bcgsc / pori_graphkb_schema

Shared package between the API and GUI for GraphKB which holds the schema definitions and schema-related functions

GraphKB Schema

This repository is part of the platform for oncogenomic reporting and interpretation.

This is the package which defines the schema logic used to create the database, build the API and GUI. It is a dependency of both the API and GUI and uses the parser package.

This is where all database constraints and swagger metadata associated with a particular database model is defined

Deployment

This package is installed on our local npm server. To install simply add to your package.json as you would with any other package and supply the registry argument to npm install

Getting Started (For Developers)

Install the dependencies

npm install

Then run the tests

npm run test

Using with OrientJS

To avoid requiring orientjs in this package, the RID class is defaulted to the builtin String class. It is expected that if you want your RID strings cast to RID objects (orientjs.RID or orientjs.RecordID for orientjs 3.X.X) that you will patch this after import. For example

const {RID} = require('orientjs');
const {constants, schema} = require('@bcgsc-pori/graphkb-schema');

const {PERMISSIONS} = constants;

constants.RID = RID; // IMPORTANT: Without this all castToRID will do is convert to a string

Migrating from v3 to v4

To facilitate more reuseable typing schemes ClassModel and Property classes have been removed and now are simply objects. All interactions with these models should go through the schema class instead of interacting directly with the model and property objects. Return types are given only when they differ.

v3 (ClassModel methods)	v4 equivalent (SchemaDefinition methods)	Notes
properties	getProperties(modelName: string)
required	requiredProperties(modelName: string)
optional	optionalProperties(modelName: string)
getActiveProperties()	activeProperties(modelName: string)
inherits	ancestors(modelName: string)
subclasses: ClassModel[]	children(modelName: string): string[]
descendantTree(boolean): ClassModel[]	descendants(modelName: string, opt: { excludeAbstract?: boolean, includeSelf?: boolean }): string[]	must be called with includeSelf=true to match v3 edition
queryProperties: Property[]	queryableProperties(modelName: string): PropertyDefinition[]
inheritsProperty(propName: string)	inheritsProperty(modelName: string, propName: string)
toJSON	N/A
formatRecord(record: GraphRecord, opt = {})	formatRecord(modelName: string, record: GraphRecord, opt = {})

pori_graphkb_schema's Issues

Convert to Typescript

Convert to typescript. In order to support better type-checking we will be moving this and related repositories to typescript. This must be tested with the current implementations of the client and api and should support use in node as a commonjs module still

depends on

• bcgsc/pori_graphkb_parser#13

Error on editing existing user

Describe the bug

When trying to edit a user in the admin interface I see the following error

See attached console log
graphkbdev.bcgsc.ca-1651010819639.log

To Reproduce

Pick an existing user, attempt to edit their details

Add new Phenotype Class

In order to support loading the Human Phenotype ontology (see https://hpo.jax.org/) and linking these terms from CIViC statements it would be helpful to add a phenotype class to GraphKB. This will require

• Define the new class in this package
• Add a migration to GraphKB API to apply/create the new class
• Ensure this new class is included in the class-based permissions object

This new class should subclass ontology