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Add a "my sequences page" displaying released sequences (#1037)
* wip * still types to fix * add link * fix types and more * remove download dialog * remove redundancies * Update my_sequences.astro * Update website/src/routes.ts Co-authored-by: Fabian Engelniederhammer <[email protected]> * Update website/src/pages/[organism]/my_sequences/[group].astro Co-authored-by: Fabian Engelniederhammer <[email protected]> * Update website/src/pages/[organism]/my_sequences/[group].astro Co-authored-by: Fabian Engelniederhammer <[email protected]> * refactor(website): use GroupManagementClient * refactor to reduce code duplication * improve error message * add back group functionality with better exclude option * lots of fixes * add underline to link * get user groups not all groups --------- Co-authored-by: Fabian Engelniederhammer <[email protected]> Co-authored-by: Fabian Engelniederhammer <[email protected]>
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Feb 20, 2024
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| import { type FC } from 'react'; | ||
|
|
||
| import { routes } from '../../routes'; | ||
|
|
||
| type GroupSelectorProps = { | ||
| groupNames: string[]; | ||
| selectedGroupName: string; | ||
| organism: string; | ||
| }; | ||
| export const GroupSelector: FC<GroupSelectorProps> = ({ groupNames, selectedGroupName, organism }) => { | ||
| return ( | ||
| <select | ||
| className='mt-4 select select-bordered' | ||
| onChange={(event) => { | ||
| const newGroup = event.target.value; | ||
| const page = routes.mySequencesPage(organism, newGroup); | ||
| location.href = page; | ||
| }} | ||
| > | ||
| {groupNames.map((groupName: string) => ( | ||
| <option selected={groupName === selectedGroupName} value={groupName} key={groupName}> | ||
| {groupName} | ||
| </option> | ||
| ))} | ||
| </select> | ||
| ); | ||
| }; |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| --- | ||
| import BaseLayout from '../../layouts/BaseLayout.astro'; | ||
| import { routes } from '../../routes'; | ||
| import { GroupManagementClient } from '../../services/groupManagementClient'; | ||
| import { getAccessToken } from '../../utils/getAccessToken'; | ||
| const accessToken = getAccessToken(Astro.locals.session)!; | ||
| const groupsResult = await GroupManagementClient.create().getGroupsOfUser(accessToken); | ||
| const organism = Astro.params.organism; | ||
| let noGroups = false; | ||
| let errorMessage = ''; | ||
| if (groupsResult.isOk()) { | ||
| if (groupsResult.value.length > 0) { | ||
| return Astro.redirect(routes.mySequencesPage(organism, groupsResult.value[0].groupName)); | ||
| } | ||
| noGroups = true; | ||
| } else { | ||
| errorMessage = groupsResult.error.detail; | ||
| } | ||
| --- | ||
|
|
||
| <BaseLayout title='My Sequences'> | ||
| <div> | ||
| <p> | ||
| { | ||
| noGroups && ( | ||
| <div> | ||
| To access sequence-management pages your account needs to be part of a group. Please{' '} | ||
| <a href={routes.whereYouCreateAGroup()}>create a group</a>, or ask an existing group admin to | ||
| add you to their group. | ||
| </div> | ||
| ) | ||
| } | ||
| {errorMessage && <div class='bg-red-500'>{errorMessage}</div>} | ||
| </p> | ||
| </div> | ||
| </BaseLayout> |
111 changes: 111 additions & 0 deletions
111
website/src/pages/[organism]/my_sequences/[group].astro
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,111 @@ | ||
| --- | ||
| import { GroupSelector } from '../../../components/MySequencesPage/GroupSelector'; | ||
| import { SearchForm } from '../../../components/SearchPage/SearchForm'; | ||
| import { SearchPagination } from '../../../components/SearchPage/SearchPagination'; | ||
| import { Table } from '../../../components/SearchPage/Table'; | ||
| import ErrorBox from '../../../components/common/ErrorBox.astro'; | ||
| import BaseLayout from '../../../layouts/BaseLayout.astro'; | ||
| import { MY_SEQUENCES } from '../../../routes'; | ||
| import { GroupManagementClient } from '../../../services/groupManagementClient'; | ||
| import { pageSize } from '../../../settings'; | ||
| import { getAccessToken } from '../../../utils/getAccessToken'; | ||
| import { processParametersAndFetchSearch } from '../../../utils/processParametersAndFetchSearch'; | ||
| const group = Astro.params.group!; | ||
| const accessToken = getAccessToken(Astro.locals.session)!; | ||
| const groupsResult = await GroupManagementClient.create().getGroupsOfUser(accessToken); | ||
| if (groupsResult.isOk() === false) { | ||
| return new Response(undefined, { | ||
| status: 500, | ||
| message: 'Failed to get groups', | ||
| }); | ||
| } | ||
| const groups = groupsResult.value; | ||
| const groupNames = groups.map((group: { groupName: string }) => group.groupName); | ||
| const groupExists = groupNames.includes(group); | ||
| if (groupExists === false) { | ||
| return new Response(undefined, { | ||
| status: 404, | ||
| }); | ||
| } | ||
| const { | ||
| cleanedOrganism, | ||
| organism, | ||
| data, | ||
| page, | ||
| metadataFilter, | ||
| mutationFilter, | ||
| referenceGenomesSequenceNames, | ||
| schema, | ||
| clientConfig, | ||
| orderBy, | ||
| } = await processParametersAndFetchSearch(Astro, group); | ||
| --- | ||
|
|
||
| <BaseLayout title={`${cleanedOrganism.displayName} - My sequences`}> | ||
| <h1 class='title'>Viewing sequences for group {group}</h1> | ||
| { | ||
| groupNames.length > 1 && ( | ||
| <> | ||
| Choose group: | ||
| <GroupSelector groupNames={groupNames} selectedGroupName={group} organism={organism} client:load /> | ||
| </> | ||
| ) | ||
| } | ||
|
|
||
| <div class='flex flex-col md:flex-row gap-8 md:gap-4'> | ||
| <div class='md:w-72'> | ||
| <SearchForm | ||
| organism={organism} | ||
| filters={metadataFilter} | ||
| initialMutationFilter={mutationFilter} | ||
| clientConfig={clientConfig} | ||
| referenceGenomesSequenceNames={referenceGenomesSequenceNames} | ||
| classOfSearchPage={MY_SEQUENCES} | ||
| group={group} | ||
| client:only='react' | ||
| /> | ||
| </div> | ||
| { | ||
| data.match( | ||
| (data) => ( | ||
| <div class='flex-1'> | ||
| <div class='mt-4 mb-1'> | ||
| Search returned {data.totalCount.toLocaleString()} | ||
| sequence{data.totalCount === 1 ? '' : 's'} | ||
| </div> | ||
| <Table | ||
| organism={organism} | ||
| data={data.data} | ||
| schema={schema} | ||
| metadataFilter={metadataFilter} | ||
| mutationFilter={mutationFilter} | ||
| page={page} | ||
| orderBy={orderBy} | ||
| classOfSearchPage={MY_SEQUENCES} | ||
| group={group} | ||
| client:load | ||
| /> | ||
|
|
||
| <div class='mt-4 flex justify-center'> | ||
| <SearchPagination | ||
| client:only='react' | ||
| count={Math.ceil(data.totalCount / pageSize)} | ||
| page={page} | ||
| metadataFilter={metadataFilter} | ||
| mutationFilter={mutationFilter} | ||
| orderBy={orderBy} | ||
| organism={organism} | ||
| classOfSearchPage={MY_SEQUENCES} | ||
| group={group} | ||
| /> | ||
| </div> | ||
| </div> | ||
| ), | ||
| (error) => <ErrorBox title='Failed searching sequences' message={error.detail} />, | ||
| ) | ||
| } | ||
| </div> | ||
| </BaseLayout> |
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