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fix linting issues #1508

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fix linting issues #1508

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f60745b
fix linting issues
zy4 May 11, 2023
84a06f2
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zy4 May 11, 2023
a390f99
ignore
zy4 May 11, 2023
0a8e15c
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zy4 May 11, 2023
1c45662
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zy4 May 11, 2023
d20033d
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zy4 May 11, 2023
76982cb
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zy4 May 11, 2023
5ae95b2
find correct prettierignore
zy4 May 11, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/frontend.yml
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Expand Up @@ -81,4 +81,4 @@ jobs:
eslint_dir: ./frontend/src
eslint_extensions: ts,vue
prettier: true
prettier_dir: ./frontend/src
prettier_dir: ./frontend
1 change: 1 addition & 0 deletions frontend/.eslintrc.js
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Expand Up @@ -3,6 +3,7 @@ module.exports = {
env: {
browser: true,
es2021: true,
node: true,
},
extends: ['plugin:vue/recommended', 'eslint:recommended', '@vue/typescript/recommended', 'prettier'],
ignorePatterns: ['**/*.min.js'],
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4 changes: 2 additions & 2 deletions frontend/.prettierignore
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@@ -1,4 +1,4 @@
node_modules
/dist
*.min.js
package.json
**/*.min.*
package.json
208 changes: 103 additions & 105 deletions frontend/src/components/jobs/result-tabs/PLMBlastResultsTab.vue
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@@ -1,141 +1,139 @@
<template>
<Loading v-if="loading" :message="$t('loading')"/>
<div v-else class="font-small">
<b v-if="total === 0" v-text="$t('jobs.results.plmblast.noResults')"></b>
<div v-else>
<div class="result-options">
<a @click="scrollTo('visualization')">{{ $t('jobs.results.hitlist.visLink') }}</a>
<a class="mr-4" @click="scrollTo('hits')">{{ $t('jobs.results.hitlist.hitsLink') }}</a>
<a class="border-right mr-4"></a>
<a @click="download" v-text="$t('jobs.results.actions.downloadCSV')"></a>
<Loading v-if="loading" :message="$t('loading')" />
<div v-else class="font-small">
<b v-if="total === 0" v-text="$t('jobs.results.plmblast.noResults')"></b>
<div v-else>
<div class="result-options">
<a @click="scrollTo('visualization')">{{ $t('jobs.results.hitlist.visLink') }}</a>
<a class="mr-4" @click="scrollTo('hits')">{{ $t('jobs.results.hitlist.hitsLink') }}</a>
<a class="border-right mr-4"></a>
<a @click="download" v-text="$t('jobs.results.actions.downloadCSV')"></a>
</div>

</div>
<div v-html="$t('jobs.results.plmblast.numHits', { num: total })"></div>

<div v-html="$t('jobs.results.plmblast.numHits', { num: total })"></div>
<div ref="visualization" class="result-section">
<h4>{{ $t('jobs.results.hitlist.vis') }}</h4>
<hit-map :job="job" @resubmit-section="resubmitSection" />
</div>

<div ref="visualization" class="result-section">
<h4>{{ $t('jobs.results.hitlist.vis') }}</h4>
<hit-map :job="job" @resubmit-section="resubmitSection"/>
</div>

<div ref="hits" class="result-section">
<h4 class="mb-4">
{{ $t('jobs.results.hitlist.hits') }}
</h4>
<hit-list-table :job="job" :fields="hitListFields"/>
</div>
<div ref="hits" class="result-section">
<h4 class="mb-4">
{{ $t('jobs.results.hitlist.hits') }}
</h4>
<hit-list-table :job="job" :fields="hitListFields" />
</div>
</div>
</div>
</div>
</template>

<script lang="ts">
import Loading from '@/components/utils/Loading.vue';
import HitListTable from '@/components/jobs/result-tabs/sections/HitListTable.vue';
import HitMap from '@/components/jobs/result-tabs/sections/HitMap.vue';
import SearchResultTabMixin from '@/mixins/SearchResultTabMixin';
import EventBus from '@/util/EventBus';
import {resultsService} from '@/services/ResultsService';
import { resultsService } from '@/services/ResultsService';
import Logger from 'js-logger';
const logger = Logger.get('PLMBlastResultsTab');

import { PLMBLASTAlignmentItem } from '@/types/toolkit/results';

export default SearchResultTabMixin.extend({
name: 'PLMBlastResultsTab',
components: {
Loading,
HitListTable,
HitMap,
},
data() {
return {
alignments: undefined as PLMBLASTAlignmentItem[] | undefined,
hitListFields: [
{
key: 'num',
label: this.$t('jobs.results.plmblast.table.num'),
sortable: true,
},
{
key: 'acc',
label: this.$t('jobs.results.plmblast.table.accession'),
sortable: true,
},
{
key: 'name',
label: this.$t('jobs.results.plmblast.table.description'),
sortable: true,
},
{
key: 'eval',
label: this.$t('jobs.results.plmblast.table.eValue'),
class: 'no-wrap',
sortable: true,
},
{
key: 'bitScore',
label: this.$t('jobs.results.plmblast.table.bitscore'),
sortable: true,
},
{
key: 'hitLen',
label: this.$t('jobs.results.plmblast.table.hit_len'),
sortable: true,
},
{
key: 'matchLen',
label: this.$t('jobs.results.plmblast.table.match_len'),
sortable: true,
name: 'PLMBlastResultsTab',
components: {
Loading,
HitListTable,
HitMap,
},
data() {
return {
alignments: undefined as PLMBLASTAlignmentItem[] | undefined,
hitListFields: [
{
key: 'num',
label: this.$t('jobs.results.plmblast.table.num'),
sortable: true,
},
{
key: 'acc',
label: this.$t('jobs.results.plmblast.table.accession'),
sortable: true,
},
{
key: 'name',
label: this.$t('jobs.results.plmblast.table.description'),
sortable: true,
},
{
key: 'eval',
label: this.$t('jobs.results.plmblast.table.eValue'),
class: 'no-wrap',
sortable: true,
},
{
key: 'bitScore',
label: this.$t('jobs.results.plmblast.table.bitscore'),
sortable: true,
},
{
key: 'hitLen',
label: this.$t('jobs.results.plmblast.table.hit_len'),
sortable: true,
},
{
key: 'matchLen',
label: this.$t('jobs.results.plmblast.table.match_len'),
sortable: true,
},
],
};
},
computed: {
filename(): string {
if (!this.viewOptions.filename) {
return '';
}
return this.viewOptions.filename.replace(':jobID', this.job.jobID);
},
],
};
},
computed: {
filename(): string {
if (!this.viewOptions.filename) {
return '';
}
return this.viewOptions.filename.replace(':jobID', this.job.jobID);
},
},
methods: {
download(): void {
const toolName = this.tool.name;
const downloadFilename = `${toolName}_${this.job.jobID}.hits.csv`;
resultsService.downloadFile(this.job.jobID, this.filename, downloadFilename).catch((e) => {
logger.error(e);
});
methods: {
download(): void {
const toolName = this.tool.name;
const downloadFilename = `${toolName}_${this.job.jobID}.hits.csv`;
resultsService.downloadFile(this.job.jobID, this.filename, downloadFilename).catch((e) => {
logger.error(e);
});
},
},
},
});
</script>

<style lang="scss" scoped>
.result-section {
padding-top: 3.5rem;
padding-top: 3.5rem;
}

.alignments-table {
font-size: 0.95em;
font-size: 0.95em;

.blank-row {
height: 0.8rem;
}
.blank-row {
height: 0.8rem;
}

.sequence td {
word-break: keep-all;
white-space: nowrap;
font-family: $font-family-monospace;
padding: 0 1rem 0 0;
}
.sequence td {
word-break: keep-all;
white-space: nowrap;
font-family: $font-family-monospace;
padding: 0 1rem 0 0;
}

a {
cursor: pointer;
color: $primary;
a {
cursor: pointer;
color: $primary;

&:hover {
color: $tk-dark-green;
&:hover {
color: $tk-dark-green;
}
}
}
}
</style>
3 changes: 2 additions & 1 deletion frontend/src/i18n/lang/modules/tools-en.ts
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Expand Up @@ -479,7 +479,8 @@ export default {
'<a href="https://doi.org/10.1093/nar/gkaa1079" target="_blank" rel="noopener">' +
'Nucleic Acids Res. 2021;49(D1):D266-D273</a>.<br><br>',
hhpred_manual: '',
plmblast: 'pLM-BLAST – distant homology detection based on direct comparison of sequence representations from ' +
plmblast:
'pLM-BLAST – distant homology detection based on direct comparison of sequence representations from ' +
'protein language models.<br> Kaminski K, Ludwiczak K, Alva V, Dunin-Horkawicz S. bioRxiv. 2022.',
},
};
1 change: 0 additions & 1 deletion frontend/src/types/toolkit/results.ts
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Expand Up @@ -77,7 +77,6 @@ export interface PLMBLASTAlignmentItem extends SearchAlignmentItem {
matchLen: number;
}


export interface PSIBLASTAlignmentItem extends SearchAlignmentItem {
fastaLink: string;
eval: number;
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