eusda v3.0.0

eusda

This is a simple development of a package that allows to have a database in MongoDB with nutrition data obtained of USDA (United States Department of Agriculture). You can change the url and download other type of data for your database.

Installation

You need node.js and npm.

npm install -d eusda

Usage from command line

You can use --help option to see what you can do:

Options:
  -v --version        Print eusda version
  -h, --help          output usage information

Commands:
  config              Show the config options.
  download [options]  Download data from USDA
  usda [options]      Config the URLs
  insert              Insert data from ./files/json/usda.json to the database.

Commands:

config: It shows the config file. download: It is used to download data.

• Options: You can see the command options using --help:

  Usage: app download [options]
  
  Download data from eusda
  
  Options:
  -u, --usda       USDA data version
  -s, --set <url>  Download data from another USDA url       
  -h, --help       output usage information

usda: Is is used to work with the urls.

• Options: You can see the command options using --help:

  Usage: app eusda [options]
  
  Config the URLs
  
  Options:
  -a, --add <path> <version> <url>  Add a new url to the config options
  -s, --show                        Show the available urls
  -d, --default <path> <version>    Set a default url
  -h, --help                        output usage information

insert: It inserts data in your database (MongoDB).

Eusda Tutorial

Install it with

npm i -g eusda

The first time it will ask you some questions to configure the database.

Here is an example of how to configure it locally with a default file:

[.../tfg-kathrina-arrocha-umpierrez/deploy(master)]$ eusda
The directory 'files' was created.
The directory 'zip' was created.
The directory 'unzip' was created.
The directory 'json' was created.
███████╗██╗   ██╗███████╗██████╗  █████╗
██╔════╝██║   ██║██╔════╝██╔══██╗██╔══██╗
█████╗  ██║   ██║███████╗██║  ██║███████║
██╔══╝  ██║   ██║╚════██║██║  ██║██╔══██║
███████╗╚██████╔╝███████║██████╔╝██║  ██║
╚══════╝ ╚═════╝ ╚══════╝╚═════╝ ╚═╝  ╚═╝

? Do you want to use a default configuration file?  Yes.
? Where will your config file be?  I want to use this directory.
New directory: /Volumes/2020/TFG/tfg-kathrina-arrocha-umpierrez/deploy/config/eusda
New file: /Volumes/2020/TFG/tfg-kathrina-arrocha-umpierrez/deploy/config/eusda/default.json

this will create the following tree:

[.../tfg-kathrina-arrocha-umpierrez/deploy(master)]$ tree
.
├── config
|    └── eusda
│         └── default.json
└── files
    ├── json
    ├── unzip
    └── zip

6 directories, 1 file

The command eusda config shows the contents of the configuration file:

[.../tfg-kathrina-arrocha-umpierrez/deploy(master)]$ eusda config
eusda 2.0.6

The configuration used is:

Config {
  db:
   { host: '127.0.0.1',
     port: 27017,
     name: 'eusda',
     collectionUSDA: 'food' },
  usda:
   { urls:
      { default: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/SR/sr28/dnload/sr28abxl.zip',
        sr28: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/SR/sr28/dnload/sr28abxl.zip',
        sr27: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/sr27/dnload/sr27abxl.zip',
        sr26: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/sr26/dnload/sr26abxl.zip',
        sr25: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/sr25/dnload/sr25abxl.zip',
        sr24: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/sr24/dnload/sr24abxl.zip',
        sr23: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/sr23/dnload/sr23abxl.zip',
        sr22: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/sr22/dnload/sr22abxl.zip',
        sr21: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/sr21/dnload/sr21abxl.zip',
        sr20: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/sr20/sr20abxl.zip',
        sr19: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/sr19/sr19abxl.zip',
        sr18: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/sr18/sr18abxl.zip',
        sr17: 'https://www.ars.usda.gov/ARSUserFiles/80400535/DATA/sr17/sr17abxl.zip' } },
  files: { zip: 'data.zip', json: 'usda.json', dish: 'dishes.json' },
  directories_path:
   { zip: './files/zip/',
     unzip: './files/unzip/',
     json: './files/json/' 
   }
  }

With the command download you can download the default version:

[.../tfg-kathrina-arrocha-umpierrez/deploy(master)]$ eusda download
eusda 2.0.6

 Downloading from USDA, using version sr28
        You can choose another version in this URL:
        https://www.ars.usda.gov/northeast-area/beltsville-md-bhnrc/beltsville-human-nutrition-research-center/methods-and-application-of-food-composition-laboratory/mafcl-site-pages/sr11-sr28/
       Then, you should change it in our configuration file: ./config/default.json

Extracted files
Converting excel file to json...
Process successfully completed
New json file created in ./files/json/

The new tree structure is:

[.../tfg-kathrina-arrocha-umpierrez/deploy(master)]$ tree -s
.
├── [       4096]  config
│   └── [       4096]  eusda
│       └── [       1559]  default.json
└── [       4096]  files
    ├── [       4096]  json
    │   └── [   11787549]  usda.json
    ├── [       4096]  unzip
    │   ├── [    2486334]  ABBREV.xlsx
    │   └── [     653211]  sr28_doc.pdf
    └── [       4096]  zip
        └── [    3050195]  data.zip

6 directories, 5 files

Observe the size of the file files/json/usda.json: it contains the whole data base in JSON format. For instance, to get the 2nd item description we can use jq:

[.../tfg-kathrina-arrocha-umpierrez/deploy(master)]$ jq .[1].shrt_desc files/json/usda.json
"BUTTER,WHIPPED,W/ SALT"

Be sure MongoDB is installed and mongod is running. If not, install it, confifure it and run it:

[.../tfg-kathrina-arrocha-umpierrez/deploy(master)]$ mkdir mongo-database
[.../tfg-kathrina-arrocha-umpierrez/deploy(master)]$ cd mongo-database/
[.../deploy/mongo-database(master)]$ mongod --dbpath .
2020-06-04T11:33:33.492+0100 I  CONTROL  [main] Automatically disabling TLS 1.0, to force-enable TLS 1.0 specify --sslDisabledProtocols 'none'
2020-06-04T11:33:33.522+0100 I  CONTROL  [initandlisten] MongoDB starting : pid=9774 port=27017 dbpath=. 64-bit host=sanclemente-2.local
...

This commands start mongod in the directory mongo-database:

[.../tfg-kathrina-arrocha-umpierrez/deploy(master)]$ tree mongo-database/
mongo-database/
├── WiredTiger
├── WiredTiger.lock
├── WiredTiger....
├── _mdb_catalog.wt
├── collection-.....wt
├── diagnostic.data
│   ├── metrics.2020-06-04T10-33-42Z-00000
│   └── metrics.interim
├── index-6--5.....wt
├── journal
│   └── WiredTigerPreplog....
├── mongod.lock
├── sizeStorer.wt
└── storage.bson

2 directories, 21 files

Now we can upload the json file inside the mongo database with

.../tfg-kathrina-arrocha-umpierrez/deploy(master)]$ eusda insert
eusda 2.0.6
Inserting data in the collection: food
Data was successfully inserted

Now, the database and collection with the data should have been created. exit. To check it, you can do this:

$ mongo
> show dbs
admin    0.000GB
config   0.000GB
eusda  0.003GB
local    0.000GB
> use eusda
switched to db eusda
> show collections
food