Codify that the fromsequenceadapter only takes a single feature conve…

…ring refseq
GMOD · Feb 19, 2021 · 125c8fc · 125c8fc
1 parent ed0d12f
commit 125c8fc
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Showing 2 changed files with 20 additions and 40 deletions.
diff --git a/packages/core/assemblyManager/assemblyManager.ts b/packages/core/assemblyManager/assemblyManager.ts
@@ -9,7 +9,10 @@ import {
 } from 'mobx-state-tree'
 import { when } from '../util'
 import { readConfObject } from '../configuration'
-import { AnyConfigurationModel } from '../configuration/configurationSchema'
+import {
+  AnyConfigurationModel,
+  AnyConfigurationSchemaType,
+} from '../configuration/configurationSchema'
 
 import assemblyFactory from './assembly'
 import PluginManager from '../PluginManager'
@@ -32,7 +35,7 @@ export default function assemblyManagerFactory(
         return [
           ...getParent(self).jbrowse.assemblies,
           ...(getParent(self).session.sessionAssemblies || []),
-        ]
+        ] as AnyConfigurationModel[]
       },
 
       get rpcManager() {
@@ -125,12 +128,8 @@ export default function assemblyManagerFactory(
           self,
           reaction(
             // have to slice it to be properly reacted to
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            () => self.assemblyList as any,
-            (
-              assemblyConfigs: Instance<typeof Assembly> &
-                AnyConfigurationModel[],
-            ) => {
+            () => self.assemblyList,
+            assemblyConfigs => {
               self.assemblies.forEach(asm => {
                 if (!asm.configuration) {
                   this.removeAssembly(asm)

diff --git a/plugins/config/src/FromConfigAdapter/FromConfigSequenceAdapter.test.ts b/plugins/config/src/FromConfigAdapter/FromConfigSequenceAdapter.test.ts
@@ -7,47 +7,28 @@ test('adapter can fetch sequences', async () => {
     {
       uniqueId: 'one',
       refName: 'ctgA',
-      start: 250,
-      end: 400,
+      start: 0,
+      end: 150,
       seq:
         'ccaaaccgtcaattaaccggtatcttctcggaaacggcggttctctcctagatagcgatctgtggtctcaccatgcaatttaaacaggtgagtaaagattgctacaaatacgagactagctgtcaccagatgctgttcatctgttggctc',
     },
-    {
-      uniqueId: 'two',
-      refName: 'ctgA',
-      start: 150,
-      end: 250,
-      seq:
-        'attctgattcagcctgacttctcttggaaccctgcccataaatcaaagggttagtgcggccaaaacgttggacaacggtattagaagaccaacctgacca',
-    },
-    {
-      uniqueId: 'three',
-      refName: 'ctgB',
-      start: 50,
-      end: 60,
-      seq: 'TACATGCTAGC',
-    },
   ]
   const adapter = new Adapter(sequenceConfigSchema.create({ features }))
   const result = adapter.getFeatures({
     refName: 'ctgA',
     start: 0,
-    end: 500,
+    end: 50,
   })
   const featuresArray = await result.pipe(toArray()).toPromise()
-  expect(featuresArray.length).toBe(2)
-})
+  expect(featuresArray.length).toBe(1)
+  expect(featuresArray[0].get('seq')).toBe(features[0].seq.slice(0, 50))
 
-test('adapter can fetch regions 1', async () => {
-  const features = [
-    { uniqueId: 'one', refName: 'ctgA', start: 250, end: 400 },
-    { uniqueId: 'two', refName: 'ctgA', start: 150, end: 300 },
-    { uniqueId: 'three', refName: 'ctgB', start: 50, end: 60 },
-  ]
-  const adapter = new Adapter(sequenceConfigSchema.create({ features }))
-  const result = await adapter.getRegions()
-  expect(result).toEqual([
-    { refName: 'ctgA', start: 150, end: 400 },
-    { refName: 'ctgB', start: 50, end: 60 },
-  ])
+  const result2 = adapter.getFeatures({
+    refName: 'ctgA',
+    start: 100,
+    end: 150,
+  })
+  const featuresArray2 = await result2.pipe(toArray()).toPromise()
+  expect(featuresArray2.length).toBe(1)
+  expect(featuresArray2[0].get('seq')).toBe(features[0].seq.slice(100, 150))
 })