@apollo-annotation/mst 0.3.13 → 1.0.0

package/package.json

@@ -1,6 +1,11 @@
 {
   "name": "@apollo-annotation/mst",
-  "version": "0.3.13",
+  "version": "1.0.0",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/Apollo3.git",
+    "directory": "packages/apollo-mst"
+  },
   "sideEffects": false,
   "type": "module",
   "exports": "./dist/index.js",

package/src/AnnotationFeatureModel.ts

@@ -4,18 +4,19 @@
 import { getSession, intersection2 } from '@jbrowse/core/util'
 import {
   type IAnyModelType,
+  type IAnyStateTreeNode,
   type IMSTMap,
   type Instance,
   type SnapshotIn,
   type SnapshotOrInstance,
   cast,
+  getParent,
   getParentOfType,
   getSnapshot,
+  hasParent,
   types,
 } from '@jbrowse/mobx-state-tree'
 
-import { ApolloAssembly } from './index.js'
-
 const LateAnnotationFeature = types.late(
   (): IAnyModelType => AnnotationFeatureModel,
 )
@@ -291,40 +292,6 @@ export const AnnotationFeatureModel = types
         transcript.filter((transcriptPart) => transcriptPart.type === 'CDS'),
       )
     },
-    get looksLikeGene(): boolean {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      const session = getSession(self) as any
-      const { apolloDataStore } = session
-      const { featureTypeOntology } = apolloDataStore.ontologyManager
-      if (!featureTypeOntology) {
-        return false
-      }
-      const children = self.children as Children
-      if (!children?.size) {
-        return false
-      }
-      const isGene =
-        featureTypeOntology.isTypeOf(self.type, 'gene') ||
-        featureTypeOntology.isTypeOf(self.type, 'pseudogene')
-      if (!isGene) {
-        return false
-      }
-      for (const [, child] of children) {
-        if (
-          featureTypeOntology.isTypeOf(child.type, 'transcript') ||
-          featureTypeOntology.isTypeOf(child.type, 'pseudogenic_transcript')
-        ) {
-          const { children: grandChildren } = child
-          if (!grandChildren?.size) {
-            return false
-          }
-          return [...grandChildren.values()].some((grandchild) =>
-            featureTypeOntology.isTypeOf(grandchild.type, 'exon'),
-          )
-        }
-      }
-      return false
-    },
   }))
   .actions((self) => ({
     setAttributes(attributes: Map<string, string[]>) {
@@ -431,7 +398,18 @@ export const AnnotationFeatureModel = types
       return feature as AnnotationFeature
     },
     get assemblyId(): string {
-      return getParentOfType(self, ApolloAssembly)._id
+      // Not using getParentOfType because importing ApolloAssembly would create
+      // a circular module dependency
+      let node: IAnyStateTreeNode = self
+      while (hasParent(node)) {
+        node = getParent(node)
+        if ('refSeqs' in node && '_id' in node) {
+          return node._id as string
+        }
+      }
+      throw new Error(
+        'AnnotationFeatureModel: could not find parent ApolloAssembly',
+      )
     },
   }))
 

package/src/ApolloAssembly.ts

@@ -2,10 +2,7 @@ import { type Instance, type SnapshotIn, types } from '@jbrowse/mobx-state-tree'
 
 import { ApolloRefSeq } from './ApolloRefSeq.js'
 
-export type BackendDriverType =
-  | 'CollaborationServerDriver'
-  | 'InMemoryFileDriver'
-  | 'DesktopFileDriver'
+export type BackendDriverType = 'CollaborationServerDriver' | 'LocalDriver'
 
 export const ApolloAssembly = types
   .model('ApolloAssembly', {
@@ -15,8 +12,7 @@ export const ApolloAssembly = types
     backendDriverType: types.optional(
       types.enumeration('backendDriverType', [
         'CollaborationServerDriver',
-        'InMemoryFileDriver',
-        'DesktopFileDriver',
+        'LocalDriver',
       ]),
       'CollaborationServerDriver',
     ),