@apollo-annotation/shared 0.1.18 → 0.1.20

package/test_data/one_cds.gff3

@@ -0,0 +1,9 @@
+##gff-version 3
+##sequence-region   chr1 1000 9000
+#example01
+chr1	.	gene	1000	9000	.	+	.	ID=gene10001;Name=EDEN;testid=t003
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004,t001,t004
+chr1	.	exon	1050	1500	.	+	.	ID=exon10001;Parent=mRNA10001;testid=t007
+chr1	.	exon	5000	5500	.	+	.	ID=exon10004;Parent=mRNA10001;testid=t010
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t012,t013,t014
+chr1	.	CDS	5000	5000	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t015,t014

package/test_data/one_cds.json

@@ -0,0 +1,67 @@
+{
+  "_id": "66d70e4ccc30b55b65e5f619",
+  "refSeq": "chr1",
+  "type": "gene",
+  "min": 999,
+  "max": 9000,
+  "strand": 1,
+  "children": {
+    "66d70e4ccc30b55b65e5f618": {
+      "_id": "66d70e4ccc30b55b65e5f618",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 1049,
+      "max": 9000,
+      "strand": 1,
+      "children": {
+        "66d70e4ccc30b55b65e5f615": {
+          "_id": "66d70e4ccc30b55b65e5f615",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 1049,
+          "max": 1500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10001"],
+            "testid": ["t007"]
+          }
+        },
+        "66d70e4ccc30b55b65e5f616": {
+          "_id": "66d70e4ccc30b55b65e5f616",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 4999,
+          "max": 5500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10004"],
+            "testid": ["t010"]
+          }
+        },
+        "66d70e4ccc30b55b65e5f617": {
+          "_id": "66d70e4ccc30b55b65e5f617",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 1200,
+          "max": 5000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds10001"],
+            "gff_name": ["edenprotein.1"],
+            "testid": ["t012", "t013", "t014", "t015"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA10001"],
+        "gff_name": ["EDEN.1"],
+        "testid": ["t004", "t001", "t004"]
+      }
+    }
+  },
+  "attributes": {
+    "gff_id": ["gene10001"],
+    "gff_name": ["EDEN"],
+    "testid": ["t003"]
+  }
+}

package/test_data/two_cds.gff3

@@ -0,0 +1,9 @@
+##gff-version 3
+##sequence-region   chr1 1000 9000
+#example01
+chr1	.	gene	1000	9000	.	+	.	ID=gene10001;Name=EDEN;testid=t003
+chr1	.	mRNA	1050	9000	.	+	.	ID=mRNA10001;Parent=gene10001;Name=EDEN.1;testid=t004,t001,t004
+chr1	.	exon	1050	1500	.	+	.	ID=exon10001;Parent=mRNA10001;testid=t007
+chr1	.	exon	5000	5500	.	+	.	ID=exon10004;Parent=mRNA10001;testid=t010
+chr1	.	CDS	1201	1500	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t012,t013,t014
+chr1	.	CDS	5000	5000	.	+	0	ID=cds10001;Parent=mRNA10001;Name=edenprotein.1;testid=t014

package/test_data/two_cds.json

@@ -0,0 +1,67 @@
+{
+  "_id": "66d70f3b9c7a7460925687a3",
+  "refSeq": "chr1",
+  "type": "gene",
+  "min": 999,
+  "max": 9000,
+  "strand": 1,
+  "children": {
+    "66d70f3b9c7a7460925687a2": {
+      "_id": "66d70f3b9c7a7460925687a2",
+      "refSeq": "chr1",
+      "type": "mRNA",
+      "min": 1049,
+      "max": 9000,
+      "strand": 1,
+      "children": {
+        "66d70f3b9c7a74609256879f": {
+          "_id": "66d70f3b9c7a74609256879f",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 1049,
+          "max": 1500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10001"],
+            "testid": ["t007"]
+          }
+        },
+        "66d70f3b9c7a7460925687a0": {
+          "_id": "66d70f3b9c7a7460925687a0",
+          "refSeq": "chr1",
+          "type": "exon",
+          "min": 4999,
+          "max": 5500,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["exon10004"],
+            "testid": ["t010"]
+          }
+        },
+        "66d70f3b9c7a7460925687a1": {
+          "_id": "66d70f3b9c7a7460925687a1",
+          "refSeq": "chr1",
+          "type": "CDS",
+          "min": 1200,
+          "max": 5000,
+          "strand": 1,
+          "attributes": {
+            "gff_id": ["cds10001"],
+            "gff_name": ["edenprotein.1"],
+            "testid": ["t012", "t013", "t014"]
+          }
+        }
+      },
+      "attributes": {
+        "gff_id": ["mRNA10001"],
+        "gff_name": ["EDEN.1"],
+        "testid": ["t004", "t001", "t004"]
+      }
+    }
+  },
+  "attributes": {
+    "gff_id": ["gene10001"],
+    "gff_name": ["EDEN"],
+    "testid": ["t003"]
+  }
+}

package/tsconfig.json

@@ -12,8 +12,8 @@
   },
   "include": ["./src"],
   "references": [
-    { "path": "../apollo-mst"},
-    { "path": "../apollo-schemas"},
-    { "path": "../apollo-common"},
-  ]
+    { "path": "../apollo-mst" },
+    { "path": "../apollo-schemas" },
+    { "path": "../apollo-common" },
+  ],
 }

package/src/Changes/DiscontinuousLocationEndChange.ts

@@ -1,182 +0,0 @@
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-/* eslint-disable @typescript-eslint/require-await */
-import {
-  ChangeOptions,
-  ClientDataStore,
-  FeatureChange,
-  LocalGFF3DataStore,
-  SerializedFeatureChange,
-  ServerDataStore,
-} from '@apollo-annotation/common'
-
-interface SerializedDiscontinuousLocationEndChangeBase
-  extends SerializedFeatureChange {
-  typeName: 'DiscontinuousLocationEndChange'
-}
-
-interface DiscontinuousLocationEndChangeDetails {
-  featureId: string
-  oldEnd: number
-  newEnd: number
-  index: number
-}
-
-interface SerializedDiscontinuousLocationEndChangeSingle
-  extends SerializedDiscontinuousLocationEndChangeBase,
-    DiscontinuousLocationEndChangeDetails {}
-
-interface SerializedDiscontinuousLocationEndChangeMultiple
-  extends SerializedDiscontinuousLocationEndChangeBase {
-  changes: DiscontinuousLocationEndChangeDetails[]
-}
-
-type SerializedDiscontinuousLocationEndChange =
-  | SerializedDiscontinuousLocationEndChangeSingle
-  | SerializedDiscontinuousLocationEndChangeMultiple
-
-export class DiscontinuousLocationEndChange extends FeatureChange {
-  typeName = 'DiscontinuousLocationEndChange' as const
-  changes: DiscontinuousLocationEndChangeDetails[]
-
-  constructor(
-    json: SerializedDiscontinuousLocationEndChange,
-    options?: ChangeOptions,
-  ) {
-    super(json, options)
-    this.changes = 'changes' in json ? json.changes : [json]
-  }
-
-  toJSON(): SerializedDiscontinuousLocationEndChange {
-    const { assembly, changedIds, changes, typeName } = this
-    if (changes.length === 1) {
-      const [{ featureId, index, newEnd, oldEnd }] = changes
-      return {
-        typeName,
-        changedIds,
-        assembly,
-        featureId,
-        oldEnd,
-        newEnd,
-        index,
-      }
-    }
-    return { typeName, changedIds, assembly, changes }
-  }
-
-  async executeOnServer(backend: ServerDataStore) {
-    const { featureModel, session } = backend
-    const { changes, logger } = this
-    for (const change of changes) {
-      const { featureId, index, newEnd, oldEnd: expectedOldEnd } = change
-      const topLevelFeature = await featureModel
-        .findOne({ allIds: featureId })
-        .session(session)
-        .exec()
-
-      if (!topLevelFeature) {
-        const errMsg = `ERROR: The following featureId was not found in database ='${featureId}'`
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-
-      const feature = this.getFeatureFromId(topLevelFeature, featureId)
-      if (!feature) {
-        const errMsg = 'ERROR when searching feature by featureId'
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      logger.debug?.(`*** Found feature: ${JSON.stringify(feature)}`)
-      if (
-        !feature.discontinuousLocations ||
-        feature.discontinuousLocations.length === 0
-      ) {
-        const errMsg =
-          'Must use "LocationEndChange" to change a feature end that does not have discontinuous locations'
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      const oldEnd = feature.discontinuousLocations[index].end
-      if (oldEnd !== expectedOldEnd) {
-        const errMsg = `Location's current end value ${oldEnd} doesn't match with expected value ${expectedOldEnd}`
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      const { start } = feature.discontinuousLocations[index]
-      if (newEnd <= start) {
-        const errMsg = `location end (${newEnd}) can't be smaller than location start (${start})`
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      const nextLocation = feature.discontinuousLocations[index + 1]
-      if (nextLocation && newEnd >= nextLocation.start) {
-        const errMsg = `Location end (${newEnd}) can't be larger than  the next location's start (${nextLocation.start})`
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      feature.discontinuousLocations[index].end = newEnd
-      if (index === feature.discontinuousLocations.length - 1) {
-        feature.end = newEnd
-      }
-
-      try {
-        if (topLevelFeature._id.equals(feature._id)) {
-          topLevelFeature.markModified('discontinuousLocations')
-        } else {
-          topLevelFeature.markModified('children')
-        }
-        await topLevelFeature.save()
-      } catch (error) {
-        logger.debug?.(`*** FAILED: ${error}`)
-        throw error
-      }
-    }
-  }
-
-  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
-    throw new Error('executeOnLocalGFF3 not implemented')
-  }
-
-  async executeOnClient(dataStore: ClientDataStore) {
-    if (!dataStore) {
-      throw new Error('No data store')
-    }
-    for (const [idx, changedId] of this.changedIds.entries()) {
-      const feature = dataStore.getFeature(changedId)
-      if (!feature) {
-        throw new Error(`Could not find feature with identifier "${changedId}"`)
-      }
-      const { index, newEnd } = this.changes[idx]
-      feature.setCDSDiscontinuousLocationEnd(newEnd, index)
-    }
-  }
-
-  getInverse() {
-    const { assembly, changedIds, changes, logger, typeName } = this
-    const inverseChangedIds = [...changedIds].reverse()
-    const inverseChanges = [...changes].reverse().map((change) => ({
-      featureId: change.featureId,
-      oldEnd: change.newEnd,
-      newEnd: change.oldEnd,
-      index: change.index,
-    }))
-    return new DiscontinuousLocationEndChange(
-      {
-        changedIds: inverseChangedIds,
-        typeName,
-        changes: inverseChanges,
-        assembly,
-      },
-      { logger },
-    )
-  }
-}
-
-export function isDiscontinuousLocationEndChange(
-  change: unknown,
-): change is DiscontinuousLocationEndChange {
-  return (
-    (change as DiscontinuousLocationEndChange).typeName ===
-    'DiscontinuousLocationEndChange'
-  )
-}

package/src/Changes/DiscontinuousLocationStartChange.ts

@@ -1,182 +0,0 @@
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-/* eslint-disable @typescript-eslint/require-await */
-import {
-  ChangeOptions,
-  ClientDataStore,
-  FeatureChange,
-  LocalGFF3DataStore,
-  SerializedFeatureChange,
-  ServerDataStore,
-} from '@apollo-annotation/common'
-
-interface SerializedDiscontinuousLocationStartChangeBase
-  extends SerializedFeatureChange {
-  typeName: 'DiscontinuousLocationStartChange'
-}
-
-interface DiscontinuousLocationStartChangeDetails {
-  featureId: string
-  oldStart: number
-  newStart: number
-  index: number
-}
-
-interface SerializedDiscontinuousLocationStartChangeSingle
-  extends SerializedDiscontinuousLocationStartChangeBase,
-    DiscontinuousLocationStartChangeDetails {}
-
-interface SerializedDiscontinuousLocationStartChangeMultiple
-  extends SerializedDiscontinuousLocationStartChangeBase {
-  changes: DiscontinuousLocationStartChangeDetails[]
-}
-
-type SerializedDiscontinuousLocationStartChange =
-  | SerializedDiscontinuousLocationStartChangeSingle
-  | SerializedDiscontinuousLocationStartChangeMultiple
-
-export class DiscontinuousLocationStartChange extends FeatureChange {
-  typeName = 'DiscontinuousLocationStartChange' as const
-  changes: DiscontinuousLocationStartChangeDetails[]
-
-  constructor(
-    json: SerializedDiscontinuousLocationStartChange,
-    options?: ChangeOptions,
-  ) {
-    super(json, options)
-    this.changes = 'changes' in json ? json.changes : [json]
-  }
-
-  toJSON(): SerializedDiscontinuousLocationStartChange {
-    const { assembly, changedIds, changes, typeName } = this
-    if (changes.length === 1) {
-      const [{ featureId, index, newStart, oldStart }] = changes
-      return {
-        typeName,
-        changedIds,
-        assembly,
-        featureId,
-        oldStart,
-        newStart,
-        index,
-      }
-    }
-    return { typeName, changedIds, assembly, changes }
-  }
-
-  async executeOnServer(backend: ServerDataStore) {
-    const { featureModel, session } = backend
-    const { changes, logger } = this
-    for (const change of changes) {
-      const { featureId, index, newStart, oldStart: expectedOldStart } = change
-      const topLevelFeature = await featureModel
-        .findOne({ allIds: featureId })
-        .session(session)
-        .exec()
-
-      if (!topLevelFeature) {
-        const errMsg = `ERROR: The following featureId was not found in database ='${featureId}'`
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-
-      const feature = this.getFeatureFromId(topLevelFeature, featureId)
-      if (!feature) {
-        const errMsg = 'ERROR when searching feature by featureId'
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      logger.debug?.(`*** Found feature: ${JSON.stringify(feature)}`)
-      if (
-        !feature.discontinuousLocations ||
-        feature.discontinuousLocations.length === 0
-      ) {
-        const errMsg =
-          'Must use "LocationStartChange" to change a feature start that does not have discontinuous locations'
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      const oldStart = feature.discontinuousLocations[index].start
-      if (oldStart !== expectedOldStart) {
-        const errMsg = `Location's current start value ${oldStart} doesn't match with expected value ${expectedOldStart}`
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      const { end } = feature.discontinuousLocations[index]
-      if (newStart >= end) {
-        const errMsg = `location start (${newStart}) can't be larger than location end (${end})`
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      const previousLocation = feature.discontinuousLocations[index - 1]
-      if (previousLocation && newStart <= previousLocation.end) {
-        const errMsg = `Location start (${newStart}) can't be larger than  the previous location's end (${previousLocation.end})`
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      feature.discontinuousLocations[index].start = newStart
-      if (index === 0) {
-        feature.start = newStart
-      }
-
-      try {
-        if (topLevelFeature._id.equals(feature._id)) {
-          topLevelFeature.markModified('discontinuousLocations')
-        } else {
-          topLevelFeature.markModified('children')
-        }
-        await topLevelFeature.save()
-      } catch (error) {
-        logger.debug?.(`*** FAILED: ${error}`)
-        throw error
-      }
-    }
-  }
-
-  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
-    throw new Error('executeOnLocalGFF3 not implemented')
-  }
-
-  async executeOnClient(dataStore: ClientDataStore) {
-    if (!dataStore) {
-      throw new Error('No data store')
-    }
-    for (const [idx, changedId] of this.changedIds.entries()) {
-      const feature = dataStore.getFeature(changedId)
-      if (!feature) {
-        throw new Error(`Could not find feature with identifier "${changedId}"`)
-      }
-      const { index, newStart } = this.changes[idx]
-      feature.setCDSDiscontinuousLocationStart(newStart, index)
-    }
-  }
-
-  getInverse() {
-    const { assembly, changedIds, changes, logger, typeName } = this
-    const inverseChangedIds = [...changedIds].reverse()
-    const inverseChanges = [...changes].reverse().map((change) => ({
-      featureId: change.featureId,
-      oldStart: change.newStart,
-      newStart: change.oldStart,
-      index: change.index,
-    }))
-    return new DiscontinuousLocationStartChange(
-      {
-        changedIds: inverseChangedIds,
-        typeName,
-        changes: inverseChanges,
-        assembly,
-      },
-      { logger },
-    )
-  }
-}
-
-export function isDiscontinuousLocationStartChange(
-  change: unknown,
-): change is DiscontinuousLocationStartChange {
-  return (
-    (change as DiscontinuousLocationStartChange).typeName ===
-    'DiscontinuousLocationStartChange'
-  )
-}