Merge pull request #1316 from research-software-directory/1312-openal…

…ex-support

Better OpenAlex support

documentation/docs/01-users/05-adding-software.md

@@ -164,19 +164,19 @@ This section allows you to add mentions to your software page. You can use this
 
 ### Reference papers
 
-Use the *Search* box on the right hand side to find papers by DOI or title. All the relevant data about the publication will be retrieved automatically. A background scraper will use [OpenAlex](https://openalex.org/) to collect all citations of reference papers that have a DOI or an OpenAlex ID.
+Use the *Search* box on the right hand side to find papers by DOI, OpenAlex ID or title. All the relevant data about the publication will be retrieved automatically. A background scraper will use [OpenAlex](https://openalex.org/) to collect all citations of reference papers that have a DOI or an OpenAlex ID.
 
 ### Citations
 
-These are the citations of the reference papers that the RSD scraper was able to find on [OpenAlex](https://openalex.org/. It can take a few minutes before the citations are harvested.
+These are the citations of the reference papers that the RSD scraper was able to find on [OpenAlex](https://openalex.org/). It can take a few minutes before the citations are harvested.
 
 :::warning
 You cannot edit the content of this section. All entries are automatically harvested and generated by the RSD scraper. The mentions found are displayed in the mentions section of the software page.
 :::
 
 ### Related output
 
-Here you can add all additional related output. Use search to find papers or other publications by DOI or title. It is also possible to bulk add mentions, that have a DOI (use the *Import* button). On the popup, you can add one DOI per line, with a maximum of 50. After clicking on the *Next* button, we will fetch the data, which can take a moment. When that is done, you will see an overview of the data we fetched, including possible errors, where you can check the data and possibly disable some of the mentions.
+Here you can add all additional related output. Use search to find papers or other publications by DOI, OpenAlex ID or title. It is also possible to bulk add mentions, that have a DOI (use the *Import* button). On the popup, you can add one DOI per line, with a maximum of 50. After clicking on the *Next* button, we will fetch the data, which can take a moment. When that is done, you will see an overview of the data we fetched, including possible errors, where you can check the data and possibly disable some of the mentions.
 
 ## Testimonials
 

documentation/docs/01-users/07-adding-projects.md

@@ -95,7 +95,7 @@ Here you can add output that was produced by the project itself, such as papers,
 
 #### Add output
 
-To add an item, the search bar on the left can be used to search the RSD, [Crossref](https://crossref.org), and [DataCite](https://datacite.org) databases using the **Title** or **DOI** of the research output. An item can be added by selecting it from the list of the search results. The RSD will automatically classify the item based on the available metadata.
+To add an item, the search bar on the left can be used to search the RSD, [Crossref](https://www.crossref.org), [DataCite](https://datacite.org) and [OpenAlex](https://openalex.org/) databases using the **Title**, **DOI** or **OpenAlex ID** of the research output. An item can be added by selecting it from the list of the search results. The RSD will automatically classify the item based on the available metadata.
 
 #### Import output
 
@@ -124,7 +124,7 @@ Here you can add mentions of your project that cannot be found automatically by
 
 #### Search publication
 
-To add an item, the search bar on the left can be used to search the RSD, [Crossref](https://crossref.org), and [DataCite](https://datacite.org) databases using the **Title** or **DOI** of the research output. An item can be added by selecting it from the list of search results. The RSD will automatically classify the item based on the available metadata.
+To add an item, the search bar on the left can be used to search the RSD, [Crossref](https://www.crossref.org), [DataCite](https://datacite.org) and [OpenAlex](https://openalex.org/) databases using the **Title**, **DOI** or **OpenAlex ID** of the research impact item. An item can be added by selecting it from the list of search results. The RSD will automatically classify the item based on the available metadata.
 
 #### Import publication
 

frontend/components/admin/mentions/MentionsOverview.tsx

@@ -49,10 +49,14 @@ export default function MentionsOverview() {
 
     const searchTypeTerm: SearchTermInfo = extractSearchTerm(sanitisedSearch)
     const termEscaped = encodeURIComponent(sanitisedSearch)
-    if (searchTypeTerm.type === 'doi') {
-      return `doi=eq.${termEscaped}`
+    switch (searchTypeTerm.type) {
+      case 'doi':
+        return `doi=eq.${termEscaped}`
+      case 'openalex':
+        return `openalex_id=eq.${termEscaped}`
+      case 'title':
+        return `or=(title.ilike.*${termEscaped}*,authors.ilike.*${termEscaped}*,journal.ilike.*${termEscaped}*,url.ilike.*${termEscaped}*,note.ilike.*${termEscaped}*,openalex_id.ilike.*${termEscaped}*)`
     }
-    return `or=(title.ilike.*${termEscaped}*,authors.ilike.*${termEscaped}*,journal.ilike.*${termEscaped}*,url.ilike.*${termEscaped}*,note.ilike.*${termEscaped}*,openalex_id.ilike.*${termEscaped}*)`
   }
 
   function sanitiseSearch(search: string): string | undefined {

frontend/components/mention/EditMentionModal.tsx

@@ -65,7 +65,7 @@ export default function EditMentionModal({open, onCancel, onSubmit, item, pos, t
   const formData = watch()
   // need to clear image_url error manually after the type change
   // and dynamic rules change from required to not required
-  if (formData.mention_type!=='highlight' && errors?.hasOwnProperty('image_url')){
+  if (formData.mention_type !== 'highlight' && errors?.hasOwnProperty('image_url')) {
     clearErrors('image_url')
   }
 
@@ -130,23 +130,6 @@ export default function EditMentionModal({open, onCancel, onSubmit, item, pos, t
             width: ['100%'],
             padding: '1rem 1.5rem'
           }}>
-          {isAdmin &&
-        <>
-          <ControlledTextField
-            control={control}
-            options={{
-              name: 'doi',
-              label: config.doi.label,
-              useNull: true,
-              defaultValue: formData?.doi,
-              helperTextMessage: config.doi.help,
-              helperTextCnt: `${formData?.doi?.length || 0}/${config.doi.validation.maxLength.value}`,
-            }}
-            rules={config.doi.validation}
-          />
-          <div className="py-2"></div>
-        </>
-          }
           <ControlledTextField
             control={control}
             options={{
@@ -286,26 +269,39 @@ export default function EditMentionModal({open, onCancel, onSubmit, item, pos, t
             rules={config.note.validation}
           />
           {isAdmin &&
-        <>
-          <div className="py-2"></div>
-          <ControlledTextField
-            control={control}
-            options={{
-              name: 'openalex_id',
-              label: config.openalex_id.label,
-              useNull: true,
-              defaultValue: formData?.openalex_id,
-              helperTextMessage: config.openalex_id.help,
-            }}
-            rules={config.openalex_id.validation}
-          />
-          <div className="py-2"></div>
-        </>
+            <>
+              <div className="py-2"></div>
+              <ControlledTextField
+                control={control}
+                options={{
+                  name: 'doi',
+                  label: config.doi.label,
+                  useNull: true,
+                  defaultValue: formData?.doi,
+                  helperTextMessage: config.doi.help,
+                  helperTextCnt: `${formData?.doi?.length || 0}/${config.doi.validation.maxLength.value}`,
+                }}
+                rules={config.doi.validation}
+              />
+              <div className="py-2"></div>
+              <ControlledTextField
+                control={control}
+                options={{
+                  name: 'openalex_id',
+                  label: config.openalex_id.label,
+                  useNull: true,
+                  defaultValue: formData?.openalex_id,
+                  helperTextMessage: config.openalex_id.help,
+                }}
+                rules={config.openalex_id.validation}
+              />
+              <div className="py-2"></div>
+            </>
           }
           {!isAdmin &&
-        <Alert severity="warning" sx={{marginTop: '1rem'}}>
-          The information can not be edited after creation.
-        </Alert>}
+            <Alert severity="warning" sx={{marginTop: '1rem'}}>
+              The information can not be edited after creation.
+            </Alert>}
         </DialogContent>
         <DialogActions sx={{
           padding: '1rem 1.5rem',

frontend/components/mention/FindMentionInfoPanel.tsx

@@ -1,5 +1,7 @@
 // SPDX-FileCopyrightText: 2022 - 2023 Dusan Mijatovic (dv4all)
 // SPDX-FileCopyrightText: 2022 - 2023 dv4all
+// SPDX-FileCopyrightText: 2024 Ewan Cahen (Netherlands eScience Center) <e[email protected]>
+// SPDX-FileCopyrightText: 2024 Netherlands eScience Center
 //
 // SPDX-License-Identifier: Apache-2.0
 
@@ -12,7 +14,7 @@ export default function FindMentionInfoPanel({children}:{children:any}) {
       icon={false}
     >
       {/* <AlertTitle>Add existing publication</AlertTitle> */}
-      We search in <strong> <a href="https://crossref.org" target="_blank">Crossref</a>, <a href="https://datacite.org" target="_blank">DataCite</a></strong> and the RSD.
+      We search in <strong> <a href="https://www.crossref.org/" target="_blank">Crossref</a>, <a href="https://datacite.org" target="_blank">DataCite</a>, <a href="https://openalex.org/" target="_blank">OpenAlex</a></strong> and the RSD.
       All metadata will be imported automatically.
       { children }
     </Alert>

frontend/components/mention/FindMentionSection.tsx

@@ -1,20 +1,21 @@
 // SPDX-FileCopyrightText: 2022 - 2023 Dusan Mijatovic (dv4all)
-// SPDX-FileCopyrightText: 2022 - 2023 Ewan Cahen (Netherlands eScience Center) <[email protected]>
 // SPDX-FileCopyrightText: 2022 - 2023 dv4all
+// SPDX-FileCopyrightText: 2022 - 2024 Ewan Cahen (Netherlands eScience Center) <[email protected]>
 // SPDX-FileCopyrightText: 2022 - 2024 Netherlands eScience Center
 // SPDX-FileCopyrightText: 2024 Dusan Mijatovic (Netherlands eScience Center)
 //
 // SPDX-License-Identifier: Apache-2.0
 
 import {useAuth} from '~/auth'
 import {MentionItemProps} from '~/types/Mention'
-import {getMentionByDoiFromRsd} from '~/utils/editMentions'
+import {getMentionByDoiFromRsd, getMentionByOpenalexIdFromRsd} from '~/utils/editMentions'
 import {getMentionByDoi} from '~/utils/getDOI'
 import EditSectionTitle from '~/components/layout/EditSectionTitle'
 import FindMention from '~/components/mention/FindMention'
 import FindMentionInfoPanel from '~/components/mention/FindMentionInfoPanel'
 import useEditMentionReducer from '~/components/mention/useEditMentionReducer'
 import {extractSearchTerm} from '~/components/software/edit/mentions/utils'
+import {getMentionByOpenalexId} from '~/utils/getOpenalex'
 
 type FindProjectMentionProps={
   id:string,
@@ -39,35 +40,57 @@ export default function FindMentionSection({id,config,findPublicationByTitle}:Fi
   const {session: {token}} = useAuth()
   const {onAdd} = useEditMentionReducer()
 
-  async function findPublication(searchFor: string) {
+  async function findPublication(searchFor: string): Promise<MentionItemProps[]> {
     const searchData = extractSearchTerm(searchFor)
-    if (searchData.type === 'doi') {
-      searchFor = searchData.term
-      // look first at RSD
-      const rsd = await getMentionByDoiFromRsd({
-        doi: searchFor,
-        token
-      })
-      if (rsd?.status === 200 && rsd.message?.length === 1) {
-        // return first found item in RSD
-        const item:MentionItemProps = rsd.message[0]
-        return [item]
+    switch (searchData.type) {
+      case 'doi': {
+        searchFor = searchData.term
+        // look first at RSD
+        const rsd = await getMentionByDoiFromRsd({
+          doi: searchFor,
+          token
+        })
+        if (rsd?.status === 200 && rsd.message?.length === 1) {
+          // return first found item in RSD
+          const item: MentionItemProps = rsd.message[0]
+          return [item]
+        }
+        // else find by DOI
+        const resp = await getMentionByDoi(searchFor)
+        if (resp?.status === 200) {
+          return [resp.message as MentionItemProps]
+        }
+        return []
       }
-      // else find by DOI
-      const resp = await getMentionByDoi(searchFor)
-      if (resp?.status === 200) {
-        return [resp.message as MentionItemProps]
+      case 'openalex': {
+        searchFor = searchData.term
+        // look first at RSD
+        const rsd = await getMentionByOpenalexIdFromRsd({
+          id: searchFor,
+          token
+        })
+        if (rsd?.status === 200 && rsd.message?.length === 1) {
+          // return first found item in RSD
+          const item: MentionItemProps = rsd.message[0]
+          return [item]
+        }
+        // else find by DOI
+        const resp = await getMentionByOpenalexId(searchFor)
+        if (resp?.status === 200) {
+          return [resp.message as MentionItemProps]
+        }
+        return []
+      }
+      case 'title': {
+        searchFor = searchData.term
+        // find by title
+        const mentions = await findPublicationByTitle({
+          id: id,
+          searchFor,
+          token
+        })
+        return mentions
       }
-      return []
-    } else{
-      searchFor = searchData.term
-      // find by title
-      const mentions = await findPublicationByTitle({
-        id: id,
-        searchFor,
-        token
-      })
-      return mentions
     }
   }
 

frontend/components/mention/ImportMentions/apiImportMentions.tsx

@@ -17,11 +17,11 @@ import useEditMentionReducer from '../useEditMentionReducer'
 
 export type DoiBulkImportReport = Map<string, SearchResult> | null
 
-export function useValidateInputList(token:string) {
+export function useValidateInputList(token: string) {
   const {mentions} = useEditMentionReducer()
   const [validating, setValidating] = useState(false)
 
-  async function validateInput(value:string) {
+  async function validateInput(value: string) {
     setValidating(true)
     const doiList = value.split(/\r\n|\n|\r/)
     const searchResults = await validateInputList(doiList, mentions, token)
@@ -48,21 +48,24 @@ export async function validateInputList(doiList: string[], mentions: MentionItem
     // filter valid DOI type entries
     .filter(search => {
       // debugger
-      if (search.type === 'doi') {
-        // convert to lower case
-        const doi = search.term.toLowerCase()
-        // validate if not already included
-        const found = mentions.find(mention => mention.doi?.toLowerCase() === doi)
-        if (found) {
-          // flag item with DOI already processed
-          mentionResultPerDoi.set(doi, {doi ,status: 'alreadyImported', include: false})
-          return false
+      switch (search.type) {
+        case 'doi': {
+          // convert to lower case
+          const doi = search.term.toLowerCase()
+          // validate if not already included
+          const found = mentions.find(mention => mention.doi?.toLowerCase() === doi)
+          if (found) {
+            // flag item with DOI already processed
+            mentionResultPerDoi.set(doi, {doi, status: 'alreadyImported', include: false})
+            return false
+          }
+          return true
         }
-        return true
-      } else {
-        // flag invalid DOI entries
-        mentionResultPerDoi.set(search.term, {doi:search.term, status: 'invalidDoi', include: false})
-        return false
+        case 'openalex':
+        case 'title':
+          // flag invalid DOI entries
+          mentionResultPerDoi.set(search.term, {doi: search.term, status: 'invalidDoi', include: false})
+          return false
       }
     })
     // extract DOI string from serch info
@@ -164,16 +167,16 @@ export async function validateInputList(doiList: string[], mentions: MentionItem
     // flag dois that are not updated
     doisNotInDatabase.forEach(doi => {
       if (!mentionResultPerDoi.has(doi)) {
-        mentionResultPerDoi.set(doi, {doi,status: 'unknown', include: false})
+        mentionResultPerDoi.set(doi, {doi, status: 'unknown', include: false})
       }
     })
   }
 
   return mentionResultPerDoi
 }
 
-export async function linkMentionToEntity({ids, table, entityName,entityId, token}: {
-  ids: string[], table: string, entityName: string, entityId:string, token: string
+export async function linkMentionToEntity({ids, table, entityName, entityId, token}: {
+  ids: string[], table: string, entityName: string, entityId: string, token: string
 }) {
   try {
     const url = `/api/v1/${table}`
@@ -207,7 +210,7 @@ export async function addMentions({mentions, token}: { mentions: MentionItemProp
       body: JSON.stringify(mentions)
     })
     if (resp.status === 201) {
-      const json:MentionItemProps[] = await resp.json()
+      const json: MentionItemProps[] = await resp.json()
       return {
         status: 200,
         message: json

frontend/components/mention/config.ts

@@ -6,13 +6,13 @@
 // SPDX-License-Identifier: Apache-2.0
 
 import {MentionByType, MentionTypeKeys} from '~/types/Mention'
-import {doiRegexStrict} from '~/components/software/edit/mentions/utils'
+import {DOI_REGEX_STRICT} from '~/components/software/edit/mentions/utils'
 
 export const findMention={
   // title: 'Add publication',
   // subtitle: 'We search in Crossref, DataCite and RSD databases',
-  label: 'Search by DOI or publication title',
-  help: 'Valid DOI or at least first 2 letters of publication title',
+  label: 'Search by DOI, OpenAlex ID or publication title',
+  help: 'Valid DOI, OpenAlex ID or at least first 2 letters of publication title',
   validation: {
     // custom validation rule, not in use by react-hook-form
     minLength: 2,
@@ -31,7 +31,7 @@ export const mentionModal = {
         message: 'Maximum length is 255'
       },
       pattern: {
-        value: doiRegexStrict,
+        value: DOI_REGEX_STRICT,
         message: 'The DOI should look like 10.XXX/XXX'
       }
     }

frontend/components/projects/edit/mentions/impact/impactForProjectApi.test.ts

@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: 2022 Dusan Mijatovic (dv4all) (dv4all)
 // SPDX-FileCopyrightText: 2022 dv4all
 // SPDX-FileCopyrightText: 2024 Dusan Mijatovic (Netherlands eScience Center)
+// SPDX-FileCopyrightText: 2024 Ewan Cahen (Netherlands eScience Center) <[email protected]>
 // SPDX-FileCopyrightText: 2024 Netherlands eScience Center
 //
 // SPDX-License-Identifier: Apache-2.0
@@ -34,7 +35,7 @@ it('findPublicationByTitle', async () => {
     token: 'TEST-TOKEN'
   }
 
-  const expectedUrl = `/api/fe/mention/impact?id=${props.id}&search=${encodeURIComponent(props.searchFor)}`
+  const expectedUrl = `/api/fe/mention/find_by_title?id=${props.id}&search=${encodeURIComponent(props.searchFor)}&relation_type=impact`
   const expectBody = {
     'headers': {
       'Authorization': `Bearer ${props.token}`,