support snpedia

Author: jynlix

config.js

@@ -2,7 +2,8 @@ const config = {
   srcdb:{
     'HGNC': 'http://rest.genenames.org/fetch/status/Approved',
     'entrez': 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=gene&retmode=json&id=',
-    'ensembl': 'https://rest.ensembl.org/lookup/symbol/homo_sapiens/'
+    'ensembl': 'https://rest.ensembl.org/lookup/symbol/homo_sapiens/',
+    'snpedia': 'https://bots.snpedia.com/api.php'
   },
   targetdb: {
     host: 'localhost',

db/initdb.sql

@@ -16,5 +16,22 @@ create table genes (
   location varchar(10) not null,
   region_start int not null,
   region_end int not null,
-  band varchar(32) not null
+  band varchar(50) not null
+);
+
+create table snp (
+  id serial primary key,
+  rsid int not null,
+  description text,
+  genes_id int
+);
+
+create table genotypes (
+  id serial primary key,
+  pair varchar(10),
+  orientation varchar(10),
+  magnitude int,
+  repute varchar(10),
+  summary text,
+  snp_id int
 );

doc/schema.pdf

@@ -0,0 +1,36 @@
+const commander = require('commander');
+const {createSnps, createGenotypes, translateSnps, translateGenotypes} = require('./snpedia');
+
+commander
+    .version('1.0.0')
+    .description('Create different genetic databases locally.');
+
+commander
+    .command('createsnps')
+    .description('Create snps from snpedia if not exist.')
+    .action(()=>{
+	createSnps();
+    });
+
+commander
+    .command('creategenotypes')
+    .description('Create all genotypes of a snp')
+    .action(()=>{
+        createGenotypes();
+    });
+
+commander
+    .command('translatesnps')
+    .description('Translate snps into Chinese')
+    .action(()=>{
+	translateSnps();
+    });
+
+commander
+    .command('translategenotypes')
+    .description('Translate genotypes into Chinese')
+    .action(()=>{
+        translateGenotypes();
+    });
+
+commander.parse(process.argv);

genedb.js

@@ -29,13 +29,13 @@ var genes = seq.define('genes', {
       type: Sequelize.INTEGER,
     },
     band:{
-      type: Sequelize.STRING(32)
+      type: Sequelize.STRING(50)
     }
  },
   {
     underscored: true,
     freezeTableName: true // Model tableName will be the same as the model name
   });
 
-genes.belongsTo(chromosome);
+//genes.belongsTo(chromosome);
 module.exports=genes;

model/genes.js

@@ -0,0 +1,35 @@
+var seq = require('./seq.js');
+var Sequelize = require('sequelize');
+var snps = require('./snp.js');
+var genotypes = seq.define('genotypes', {
+    id: {
+      type: Sequelize.INTEGER,
+      autoIncrement: true,
+      primaryKey: true
+    },
+    pair: {
+      type: Sequelize.TEXT,
+    },
+    magnitude:{
+      type: Sequelize.FLOAT,
+    },
+    repute:{
+      type: Sequelize.STRING(10),
+    },
+    summary:{
+      type:Sequelize.TEXT,
+    },
+    snp_id: {
+      type: Sequelize.INTEGER,
+    },
+    name: {
+      type: Sequelize.STRING(50),
+    }
+ },
+  {
+    underscored: true,
+    freezeTableName: true // Model tableName will be the same as the model name
+  });
+
+genotypes.belongsTo(snps);
+module.exports=genotypes;

model/genotypes.js

@@ -11,9 +11,11 @@ var sequelize = new seq(
             timestamps: false //为模型添加 createdAt 和 updatedAt 两个时间戳字段（true or false）
         },
         pool: { //使用连接池连接，默认为true
-            max: 50,
+            max: 80,
             min: 0,
-            idle: 30000
+            idle: 1000,
+	    evict: 1000,
+	    acquire: 200000
         },
     });
 

model/seq.js

@@ -0,0 +1,35 @@
+var seq = require('./seq.js');
+var Sequelize = require('sequelize');
+var gene = require('./genes.js');
+var snps = seq.define('snp', {
+    id: {
+      type: Sequelize.INTEGER,
+      autoIncrement: true,
+      primaryKey: true
+    },
+    description:{
+      type: Sequelize.TEXT,
+    },
+    rsid: {
+      type: Sequelize.STRING(50),
+    },
+    alias: {
+      type: Sequelize.STRING(50),
+    },
+    genes_id: {
+      type: Sequelize.INTEGER,
+    },
+    position:{
+      type: Sequelize.INTEGER
+    },
+    orientation:{
+      type: Sequelize.STRING(10)
+    }
+ },
+  {
+    underscored: true,
+    freezeTableName: true // Model tableName will be the same as the model name
+  });
+
+snps.belongsTo(gene,{foreignKey:'genes_id'});
+module.exports=snps;

model/snp.js

@@ -23,8 +23,15 @@
   },
   "homepage": "https://github.com/genostack/genedb#readme",
   "dependencies": {
+    "commander": "^2.18.0",
+    "google-translate-api": "^2.3.0",
     "google-translate-api-cn": "^1.0.1",
+    "mwbot": "^1.0.10",
     "node-fetch": "^2.2.0",
-    "sequelize": "^4.38.0"
+    "pg": "^7.4.3",
+    "pg-hstore": "^2.3.2",
+    "sequelize": "^4.38.0",
+    "xmldom": "^0.1.27",
+    "xpath": "0.0.27"
   }
 }