@apollo-annotation/shared 0.3.5 → 0.3.7

package/src/Operations/GetFeaturesOperation.ts

@@ -1,10 +1,10 @@
 /* eslint-disable @typescript-eslint/require-await */
 import {
-  LocalGFF3DataStore,
+  type LocalGFF3DataStore,
   Operation,
-  OperationOptions,
-  SerializedOperation,
-  ServerDataStore,
+  type OperationOptions,
+  type SerializedOperation,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
 
 interface SerializedGetFeaturesOperation extends SerializedOperation {

package/src/Validations/CoreValidation.ts

@@ -1,9 +1,10 @@
 /* eslint-disable @typescript-eslint/require-await */
-import { Change } from '@apollo-annotation/common'
+import { type Change } from '@apollo-annotation/common'
+
+import { type TypeChange } from '../Changes'
 
-import { TypeChange } from '../Changes'
-import soSequenceTypes from './soSequenceTypes'
 import { Validation } from './Validation'
+import soSequenceTypes from './soSequenceTypes'
 
 export function isTypeChange(thing: Change): thing is TypeChange {
   return 'oldType' in thing && 'newType' in thing

package/src/Validations/ParentChildValidation.ts

@@ -1,16 +1,18 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-import { Change } from '@apollo-annotation/common'
-import { Feature, FeatureDocument } from '@apollo-annotation/schemas'
-import { ClientSession, Model } from 'mongoose'
+
+import { type Change } from '@apollo-annotation/common'
+import { type Feature, type FeatureDocument } from '@apollo-annotation/schemas'
+import { type ClientSession, type Model } from 'mongoose'
 
 import {
-  LocationEndChange,
-  LocationStartChange,
+  type LocationEndChange,
+  type LocationStartChange,
   isLocationEndChange,
   isLocationStartChange,
 } from '../Changes'
-import { Validation, ValidationResult } from './Validation'
+import { getPrintableId } from '../util'
+
+import { Validation, type ValidationResult } from './Validation'
 
 export class ParentChildValidation extends Validation {
   name = 'ParentChildValidation' as const
@@ -79,7 +81,7 @@ export class ParentChildValidation extends Validation {
         (childFeature.max > feature.max || childFeature.min < feature.min)
       ) {
         throw new Error(
-          `Feature "${childFeature._id}" exceeds the bounds of its parent, "${feature._id}"`,
+          `Feature ${getPrintableId(childFeature)} exceeds the bounds of its parent, ${getPrintableId(feature)}`,
         )
       }
       this.checkChildFeatureBoundaries(childFeature)

package/src/Validations/Validation.ts

@@ -1,10 +1,10 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/require-await */
-import { Change, ClientDataStore } from '@apollo-annotation/common'
-import { FeatureDocument } from '@apollo-annotation/schemas'
-import type { ExecutionContext } from '@nestjs/common'
-import type { Reflector } from '@nestjs/core'
-import { ClientSession, Model } from 'mongoose'
+import { type Change, type ClientDataStore } from '@apollo-annotation/common'
+import { type FeatureDocument } from '@apollo-annotation/schemas'
+import { type ExecutionContext } from '@nestjs/common'
+import { type Reflector } from '@nestjs/core'
+import { type ClientSession, type Model } from 'mongoose'
 
 export interface Context {
   context: ExecutionContext

package/src/Validations/ValidationSet.ts

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

package/src/util.ts

@@ -1,3 +1,6 @@
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+import { type Feature } from '@apollo-annotation/schemas'
+
 export function splitStringIntoChunks(
   input: string,
   chunkSize: number,
@@ -9,3 +12,16 @@ export function splitStringIntoChunks(
   }
   return chunks
 }
+
+export function getPrintableId(feature: Feature): string {
+  const ff = feature as unknown as AnnotationFeature
+  const gff_id = ff.attributes.get('gff_id')?.join(',')
+  if (gff_id) {
+    return `ID=${gff_id} (_id: ${feature._id.toString()})`
+  }
+  const gff_name = ff.attributes.get('gff_name')?.join(',')
+  if (gff_name) {
+    return `Name=${gff_name} (_id: ${feature._id.toString()})`
+  }
+  return `_id: ${feature._id.toString()}`
+}

package/test_data/example01.json

@@ -30,7 +30,7 @@
           "refSeq": "chr1",
           "type": "exon",
           "min": 1049,
-          "max": 1500,
+          "max": 1499,
           "strand": 1,
           "attributes": {
             "gff_id": ["exon10002"]
@@ -100,7 +100,7 @@
           "refSeq": "chr1",
           "type": "exon",
           "min": 1049,
-          "max": 1500,
+          "max": 1499,
           "strand": 1,
           "attributes": {
             "gff_id": ["exon10002"]
@@ -159,7 +159,7 @@
           "refSeq": "chr1",
           "type": "exon",
           "min": 1299,
-          "max": 1500,
+          "max": 1499,
           "strand": 1,
           "attributes": {
             "gff_id": ["exon10001"]

package/test_data/example02.json

@@ -19,7 +19,7 @@
           "refSeq": "chr1",
           "type": "exon",
           "min": 11049,
-          "max": 11500,
+          "max": 11499,
           "strand": 1,
           "attributes": {
             "gff_id": ["exon20001"]
@@ -89,7 +89,7 @@
           "refSeq": "chr1",
           "type": "exon",
           "min": 11049,
-          "max": 11500,
+          "max": 11499,
           "strand": 1,
           "attributes": {
             "gff_id": ["exon20002"]
@@ -148,7 +148,7 @@
           "refSeq": "chr1",
           "type": "exon",
           "min": 11299,
-          "max": 11500,
+          "max": 11499,
           "strand": 1,
           "attributes": {
             "gff_id": ["exon20003"]

package/test_data/example04.json

@@ -19,7 +19,7 @@
           "refSeq": "chr1",
           "type": "exon",
           "min": 31049,
-          "max": 31500,
+          "max": 31499,
           "strand": 1,
           "attributes": {
             "gff_id": ["exon40001"]
@@ -89,7 +89,7 @@
           "refSeq": "chr1",
           "type": "exon",
           "min": 31049,
-          "max": 31500,
+          "max": 31499,
           "strand": 1,
           "attributes": {
             "gff_id": ["exon40001"]
@@ -148,7 +148,7 @@
           "refSeq": "chr1",
           "type": "exon",
           "min": 31299,
-          "max": 31500,
+          "max": 31499,
           "strand": 1,
           "attributes": {
             "gff_id": ["exon40002"]