Fix linting errors again, mostly indentation changes

nextstrain · May 30, 2020 · 61e7d28 · 61e7d28
1 parent 1a71ae5
commit 61e7d28
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Showing 6 changed files with 244 additions and 245 deletions.
diff --git a/cli/server/handleGenomeDbs.js b/cli/server/handleGenomeDbs.js
@@ -1,10 +1,8 @@
 const fs = require('fs');
 const path = require("path");
-const through = require('through2');
 const {PassThrough} = require('stream');
 const Engine = require('nedb');
 const fasta = require('bionode-fasta');
-const bodyParser = require('body-parser');
 
 const { promisify } = require('util');
 
@@ -35,7 +33,7 @@ const fetchRecords = (ids, dbPath) =>
         if (err) {
           console.log('EE');
           reject(err);
-        } else if (docs.length == 0) {
+        } else if (docs.length === 0) {
           console.log("No record found!");
           resolve(docs);
         } else {
@@ -54,11 +52,11 @@ const fetchRecords = (ids, dbPath) =>
 const getGenomeDB = (datasetsPath) => {
   return async (req, res) => { // eslint-disable-line consistent-return
     try {
-      let prefix = req.body.prefix
-          .replace(/^\//, '')
-          .replace(/\/$/, '')
-          .split("/")
-          .join("_");
+      const prefix = req.body.prefix
+            .replace(/^\//, '')
+            .replace(/\/$/, '')
+            .split("/")
+            .join("_");
       const dbPath = datasetsPath + '/genomeDbs/' + prefix + '.db';
       if (!req.body.ids || req.body.ids.length === 0) {
         res.setHeader('Content-Type', 'application/json');
@@ -70,8 +68,8 @@ const getGenomeDB = (datasetsPath) => {
         return;
       }
       res.setHeader('Content-Type', 'text/plain');
-      var db = await fetchRecords(req.body.ids, dbPath);
-      db.forEach(v=> {
+      const db = await fetchRecords(req.body.ids, dbPath);
+      db.forEach((v) => {
         const wrappedSeq = v.seq.match(/.{1,80}/g).join('\n') + '\n';
         res.write('>' + v.id + '\n');
         res.write(wrappedSeq);
@@ -83,27 +81,6 @@ const getGenomeDB = (datasetsPath) => {
   };
 };
 
-/**
-   @param {string} path Path to datasetDir so we can create database if corresponding fasta
-   files exists for aupsice input JSON file
-*/
-const prepareDbs = async (path) => {
-  try {
-    const files = await readdir(path);
-    const v2Files = files.filter((file) => (
-      file.endsWith(".fasta")
-    ));
-    v2Files.forEach((v) => {
-      makeDB(path, path + '/' + v);
-    });
-
-
-  } catch (err) {
-    // utils.warn(`Couldn't collect available dataset files (path searched: ${path})`);
-    // utils.verbose(err);
-  }
-};
-
 /**
    @param {string} dbRoot Path to directory where genome database should be saved
    @param {string} fastaPath Path to fasta file to use as input to create database
@@ -129,7 +106,7 @@ const makeDB = (dbRoot, fastaPath) => new Promise((resolve, reject) => {
   let rc = 0;
 
   processRecord.on('data', (rec) => {
-    obj = JSON.parse(rec);
+    const obj = JSON.parse(rec);
     const outrec = {id: obj.id, seq: obj.seq, source: fastaPath};
     db.insert(outrec);
     rc++;
@@ -149,6 +126,28 @@ const makeDB = (dbRoot, fastaPath) => new Promise((resolve, reject) => {
     .pipe(processRecord);
 
 });
+
+/**
+   @param {string} path Path to datasetDir so we can create database if corresponding fasta
+   files exists for aupsice input JSON file
+*/
+const prepareDbs = async (localPath) => {
+  try {
+    const files = await readdir(localPath);
+    const v2Files = files.filter((file) => (
+      file.endsWith(".fasta")
+    ));
+    v2Files.forEach((v) => {
+      makeDB(localPath, localPath + '/' + v);
+    });
+
+
+  } catch (err) {
+    // utils.warn(`Couldn't collect available dataset files (path searched: ${locaPath})`);
+    // utils.verbose(err);
+  }
+};
+
 module.exports = {
   fetchRecords,
   getDbPath,

diff --git a/cli/server/parseNarrative.js b/cli/server/parseNarrative.js
@@ -60,7 +60,7 @@ const makeFrontMatterBlock = (frontMatter) => {
       markdown.push(`#### License: ${license}`);
     }
   }
-  
+
   const block = new Proxy({}, blockProxyHandler);
   block.url = frontMatter.dataset;
   block.contents = markdown.join("\n");

diff --git a/docs-src/website/siteConfig.js b/docs-src/website/siteConfig.js
@@ -17,7 +17,7 @@ const siteConfig = {
 
   // Header links in the top nav bar
   headerLinks: [
-    {doc: 'introduction/overview', label: 'Docs'},
+    {doc: 'introduction/overview', label: 'Docs'}
     // {doc: 'tutorial/overview', label: 'Tutorial'}
   ],
 

diff --git a/docs/js/scrollSpy.js b/docs/js/scrollSpy.js
@@ -18,7 +18,7 @@
       // throttle
       return;
     }
-    timer = setTimeout(function() {
+    timer = setTimeout(function () {
       timer = null;
       let activeNavFound = false;
       const headings = findHeadings(); // toc nav anchors
@@ -48,7 +48,7 @@
           } else {
             console.error('Can not find header element', {
               id: next,
-              heading,
+              heading
             });
           }
         }
@@ -68,9 +68,9 @@
 
   document.addEventListener('scroll', onScroll);
   document.addEventListener('resize', onScroll);
-  document.addEventListener('DOMContentLoaded', function() {
+  document.addEventListener('DOMContentLoaded', function () {
     // Cache the headings once the page has fully loaded.
     headingsCache = findHeadings();
     onScroll();
   });
-})();
+}());
diff --git a/src/components/download/downloadModal.js b/src/components/download/downloadModal.js
@@ -138,17 +138,17 @@ class DownloadModal extends React.Component {
   }
   formatPublications(pubs) {
     return (
-        <span>
+      <span>
         <ul>
-        {pubs.map((pub) => (
+          {pubs.map((pub) => (
             <li key={pub.href}>
-            <a href={pub.href} target="_blank" rel="noreferrer noopener">
-            {pub.author}, {pub.title}, <i>{pub.journal}</i> ({pub.year})
-          </a>
+              <a href={pub.href} target="_blank" rel="noreferrer noopener">
+                {pub.author}, {pub.title}, <i>{pub.journal}</i> ({pub.year})
+              </a>
             </li>
-        ))}
-      </ul>
-        </span>
+          ))}
+        </ul>
+      </span>
     );
   }
   getFilePrefix() {
@@ -233,21 +233,21 @@ class DownloadModal extends React.Component {
     const buttonTextStyle = Object.assign({}, materialButton, {backgroundColor: "rgba(0,0,0,0)", paddingLeft: "10px", color: "white", minWidth: "300px", textAlign: "left" });
     const buttonLabelStyle = { fontStyle: "italic", fontSize: "14px", color: "lightgray" };
     return (
-        <div style={{display: "block", justifyContent: "space-around", marginLeft: "25px", width: "100%" }}>
+      <div style={{display: "block", justifyContent: "space-around", marginLeft: "25px", width: "100%" }}>
         <div style={{ width: "100%" }}>
-        {buttons.map((data) => (
+          {buttons.map((data) => (
             <div key={data[0]} onClick={data[3]} style={{cursor: 'pointer' }}>
-            {data[2]}
-            <button style={buttonTextStyle} name={data[0]}>
-            {data[0]}
-          </button>
-            <div style={{ display: "inline-block", height: "30px", verticalAlign: "top", paddingTop: "6px" }}>
-            <label style={buttonLabelStyle} htmlFor={data[0]}>{data[1]}</label>
+              {data[2]}
+              <button style={buttonTextStyle} name={data[0]}>
+                {data[0]}
+              </button>
+              <div style={{ display: "inline-block", height: "30px", verticalAlign: "top", paddingTop: "6px" }}>
+                <label style={buttonLabelStyle} htmlFor={data[0]}>{data[1]}</label>
+              </div>
             </div>
-            </div>
-        ))}
-      </div>
+          ))}
         </div>
+      </div>
     );
   }
   dismissModal() {
@@ -279,42 +279,42 @@ class DownloadModal extends React.Component {
 
     const meta = this.props.metadata;
     return (
-        <div style={infoPanelStyles.modalContainer} onClick={this.dismissModal}>
+      <div style={infoPanelStyles.modalContainer} onClick={this.dismissModal}>
         <div style={panelStyle} onClick={(e) => stopProp(e)}>
-        <p style={infoPanelStyles.topRightMessage}>
+          <p style={infoPanelStyles.topRightMessage}>
         ({t("click outside this box to return to the app")})
-      </p>
+          </p>
 
-        <div style={infoPanelStyles.modalSubheading}>
-        {meta.title} ({t("last updated")} {meta.updated})
-      </div>
+          <div style={infoPanelStyles.modalSubheading}>
+            {meta.title} ({t("last updated")} {meta.updated})
+          </div>
 
-        <div>
-        {this.createSummaryWrapper()}
-      </div>
-        <div style={infoPanelStyles.break}/>
-        {" " + t("A full list of sequence authors is available via the TSV files below")}
-        <div style={infoPanelStyles.break}/>
-        {getAcknowledgments({}, {preamble: {fontWeight: 300}, acknowledgments: {fontWeight: 300}})}
+          <div>
+            {this.createSummaryWrapper()}
+          </div>
+          <div style={infoPanelStyles.break}/>
+          {" " + t("A full list of sequence authors is available via the TSV files below")}
+          <div style={infoPanelStyles.break}/>
+          {getAcknowledgments({}, {preamble: {fontWeight: 300}, acknowledgments: {fontWeight: 300}})}
 
-        <div style={infoPanelStyles.modalSubheading}>
-        {t("Data usage policy")}
-      </div>
-        {t("Data usage part 1") + " " + t("Data usage part 2")}
+          <div style={infoPanelStyles.modalSubheading}>
+            {t("Data usage policy")}
+          </div>
+          {t("Data usage part 1") + " " + t("Data usage part 2")}
 
-        <div style={infoPanelStyles.modalSubheading}>
-        {t("Please cite the authors who contributed genomic data (where relevant), as well as")+":"}
-      </div>
-        {this.formatPublications(this.getRelevantPublications())}
+          <div style={infoPanelStyles.modalSubheading}>
+            {t("Please cite the authors who contributed genomic data (where relevant), as well as")+":"}
+          </div>
+          {this.formatPublications(this.getRelevantPublications())}
 
 
-        <div style={infoPanelStyles.modalSubheading}>
-        {t("Download data")}:
-      </div>
-        {this.downloadButtons()}
+          <div style={infoPanelStyles.modalSubheading}>
+            {t("Download data")}:
+          </div>
+          {this.downloadButtons()}
 
-      </div>
         </div>
+      </div>
     );
   }
 }