@apollo-annotation/shared 0.3.4 → 0.3.6

package/src/GFF3/gff3ToAnnotationFeature.test.ts

@@ -1,13 +1,13 @@
 /* eslint-disable @typescript-eslint/no-floating-promises */
-import { describe, it } from 'node:test'
 import { readFileSync } from 'node:fs'
+import { describe, it } from 'node:test'
 
-import gff, { GFF3Feature } from '@gmod/gff'
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import gff, { type GFF3Feature } from '@gmod/gff'
 import { assert, use } from 'chai'
 import chaiExclude from 'chai-exclude'
 
 import { gff3ToAnnotationFeature } from './gff3ToAnnotationFeature'
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
 use(chaiExclude)
 

package/src/GFF3/gff3ToAnnotationFeature.ts

@@ -1,5 +1,5 @@
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import { GFF3Feature, GFF3FeatureLineWithRefs } from '@gmod/gff'
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import { type GFF3Feature, type GFF3FeatureLineWithRefs } from '@gmod/gff'
 import { doesIntersect2 } from '@jbrowse/core/util'
 import ObjectID from 'bson-objectid'
 
@@ -199,6 +199,7 @@ function convertChildren(
       exonFeatures,
       utrFeatures,
       processedCDS[0].refSeq,
+      featureIds,
     )
     for (const exon of missingExons) {
       convertedChildren[exon._id] = exon
@@ -216,6 +217,7 @@ function inferMissingExons(
   existingExons: GFF3Feature[],
   utrFeatures: GFF3Feature[],
   refSeq: string,
+  featureIds?: string[],
 ): AnnotationFeatureSnapshot[] {
   // Convert utrFeatures from GFF3Feature to AnnotationFeatureSnapshot
   const utrExons: AnnotationFeatureSnapshot[] = []
@@ -326,6 +328,13 @@ function inferMissingExons(
     }
   }
   const mergedExons = mergeAnnotationFeatures(missingExons)
+  if (featureIds) {
+    for (const exon of mergedExons) {
+      if (!featureIds.includes(exon._id)) {
+        featureIds.push(exon._id)
+      }
+    }
+  }
   return mergedExons
 }
 

package/src/GFF3/gffReservedKeys.ts

@@ -59,3 +59,28 @@ export const internalToGFF: Record<GFFInternalAttribute, GFFReservedAttribute> =
     gff_ontology_term: 'Ontology_term',
     gff_is_circular: 'Is_circular',
   }
+
+export function isGFFInternalAttribute(
+  attribute: string,
+): attribute is GFFInternalAttribute {
+  return attribute in internalToGFF
+}
+
+export type GFFColumn = 'score' | 'source'
+export type GFFColumnInternal = 'gff_score' | 'gff_source'
+export const gffColumnToInternal: Record<GFFColumn, GFFColumnInternal> = {
+  score: 'gff_score',
+  source: 'gff_source',
+}
+export function isGFFColumn(attribute: string): attribute is GFFColumn {
+  return attribute in gffColumnToInternal
+}
+export const gffInternalToColumn: Record<GFFColumnInternal, GFFColumn> = {
+  gff_score: 'score',
+  gff_source: 'source',
+}
+export function isGFFColumnInternal(
+  column: string,
+): column is GFFColumnInternal {
+  return column in gffInternalToColumn
+}

package/src/Messages.ts

@@ -1,5 +1,5 @@
-import { SerializedChange } from '@apollo-annotation/common'
-import { CheckResultSnapshot } from '@apollo-annotation/mst'
+import { type SerializedChange } from '@apollo-annotation/common'
+import { type CheckResultSnapshot } from '@apollo-annotation/mst'
 
 interface BaseMessage {
   channel: string

package/src/Operations/GetAssembliesOperation.ts

@@ -1,9 +1,9 @@
 /* eslint-disable @typescript-eslint/require-await */
 import {
-  LocalGFF3DataStore,
+  type LocalGFF3DataStore,
   Operation,
-  SerializedOperation,
-  ServerDataStore,
+  type SerializedOperation,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
 
 interface SerializedGetAssembliesOperation extends SerializedOperation {

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 +1,17 @@
 /* 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 { Validation, type ValidationResult } from './Validation'
 
 export class ParentChildValidation extends Validation {
   name = 'ParentChildValidation' as const

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/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"]