Merge pull request #492 from akmorrow13/add-in-flow-2

lint and tests passing with new flow version

.eslintrc.json

@@ -0,0 +1,39 @@
+
+{
+	"parser": "babel-eslint",
+	"parserOptions": {
+		"ecmaVersion": 6,
+		"sourceType": "module",
+		"ecmaFeatures": {
+			"jsx": true,
+			"modules": true,
+			"experimentalObjectRestSpread": true
+		}
+	},
+	"plugins": [
+		"react"
+	],
+	"env": {
+    	"browser": true,
+    	"node": true,
+    	"es6": true
+	},
+	"extends": ["eslint:recommended", "plugin:react/recommended"],
+	"rules": {
+		"semi": ["error", "always"],
+		"quotes": ["off", "double"],
+		"no-tabs": "off",
+		"new-cap": "off",
+		"no-unused-vars": ["error", {"args": "none"}],
+		"no-console": ["error", { "allow": ["warn", "error", "log"] }],
+		"react/no-find-dom-node": "warn",
+		"react/no-string-refs": "warn"
+
+	},
+	"settings": {
+		"react": {
+			"pragma": "React",
+			"version": "15.6.1"
+		}
+	}
+}

.flowconfig

@@ -1,4 +1,5 @@
 [ignore]
+.*node_modules/config-chain/test/*
 .*node_modules/flow-bin.*
 .*node_modules/jsxhint.*
 .*node_modules/.*mocha.*
@@ -30,7 +31,7 @@
 
 [libs]
 lib
-types
 node_modules/data-canvas/flowtype
 
 [options]
+suppress_comment= \\(.\\|\n\\)*\\$FlowIgnore

.travis.yml

@@ -1,7 +1,7 @@
 sudo: false  # Use container-based infrastructure
 language: node_js
 node_js:
-  - "5.1"
+  - "6.14"
 
 script: >
     npm run build &&

lib/q.js

@@ -23,6 +23,7 @@ declare module "q" {
         promise: Promise<T>;
         resolve(value: T): void;
         reject(reason: any): void;
+        delay(time: number):void;
         notify(value: any): void;
         makeNodeResolver(): (reason: any, value: T) => void;
     }
@@ -44,7 +45,7 @@ declare module "q" {
         /**
          * The then method from the Promises/A+ specification, with an additional progress handler.
          */
-        then<U>(onFulfill?: (value: T) => U | IPromise<U>, onReject?: (error: any) => U | IPromise<U>, onProgress?: Function): Promise<U>;
+        then<T, U>(onFulfill?: (value: T) => U | IPromise<U> | Promise<U>, onReject?: (error: any) => U | IPromise<U>, onProgress?: Function): Promise<U>;
 
         /**
          * Like then, but "spreads" the array into a variadic fulfillment handler. If any of the promises in the array are rejected, instead calls onRejected with the first rejected promise's rejection reason.
@@ -164,13 +165,13 @@ declare module "q" {
     }
 
     // If no value provided, returned promise will be of void type
-    declare function when<T, U>(): Promise<void>;
+    declare function when(): Promise<void>;
 
     // if no fulfill, reject, or progress provided, returned promise will be of same type
-    declare function when<T, U>(value: T | IPromise<T>): Promise<T>;
+    declare function when<T, U>(value: T | IPromise<T>,): Promise<T>;
 
     // If a non-promise value is provided, it will not reject or progress
-    declare function when<T, U>(value: T | IPromise<T>, onFulfilled: (val: T) => U | IPromise<U>, onRejected?: (reason: any) => U | IPromise<U>, onProgress?: (progress: any) => any): Promise<U>;
+    declare function when<T, U>(value: T | IPromise<T>, onFulfilled: (val: T) => U | IPromise<U>, onRejected?: (reason: any) => U | IPromise<U>, onProgress?: (progress: any) => any, ...rest: Array<void>): Promise<U>;
 
     /**
      * Currently "impossible" (and I use the term loosely) to implement due to TypeScript limitations as it is now.
@@ -200,8 +201,10 @@ declare module "q" {
     /**
      * Returns a promise that is fulfilled with an array containing the fulfillment value of each promise, or is rejected with the same rejection reason as the first promise to be rejected.
      */
-    declare function all<A, B, C>(promises: [Promise<A>, Promise<B>, Promise<C>]): Promise<[A, B, C]>;
-    declare function all<A, B, C>(promises: [Promise<A>, Promise<B>]): Promise<[A, B]>;
+    declare function all(promises: Promise<any>[]): Promise<any>; // catch all
+    // declare function all<A, B, C, D>(promises: [Promise<A>, Promise<B>, Promise<C>, Promise<D>]): Promise<[A, B, C, D]>;
+    // declare function all<A, B, C>(promises: [Promise<A>, Promise<B>, Promise<C>]): Promise<[A, B, C]>;    
+    // declare function all<A, B>(promises: [Promise<A>, Promise<B>]): Promise<[A, B]>;
 
     /**
      * Returns a promise that is fulfilled with an array of promise state snapshots, but only after all the original promises have settled, i.e. become either fulfilled or rejected.
@@ -314,4 +317,6 @@ declare module "q" {
      * Calling resolve with a non-promise value causes promise to be fulfilled with that value.
      */
     declare function resolve<T>(object: T): Promise<T>;
+
+    declare function delay<T>(time: number): Promise<T>;
 }

lib/underscore.js

@@ -6,7 +6,7 @@ declare module "underscore" {
   declare function clone<T>(obj: T): T;
 
   declare function isEqual<S, T>(a: S, b: T): boolean;
-  declare function range(a: number, b: number): Array<number>;
+  declare function range(a?: number, b: number, c?: number): Array<number>;
   declare function extend<S, T>(o1: S, o2: T): S & T;
 
   declare function zip<S, T>(a1: S[], a2: T[]): Array<[S, T]>;
@@ -41,11 +41,12 @@ declare module "underscore" {
 
   declare function groupBy<K, T>(a: Array<T>, iteratee: (val: T, index: number)=>K): {[key:K]: T[]};
 
-  declare function min<T>(a: Array<T>|{[key:any]: T}): T;
+  declare function min<T>(a: Array<T>|{[key:any]: T}, iteratee: (val: T)=>any): T;
   declare function max<T>(a: Array<T>|{[key:any]: T}): T;
 
   declare function values<T>(o: {[key: any]: T}): T[];
   declare function flatten(a: Array<any>): Array<any>;
+  declare function flatten(a: Array<any>, shallow?: boolean): Array<any>;
 
   declare function reduce<T, R>(a: T[], fn: (memo: R, val: T, idx: number, list: T[])=>R, memo?: R): R;
   declare function reduce<K, T, R>(a: {[key:K]: T}, fn: (memo: R, val: T, key: K, o: {[key:K]: T})=>R, memo?: R): R;

package.json

@@ -65,14 +65,22 @@
   "devDependencies": {
     "arraybuffer-slice": "^0.1.2",
     "babel": "^5.8.23",
+    "babel-eslint" : "8.2.6",
     "babel-core": "^5.8.23",
     "babelify": "^6.3.0",
     "browserify": "^10.2.4",
     "chai": "^2.0.0",
     "coveralls": "2.10.x",
     "envify": "^3.4.0",
+    "eslint": "^5.4.0",
+    "eslint-config-standard": "^11.0.0",
+    "eslint-plugin-import": "^2.14.0",
+    "eslint-plugin-node": "^7.0.1",
+    "eslint-plugin-promise": "^4.0.0",
+    "eslint-plugin-standard": "^3.1.0",
+    "eslint-plugin-react": "7.11.1",
     "exorcist": "^0.4.0",
-    "flow-bin": "^0.21.0",
+    "flow-bin": "^0.79.1",
     "http-server": "^0.8.0",
     "istanbul": "^0.3.17",
     "jsxhint": "git://github.com/strml/JSXHint.git",

scripts/lint.sh

@@ -19,4 +19,4 @@ if [[ $package_version != $code_version ]]; then
 fi
 
 # Run the usual linter
-./node_modules/.bin/jsxhint --es6module --harmony 'src/main/**/*.js' 'src/test/**/*.js'
+./node_modules/.bin/eslint src/**/**/*.js

src/main/Alignment.js

@@ -2,7 +2,9 @@
  * Interface for alignments, shared between BAM and GA4GH backends.
  * @flow
  */
-
+'use strict';
+
+import type {GenomeRange} from './types';
 import type ContigInterval from './ContigInterval';
 
 // "CIGAR" operations express how a sequence aligns to the reference: does it
@@ -13,6 +15,11 @@ export type CigarOp = {
   length: number
 }
 
+// converts a string into a Strand element. Must be '+' or '-'. Any other
+// strings will be converted to '.'.
+function strToStrand(str: string): Strand {
+  return str && str == '+' ? '+' : (str && str == '-' ? '-' : '.'); // either +, - or .
+}
 
 export type Strand = '-' | '+' | '.';
 
@@ -46,3 +53,7 @@ export type AlignmentDataSource = {
   once: (event: string, handler: Function) => void;
   off: (event: string) => void;
 };
+
+module.exports = {
+  strToStrand
+};

src/main/ContigInterval.js

@@ -1,6 +1,8 @@
 /* @flow */
 'use strict';
 
+import type {GenomeRange} from './types';
+
 import Interval from './Interval';
 import {flatMap} from './utils';
 
@@ -108,10 +110,10 @@ class ContigInterval<T: (number|string)> {
   }
 
   // Comparator for use with Array.prototype.sort
-  static compare(a: ContigInterval, b: ContigInterval): number {
-    if (a.contig > b.contig) {
+  static compare<T: (string|number)>(a: ContigInterval<T>, b: ContigInterval<T>): number {
+    if (a.contig.toString() > b.contig.toString()) {
       return -1;
-    } else if (a.contig < b.contig) {
+    } else if (a.contig.toString() < b.contig.toString()) {
       return +1;
     } else {
       return a.start() - b.start();
@@ -120,7 +122,7 @@ class ContigInterval<T: (number|string)> {
 
   // Sort an array of intervals & coalesce adjacent/overlapping ranges.
   // NB: this may re-order the intervals parameter
-  static coalesce(intervals: ContigInterval[]): ContigInterval[] {
+  static coalesce<T: (string|number)>(intervals: ContigInterval<T>[]): ContigInterval<T>[] {
     intervals.sort(ContigInterval.compare);
 
     var rs = [];
@@ -143,7 +145,7 @@ class ContigInterval<T: (number|string)> {
   }
 
   static fromGenomeRange(range: GenomeRange): ContigInterval<string> {
-    return new ContigInterval(range.contig, range.start, range.stop);
+    return new ContigInterval(range.contig.toString(), range.start, range.stop);
   }
 }
 

src/main/Controls.js

@@ -4,7 +4,7 @@
  */
 'use strict';
 
-import type {PartialGenomeRange} from './types';
+import type {GenomeRange, PartialGenomeRange} from './types';
 
 import React from 'react';
 import _ from 'underscore';
@@ -18,7 +18,7 @@ type Props = {
   onChange: (newRange: GenomeRange)=>void;
 };
 
-class Controls extends React.Component {
+class Controls extends React.Component<Props> {
   props: Props;
   state: void;  // no state
 
@@ -50,14 +50,14 @@ class Controls extends React.Component {
       if (altContig) range.contig = altContig;
     }
 
-    return (_.extend({}, this.props.range, range) : any);
+    return (_.extend(_.clone(this.props.range), range) : any);
   }
 
-  handleContigChange(e: SyntheticEvent) {
+  handleContigChange(e: SyntheticEvent<>) {
     this.props.onChange(this.completeRange({contig: this.refs.contig.value}));
   }
 
-  handleFormSubmit(e: SyntheticEvent) {
+  handleFormSubmit(e: SyntheticEvent<>) {
     e.preventDefault();
     var range = this.completeRange(utils.parseRange(this.refs.position.value));
     this.props.onChange(range);

src/main/LocalStringFile.js

@@ -24,7 +24,7 @@ class LocalStringFile extends AbstractFile {
     }
   }
 
-  getBytes(start: number, length: number): Q.Promise<ArrayBuffer> {
+  getBytes(start: number, length: number): Q.Promise<?ArrayBuffer> {
     if (length < 0) {
       return Q.reject(`Requested <0 bytes (${length})`);
     }
@@ -41,7 +41,7 @@ class LocalStringFile extends AbstractFile {
   }
 
   // Read the entire file -- not recommended for large files!
-  getAll(): Q.Promise<ArrayBuffer> {
+  getAll(): Q.Promise<?ArrayBuffer> {
    var buf = this.getFromCache(0, this.fileLength - 1);
    return Q.when(buf);
   }

src/main/Menu.js

@@ -30,10 +30,10 @@ type Props = {
   onSelect: (key: string) => void;
 };
 
-class Menu extends React.Component<void, Props, void> {
+class Menu extends React.Component<Props> {
   props: Props;
 
-  clickHandler(idx: number, e: SyntheticMouseEvent) {
+  clickHandler(idx: number, e: SyntheticMouseEvent<>) {
     e.preventDefault();
     var item = this.props.items[idx];
     if (typeof(item) == 'string') return;  // for flow

src/main/RemoteFile.js

@@ -150,14 +150,14 @@ class RemoteFile extends AbstractFile{
   promiseXHR(xhr: XMLHttpRequest): Q.Promise<[any, Event]> {
     var url = this.url;
     var deferred = Q.defer();
-    xhr.addEventListener('load', function(e) {
+    xhr.addEventListener('load', function(e: any) {
       if (this.status >= 400) {
         deferred.reject(`Request for ${url} failed with status: ${this.status} ${this.statusText}`);
       } else {
         deferred.resolve([this.response, e]);
       }
     });
-    xhr.addEventListener('error', function(e) {
+    xhr.addEventListener('error', function(e: any) {
       deferred.reject(`Request for ${url} failed with status: ${this.status} ${this.statusText}`);
     });
     this.numNetworkRequests++;

src/main/RemoteRequest.js

@@ -71,14 +71,14 @@ class RemoteRequest {
   promiseXHR(xhr: XMLHttpRequest): Q.Promise<[any, Event]> {
     var url = this.url;
     var deferred = Q.defer();
-    xhr.addEventListener('load', function(e) {
+    xhr.addEventListener('load', function(e: any) {
       if (this.status >= 400) {
         deferred.reject(`Request for ${url} failed with status: ${this.status} ${this.statusText}`);
       } else {
         deferred.resolve([this.response, e]);
       }
     });
-    xhr.addEventListener('error', function(e) {
+    xhr.addEventListener('error', function(e: any) {
       deferred.reject(`Request for ${url} failed with status: ${this.status} ${this.statusText}`);
     });
     this.numNetworkRequests++;