bionode-fasta - npm Package Compare versions

Comparing version 0.4.1 to 0.4.2

package.json

 {
   "name": "bionode-fasta",
   "description": "Streamable FASTA parser",
-  "version": "0.4.1",
+  "version": "0.4.2",
   "homepage": "http://bionode.io",
@@ -23,4 +23,7 @@ "repository": {
   "devDependencies": {
+    "async": "~0.9.0",
     "beefy": "^2.1.0",
-    "browserify": "^5.9.3",
+    "browserify": "git+https://github.com/bmpvieira/node-browserify#3.46.1/http-browserify-1.6.0-pull-53-61-62",
+    "browserify-fs": "~1.0.0",
+    "request": "~2.40.0",
     "contributor": "~0.1.22",
@@ -49,4 +52,8 @@ "coveralls": "~2.11.1",
   },
+  "browser": {
+    "fs": "browserify-fs"
+  },
   "scripts": {
     "test": "node test/bionode-fasta.js | tap-spec",
+    "test-browser": "browserify test/bionode-fasta.js | testling -x 'open -a \"Google Chrome\"' | tap-spec",
     "coverage": "istanbul cover test/bionode-fasta.js --report lcovonly -- | tap-spec && rm -rf ./coverage",
@@ -53,0 +60,0 @@ "coveralls": "istanbul cover test/bionode-fasta.js --report lcovonly -- | tap-spec && cat ./coverage/lcov.info | ./node_modules/.bin/coveralls && rm -rf ./coverage",

test/bionode-fasta.js

 var fs = require('fs')
 var test = require('tape')
+var request = require('request')
+var async = require('async')
 var fasta = require('../')
 var data = require('./data')
+var zlib = require('zlib')
+var through = require('through2')
+var buffer = require('buffer')
 
-var file = fs.readFileSync('./test/test.fasta')
 
+// Node.js fs is implemented in the browser by browserify-fs using leveldb.
+// So we need to fetch the file and save it locally (server) or in leveldb (client) with fs.
+// Because Cross-Origin Resource Sharing (CORS) isn't enabled on GitHub, we need
+// to use a proxy to access the file.
 
-test('Read a fasta file and pipe content to parser.', function (t) {
-  t.plan(3)
-  var msg
-  var pushFunc
+async.eachSeries(['test.fasta', 'test.fasta.gz'], download, startTests)
 
-
-  msg = 'should return a Buffer for each sequence'
-  testPipeParser(msg, fasta(), true)
-
-  msg = 'should return an Object for each sequence'
-  testPipeParser(msg, fasta({ objectMode: true }))
-
-  msg = 'should return an Object for each sequence (shortcut version)'
-  testPipeParser(msg, fasta.obj())
-
-
-  function testPipeParser(msg, parser, jsparse) {
-    var result = []
-
-    parser
-    .on('data', pushResult)
-    .on('end', function() { t.deepEqual(result, data.fasta, msg) })
-
-    function pushResult(data) {
-      if (jsparse) { data = JSON.parse(data.toString()) }
-      result.push(data)
-    }
-
-    parser.write(file)
-    parser.end()
+function download(file, callback) {
+  var proxy = 'http://cors.inb.io/'
+  var rooturl = 'https://raw.githubusercontent.com/bionode/bionode-fasta/master/test/'
+  fs.mkdir('test', gotDir)
+  function gotDir() {
+    var get = request(proxy + rooturl + file, {encoding: null})
+    var write = fs.createWriteStream('test/' + file)
+    get.pipe(write)
+    write.on('close', callback)
   }
-})
+}
 
-testFilename('./test/test.fasta')
-testFilename('./test/test.fasta.gz')
-testFilename('./test/test.fasta', true)
-testFilename('./test/test.fasta.gz', true)
-
-function testFilename(file, includePath) {
-  var solution = JSON.parse(JSON.stringify(data.fasta))
-  var extramsg = ''
-  if (includePath) {
-    extramsg = ' (add path to results)'
-    solution.forEach(addPath)
-    function addPath(obj, i) {
-      obj.path = file
-      solution[i] = obj
-    }
-  }
-
-  if ('gz' === file.split('.').pop()) {
-    extramsg += ' (read gzipped file)'
-  }
-
-  test('Use parser to read file by passing filename' + extramsg, function (t) {
+function startTests() {
+  test('Read a fasta file and pipe content to parser.', function (t) {
     t.plan(3)
     var msg
-    var parser
     var pushFunc
 
-
     msg = 'should return a Buffer for each sequence'
-    parser = includePath ? fasta({ includePath: true }, file) : fasta(file)
-    testFilenamePipe(msg, parser, true)
+    testPipeParser(msg, fasta(), true)
 
     msg = 'should return an Object for each sequence'
-    var options = { objectMode: true }
-    if (includePath) { options.includePath = true }
-    parser = fasta(options, file)
-    testFilenamePipe(msg, parser)
+    testPipeParser(msg, fasta({ objectMode: true }))
 
     msg = 'should return an Object for each sequence (shortcut version)'
-    parser = includePath ? fasta.obj({ includePath: true }, file) : fasta.obj(file)
-    testFilenamePipe(msg, parser)
+    testPipeParser(msg, fasta.obj())
 
 
-    function testFilenamePipe(msg, parser, jsparse) {
+    function testPipeParser(msg, parser, jsparse) {
       var result = []
-      parser
+
+      fs.createReadStream('test/test.fasta')
+      .pipe(parser)
       .on('data', pushResult)
-      .on('end', function() { t.deepEqual(result, solution, msg) })
+      .on('end', function() { t.deepEqual(result, data.fasta, msg) })
+
       function pushResult(data) {
@@ -97,53 +62,111 @@ if (jsparse) { data = JSON.parse(data.toString()) }
 
-  test('Use parser to read file by passing filename and get results with callback' + extramsg, function (t) {
-    t.plan(6)
+  testFilename('test/test.fasta')
+  testFilename('test/test.fasta.gz')
+  testFilename('test/test.fasta', true)
+  testFilename('test/test.fasta.gz', true)
 
+
+  function testFilename(file, includePath) {
+    var solution = JSON.parse(JSON.stringify(data.fasta))
+    var extramsg = ''
     if (includePath) {
-      fasta({ includePath: true }, file, callback1)
+      extramsg = ' (add path to results)'
+      solution.forEach(addPath)
+      function addPath(obj, i) {
+        obj.path = file
+        solution[i] = obj
+      }
     }
-    else {
-      fasta(file, callback1)
+
+    if ('gz' === file.split('.').pop()) {
+      extramsg += ' (read gzipped file)'
     }
-    function callback1(err, result) {
-      t.error(err, 'callback error should be null')
-      var objects = []
-      result.toString().split('\n').forEach(pushObject)
-      function pushObject(obj) {
-        if (obj !== '') {
-          objects.push(JSON.parse(obj))
+
+
+    test('Use parser to read file by passing filename' + extramsg, function (t) {
+      t.plan(3)
+      var msg
+      var parser
+      var pushFunc
+
+      msg = 'should return a Buffer for each sequence'
+      parser = includePath ? fasta({ includePath: true }, file) : fasta(file)
+      testFilenamePipe(msg, parser, true)
+
+      msg = 'should return an Object for each sequence'
+      var options = { objectMode: true }
+      if (includePath) { options.includePath = true }
+      parser = fasta(options, file)
+      testFilenamePipe(msg, parser)
+
+      msg = 'should return an Object for each sequence (shortcut version)'
+      parser = includePath ? fasta.obj({ includePath: true }, file) : fasta.obj(file)
+      testFilenamePipe(msg, parser)
+
+      function testFilenamePipe(msg, parser, jsparse) {
+        var result = []
+        parser
+        .on('data', pushResult)
+        .on('end', function() { t.deepEqual(result, solution, msg) })
+        function pushResult(data) {
+          if (jsparse) { data = JSON.parse(data.toString()) }
+          result.push(data)
         }
       }
-      var msg = 'should return a Buffer with all sequences objects separated by newline'
-      t.deepEqual(objects, solution, msg)
-    }
+    })
 
 
-    var options = { objectMode: true }
-    if (includePath) { options.includePath = true }
-    fasta(options, file, function(err, result) {
-      t.error(err, 'callback error should be null')
-      var msg = 'should return an array of Objects'
-      t.deepEqual(result, solution, msg)
+    test('Use parser to read file by passing filename and get results with callback' + extramsg, function (t) {
+      t.plan(6)
+
+      if (includePath) {
+        fasta({ includePath: true }, file, callback1)
+      }
+      else {
+        fasta(file, callback1)
+      }
+      function callback1(err, result) {
+        t.error(err, 'callback error should be null')
+        var objects = []
+        result.toString().split('\n').forEach(pushObject)
+        function pushObject(obj) {
+          if (obj !== '') {
+            objects.push(JSON.parse(obj))
+          }
+        }
+        var msg = 'should return a Buffer with all sequences objects separated by newline'
+        t.deepEqual(objects, solution, msg)
+      }
+
+
+      var options = { objectMode: true }
+      if (includePath) { options.includePath = true }
+      fasta(options, file, function(err, result) {
+        t.error(err, 'callback error should be null')
+        var msg = 'should return an array of Objects'
+        t.deepEqual(result, solution, msg)
+      })
+
+
+      if (includePath) {
+        fasta.obj({ includePath: true }, file, callback2)
+      }
+      else {
+        fasta.obj(file, callback2)
+      }
+      function callback2(err, result) {
+        t.error(err, 'callback error should be null')
+        var msg = 'should return an array of Objects'
+        t.deepEqual(result, solution, msg)
+      }
     })
+  }
 
 
-    if (includePath) {
-      fasta.obj({ includePath: true }, file, callback2)
-    }
-    else {
-      fasta.obj(file, callback2)
-    }
-    function callback2(err, result) {
-      t.error(err, 'callback error should be null')
-      var msg = 'should return an array of Objects'
-      t.deepEqual(result, solution, msg)
-    }
+  test('Errors should be caught', function(t) {
+    t.plan(1)
+    var msg = 'should return a ENOENT error for non-existing path'
+    fasta('./nosuchfile.fasta')
+    .on('error', function(error) { t.equal(error.code, 'ENOENT', msg) })
   })
 }
-
-test('Errors should be caught', function(t) {
-  t.plan(1)
-  var msg = 'should return a ENOENT error for non-existing path'
-  fasta('./nosuchfile.fasta')
-  .on('error', function(error) { t.equal(error.code, 'ENOENT', msg) })
-})

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Worsened metrics

Total package byte prevSize

614163

decreased by-0.13%

Dev dependency count

12

increased by33.33%

Number of package files

27

decreased by-6.9%

Lines of code

1841

decreased by-2.33%

No dependency changes