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.
You need node.js and npm.
npm install -d eusda
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.
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).
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.
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? 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