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766 add feature to download list of included papers as csv (#796)
* feat: added download button and logic to convert to bibtex * feat: added feature to download curation CSVs and bibtex files * feat: added window * feat: added testing * fix: remove unused imports * fix: failing cypress tests
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3 changes: 0 additions & 3 deletions
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compose/neurosynth-frontend/src/__mocks__/react-query/useIsFetching.ts
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compose/neurosynth-frontend/src/__mocks__/react-query/useMutation.ts
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compose/neurosynth-frontend/src/__mocks__/react-query/useQueryClient.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,20 @@ | ||
| import { Style } from 'index'; | ||
|
|
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| const GlobalStyles: Style = { | ||
| colorPulseAnimation: { | ||
| animation: 'pulse 2s infinite', | ||
| '@keyframes pulse': { | ||
| '0%': { | ||
| backgroundColor: 'success.light', | ||
| }, | ||
| '50%': { | ||
| backgroundColor: 'white', | ||
| }, | ||
| '100%': { | ||
| backgroundColor: 'success.light', | ||
| }, | ||
| }, | ||
| }, | ||
| }; | ||
|
|
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| export default GlobalStyles; |
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compose/neurosynth-frontend/src/hooks/external/useGetBibtexCitations.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,100 @@ | ||
| import axios, { AxiosError } from 'axios'; | ||
| import { stringToNumber } from 'helpers/utils'; | ||
| import { ICurationStubStudy } from 'pages/Curation/Curation.types'; | ||
| import { useMutation } from 'react-query'; | ||
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| const stringAsAuthorArray = (authors: string): IBibtex['author'] => { | ||
| const authorsStringToArray = authors.split(', ').map((author) => { | ||
| const nameAsArray = author.split(' '); | ||
| if (nameAsArray.length === 0) { | ||
| return { given: '', family: '' }; | ||
| } else if (nameAsArray.length === 1) { | ||
| return { given: nameAsArray[0], family: '' }; | ||
| } else { | ||
| const givenNames = nameAsArray.slice(0, nameAsArray.length - 1).join(' '); | ||
| return { given: givenNames, family: nameAsArray[nameAsArray.length - 1] }; | ||
| } | ||
| }); | ||
| return authorsStringToArray; | ||
| }; | ||
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| const generateBibtexNote = (study: ICurationStubStudy) => { | ||
| let bibtexNote = ''; | ||
| if (study.pmid) bibtexNote = `PMID: ${study.pmid}`; | ||
| if (study.pmcid) bibtexNote = `${bibtexNote}; PMCID: ${study.pmcid}`; | ||
| if (study.neurostoreId) bibtexNote = `${bibtexNote}; Neurosynth ID: ${study.neurostoreId}`; | ||
| if (study.identificationSource.label) { | ||
| bibtexNote = `${bibtexNote}; Source: ${study.identificationSource.label}`; | ||
| } | ||
| if (study.tags.length > 0) { | ||
| const tagString = study.tags.reduce( | ||
| (prev, curr, index, arr) => | ||
| `${prev}${curr.label}${index === arr.length - 1 ? '' : ','}`, | ||
| '' | ||
| ); | ||
| bibtexNote = `${bibtexNote}; Tags: ${tagString}`; | ||
| } | ||
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| return bibtexNote; | ||
| }; | ||
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| // this is not the complete Bibtex type. There are other other types | ||
| // as described here: https://bibtex.eu/types/article/ however these are the most significant | ||
| export interface IBibtex { | ||
| author: { given: string; family: string }[]; | ||
| title: string; | ||
| DOI: string; | ||
| note?: string; | ||
| URL: string; | ||
| abstract: string; | ||
| issued: { | ||
| 'date-parts'?: [number, number, number][]; | ||
| }; | ||
| 'container-title': string; // journal | ||
| type: string; // article-journal for papers | ||
| } | ||
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| // if we do not receive bibtex data from the api, then we create our own with the data we have | ||
| export const generateBibtex = (study: ICurationStubStudy): IBibtex => { | ||
| const { isValid, value } = stringToNumber(study.articleYear || ''); | ||
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| return { | ||
| title: study.title, | ||
| type: 'article-journal', | ||
| DOI: study.doi || '', | ||
| URL: study.articleLink || '', | ||
| abstract: study.abstractText || '', | ||
| note: generateBibtexNote(study), | ||
| issued: { | ||
| 'date-parts': isValid ? [[value, 0, 0]] : undefined, | ||
| }, | ||
| 'container-title': study.journal || '', | ||
| author: stringAsAuthorArray(study.authors || ''), | ||
| }; | ||
| }; | ||
|
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| /** | ||
| * NOTE: this is a get request but we use useMutation so that we can query the data imperatively. | ||
| * This means that there is no smart refetching | ||
| * https://github.com/TanStack/query/discussions/3675 | ||
| */ | ||
|
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| const useGetBibtexCitations = () => { | ||
| return useMutation<IBibtex, AxiosError, ICurationStubStudy, unknown>(async (study) => { | ||
| let res: IBibtex; | ||
| try { | ||
| res = ( | ||
| await axios.get<{ message: IBibtex }>( | ||
| `https://api.crossref.org/v1/works/${study.doi}` | ||
| ) | ||
| ).data.message; | ||
| } catch (e) { | ||
| res = generateBibtex(study); | ||
| } | ||
| // add a note with relevant neurosynth related data for provenance | ||
| res.note = generateBibtexNote(study); | ||
| return res; | ||
| }); | ||
| }; | ||
|
|
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| export default useGetBibtexCitations; |
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compose/neurosynth-frontend/src/pages/Curation/Curation.helpers.ts
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,9 @@ | ||
| export const downloadFile = (filename: string, fileContents: BlobPart, contentType: string) => { | ||
| const blob = new Blob([fileContents], { type: contentType }); | ||
| const element = window.document.createElement('a'); | ||
| element.href = window.URL.createObjectURL(blob); | ||
| element.download = filename; | ||
| window.document.body.appendChild(element); | ||
| element.click(); | ||
| window.document.body.removeChild(element); | ||
| }; |
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