@apollo-annotation/shared 0.3.10 → 0.3.12

package/src/Validations/ValidationSet.ts

@@ -1,12 +1,8 @@
-import { type Change, type ClientDataStore } from '@apollo-annotation/common'
-import { type FeatureDocument } from '@apollo-annotation/schemas'
-import { type ClientSession, type Model } from 'mongoose'
+import type { Change, ClientDataStore } from '@apollo-annotation/common'
+import type { FeatureDocument } from '@apollo-annotation/schemas'
+import type { ClientSession, Model } from 'mongoose'
 
-import {
-  type Context,
-  type Validation,
-  type ValidationResult,
-} from './Validation'
+import type { Context, Validation, ValidationResult } from './Validation.js'
 
 export class ValidationResultSet {
   results: ValidationResult[] = []

package/src/Validations/index.ts

@@ -1,4 +1,4 @@
-export * from './Validation'
-export * from './ValidationSet'
-export * from './CoreValidation'
-export * from './ParentChildValidation'
+export * from './Validation.js'
+export * from './ValidationSet.js'
+export * from './CoreValidation.js'
+export * from './ParentChildValidation.js'

package/src/declare.d.ts

@@ -0,0 +1,58 @@
+declare module 'bson-objectid' {
+  import type { Buffer } from 'node:buffer'
+
+  export default ObjectID
+
+  declare const ObjectID: ObjectIDCtor
+
+  declare interface ObjectID {
+    readonly id: string
+    readonly str: string
+
+    toHexString(): string
+    equals(other: ObjectID): boolean
+    getTimestamp(): Date
+  }
+
+  declare interface ObjectIDCtor {
+    (hexStringOrIdStringOrArrayOrBuffer?: string | number[] | Buffer): ObjectID
+
+    new (
+      hexStringOrIdStringOrArrayOrBuffer?: string | number[] | Buffer,
+    ): ObjectID
+
+    createFromTime(time: number): ObjectID
+    createFromHexString(hexString: string): ObjectID
+    isValid(hexStringOrObjectID: string | ObjectID): boolean
+    toString(): string
+  }
+}
+
+declare module 'jwt-decode' {
+  export class InvalidTokenError extends Error {}
+
+  export interface JwtDecodeOptions {
+    header?: boolean
+  }
+
+  export interface JwtHeader {
+    type?: string
+    alg?: string
+  }
+
+  export interface JwtPayload {
+    iss?: string
+    sub?: string
+    aud?: string[] | string
+    exp?: number
+    nbf?: number
+    iat?: number
+    jti?: string
+  }
+
+  // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-parameters, @typescript-eslint/no-unnecessary-type-constraint
+  export default function jwtDecode<T extends unknown>(
+    token: string,
+    options?: JwtDecodeOptions,
+  ): T
+}

package/src/index.ts

@@ -1,8 +1,8 @@
-export * from './Changes'
-export * from './Operations'
-export * from './Validations'
-export * from './Common'
-export * from './Checks'
-export * from './util'
-export * from './Messages'
-export * from './GFF3'
+export * from './Changes/index.js'
+export * from './Operations/index.js'
+export * from './Validations/index.js'
+export * from './Common/index.js'
+export * from './Checks/index.js'
+export * from './util.js'
+export * from './Messages.js'
+export * from './GFF3/index.js'

package/src/util.ts

@@ -1,6 +1,6 @@
-import { type AnnotationFeature } from '@apollo-annotation/mst'
-import { type Feature } from '@apollo-annotation/schemas'
-import { type IKeyValueMap } from 'mobx'
+import type { AnnotationFeature } from '@apollo-annotation/mst'
+import type { Feature } from '@apollo-annotation/schemas'
+import type { IKeyValueMap } from 'mobx'
 
 export function splitStringIntoChunks(
   input: string,

package/test_data/single_feature_mutliple_locations.gff3

@@ -0,0 +1,5 @@
+TMUE_LG1	translated_feature	polypeptide_motif	212019	212160	.	-	.	ID=motif:TMUE_1000004293-hmmpanther.1
+TMUE_LG1	translated_feature	polypeptide_motif	212780	212850	.	-	.	ID=motif:TMUE_1000004293-hmmpanther.1
+TMUE_LG1	translated_feature	polypeptide_motif	212905	213031	.	-	.	ID=motif:TMUE_1000004293-hmmpanther.1
+TMUE_LG1	translated_feature	polypeptide_motif	213184	213299	.	-	.	ID=motif:TMUE_1000004293-hmmpanther.1
+TMUE_LG1	translated_feature	polypeptide_motif	213369	213480	.	-	.	ID=motif:TMUE_1000004293-hmmpanther.1

package/test_data/single_feature_mutliple_locations.json

@@ -0,0 +1,76 @@
+[
+  {
+    "_id": "69b44de19e27d84db8a9bd71",
+    "refSeq": "TMUE_LG1",
+    "type": "apollo_feature_container",
+    "min": 212018,
+    "max": 213480,
+    "strand": -1,
+    "children": {
+      "69b44de19e27d84db8a9bd6c": {
+        "_id": "69b44de19e27d84db8a9bd6c",
+        "refSeq": "TMUE_LG1",
+        "type": "polypeptide_motif",
+        "min": 212018,
+        "max": 212160,
+        "strand": -1,
+        "attributes": {
+          "gff_source": ["translated_feature"],
+          "gff_id": ["motif:TMUE_1000004293-hmmpanther.1"]
+        }
+      },
+      "69b44de19e27d84db8a9bd6d": {
+        "_id": "69b44de19e27d84db8a9bd6d",
+        "refSeq": "TMUE_LG1",
+        "type": "polypeptide_motif",
+        "min": 212779,
+        "max": 212850,
+        "strand": -1,
+        "attributes": {
+          "gff_source": ["translated_feature"],
+          "gff_id": ["motif:TMUE_1000004293-hmmpanther.1"]
+        }
+      },
+      "69b44de19e27d84db8a9bd6e": {
+        "_id": "69b44de19e27d84db8a9bd6e",
+        "refSeq": "TMUE_LG1",
+        "type": "polypeptide_motif",
+        "min": 212904,
+        "max": 213031,
+        "strand": -1,
+        "attributes": {
+          "gff_source": ["translated_feature"],
+          "gff_id": ["motif:TMUE_1000004293-hmmpanther.1"]
+        }
+      },
+      "69b44de19e27d84db8a9bd6f": {
+        "_id": "69b44de19e27d84db8a9bd6f",
+        "refSeq": "TMUE_LG1",
+        "type": "polypeptide_motif",
+        "min": 213183,
+        "max": 213299,
+        "strand": -1,
+        "attributes": {
+          "gff_source": ["translated_feature"],
+          "gff_id": ["motif:TMUE_1000004293-hmmpanther.1"]
+        }
+      },
+      "69b44de19e27d84db8a9bd70": {
+        "_id": "69b44de19e27d84db8a9bd70",
+        "refSeq": "TMUE_LG1",
+        "type": "polypeptide_motif",
+        "min": 213368,
+        "max": 213480,
+        "strand": -1,
+        "attributes": {
+          "gff_source": ["translated_feature"],
+          "gff_id": ["motif:TMUE_1000004293-hmmpanther.1"]
+        }
+      }
+    },
+    "attributes": {
+      "gff_source": ["translated_feature"],
+      "gff_id": ["motif:TMUE_1000004293-hmmpanther.1"]
+    }
+  }
+]

package/tsconfig.json

@@ -1,14 +1,16 @@
 {
-  "extends": "../../tsconfig-base.json",
+  "extends": "../../tsconfig",
   "compilerOptions": {
     "composite": true,
     "incremental": true,
     "outDir": "./dist",
     "rootDir": "./src",
-    "target": "ES2022",
-    "lib": ["ES2022", "DOM"],
-    "module": "CommonJS",
     "tsBuildInfoFile": "./dist/tsconfig.tsbuildinfo",
+    // TODO: enable this and fix the problems it reveals
+    "noUncheckedIndexedAccess": false,
+    // For nodejs:
+    "lib": ["esnext"],
+    "types": ["node"],
   },
   "include": ["./src"],
   "references": [