protocolsio-schemas

This package is meant to provide a collection of schemas that model all objects available in the Protocols.io v3 api. As well a jsonschema validator object is provided that allows you to validate any instance of a Protocols.io object to check if it is valid according to the schema. All schemas are implemented using JSON-SCHEMA.

View the NPM page here

Index

• Installation
• Quick Start
• Available Imports
• Objects
  • User
  • Image
  • Reagent
  • Comment
  • Small Protocol
  • Protocol
  • Step
  • Step Component
  • Step Component Type
  • Case
• Object Validation
• Development
  • Project Structure
  • Running Tests

Installation

npm install --save protocolsio-schemas

Quick Start

import { ProtocolsIOValidator, User } from 'protocolsio-schemas'
let u = {
  "name": "Vladimir Frolov",
  "affiliation": null,
  "username": "vladimir-frolov10",
  "link": null,
  "image": {
    "source": "https://s3.amazonaws.com/pr-journal/djqbjf6.jpg",
    "placeholder": "https://s3.amazonaws.com/pr-journal/djqbjf6.jpg"
  }
}

console.log(ProtocolsIOValidator.validate(u, User))

Available Imports

Import any object from the protocolsio-schema package using its object name.

import {
  User, Image, Reagent,
  Comment, SmallProtocol, Protocol,
  Step, StepComponent, Case,
  StepComponentType1, StepComponentType3, StepComponentType4,
  StepComponentType6, StepComponentType7, StepComponentType8,
  StepComponentType9, StepComponentType13, StepComponentType15,
  StepComponentType17, StepComponentType18, StepComponentType19,
  StepComponentType20, StepComponentType21, StepComponentType22,
  StepComponentType24, StepComponentType25, StepComponentType26,
} from 'protocolsio-schema'

Objects

Note: Under guidance from the Protocols.IO API developer the following fields are currently the only ones that can be confidently said to never be null: id, title, uri, and created_on. Code your checks around this appropriately.

User

| property | type | description | |----|---|---| | name | string | user full name | | affiliation | string OR null | user affiliation | | username | string OR null | username | | link | string OR null | external url. | | image | Image | user profile image |

Image

| property | type | description | |----|---|---| | source | string OR null | link to the image. | | placeholder | string OR null | link to the image placeholder or original image link of placeholder is not exist |

Reagent

| property | type | description | |----|---|---| | id | integer | unique reagent integer identifier. | | mol_weight | number | molarity weight | | name | string | name of reagent. | | linfor | string | linear formula | | url | string OR null | external url | | sku | string | reagent sku. | | vendor | User | reagent vendor. |

Comment

| property | type | description | |----|---|---| | id | integer | unique comment integer identifier. | | parent_id | integer | id of parent comment. | | title | string | title of comment. | | body | string | body of comment. | | created_on | integer | unix timestamp. date/time of comment creation. | | changed_on | integer | unix timestamp. date/time when comment was modified last time. | | creator | User | comment creator. | | comments | Array<Comment> | comment replies. |

Small Protocol

| property | type | description | |----|---|---| | id | integer | unique protocol integer identifier. | | title | string | protocol title. | | image | Image | protocol image. | | version_id | integer | 0...n. Version number of this protocol. | | doi | string OR null | DOI of this protocol. | | uri | string | unique protocol text identifier. | | published_on | integer OR null | unix timestamp. date/time when this protocol was published. |

Protocol

| property | type | description | |----|---|---| | id | integer | unique protocol integer identifier. | | title | string | protocol title. | | image | Image | protocol image. | | doi | string | DOI of this protocol. | | uri | string | unique protocol text identifier. | | published_on | integer OR null | unix timestamp. date/time when this protocol was published. | | created_on | integer | unix timestamp. date/time of protocol creation. | | creator | User | protocol creator | | public | integer | 1 or 0. 1 means that this protocol is public and 0 otherwise. | | versions | Array<SmallProtocol> | list of versions | | version_id | integer | 0...n. Version number of this protocol. | | link | string | Link to this protocol. | | number_of_steps | integer OR null | number of steps of this protocol. | | authors | Array<User> | list of user or empty array | | steps | Array<Step> | All of the steps in this protocol. | | materials | Array<Reagent> | Reagents required for this protocol. |

Step

| property | type | description | |----|---|---| | id | integer | unique step integer identifier. | | guid | string | unique step guid. | | previous_id | integer | id of previous step. | | previous_guid | string OR null | guid of previous step. | | modified_on | integer | unix timestamp. date/time when step was modified. | | components | StepComponent | list of step components. |

Step Component

| property | type | description | |----|---|---| | id | integer | unique step integer identifier. | | guid | string | unique step guid. | | order_id | integer | sequence number of component in the list starting from 0. | | type_id | integer | type of of component, one of step component types. | | title | string | name of component. | | source | Array<StepComponentType> | variative object of component, can be determine by type_id |

Step Component Type

There are LOTS of Step Component Types: Read More Here

Case

| property | type | description | |----|---|---| | title | string | title of a case. | | label | string OR null | label of a case. | | step_id | integer OR null | linked step id. | | step_guid | string OR null | linked step guid. |

Object Validation

To validate an object after constructing it you simply need to import the ProtocolsIOValidator object and the associated object schema. Once you have done that you can get a validation object by running the validate() function of the validator.

Following is an example of constructing and validating a Protocols.io User object.

import { ProtocolsIOValidator, User } from 'protocolsio-schemas'
let u = {
  "name": "Vladimir Frolov",
  "affiliation": null,
  "username": "vladimir-frolov10",
  "link": null,
  "image": {
    "source": "https://s3.amazonaws.com/pr-journal/djqbjf6.jpg",
    "placeholder": "https://s3.amazonaws.com/pr-journal/djqbjf6.jpg"
  }
}

console.log(ProtocolsIOValidator.validate(u, User))

Example Validator Output

ValidatorResult {
  instance:
   { name: 'Vladimir Frolov',
     affiliation: null,
     username: 'vladimir-frolov10',
     link: null,
     image:
      { source: 'https://s3.amazonaws.com/pr-journal/djqbjf6.jpg',
        placeholder: 'https://s3.amazonaws.com/pr-journal/djqbjf6.jpg' } },
  schema:
   { id: '/ProtocolsIO/User',
     title: 'User',
     description: 'A Protocols.io User object. http://apidoc.protocols.io/v3/#user-object',
     type: 'object',
     properties:
      { name: [Object],
        affiliation: [Object],
        username: [Object],
        link: [Object],
        image: [Object] },
     required: [ 'name', 'affiliation', 'username', 'link', 'image' ] },
  propertyPath: 'instance',
  errors: [],
  throwError: undefined,
  disableFormat: false }

The ProtocolsIOValidator is an instance of the Validator class from the json schema package. To learn more about what validate returns and how it works please visit the jsonschema documentation

Development

Project Structure

All of the source code is written in ES6 javascript. You will find all ES6 source code under /src. Within that folder you will find a /test and /schemas folder. Schemas contains a JSON-SCHEMA spec for each object. Tests contains a validation script for each object that runs the validate function on several several test objects.

Building Project

After making changes to any of the code in the /src/ folder simply run the following command in the root folder of the project.

npm run build

Running Tests

In the root folder of the project run the following command to run tests.

npm run test