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UmmulkiramRUmmulkiramR
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Merge pull request #10 from overture-stack/authorization_switch_impl
Authorization switch impl
2 parents 91b0c9a + 39d02d5 commit f970e04

20 files changed

+653
-181
lines changed

‎.dockerignore‎

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target
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Dockerfile
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docker-compose.yml
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README.md
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Makefile
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.*
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!.mvn
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npm-debug.log
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node_modules
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dist
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coverage
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*.drawio

‎.env.example‎

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@@ -1,8 +1,7 @@
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NODE_ENV=development
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PORT=
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#DB connection details
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# --- DB connection details ---
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DB_HOST=
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DB_PORT=
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DB_USERNAME=
@@ -11,9 +10,28 @@ DB_NAME=
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DB_SYNCHRONIZE=true
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DB_SCHEMA:
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#list of permissions.
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SCOPES= []
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EGO_URL: "https://ego.url"
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# ----- Auth -----
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# client id and secret as present is keycloak or ego for this service
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CLIENT_ID=
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CLIENT_SECRET=
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# scopes as defined in EGO or KEYCLOAK eg. DICTIONARY.WRITE (For Keycloak DICTIONAY is the rsname i.e resource name and WRITE is the scope)
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# AUTH_WRITE_SCOPES property can be empty or absent for AUTH_STRATEGY = NONE.
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AUTH_WRITE_SCOPES=[]
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AUTH_STRATEGY= # valid values -> EGO or KEYCLOAK or NONE
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AUTH_SERVER_URL: # "https://ego.url" OR "http://localhost/realms/keycloak-realm". This property will be empty or absent for AUTH_STRATEGY = NONE
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# SECURED_API can be used to specify which of the APIs need authentication.
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# Can be empty or absent for AUTH_STRATEGY = NONE.
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# If omitted for AUTH_STRATEGY != NONE then all apis will need authentication by default.
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SECURED_API = ["CREATE", "FIND"]
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AUTH_PUBLICKEY_CACHE = 1d
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# ----- Entity Details -----
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# list of valid entity types
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ENTITY_LIST=["donor", "specimen", "sample"]
@@ -25,12 +43,10 @@ REQUEST_ROUTE=/:column1/:column2/:column3
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DB_SEQUENCES=
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# Repeat the below set for each entity type.
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# Sequences in defaultValue can be given as "nextval('argo.specimen_seq')" or "0" or "'A'".
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# The unique property under the columns array is not mandatory - default value for unique is false
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# The index property (in the end) holds the columns for composite unique index creation
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<ENTITY_TYPE>_SCHEMA={"tablename": "tablename", "columns": [{"name": "entityId","type": "varchar", "defaultValue": "default-value or sequence call", "unique": true}, {"name": "column1", "type": "db-datatype", "defaultValue": "default-value or sequence call", "unique": false},{"name": "column2", "type": "db-datatype", "defaultValue": "default-value or sequence call"}], "index": ["column1", "column2"]}
48+
# The index property (in the end) holds the columns for composite unique index creation. Note: This is an array of list of columns where each list constitutes a composite index.
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<ENTITY_TYPE>_SCHEMA={"tablename": "tablename", "columns": [{"name": "entityId","type": "varchar", "defaultValue": "default-value or sequence call", "unique": true}, {"name": "column1", "type": "db-datatype", "defaultValue": "default-value or sequence call", "unique": false},{"name": "column2", "type": "db-datatype", "defaultValue": "default-value or sequence call"}], "index": [[column list for composite index 1], [column list for composite index 2]]}
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# <ENTITY_TYPE>_SEARCH is the structure of the request/search-criteria/saved-entity. Should match column names in <ENTITY_TYPE>_SCHEMA.
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# values against each of the keys should remain blank.
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<ENTITY_TYPE>_SEARCH>={"column1":"", "column2":"", "column3": ""}
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‎Dockerfile‎

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FROM node:20-alpine as builder
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# Create app directory
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WORKDIR /app
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RUN chown -R node:node /app
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USER node
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# copy the package json and install first to optimize docker cache for node modules
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COPY package.json /app/
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COPY package-lock.json /app/
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RUN npm ci
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COPY . ./
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RUN npm run build
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# Runtime image
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FROM node:20-alpine
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ENV APP_UID=9999
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ENV APP_GID=9999
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RUN apk --no-cache add shadow
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RUN groupmod -g $APP_GID node
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RUN usermod -u $APP_UID -g $APP_GID node
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WORKDIR /app
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RUN chown -R node:node /app
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USER node
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RUN mkdir dist && mkdir node_modules
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COPY --from=builder /app/dist ./dist
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COPY --from=builder /app/node_modules ./node_modules
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COPY --from=builder /app/package.json .
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COPY --from=builder /app/package-lock.json .
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EXPOSE 3221
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CMD node dist/server.js

‎Jenkinsfile‎

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@Library(value='jenkins-pipeline-library@master', changelog=false) _
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pipelineOVERTUREIDGeneration()

‎package-lock.json‎

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‎package.json‎

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"jsonwebtoken": "^9.0.2",
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"memoizee": "^0.4.15",
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"ms": "^2.1.3",
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"openid-client": "^5.6.5",
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"pg": "^8.11.3",
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"swagger-ui-express": "^5.0.0",
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"typeorm": "^0.3.19",

‎src/config-validator.ts‎

Lines changed: 87 additions & 60 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
1-
import { z, ZodRecord, ZodString } from 'zod';
2-
import { SchemaInfo } from './middlewares/datasource';
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import {z, ZodEnum, ZodRecord, ZodString} from 'zod';
2+
import { SchemaInfo } from './middlewares/datasource.js';
33

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function getRequiredEnvVar(name: string) {
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const property = process.env[name];
@@ -27,6 +27,15 @@ export const getRequiredString = (name: string): string => {
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return stringValue.data;
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};
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export const getString = (name: string): string => {
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const value = process.env[name] || '';
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const stringValue = z.string().safeParse(value);
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if (!stringValue.success) {
34+
throw new Error(`Environment variable ${name} in config is not a valid string`);
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}
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return stringValue.data;
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};
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export const getUrl = (name: string): string => {
3140
const value = process.env[name] || 'a://';
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const stringValue = z.string().url().safeParse(value);
@@ -56,73 +65,91 @@ export const getArray = (name: string): ZodString['_output'][] => {
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} catch (e) {
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throw new Error(`Environment variable ${name} is not valid. Please provide an array of strings.`)
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}
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};
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export const getEnum = <T extends [string, ...string[]]>(name: string, zEnum: ZodEnum<T>): z.infer<ZodEnum<T>> => {
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const stringValue = zEnum.safeParse(process.env[name]);
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if (!stringValue.success) {
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throw new Error(`Environment variable ${name} has an invalid value. Valid values are: ${zEnum.options}`);
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}
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return stringValue.data;
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};
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export const validateArrayContents = <T extends [string, ...string[]]>(name: string, zEnum: ZodEnum<T>, value: string | undefined = ''): z.infer<ZodEnum<T>> => {
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const stringValue = zEnum.safeParse(value);
80+
if (!stringValue.success) {
81+
throw new Error(`Environment variable ${name} has an invalid value. Valid values are: ${zEnum.options}`);
82+
}
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return stringValue.data;
6084
};
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6287
export const getRecord = (name: string): ZodRecord<ZodString, ZodString> => {
6388
const config_entry = `${name.toUpperCase()}_SEARCH`;
6489
return z.record(
65-
z.string({ invalid_type_error: 'Invalid key in ' + config_entry + '. Should be a string' }),
66-
z.string({ invalid_type_error: 'Invalid value in ' + config_entry + '. Should be a string' }),
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z.string({ invalid_type_error: `Invalid key in ${config_entry}. Should be a string` }),
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z.string({ invalid_type_error: `Invalid value in ${config_entry}. Should be a string` }),
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{ invalid_type_error: `Environment variable ${config_entry} is invalid or missing` },
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);
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};
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7196
export const getSchemaDef = (name: string): z.ZodType<SchemaInfo> => {
72-
const config_entry = name.toUpperCase() + `_SCHEMA`;
73-
return z.object(
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{
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tablename: z
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.string({
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required_error: 'tablename in ' + config_entry + ' is required',
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invalid_type_error: 'tablename in ' + config_entry + ' is invalid',
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})
80-
.trim()
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.min(1, { message: 'tablename in ' + config_entry + ' cannot be empty' }),
82-
columns: z
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.array(
84-
z.object({
85-
name: z.string({ required_error: 'column `name` in ' + config_entry + ' is missing' }),
86-
type: z.union(
87-
[
88-
z.literal('float'),
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z.literal('varchar'),
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z.literal('number'),
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z.literal('date'),
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z.literal('varchar2'),
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z.literal('string'),
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z.literal('timestamp'),
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z.literal('double'),
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z.literal('boolean'),
97-
],
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{
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invalid_type_error: '`type` in ' + config_entry + ' has an invalid value.',
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required_error: '`type` in ' + config_entry + ' is required.',
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},
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),
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defaultValue: z
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.string({ invalid_type_error: 'value for `defaultValue` in ' + config_entry + ' is invalid' })
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.optional(),
106-
unique: z.boolean({ invalid_type_error: 'value for `unique` in ' + config_entry + ' is invalid' }).optional(),
107-
}),
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{
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invalid_type_error: '`columns` in ' + config_entry + ' should be an array',
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},
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)
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.nonempty({ message: '`column` array in ' + config_entry + ' should not be empty' }),
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index: z
114-
.array(
115-
z.string({
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invalid_type_error: '`index` in ' + config_entry + ' is invalid. It should be a list of column name strings',
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}),
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{
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invalid_type_error: '`index` in ' + config_entry + ' is invalid. It should be a list of column name strings',
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required_error: '`index` in ' + config_entry + ' is missing.',
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},
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)
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.nonempty({ message: '`index` in ' + config_entry + ' is required' }),
124-
},
125-
{ invalid_type_error: 'Schema definition missing for entity <' + name + '> in the ENTITY_LIST' },
126-
);
97+
const config_entry = name.toUpperCase() + `_SCHEMA`;
98+
return z.object(
99+
{
100+
tablename: z
101+
.string({
102+
required_error: 'table name in ' + config_entry + ' is required',
103+
invalid_type_error: 'table name in ' + config_entry + ' is invalid',
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})
105+
.trim()
106+
.min(1, { message: 'table name in ' + config_entry + ' cannot be empty' }),
107+
columns: z
108+
.array(
109+
z.object({
110+
name: z.string({ required_error: 'column name in ' + config_entry + ' is missing' }),
111+
type: z.union([
112+
z.literal('float'),
113+
z.literal('varchar'),
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z.literal('number'),
115+
z.literal('date'),
116+
z.literal('varchar2'),
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z.literal('string'),
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z.literal('timestamp'),
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z.literal('double'),
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z.literal('boolean'),
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]),
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defaultValue: z
123+
.string({ invalid_type_error: 'value for defaultValue in ' + config_entry + ' is invalid' })
124+
.optional(),
125+
unique: z.boolean({ invalid_type_error: 'value for unique in ' + config_entry + ' is invalid' }).optional(),
126+
}),
127+
{
128+
invalid_type_error: 'columns in ' + config_entry + ' should be an array',
129+
},
130+
)
131+
.nonempty({ message: 'column array in ' + config_entry + ' should not be empty' }),
132+
index: z
133+
.array(
134+
z.array(
135+
z.string({
136+
invalid_type_error:
137+
'index in ' + config_entry + ' is invalid. It should be a list of column name strings',
138+
}),
139+
{
140+
invalid_type_error:
141+
'index in ' + config_entry + ' is invalid. It should be a list of column name strings',
142+
required_error: 'index in ' + config_entry + ' is missing.',
143+
},
144+
),
145+
{
146+
invalid_type_error:
147+
'index in ' + config_entry + ' is invalid. It should be a list of list of column name strings',
148+
required_error: 'index in ' + config_entry + ' is missing.',
149+
},
150+
)
151+
.nonempty({ message: 'index in ' + config_entry + ' is required' }),
152+
},
153+
{ invalid_type_error: 'Schema definition missing for entity <' + name + '> in the ENTITY_LIST' },
154+
);
127155
};
128-

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