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feat(website): Add link to reference sequence on sequence details page (
#2238) * Add insdc_accession_full to reference genomes in kubernetes configs. * Put reference sequence info into a pop up button next to header. * Do not show reference sequence link if there are no reference sequences. * Add which segment each reference corresponds to.
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108 changes: 108 additions & 0 deletions
108
website/src/components/SequenceDetailsPage/ReferenceSequenceLinkButton.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,108 @@ | ||
| import { Dialog, Transition, DialogPanel, DialogTitle } from '@headlessui/react'; | ||
| import React, { Fragment } from 'react'; | ||
|
|
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| import { type ReferenceAccession } from '../../types/referencesGenomes'; | ||
| import X from '~icons/material-symbols/close'; | ||
| import MaterialSymbolsInfoOutline from '~icons/material-symbols/info-outline'; | ||
|
|
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| export const ReferenceLink = ({ accession }: { accession: string }) => { | ||
| return ( | ||
| <a | ||
| href={'https://www.ncbi.nlm.nih.gov/nuccore/__value__'.replace('__value__', accession.toString())} | ||
| target='_blank' | ||
| className='underline hover:text-primary-500' | ||
| > | ||
| {accession} | ||
| </a> | ||
| ); | ||
| }; | ||
|
|
||
| interface Props { | ||
| reference: ReferenceAccession[]; | ||
| } | ||
|
|
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| const ReferenceSequenceLinkButton: React.FC<Props> = ({ reference }) => { | ||
| const [isOpen, setIsOpen] = React.useState(false); | ||
|
|
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| const openDialog = () => setIsOpen(true); | ||
| const closeDialog = () => setIsOpen(false); | ||
|
|
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| const isMultiSegmented = reference.length > 1; | ||
|
|
||
| return ( | ||
| <> | ||
| <button onClick={openDialog} className='text-gray-400 hover:text-primary-600 '> | ||
| <MaterialSymbolsInfoOutline className='inline-block h-6 w-5' /> | ||
| </button> | ||
| <Transition appear show={isOpen} as={Fragment}> | ||
| <Dialog as='div' className='relative z-10' onClose={closeDialog}> | ||
| <Transition.Child | ||
| as={Fragment} | ||
| enter='ease-out duration-300' | ||
| enterFrom='opacity-0' | ||
| enterTo='opacity-100' | ||
| leave='ease-in duration-200' | ||
| leaveFrom='opacity-100' | ||
| leaveTo='opacity-0' | ||
| > | ||
| <div className='fixed inset-0 bg-black bg-opacity-25' /> | ||
| </Transition.Child> | ||
|
|
||
| <div className='fixed inset-0 overflow-y-auto'> | ||
| <div className='flex min-h-full items-center justify-center p-4 text-center'> | ||
| <Transition.Child | ||
| as={Fragment} | ||
| enter='ease-out duration-300' | ||
| enterFrom='opacity-0 scale-95' | ||
| enterTo='opacity-100 scale-100' | ||
| leave='ease-in duration-200' | ||
| leaveFrom='opacity-100 scale-100' | ||
| leaveTo='opacity-0 scale-95' | ||
| > | ||
| <DialogPanel className='w-full max-w-2xl transform overflow-hidden rounded-2xl bg-white p-6 text-left align-middle shadow-xl transition-all'> | ||
| <DialogTitle as='h3' className='font-bold text-2xl mb-4 text-primary-700'> | ||
| Reference Sequence | ||
| </DialogTitle> | ||
| <button className='absolute right-2 top-2 p-1' onClick={closeDialog}> | ||
| <X className='h-6 w-6' /> | ||
| </button> | ||
| <div className='mt-4'> | ||
| {reference.filter((item) => item.insdc_accession_full !== undefined).length > | ||
| 0 && ( | ||
| <div> | ||
| <div> | ||
| Alignment and Mutation metrics use the following INSDC reference | ||
| sequence | ||
| {reference.length > 1 ? 's: ' : ': '} | ||
| </div> | ||
| <span> | ||
| {reference.map( | ||
| (currElement) => | ||
| currElement.insdc_accession_full !== undefined && ( | ||
| <div className='text-primary-700 ml-5 flex'> | ||
| {isMultiSegmented && ( | ||
| <div className='w-6 text-left mr-2'> | ||
| {currElement.name}: | ||
| </div> | ||
| )} | ||
| <ReferenceLink | ||
| accession={currElement.insdc_accession_full} | ||
| /> | ||
| </div> | ||
| ), | ||
| )} | ||
| </span> | ||
| </div> | ||
| )} | ||
| </div> | ||
| </DialogPanel> | ||
| </Transition.Child> | ||
| </div> | ||
| </div> | ||
| </Dialog> | ||
| </Transition> | ||
| </> | ||
| ); | ||
| }; | ||
|
|
||
| export default ReferenceSequenceLinkButton; |
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