From f60745b5326e251d129c1c0ce418c5a80c5a4f47 Mon Sep 17 00:00:00 2001
From: Seung-Zin Nam <seung-zin.nam@artidis.com>
Date: Thu, 11 May 2023 11:04:31 +0200
Subject: [PATCH 1/8] fix linting issues

---
 frontend/.eslintrc.js                                           | 1 +
 frontend/src/components/jobs/result-tabs/PLMBlastResultsTab.vue | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend/.eslintrc.js b/frontend/.eslintrc.js
index fbef5487d..0d444a2c7 100644
--- a/frontend/.eslintrc.js
+++ b/frontend/.eslintrc.js
@@ -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'],
diff --git a/frontend/src/components/jobs/result-tabs/PLMBlastResultsTab.vue b/frontend/src/components/jobs/result-tabs/PLMBlastResultsTab.vue
index abd6ca024..f82e0a65f 100644
--- a/frontend/src/components/jobs/result-tabs/PLMBlastResultsTab.vue
+++ b/frontend/src/components/jobs/result-tabs/PLMBlastResultsTab.vue
@@ -33,7 +33,6 @@ 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 Logger from 'js-logger';
 const logger = Logger.get('PLMBlastResultsTab');

From 84a06f2b720753a28dd491e025d44c421a149fa6 Mon Sep 17 00:00:00 2001
From: Seung-Zin Nam <seung-zin.nam@artidis.com>
Date: Thu, 11 May 2023 11:09:22 +0200
Subject: [PATCH 2/8] more

---
 .../jobs/result-tabs/PLMBlastResultsTab.vue   | 207 +++++++++---------
 frontend/src/i18n/lang/modules/tools-en.ts    |   3 +-
 frontend/src/types/toolkit/results.ts         |   1 -
 3 files changed, 105 insertions(+), 106 deletions(-)

diff --git a/frontend/src/components/jobs/result-tabs/PLMBlastResultsTab.vue b/frontend/src/components/jobs/result-tabs/PLMBlastResultsTab.vue
index f82e0a65f..5b6556595 100644
--- a/frontend/src/components/jobs/result-tabs/PLMBlastResultsTab.vue
+++ b/frontend/src/components/jobs/result-tabs/PLMBlastResultsTab.vue
@@ -1,31 +1,30 @@
 <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">
@@ -33,108 +32,108 @@ 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 {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>
diff --git a/frontend/src/i18n/lang/modules/tools-en.ts b/frontend/src/i18n/lang/modules/tools-en.ts
index fd7015998..0cc01c980 100644
--- a/frontend/src/i18n/lang/modules/tools-en.ts
+++ b/frontend/src/i18n/lang/modules/tools-en.ts
@@ -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.',
     },
 };
diff --git a/frontend/src/types/toolkit/results.ts b/frontend/src/types/toolkit/results.ts
index 1f82f75b8..0386e9967 100644
--- a/frontend/src/types/toolkit/results.ts
+++ b/frontend/src/types/toolkit/results.ts
@@ -77,7 +77,6 @@ export interface PLMBLASTAlignmentItem extends SearchAlignmentItem {
     matchLen: number;
 }
 
-
 export interface PSIBLASTAlignmentItem extends SearchAlignmentItem {
     fastaLink: string;
     eval: number;

From a390f9998f45fad3dc79c46c036ebaa0df22593f Mon Sep 17 00:00:00 2001
From: Seung-Zin Nam <seung-zin.nam@artidis.com>
Date: Thu, 11 May 2023 11:12:28 +0200
Subject: [PATCH 3/8] ignore

---
 frontend/.prettierignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend/.prettierignore b/frontend/.prettierignore
index 8d5619679..d2e40c0a3 100644
--- a/frontend/.prettierignore
+++ b/frontend/.prettierignore
@@ -1,4 +1,4 @@
 node_modules
 /dist
-*.min.js
+**/.min.js
 package.json

From 0a8e15c4787b932317be6f7c51f1cf21a94bdb0b Mon Sep 17 00:00:00 2001
From: Seung-Zin Nam <seung-zin.nam@artidis.com>
Date: Thu, 11 May 2023 11:15:53 +0200
Subject: [PATCH 4/8] more

---
 frontend/.prettierignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/frontend/.prettierignore b/frontend/.prettierignore
index d2e40c0a3..0b5ce4dd1 100644
--- a/frontend/.prettierignore
+++ b/frontend/.prettierignore
@@ -2,3 +2,4 @@ node_modules
 /dist
 **/.min.js
 package.json
+modules/msa/msa.min.js
\ No newline at end of file

From 1c456626f98534a65061c2d98032496a09f14d0c Mon Sep 17 00:00:00 2001
From: Seung-Zin Nam <seung-zin.nam@artidis.com>
Date: Thu, 11 May 2023 11:19:38 +0200
Subject: [PATCH 5/8] more

---
 frontend/.prettierignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend/.prettierignore b/frontend/.prettierignore
index 0b5ce4dd1..6fcca6e0f 100644
--- a/frontend/.prettierignore
+++ b/frontend/.prettierignore
@@ -2,4 +2,4 @@ node_modules
 /dist
 **/.min.js
 package.json
-modules/msa/msa.min.js
\ No newline at end of file
+src/modules/msa/msa.min.js
\ No newline at end of file

From d20033d6e9e7c0dc40d477de75952487dea69cd6 Mon Sep 17 00:00:00 2001
From: Seung-Zin Nam <seung-zin.nam@artidis.com>
Date: Thu, 11 May 2023 11:21:44 +0200
Subject: [PATCH 6/8] more

---
 frontend/.prettierignore | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/frontend/.prettierignore b/frontend/.prettierignore
index 6fcca6e0f..0dce32caa 100644
--- a/frontend/.prettierignore
+++ b/frontend/.prettierignore
@@ -1,5 +1,4 @@
 node_modules
 /dist
-**/.min.js
-package.json
-src/modules/msa/msa.min.js
\ No newline at end of file
+*.min.*
+package.json
\ No newline at end of file

From 76982cbcf839cc4756b59cedff36698b8af4c8a7 Mon Sep 17 00:00:00 2001
From: Seung-Zin Nam <seung-zin.nam@artidis.com>
Date: Thu, 11 May 2023 11:30:49 +0200
Subject: [PATCH 7/8] more

---
 frontend/.prettierignore | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend/.prettierignore b/frontend/.prettierignore
index 0dce32caa..37dc5e256 100644
--- a/frontend/.prettierignore
+++ b/frontend/.prettierignore
@@ -1,4 +1,4 @@
 node_modules
 /dist
-*.min.*
+**/*.min.*
 package.json
\ No newline at end of file

From 5ae95b2d4c176bfb1040ba0a87b11296e6464d36 Mon Sep 17 00:00:00 2001
From: Seung-Zin Nam <seung-zin.nam@artidis.com>
Date: Thu, 11 May 2023 20:28:09 +0200
Subject: [PATCH 8/8] find correct prettierignore

---
 .github/workflows/frontend.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/frontend.yml b/.github/workflows/frontend.yml
index 520b04974..073efe68e 100644
--- a/.github/workflows/frontend.yml
+++ b/.github/workflows/frontend.yml
@@ -81,4 +81,4 @@ jobs:
           eslint_dir: ./frontend/src
           eslint_extensions: ts,vue
           prettier: true
-          prettier_dir: ./frontend/src
+          prettier_dir: ./frontend