Automate style fixes as part of linting

raejohanek · Jan 8, 2017 · dbacd6e · dbacd6e
1 parent 1832696
commit dbacd6e
Show file tree

Hide file tree

Showing 21 changed files with 1,074 additions and 1,413 deletions.
diff --git a/dist/js/ideogram.js b/dist/js/ideogram.js
diff --git a/dist/js/ideogram.min.js b/dist/js/ideogram.min.js
diff --git a/dist/js/ideogram.min.js.map b/dist/js/ideogram.min.js.map
diff --git a/gulpfile.js b/gulpfile.js
@@ -8,13 +8,19 @@ var flatten = require('gulp-flatten');
 var ignore = require('gulp-ignore');
 var order = require('gulp-order');
 var eslint = require('gulp-eslint');
+var gulpIf = require('gulp-if');
 var sourcemaps = require('gulp-sourcemaps');
 
 var paths = {
   scripts: 'src/js/**/*.js',
   styles: 'src/css/**/*.css'
 }
 
+function isFixed(file) {
+	// Has ESLint fixed the file contents?
+	return file.eslint != null && file.eslint.fixed;
+}
+
 gulp.task('default', function () {
 
   gulp
@@ -29,8 +35,12 @@ gulp.task('default', function () {
 
 gulp.task('lint', function() {
   return gulp.src([paths.scripts, '!src/js/lib.js'])
-    .pipe(eslint())
-    .pipe(eslint.format())
+    .pipe(eslint({
+      fix: true
+    }))
+    .pipe(eslint.format()) // write style issues to stdout
+    // if fixed, write the file to dest
+    .pipe(gulpIf(isFixed, gulp.dest('src/js')));
 });
 
 gulp.task('dist', function() {

diff --git a/package.json b/package.json
@@ -48,6 +48,7 @@
     "gulp-concat": "^2.6.0",
     "gulp-eslint": "^3.0.1",
     "gulp-flatten": "^0.3.1",
+    "gulp-if": "^2.0.2",
     "gulp-ignore": "^2.0.1",
     "gulp-mocha": "*",
     "gulp-mocha-phantomjs": "^0.11",

diff --git a/src/js/color.js b/src/js/color.js
@@ -1,39 +1,33 @@
 function Color(config) {
     // Ideogram config
-    this._config = config;
-    this._ploidy = new Ploidy(this._config);
+  this._config = config;
+  this._ploidy = new Ploidy(this._config);
 }
 
-
 Color.prototype.getArmColor = function(chrSetNumber, chrNmber, armNumber) {
-
-    if (this._config.armColors) {
-        return this._config.armColors[armNumber];
-    } else if (this._config.ancestors) {
-        return this._getPolyploidArmColor(chrSetNumber, chrNmber, armNumber);
-    } else {
-        return null;
-    }
+  if (this._config.armColors) {
+    return this._config.armColors[armNumber];
+  } else if (this._config.ancestors) {
+    return this._getPolyploidArmColor(chrSetNumber, chrNmber, armNumber);
+  } else {
+    return null;
+  }
 };
 
-
 Color.prototype.getBorderColor = function(chrSetNumber, chrNmber, armNumber) {
-
-    if (chrNmber < this._config.ploidy) {
-        return '#000';
-    } else if (this._ploidy.isExists(chrSetNumber, chrNmber, armNumber)) {
-        return '#000';
-    } else {
-        return '#fff';
-    }
+  if (chrNmber < this._config.ploidy) {
+    return '#000';
+  } else if (this._ploidy.isExists(chrSetNumber, chrNmber, armNumber)) {
+    return '#000';
+  } else {
+    return '#fff';
+  }
 };
 
-
 Color.prototype._getPolyploidArmColor = function(chrSetNumber, chrNmber, armNumber) {
-
-    if (! this._ploidy.isExists(chrSetNumber, chrNmber, armNumber)) {
-        return 'transparent';
-    } else {
-        return this._config.ancestors[this._ploidy.getAncestor(chrSetNumber, chrNmber, armNumber)];
-    }
+  if (!this._ploidy.isExists(chrSetNumber, chrNmber, armNumber)) {
+    return 'transparent';
+  } else {
+    return this._config.ancestors[this._ploidy.getAncestor(chrSetNumber, chrNmber, armNumber)];
+  }
 };
diff --git a/src/js/core.js b/src/js/core.js
@@ -66,7 +66,7 @@ var Ideogram = function(config) {
   if (!this.config.chrWidth) {
     var chrWidth = 10,
       chrHeight = this.config.chrHeight;
-    if (900 > chrHeight && chrHeight > 500) {
+    if (chrHeight < 900 && chrHeight > 500) {
       chrWidth = Math.round(chrHeight / 40);
     } else if (chrHeight >= 900) {
       chrWidth = Math.round(chrHeight / 45);
@@ -494,7 +494,6 @@ Ideogram.prototype.drawChromosomeLabels = function() {
 * Stalks are small lines that visually connect labels to their bands.
 */
 Ideogram.prototype.drawBandLabels = function(chromosomes) {
-
   var i, chr, chrs, taxid, ideo, chrModel;
 
   ideo = this;
@@ -538,29 +537,35 @@ Ideogram.prototype.drawBandLabels = function(chromosomes) {
       .data(chrModel.bands)
       .enter()
       .append("g")
-        .attr("class", function(d, i) { return "bandLabel bsbsl-" + i; })
+        .attr("class", function(d, i) {
+          return "bandLabel bsbsl-" + i;
+        })
         .attr("transform", function(d) {
           var transform = ideo._layout.getChromosomeBandLabelTranslate(d, i);
 
           var x = transform.x;
-          //var y = transform.y;
+          // var y = transform.y;
 
           textOffsets[chrModel.id].push(x + 13);
 
           return transform.translate;
         })
         .append("text")
         .attr('text-anchor', ideo._layout.getChromosomeBandLabelAnchor(i))
-        .text(function(d) { return d.name; });
+        .text(function(d) {
+          return d.name;
+        });
 
-    //var adapter = ModelAdapter.getInstance(ideo.chromosomesArray[i]);
-    //var view = Chromosome.getInstance(adapter, ideo.config, ideo);
+    // var adapter = ModelAdapter.getInstance(ideo.chromosomesArray[i]);
+    // var view = Chromosome.getInstance(adapter, ideo.config, ideo);
 
     chr.selectAll("line.bandLabelStalk")
       .data(chrModel.bands)
       .enter()
       .append("g")
-      .attr("class", function(d, i) { return "bandLabelStalk bsbsl-" + i; })
+      .attr("class", function(d, i) {
+        return "bandLabelStalk bsbsl-" + i;
+      })
       .attr("transform", function(d) {
         var x, y;
 
@@ -671,7 +676,6 @@ Ideogram.prototype.rotateChromosomeLabels = function(chr, chrIndex, orientation,
   }
 
   if (orientation === "vertical" || orientation === "") {
-
     var ci = chrIndex - 1;
 
     if (numAnnotTracks > 1 || orientation === "") {
@@ -706,12 +710,12 @@ Ideogram.prototype.rotateChromosomeLabels = function(chr, chrIndex, orientation,
 
     tracksHeight = ideo.config.annotTracksHeight;
     if (ideo.config.annotationsLayout !== "overlay") {
-      tracksHeight = tracksHeight * 2;
+      tracksHeight *= 2;
     }
 
     chrMargin = ideo.config.chrMargin * chrIndex;
     x = -(chrMargin + chrMargin2) + 3 + tracksHeight;
-    x = x / scale.x;
+    x /= scale.x;
 
     chr.selectAll("text.chrLabel")
       .attr("transform", "rotate(-90)" + scaleSvg)
@@ -991,8 +995,8 @@ Ideogram.prototype.drawSynteny = function(syntenicRegions) {
 * Initializes various annotation settings.  Constructor help function.
 */
 Ideogram.prototype.initAnnotSettings = function() {
-  if (this.config.annotationsPath || this.config.localAnnotationsPath
-    || this.annots || this.config.annotations) {
+  if (this.config.annotationsPath || this.config.localAnnotationsPath ||
+    this.annots || this.config.annotations) {
     if (!this.config.annotationHeight) {
       var annotHeight = Math.round(this.config.chrHeight / 100);
       this.config.annotationHeight = annotHeight;
@@ -1305,7 +1309,9 @@ Ideogram.prototype.drawProcessedAnnots = function(annots) {
   if (layout === "tracks") {
     chrAnnot
       .append("g")
-      .attr("id", function(d) { return d.id; })
+      .attr("id", function(d) {
+        return d.id;
+      })
       .attr("class", "annot")
       .attr("transform", function(d) {
         var y = ideo.config.chrWidth + (d.trackIndex * annotHeight * 2);
@@ -1319,12 +1325,16 @@ Ideogram.prototype.drawProcessedAnnots = function(annots) {
           return circle;
         }
       })
-      .attr("fill", function(d) { return d.color; });
+      .attr("fill", function(d) {
+        return d.color;
+      });
   } else if (layout === "overlay") {
       // Overlaid annotations appear directly on chromosomes
 
     chrAnnot.append("polygon")
-        .attr("id", function(d) { return d.id; })
+        .attr("id", function(d) {
+          return d.id;
+        })
         .attr("class", "annot")
         .attr("points", function(d) {
           x1 = d.px - 0.5;
@@ -1339,7 +1349,9 @@ Ideogram.prototype.drawProcessedAnnots = function(annots) {
             x1 + "," + y2
           );
         })
-        .attr("fill", function(d) { return d.color; });
+        .attr("fill", function(d) {
+          return d.color;
+        });
   } else if (layout === "histogram") {
     chrAnnot.append("polygon")
         // .attr("id", function(d, i) { return d.id; })
@@ -1363,7 +1375,9 @@ Ideogram.prototype.drawProcessedAnnots = function(annots) {
             x1 + "," + y2
           );
         })
-        .attr("fill", function(d) { return d.color; });
+        .attr("fill", function(d) {
+          return d.color;
+        });
   }
 
   if (ideo.onDrawAnnotsCallback) {
@@ -1638,8 +1652,8 @@ Ideogram.prototype.sortChromosomes = function(a, b) {
     bIsCP = b.type === "chloroplast",
     aIsMT = a.type === "mitochondrion",
     bIsMT = b.type === "mitochondrion";
-    //aIsPlastid = aIsMT && a.name !== "MT", // e.g. B1 in rice genome GCF_001433935.1
-    //bIsPlastid = bIsMT && b.name !== "MT";
+    // aIsPlastid = aIsMT && a.name !== "MT", // e.g. B1 in rice genome GCF_001433935.1
+    // bIsPlastid = bIsMT && b.name !== "MT";
 
   if (aIsNuclear && bIsNuclear) {
     return naturalSort(a.name, b.name);

diff --git a/src/js/filter.js b/src/js/filter.js
@@ -14,11 +14,10 @@ This method flattens that structure to e.g.
 See also: packAnnots
 */
 Ideogram.prototype.unpackAnnots = function() {
-
   var chr, annots, i,
-      unpackedAnnots = [],
-      ideo = this,
-      chrs = ideo.annots;
+    unpackedAnnots = [],
+    ideo = this,
+    chrs = ideo.annots;
 
   for (i = 0; i < chrs.length; i++) {
     chr = chrs[i];
@@ -27,21 +26,19 @@ Ideogram.prototype.unpackAnnots = function() {
   }
 
   return unpackedAnnots;
-
 };
 
 /*
   Compresses annots back to default state.  Inverse of unpackAnnots.
 */
 Ideogram.prototype.packAnnots = function(unpackedAnnots) {
-
   var chr, annot, i,
-      annots = [],
-      ideo = this,
-      chrs = ideo.annots;
+    annots = [],
+    ideo = this,
+    chrs = ideo.annots;
 
   for (chr in chrs) {
-    annots.push({'chr': chrs[chr].chr, annots: []});
+    annots.push({chr: chrs[chr].chr, annots: []});
   }
 
   for (i = 0; i < unpackedAnnots.length; i++) {
@@ -50,7 +47,6 @@ Ideogram.prototype.packAnnots = function(unpackedAnnots) {
   }
 
   return annots;
-
 };
 
 /*
@@ -59,8 +55,8 @@ Ideogram.prototype.packAnnots = function(unpackedAnnots) {
 */
 Ideogram.prototype.initCrossFilter = function() {
   var ideo = this,
-      keys = ideo.rawAnnots.keys,
-      i, facet;
+    keys = ideo.rawAnnots.keys,
+    i, facet;
 
   ideo.unpackedAnnots = ideo.unpackAnnots();
   ideo.crossfilter = crossfilter(ideo.unpackedAnnots);
@@ -103,14 +99,13 @@ Ideogram.prototype.initCrossFilter = function() {
     * Integrate server-side filtering for very large datasets
 */
 Ideogram.prototype.filterAnnots = function(selections) {
-
   var t0 = Date.now();
 
   var i, facet,
-      prevFacet = null,
-      results, fn,
-      counts = {},
-      ideo = this;
+    prevFacet = null,
+    results, fn,
+    counts = {},
+    ideo = this;
 
   if (Object.keys(selections).length === 0) {
     results = ideo.unpackedAnnots;