README.windows.md

Dav127

A Sails/Ember/D3 framework to display and interactively navigate complex datasets

Dependencies

Git

Download the most recent build from Git website: http://git-scm.com/download/win and the download should automatically start. Click the downloaded exe file, and follow the install instruction.

Database

The API server, Sails.js, supports many databases but we recommend MongoDB. Currently MySQL and MongoDB are supported but we are in the process of moving completely to MongoDB.

Install MongoDB

Click the Download button in the top right corner of the Mongodb home page: https://www.mongodb.com, it will take you to the download page, and select the version that is compatible with your Windows, and follow the install instruction to finish the installation.

If you do not know which version of Windows you are running, please go to your powershell or command prompt (cmd) and run following commands:

wmic os get caption
wmic os get osarchitecture

The 32-bit can be downloaded via: https://www.mongodb.org/dl/win32/i386

Setup MongdoDB

Create the default database folder using command prompt:

md C:\data\db

Run MongoDB via command prompt:

C:\Program Files\MongoDB\Server\3.4\bin\mongod.exe

Nodejs

Install the nodejs via the official download page: https://nodejs.org/en/download, choose the right platform and download either LTS or Current version of nodejs.
The downloaded package should also include npm as well.

Sails, Ember and Bower

Sails.js, Ember.js and Bower are Node.js packages and can be installed globally as administrator using npm via cmd (Run as administrator):

npm install -g sails
npm install -g ember-cli
npm install -g bower

Note that if you do not have administrator access, these packages will be installed locally by the npm install command detailed below.

Cloning repository and set-up

Clone the Github repository:

git clone https://github.com/Seanli52/Dav127.git

Install Sails and Ember dependencies

To install the various plug-ins and add-ons required by the project, use NPM and Bower (for the Ember-specific dependencies):

# cd into Sails directory
cd server
# Install Sails dependencies
npm install
# cd into Ember directory
cd ../frontend
# Install Ember dependencies
npm install
bower install

Note that npm install`` in server/andfrontend/will install the Sails.js and Ember.js dependencies, including Sails.js and Ember.js, into those directories. If you did not install Sails.js and Ember.js globally previously, you will need to run the local binaries. For example,emberis infrontend/node_modules/ember-cli/bin/```.

Set-up configs

Copy the example connections.js file from server/config/:

copy server/config/connections.js.example server/config/connections.js

And ensure that a MongoDB entry exists, reflecting your local settings:

  mongodb: {
    adapter: 'sails-mongo',
    host: 'localhost',
    port: 27017,
    // user: '',
    // password: '',
    // database: 'your_mongo_db_name_here'
  },

The connection setting in server/config/models.js should be set to this entry:

connection: 'mongodb'

Copy the example application.js file from frontend/app/adapters/:

copy frontend/app/adapters/application.js.example frontend/app/adapters/application.js

Ember needs to be pointed to the URL and namespace of the API in . By default, it is assumed that you are running Sails and Ember on the same machine (localhost), but change this to reflect your set-up:

# frontend/app/adapters/application.js
import DS from 'ember-data';

export default DS.RESTAdapter.extend({
  host: 'http://localhost:1776',
  namespace: 'api/v1'
});

Running

Starting Sails and Ember

You should now be able to start Sails:

cd server
sails lift

And Ember:

cd frontend
ember serve

Checking things are running

If Sails has started correctly, you should see the following if you navigate to http://localhost:1776/api/v1/geneticmaps in a browser:

{
  "geneticmaps": [],
  "meta": {
    "total": 0
  }
}

This tells us the API is working (though currently no data has been loaded).

If Ember has started correctly, you should see something like the following in the standard out after running ember serve:

Build successful - 15937ms.

Slowest Trees                                 | Total
----------------------------------------------+---------------------
Babel                                         | 11965ms

Slowest Trees (cumulative)                    | Total (avg)
----------------------------------------------+---------------------
Babel (15)                                    | 14371ms (958 ms)

Navigating to localhost:4200 in a browser, you should see a page load.

Inserting data

Two simple example genetic maps are in resources/:

# cat resources/example_map1.json
{ "geneticmap":
  {
    "name": "MyMap1",
    "chromosomes":
    [
      {
      "name": "MrChr",
      "markers":
        [
          {
          "name": "markerA",
          "position": 1
          },
          {
          "name": "markerB",
          "position": 1.5
          }
        ]
      }
    ]
  }
}

# cat resources/example_map2.json
{ "geneticmap":
  {
    "name": "MyMap2",
    "chromosomes":
    [
      {
      "name": "MyChr",
      "markers":
        [
          {
          "name": "markerA",
          "position": 0
          },
          {
          "name": "markerB",
          "position": 1.3
          }
        ]
      }
    ]
  }
}

Note that they both contain a chromosome called MyChr and two markers, markerA and markerB.

These maps can be uploaded using CURL:

curl -X POST \
     -H "Accept: application/json" -H "Content-type: application/json" \
     -d @example_map1.json \
     localhost:1776/api/v1/geneticmaps

curl -X POST \
     -H "Accept: application/json" -H "Content-type: application/json" \
     -d @example_map2.json \
     localhost:1776/api/v1/geneticmaps

The -H parameters set the headers as expected by Sails and are required. The API will return the inserted JSON if successful.

You should now be able to load localhost:4200 in a browser and select the two maps for alignment.