WIP: reference papers

research-software-directory · Oct 11, 2023 · d181665 · d181665
1 parent bd8911b
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diff --git a/database/109-mention-views.sql b/database/109-mention-views.sql
@@ -1,3 +1,4 @@
+-- SPDX-FileCopyrightText: 2023 Dusan Mijatovic (Netherlands eScience Center)
 -- SPDX-FileCopyrightText: 2023 Ewan Cahen (Netherlands eScience Center) <[email protected]>
 -- SPDX-FileCopyrightText: 2023 Netherlands eScience Center
 --
@@ -17,3 +18,61 @@ $$
 		SELECT mention FROM reference_paper_for_software
 	)
 $$;
+
+-- 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
+$$
+SELECT
+	reference_paper_for_software.software,
+	mention.id,
+	mention.doi,
+	mention.url,
+	mention.title,
+	mention.authors,
+	mention.publisher,
+	mention.publication_year,
+	mention.journal,
+	mention.page,
+	mention.image_url,
+	mention.mention_type,
+	mention.source,
+	ARRAY_AGG(
+		reference_paper_for_software.mention
+	) AS reference_paper
+FROM
+	reference_paper_for_software
+INNER JOIN
+	citation_for_mention ON citation_for_mention.mention = reference_paper_for_software.mention
+INNER JOIN
+	mention ON mention.id = citation_for_mention.citation
+GROUP BY
+	reference_paper_for_software.software,
+	mention.id,
+	mention.doi,
+	mention.url,
+	mention.title,
+	mention.authors,
+	mention.publisher,
+	mention.publication_year,
+	mention.journal,
+	mention.page,
+	mention.image_url,
+	mention.mention_type,
+	mention.source
+;
+$$;
diff --git a/frontend/components/mention/MentionItemBase.tsx b/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>
   )
 }

diff --git a/frontend/components/mention/MentionViewItem.tsx b/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}

diff --git a/frontend/components/mention/useEditMentionReducer.tsx b/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()
 

diff --git a/frontend/components/software/edit/editSoftwarePages.tsx b/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',

diff --git a/frontend/components/software/edit/mentions/EditMentionsProvider.tsx b/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,

diff --git a/frontend/components/software/edit/reference-papers/CitationItem.tsx b/frontend/components/software/edit/reference-papers/CitationItem.tsx
@@ -0,0 +1,95 @@
+// SPDX-FileCopyrightText: 2023 Dusan Mijatovic (Netherlands eScience Center)
+// SPDX-FileCopyrightText: 2023 Netherlands eScience Center
+//
+// SPDX-License-Identifier: Apache-2.0
+
+import {MentionItemProps} from '~/types/Mention'
+import {getMentionType} from '~/components/mention/config'
+import MentionAuthors from '~/components/mention/MentionAuthors'
+import MentionDoi from '~/components/mention/MentionDoi'
+import {MentionTitle} from '~/components/mention/MentionItemBase'
+import MentionPublisherItem from '~/components/mention/MentionPublisherItem'
+import useEditMentionReducer from '~/components/mention/useEditMentionReducer'
+
+export type CitationItemProps = MentionItemProps & {
+  reference_papers: string[]
+}
+
+function ReferencePapers({papers}:{papers:string[]}){
+  const {mentions} = useEditMentionReducer()
+  const reference:{doi:string,url:string}[] =[]
+
+  if (papers?.length===0 || mentions?.length===0){
+    return (
+      <div className="text-sm">
+        Referenced paper:
+      </div>
+    )
+  }
+
+  papers.forEach(uuid=>{
+    const found = mentions.find(item=>item.id === uuid)
+    if (found?.doi && found.url) reference.push({doi:found.doi, url:found.url})
+  })
+
+  if (reference.length === 0){
+    return (
+      <div className="text-sm">
+        Referenced: <i>None</i>
+      </div>
+    )
+  }
+
+  return(
+    <div className="flex flex-wrap gap-2 text-sm  text-base-content-secondary">
+      Referenced: {
+        reference.map(item=>{
+          return (
+            <a
+              key={item.url}
+              href={item.url} target="_blank" rel="noreferrer"
+              className="text-sm "
+            >
+              {item.doi}
+            </a>
+          )
+        })
+      }
+    </div>
+  )
+}
+
+
+export default function CitationItem({item}:{item:CitationItemProps}){
+  const title = getMentionType(item?.mention_type,'singular')
+  return (
+    <div data-testid="citation-view-item-body" className="py-2 px-4 hover:bg-base-200">
+      <div className="text-base-content-disabled">
+        {title}
+      </div>
+      <MentionTitle
+        title={item?.title ?? ''}
+        role="list"
+        url={item.url}
+        className="text-base"
+      />
+      <MentionAuthors
+        authors={item.authors}
+        className="text-sm text-base-content-secondary"
+      />
+      <MentionPublisherItem
+        publisher={item?.publisher ?? ''}
+        page={item?.page ?? ''}
+        publication_year={item.publication_year}
+        journal = {item.journal}
+        className="text-sm text-base-content-secondary"
+      />
+      <MentionDoi
+        url={item?.url}
+        doi={item?.doi}
+        className="text-sm"
+      />
+      <ReferencePapers papers={item.reference_papers} />
+    </div>
+  )
+}