gql - npm Package Compare versions

Comparing version 0.2.0 to 0.4.0

lib/Query.js

@@ -6,2 +6,3 @@ var EventEmitter = require('events').EventEmitter;
 var nop = require('nop');
+var roughMatch = require('./genotypeMatch');
 
@@ -18,2 +19,3 @@ function Query(opt){
 
+// all allele match
 Query.prototype.exact = function(id, genotype){
@@ -24,3 +26,3 @@ if (!id) throw new Error("Missing id in 'exact' query");
   this.add(function(snp, cb){
-    cb(null, (snp.id === id && snp.g === genotype));
+    cb(null, (snp.id === id && roughMatch(snp.g, genotype)));
   });
@@ -30,2 +32,13 @@ return this;
 
+Query.prototype.exactNot = function(id, genotype){
+  if (!id) throw new Error("Missing id in 'exactNot' query");
+  if (!genotype) throw new Error("Missing genotype in 'exactNot' query");
+
+  this.add(function(snp, cb){
+    cb(null, (snp.id === id && !roughMatch(snp.g, genotype)));
+  });
+  return this;
+};
+
+// one allele match
 Query.prototype.has = function(id, genotype){
@@ -41,7 +54,8 @@ if (!id) throw new Error("Missing id in 'has' query");
 
-Query.prototype.doesntExist = function(id){
-  if (!id) throw new Error("Missing id in 'doesntExist' query");
+Query.prototype.hasNot = function(id, genotype){
+  if (!id) throw new Error("Missing id in 'hasNot' query");
+  if (!genotype) throw new Error("Missing genotype in 'hasNot' query");
 
   this.add(function(snp, cb){
-    cb(null, (snp.id === id && !snp.g));
+    cb(null, (snp.id === id && (!snp.g || snp.g.indexOf(genotype) === -1)));
   });
@@ -51,2 +65,3 @@ return this;
 
+// any allele match
 Query.prototype.exists = function(id){
@@ -61,8 +76,7 @@ if (!id) throw new Error("Missing id in 'exists' query");
 
-Query.prototype.exactNot = function(id, genotype){
-  if (!id) throw new Error("Missing id in 'exactNot' query");
-  if (!genotype) throw new Error("Missing genotype in 'exactNot' query");
+Query.prototype.doesntExist = function(id){
+  if (!id) throw new Error("Missing id in 'doesntExist' query");
 
   this.add(function(snp, cb){
-    cb(null, (snp.id === id && snp.g !== genotype));
+    cb(null, (snp.id === id && !snp.g));
   });
@@ -72,18 +86,25 @@ return this;
 
-Query.prototype.hasNot = function(id, genotype){
-  if (!id) throw new Error("Missing id in 'hasNot' query");
-  if (!genotype) throw new Error("Missing genotype in 'hasNot' query");
-
-  this.add(function(snp, cb){
-    cb(null, (snp.id === id && (!snp.g || snp.g.indexOf(genotype) === -1)));
+// grouping queries
+Query.prototype.or = function(){
+  var args = [].slice.apply(arguments);
+  var afns = args.map(function(q){
+    return q._conditions.pop();
   });
-  return this;
-};
 
-Query.prototype.exact = function(id, genotype){
-  if (!id) throw new Error("Missing id in 'exact' query");
-  if (!genotype) throw new Error("Missing genotype in 'exact' query");
-
   this.add(function(snp, cb){
-    cb(null, (snp.id === id && snp.g === genotype));
+    var fns = afns.slice(0);
+    var matched = false;
+    var isDone = function(){
+      return matched === true || fns.length === 0;
+    };
+    var next = function(done){
+      fns.shift()(snp, function(err, isMatch){
+        if (err) return done(err);
+        matched = isMatch;
+        done();
+      });
+    };
+    async.until(isDone, next, function(err){
+      cb(err, matched);
+    });
   });
@@ -93,6 +114,5 @@ return this;
 
-// this is kind of a hack...
-Query.prototype.or = function(){
+Query.prototype.and = function(){
   var args = [].slice.apply(arguments);
-  var fns = args.map(function(q){
+  var afns = args.map(function(q){
     return q._conditions.pop();
@@ -102,5 +122,7 @@ });
   this.add(function(snp, cb){
-    var matched = false;
+    var fns = afns.slice(0);
+
+    var matched = true;
     var isDone = function(){
-      return matched === true || fns.length === 0;
+      return matched === false || fns.length === 0;
     };
@@ -121,2 +143,3 @@ var next = function(done){
 
+// base functions
 Query.prototype.add = function(fn) {
@@ -132,3 +155,2 @@ this._conditions.push(fn);
 // task system
-
 Query.prototype.needs = function(num){
@@ -135,0 +157,0 @@ this._needs = num;

package.json

 {
-   "name":"gql",
-   "description":"Query language for interpreting genome SNPs",
-   "version":"0.2.0",
-   "homepage":"http://github.com/genomejs/gql",
-   "repository":"git://github.com/genomejs/gql.git",
-   "author":"Fractal <[e-mail]> (http://wearefractal.com/)",
-   "main":"./index.js",
-   "tags": ["genomejs", "genoset", "gs144", "dna", "genetics", "genes", "query", "language"],
-   
-   "dependencies":{
-      "event-stream":"*",
-      "async":"*",
-      "nop":"*"
-   },
-   "devDependencies":{
-      "mocha":"*",
-      "should":"*"
-   },
-   "scripts":{
-      "test":"mocha"
-   },
-   "engines":{
-      "node":">= 0.4.0"
-   },
-   "licenses":[
-      {
-         "type":"MIT",
-         "url":"http://github.com/genomejs/gql/raw/master/LICENSE"
-      }
-   ]
+  "name": "gql",
+  "description": "Query language for interpreting genome SNPs",
+  "version": "0.4.0",
+  "homepage": "http://github.com/genomejs/gql",
+  "repository": "git://github.com/genomejs/gql.git",
+  "author": "Fractal <[e-mail]> (http://wearefractal.com/)",
+  "main": "./index.js",
+  "tags": [
+    "genomejs",
+    "genoset",
+    "gs144",
+    "dna",
+    "genetics",
+    "genes",
+    "query",
+    "language"
+  ],
+  "dependencies": {
+    "event-stream": "*",
+    "async": "*",
+    "nop": "*"
+  },
+  "devDependencies": {
+    "mocha": "*",
+    "should": "*"
+  },
+  "scripts": {
+    "test": "mocha"
+  },
+  "engines": {
+    "node": ">= 0.4.0"
+  },
+  "licenses": [
+    {
+      "type": "MIT",
+      "url": "http://github.com/genomejs/gql/raw/master/LICENSE"
+    }
+  ]
 }

README.md

@@ -88,3 +88,3 @@ [![Build Status](https://travis-ci.org/genomejs/gql.png?branch=master)](https://travis-ci.org/genomejs/gql)
 
-Creates a new GQL chainable query
+Creates a new GQL chainable query. Keep in mind that each condition is tested against one SNP at a time. If the condition is met then it is marked as a match and not tested again.
 
@@ -124,2 +124,18 @@ #### exact(id, genotype)
 
+#### or(conditions...)
+
+Evaluates to true if any of the argument conditions evaluates to true
+
+```javascript
+q.or(q.has("rs2032651", "A"), q.doesntExist("rs2032651"));
+```
+
+#### and(conditions...)
+
+Evaluates to true if all of the argument conditions evaluates to true
+
+```javascript
+q.and(q.exists("rs2032651"), q.has("rs2032651", "A"));
+```
+
 #### add(fn)
@@ -126,0 +142,0 @@

test/query.js

@@ -36,2 +36,17 @@ var gql = require('../');
 
+  it('should return a working query that matches roughly', function(done) {
+    var sample = {id: "test", g: "AB"};
+
+    var query = gql.query();
+    query.exact("test", "BA");
+
+    query.process(sample, function(err){
+      should.not.exist(err);
+      query.matches().length.should.equal(1);
+      query.matches().should.eql([sample]);
+      query.unmatched().length.should.equal(0);
+      done();
+    });
+  });
+
   it('should return a working query with multiple statements', function(done) {
@@ -38,0 +53,0 @@ var sample = {id: "test", g: "A"};

test/stream.js

@@ -24,2 +24,3 @@ var gql = require('../');
     faked.push({id:"rs2032651", g:"D"});
+    faked.push({id:"rs2032652", g:"AG"});
 
@@ -41,5 +42,6 @@ var query = gql.query();
     query.or(query.exact("rs17222419", "C"), query.exact("rs17222419", "T"));
+    query.and(query.exact("rs2032652", "AG"), query.has("rs2032652", "G"));
 
     es.readArray(faked).pipe(query.stream()).on('end', function(){
-      query.matches().length.should.equal(1);
+      query.matches().length.should.equal(2);
       query.matches().should.eql(faked);
@@ -46,0 +48,0 @@ query.unmatched().length.should.equal(13);

No alert changes

Improved metrics

Total package byte prevSize

26659

increased by11.82%

Number of package files

11

increased by22.22%

Lines of code

587

increased by15.32%

Number of lines in readme file

205

increased by8.47%

Worsened metrics

Number of low supply chain risk alerts

4

increased by33.33%

No dependency changes