sql

@@ -446,17 +446,9 @@ CREATE POLICY admin_all_rights ON research_domain_for_project TO rsd_admin
 
 
 -- mentions
--- TODO: not sure what to do here,
--- should a mention only be visible if you can see at least one software or project for which it relates?
 ALTER TABLE mention ENABLE ROW LEVEL SECURITY;
 
 CREATE POLICY anyone_can_read ON mention FOR SELECT TO rsd_web_anon, rsd_user
-	USING (id IN (SELECT mention FROM mention_for_software)
-		OR id IN (SELECT mention FROM output_for_project)
-		OR id IN (SELECT mention FROM impact_for_project)
-		OR id IN (SELECT mention_id FROM release_version));
-
-CREATE POLICY maintainer_can_read ON mention FOR SELECT TO rsd_user
 	USING (TRUE);
 
 CREATE POLICY maintainer_can_delete ON mention FOR DELETE TO rsd_user
@@ -484,6 +476,30 @@ CREATE POLICY admin_all_rights ON mention_for_software TO rsd_admin
 	WITH CHECK (TRUE);
 
 
+ALTER TABLE reference_paper_for_software ENABLE ROW LEVEL SECURITY;
+
+CREATE POLICY anyone_can_read ON reference_paper_for_software FOR SELECT TO rsd_web_anon, rsd_user
+	USING (software IN (SELECT id FROM software));
+
+CREATE POLICY maintainer_all_rights ON reference_paper_for_software TO rsd_user
+	USING (software IN (SELECT * FROM software_of_current_maintainer()))
+	WITH CHECK (software IN (SELECT * FROM software_of_current_maintainer()));
+
+CREATE POLICY admin_all_rights ON reference_paper_for_software TO rsd_admin
+	USING (TRUE)
+	WITH CHECK (TRUE);
+
+
+ALTER TABLE citation_for_mention ENABLE ROW LEVEL SECURITY;
+
+CREATE POLICY anyone_can_read ON citation_for_mention FOR SELECT TO rsd_web_anon, rsd_user
+	USING (mention IN (SELECT id FROM mention));
+
+CREATE POLICY admin_all_rights ON citation_for_mention TO rsd_admin
+	USING (TRUE)
+	WITH CHECK (TRUE);
+
+
 ALTER TABLE output_for_project ENABLE ROW LEVEL SECURITY;
 
 CREATE POLICY anyone_can_read ON output_for_project FOR SELECT TO rsd_web_anon, rsd_user

database/109-mention-views.sql

@@ -0,0 +1,82 @@
+-- SPDX-FileCopyrightText: 2023 Dusan Mijatovic (Netherlands eScience Center)
+-- SPDX-FileCopyrightText: 2023 Ewan Cahen (Netherlands eScience Center) <[email protected]>
+-- SPDX-FileCopyrightText: 2023 Netherlands eScience Center
+--
+-- SPDX-License-Identifier: Apache-2.0
+
+CREATE FUNCTION reference_papers_to_scrape()
+RETURNS TABLE (
+	id UUID,
+	doi CITEXT,
+	citations_scraped_at TIMESTAMPTZ,
+	known_dois CITEXT[]
+)
+LANGUAGE sql STABLE AS
+$$
+	SELECT mention.id, mention.doi, mention.citations_scraped_at, ARRAY_REMOVE(ARRAY_AGG(citation.doi), NULL)
+	FROM mention
+	LEFT JOIN citation_for_mention ON mention.id = citation_for_mention.mention
+	LEFT JOIN mention AS citation ON citation_for_mention.citation = citation.id
+	WHERE mention.id IN (
+		SELECT mention FROM reference_paper_for_software
+	)
+	GROUP BY mention.id
+$$;
+
+-- UNIQUE CITATIONS BY SOFTWARE ID
+CREATE FUNCTION citation_by_software() RETURNS TABLE (
+	software UUID,
+	id UUID,
+	doi CITEXT,
+	url VARCHAR,
+	title VARCHAR,
+	authors VARCHAR,
+	publisher VARCHAR,
+	publication_year SMALLINT,
+	journal VARCHAR,
+	page VARCHAR,
+	image_url VARCHAR,
+	mention_type mention_type,
+	source VARCHAR,
+	reference_papers UUID[]
+)LANGUAGE sql STABLE AS
+$$
+SELECT
+	reference_paper_for_software.software,
+	mention.id,
+	mention.doi,
+	mention.url,
+	mention.title,
+	mention.authors,
+	mention.publisher,
+	mention.publication_year,
+	mention.journal,
+	mention.page,
+	mention.image_url,
+	mention.mention_type,
+	mention.source,
+	ARRAY_AGG(
+		reference_paper_for_software.mention
+	) AS reference_paper
+FROM
+	reference_paper_for_software
+INNER JOIN
+	citation_for_mention ON citation_for_mention.mention = reference_paper_for_software.mention
+INNER JOIN
+	mention ON mention.id = citation_for_mention.citation
+GROUP BY
+	reference_paper_for_software.software,
+	mention.id,
+	mention.doi,
+	mention.url,
+	mention.title,
+	mention.authors,
+	mention.publisher,
+	mention.publication_year,
+	mention.journal,
+	mention.page,
+	mention.image_url,
+	mention.mention_type,
+	mention.source
+;
+$$;

frontend/components/mention/MentionItemBase.tsx

@@ -75,7 +75,7 @@ export default function MentionItemBase({item,pos,nav,type,role='find'}:MentionI
         className="text-sm"
         role={role}
       />
-      <MentionNote note={item.note} />
+      <MentionNote note={item.note ?? null} />
     </article>
   )
 }

frontend/components/mention/MentionViewItem.tsx

@@ -43,7 +43,7 @@ export default function MentionViewItem({item, pos}: {item: MentionItemProps, po
             doi={item?.doi}
             className="text-sm"
           />
-          <MentionNote note={item.note} />
+          <MentionNote note={item.note ?? null} />
         </div>
         <div className="flex justify-center items-center">
           {item?.url ? <LinkIcon /> : null}

frontend/components/mention/useEditMentionReducer.tsx

@@ -1,68 +1,72 @@
 // SPDX-FileCopyrightText: 2022 Dusan Mijatovic (dv4all)
 // SPDX-FileCopyrightText: 2022 dv4all
+// SPDX-FileCopyrightText: 2023 Dusan Mijatovic (Netherlands eScience Center)
+// SPDX-FileCopyrightText: 2023 Netherlands eScience Center
 //
 // SPDX-License-Identifier: Apache-2.0
 
-import {useContext} from 'react'
+import {useCallback, useContext} from 'react'
 import {EditMentionActionType} from './editMentionReducer'
 import EditMentionContext from './editMentionContext'
 import {MentionItemProps} from '~/types/Mention'
 
 export default function useEditMentionReducer() {
   const {state, dispatch} = useContext(EditMentionContext)
 
-  function setLoading(loading: boolean) {
+  const setLoading = useCallback((loading:boolean)=>{
     dispatch({
       type: EditMentionActionType.SET_LOADING,
       payload: loading
     })
-  }
+  // eslint-disable-next-line react-hooks/exhaustive-deps
+  },[])
 
-  function setMentions(mentions: MentionItemProps[]) {
+  const setMentions = useCallback((mentions: MentionItemProps[])=>{
     dispatch({
       type: EditMentionActionType.SET_MENTIONS,
       payload: mentions
     })
-  }
+  // eslint-disable-next-line react-hooks/exhaustive-deps
+  },[])
 
-  function onAdd(item: MentionItemProps) {
+  const onAdd = useCallback((item: MentionItemProps)=>{
     dispatch({
       type: EditMentionActionType.ON_ADD,
       payload: item
     })
-  }
+  },[dispatch])
 
-  function onNewItem() {
+  const onNewItem = useCallback(()=>{
     dispatch({
       type: EditMentionActionType.SET_EDIT_MODAL,
       payload: {
         open:true
       }
     })
-  }
+  },[dispatch])
 
-  function onSubmit(item:MentionItemProps) {
+  const onSubmit = useCallback((item:MentionItemProps)=>{
     dispatch({
       type: EditMentionActionType.ON_SUBMIT,
       payload: item
     })
-  }
+  },[dispatch])
 
-  function onUpdate(item:MentionItemProps) {
+  const onUpdate = useCallback((item:MentionItemProps)=>{
     dispatch({
       type: EditMentionActionType.ON_UPDATE,
       payload: item
     })
-  }
+  },[dispatch])
 
-  function onDelete(item:MentionItemProps) {
+  const onDelete = useCallback((item:MentionItemProps)=>{
     dispatch({
       type: EditMentionActionType.ON_DELETE,
       payload: item
     })
-  }
+  },[dispatch])
 
-  function confirmDelete(item?: MentionItemProps) {
+  const confirmDelete = useCallback((item?: MentionItemProps)=>{
     if (item) {
       // open modal
       dispatch({
@@ -81,9 +85,9 @@ export default function useEditMentionReducer() {
         }
       })
     }
-  }
+  },[dispatch])
 
-  function setEditModal(item?: MentionItemProps) {
+  const setEditModal = useCallback((item?: MentionItemProps)=>{
     if (item) {
       // show modal when item provided
       dispatch({
@@ -102,9 +106,9 @@ export default function useEditMentionReducer() {
         }
       })
     }
-  }
+  },[dispatch])
 
-  // console.group('useOutputContext')
+  // console.group('useEditMentionReducer')
   // console.log('state...', state)
   // console.groupEnd()
 

frontend/components/software/edit/editSoftwarePages.tsx

@@ -18,6 +18,7 @@ import PersonAddIcon from '@mui/icons-material/PersonAdd'
 import ContentLoader from '~/components/layout/ContentLoader'
 import HomeRepairServiceIcon from '@mui/icons-material/HomeRepairService'
 import PendingActionsIcon from '@mui/icons-material/PendingActions'
+import PostAddIcon from '@mui/icons-material/PostAdd'
 
 // import SoftwareInformation from './information'
 // import SoftwareContributors from './contributors'
@@ -28,22 +29,25 @@ import PendingActionsIcon from '@mui/icons-material/PendingActions'
 // import SoftwareMaintainers from './maintainers'
 
 // use dynamic imports instead
+const SoftwareContributors = dynamic(() => import('./contributors'),{
+  loading: ()=><ContentLoader />
+})
 const SoftwareInformation = dynamic(() => import('./information'),{
   loading: ()=><ContentLoader />
 })
-const SoftwareContributors = dynamic(() => import('./contributors'),{
+const SoftwareMaintainers = dynamic(() => import('./maintainers'),{
   loading: ()=><ContentLoader />
 })
-const SoftwareOgranisations = dynamic(() => import('./organisations'),{
+const SoftwareMentions = dynamic(() => import('./mentions'),{
   loading: ()=><ContentLoader />
 })
-const PackageManagers = dynamic(() => import('./package-managers'),{
+const SoftwareOgranisations = dynamic(() => import('./organisations'),{
   loading: ()=><ContentLoader />
 })
-const SoftwareMentions = dynamic(() => import('./mentions'),{
+const PackageManagers = dynamic(() => import('./package-managers'),{
   loading: ()=><ContentLoader />
 })
-const SoftwareTestimonials = dynamic(() => import('./testimonials'),{
+const ReferencePapers = dynamic(() => import('./reference-papers'),{
   loading: ()=><ContentLoader />
 })
 const RelatedSoftware = dynamic(() => import('./related-software'),{
@@ -52,10 +56,11 @@ const RelatedSoftware = dynamic(() => import('./related-software'),{
 const RelatedProjects = dynamic(() => import('./related-projects'),{
   loading: ()=><ContentLoader />
 })
-const SoftwareMaintainers = dynamic(() => import('./maintainers'),{
+const SoftwareTestimonials = dynamic(() => import('./testimonials'),{
   loading: ()=><ContentLoader />
 })
 
+
 export type EditSoftwarePageProps = {
   id: string
   status: string,
@@ -82,6 +87,12 @@ export const editSoftwarePage:EditSoftwarePageProps[] = [{
   icon: <FactoryIcon />,
   render: () => <SoftwareOgranisations />,
   status: 'Optional information'
+},{
+  id: 'reference-paper',
+  label: 'Reference papers',
+  icon: <PostAddIcon />,
+  render: () => <ReferencePapers />,
+  status: 'Optional information'
 },{
   id: 'mentions',
   label: 'Mentions',

frontend/components/software/edit/mentions/EditMentionsProvider.tsx

@@ -1,6 +1,8 @@
 // SPDX-FileCopyrightText: 2022 Dusan Mijatovic (dv4all)
 // SPDX-FileCopyrightText: 2022 Dusan Mijatovic (dv4all) (dv4all)
 // SPDX-FileCopyrightText: 2022 dv4all
+// SPDX-FileCopyrightText: 2023 Dusan Mijatovic (Netherlands eScience Center)
+// SPDX-FileCopyrightText: 2023 Netherlands eScience Center
 //
 // SPDX-License-Identifier: Apache-2.0
 
@@ -112,7 +114,7 @@ export default function EditMentionsProvider(props: any) {
       }
     }
     if (item.id) {
-      // existing RSD mention item to be added to project
+      // existing RSD mention item to be added to software
       const resp = await addToMentionForSoftware({
         software,
         mention: item.id,

frontend/components/software/edit/mentions/utils.ts

@@ -1,3 +1,4 @@
+// SPDX-FileCopyrightText: 2023 Dusan Mijatovic (Netherlands eScience Center)
 // SPDX-FileCopyrightText: 2023 Dusan Mijatovic (dv4all)
 // SPDX-FileCopyrightText: 2023 Ewan Cahen (Netherlands eScience Center) <[email protected]>
 // SPDX-FileCopyrightText: 2023 Netherlands eScience Center
@@ -11,8 +12,8 @@ export type SearchTermInfo = {
   term: string,
   type: 'doi' | 'title'
 }
-
 export function extractSearchTerm(query: string): SearchTermInfo{
+
   const doiRegexMatch = query.match(doiRegex)
   if (doiRegexMatch != null) {
     return {term: doiRegexMatch[0], type: 'doi'}