@jbrowse/plugin-data-management 1.4.1 → 1.5.2

package/src/AddTrackWidget/components/__snapshots__/AddTrackWidget.test.js.snap

@@ -62,168 +62,201 @@ exports[`<AddTrackWidget /> renders 1`] = `
               class="MuiCollapse-wrapperInner"
             >
               <div
-                class="makeStyles-root"
+                class="MuiPaper-root makeStyles-paper MuiPaper-elevation1 MuiPaper-rounded"
               >
                 <div
-                  class="MuiPaper-root makeStyles-paper MuiPaper-elevation1 MuiPaper-rounded"
+                  class="MuiBox-root MuiBox-root"
                 >
                   <label
                     class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-animated MuiInputLabel-shrink"
                     data-shrink="true"
-                    for="callback-editor"
                   >
                     Main file
                   </label>
+                </div>
+                <div
+                  class="MuiBox-root MuiBox-root"
+                >
                   <div
-                    class="MuiGrid-root MuiGrid-container MuiGrid-spacing-xs-1 MuiGrid-align-items-xs-center"
+                    class="MuiBox-root MuiBox-root"
                   >
                     <div
-                      class="MuiGrid-root MuiGrid-item"
+                      aria-label="file, url, or account picker"
+                      class="MuiToggleButtonGroup-root"
+                      role="group"
                     >
-                      <div
-                        aria-label="file or url picker"
-                        class="MuiToggleButtonGroup-root"
-                        role="group"
+                      <button
+                        aria-label="local file"
+                        aria-pressed="false"
+                        class="MuiButtonBase-root MuiToggleButton-root MuiToggleButtonGroup-grouped MuiToggleButtonGroup-groupedHorizontal"
+                        tabindex="0"
+                        type="button"
+                        value="file"
                       >
-                        <button
-                          aria-label="local file"
-                          aria-pressed="false"
-                          class="MuiButtonBase-root MuiToggleButton-root MuiToggleButtonGroup-grouped MuiToggleButtonGroup-groupedHorizontal"
-                          tabindex="0"
-                          type="button"
-                          value="file"
+                        <span
+                          class="MuiToggleButton-label"
                         >
-                          <span
-                            class="MuiToggleButton-label"
-                          >
-                            File
-                          </span>
-                          <span
-                            class="MuiTouchRipple-root"
-                          />
-                        </button>
-                        <button
-                          aria-label="url"
-                          aria-pressed="true"
-                          class="MuiButtonBase-root MuiToggleButton-root MuiToggleButtonGroup-grouped MuiToggleButtonGroup-groupedHorizontal MuiToggleButton-selected"
-                          tabindex="0"
-                          type="button"
-                          value="url"
+                          File
+                        </span>
+                        <span
+                          class="MuiTouchRipple-root"
+                        />
+                      </button>
+                      <button
+                        aria-label="url"
+                        aria-pressed="true"
+                        class="MuiButtonBase-root MuiToggleButton-root MuiToggleButtonGroup-grouped MuiToggleButtonGroup-groupedHorizontal MuiToggleButton-selected"
+                        tabindex="0"
+                        type="button"
+                        value="url"
+                      >
+                        <span
+                          class="MuiToggleButton-label"
                         >
-                          <span
-                            class="MuiToggleButton-label"
-                          >
-                            URL
-                          </span>
-                          <span
-                            class="MuiTouchRipple-root"
-                          />
-                        </button>
-                      </div>
+                          URL
+                        </span>
+                        <span
+                          class="MuiTouchRipple-root"
+                        />
+                      </button>
                     </div>
-                    <div
-                      class="MuiGrid-root MuiGrid-item"
+                  </div>
+                </div>
+                <div
+                  class="MuiFormControl-root MuiTextField-root MuiFormControl-fullWidth"
+                >
+                  <label
+                    class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-outlined"
+                    data-shrink="false"
+                  >
+                    Enter URL
+                  </label>
+                  <div
+                    class="MuiInputBase-root MuiOutlinedInput-root MuiInputBase-fullWidth MuiInputBase-formControl"
+                  >
+                    <input
+                      aria-invalid="false"
+                      class="MuiInputBase-input MuiOutlinedInput-input"
+                      data-testid="urlInput"
+                      type="text"
+                      value=""
+                    />
+                    <fieldset
+                      aria-hidden="true"
+                      class="PrivateNotchedOutline-root MuiOutlinedInput-notchedOutline"
                     >
-                      <div
-                        class="MuiFormControl-root MuiTextField-root MuiFormControl-fullWidth"
+                      <legend
+                        class="PrivateNotchedOutline-legendLabelled"
                       >
-                        <div
-                          class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-fullWidth MuiInput-fullWidth MuiInputBase-formControl MuiInput-formControl"
-                        >
-                          <input
-                            aria-invalid="false"
-                            class="MuiInputBase-input MuiInput-input"
-                            data-testid="urlInput"
-                            type="text"
-                            value=""
-                          />
-                        </div>
-                      </div>
-                    </div>
+                        <span>
+                          Enter URL
+                        </span>
+                      </legend>
+                    </fieldset>
                   </div>
-                  <p
-                    class="MuiFormHelperText-root"
-                  />
+                </div>
+                <p
+                  class="MuiFormHelperText-root"
+                />
+                <div
+                  class="makeStyles-spacer"
+                />
+                <div
+                  class="MuiBox-root MuiBox-root"
+                >
                   <label
                     class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-animated MuiInputLabel-shrink"
                     data-shrink="true"
-                    for="callback-editor"
                   >
                     Index file
                   </label>
+                </div>
+                <div
+                  class="MuiBox-root MuiBox-root"
+                >
                   <div
-                    class="MuiGrid-root MuiGrid-container MuiGrid-spacing-xs-1 MuiGrid-align-items-xs-center"
+                    class="MuiBox-root MuiBox-root"
                   >
                     <div
-                      class="MuiGrid-root MuiGrid-item"
+                      aria-label="file, url, or account picker"
+                      class="MuiToggleButtonGroup-root"
+                      role="group"
                     >
-                      <div
-                        aria-label="file or url picker"
-                        class="MuiToggleButtonGroup-root"
-                        role="group"
+                      <button
+                        aria-label="local file"
+                        aria-pressed="false"
+                        class="MuiButtonBase-root MuiToggleButton-root MuiToggleButtonGroup-grouped MuiToggleButtonGroup-groupedHorizontal"
+                        tabindex="0"
+                        type="button"
+                        value="file"
                       >
-                        <button
-                          aria-label="local file"
-                          aria-pressed="false"
-                          class="MuiButtonBase-root MuiToggleButton-root MuiToggleButtonGroup-grouped MuiToggleButtonGroup-groupedHorizontal"
-                          tabindex="0"
-                          type="button"
-                          value="file"
-                        >
-                          <span
-                            class="MuiToggleButton-label"
-                          >
-                            File
-                          </span>
-                          <span
-                            class="MuiTouchRipple-root"
-                          />
-                        </button>
-                        <button
-                          aria-label="url"
-                          aria-pressed="true"
-                          class="MuiButtonBase-root MuiToggleButton-root MuiToggleButtonGroup-grouped MuiToggleButtonGroup-groupedHorizontal MuiToggleButton-selected"
-                          tabindex="0"
-                          type="button"
-                          value="url"
+                        <span
+                          class="MuiToggleButton-label"
                         >
-                          <span
-                            class="MuiToggleButton-label"
-                          >
-                            URL
-                          </span>
-                          <span
-                            class="MuiTouchRipple-root"
-                          />
-                        </button>
-                      </div>
-                    </div>
-                    <div
-                      class="MuiGrid-root MuiGrid-item"
-                    >
-                      <div
-                        class="MuiFormControl-root MuiTextField-root MuiFormControl-fullWidth"
+                          File
+                        </span>
+                        <span
+                          class="MuiTouchRipple-root"
+                        />
+                      </button>
+                      <button
+                        aria-label="url"
+                        aria-pressed="true"
+                        class="MuiButtonBase-root MuiToggleButton-root MuiToggleButtonGroup-grouped MuiToggleButtonGroup-groupedHorizontal MuiToggleButton-selected"
+                        tabindex="0"
+                        type="button"
+                        value="url"
                       >
-                        <div
-                          class="MuiInputBase-root MuiInput-root MuiInput-underline MuiInputBase-fullWidth MuiInput-fullWidth MuiInputBase-formControl MuiInput-formControl"
+                        <span
+                          class="MuiToggleButton-label"
                         >
-                          <input
-                            aria-invalid="false"
-                            class="MuiInputBase-input MuiInput-input"
-                            data-testid="urlInput"
-                            type="text"
-                            value=""
-                          />
-                        </div>
-                      </div>
+                          URL
+                        </span>
+                        <span
+                          class="MuiTouchRipple-root"
+                        />
+                      </button>
                     </div>
                   </div>
-                  <p
-                    class="MuiFormHelperText-root"
+                </div>
+                <div
+                  class="MuiFormControl-root MuiTextField-root MuiFormControl-fullWidth"
+                >
+                  <label
+                    class="MuiFormLabel-root MuiInputLabel-root MuiInputLabel-formControl MuiInputLabel-animated MuiInputLabel-outlined"
+                    data-shrink="false"
+                  >
+                    Enter URL
+                  </label>
+                  <div
+                    class="MuiInputBase-root MuiOutlinedInput-root MuiInputBase-fullWidth MuiInputBase-formControl"
                   >
-                    Automatically inferred from the URL if not supplied
-                  </p>
+                    <input
+                      aria-invalid="false"
+                      class="MuiInputBase-input MuiOutlinedInput-input"
+                      data-testid="urlInput"
+                      type="text"
+                      value=""
+                    />
+                    <fieldset
+                      aria-hidden="true"
+                      class="PrivateNotchedOutline-root MuiOutlinedInput-notchedOutline"
+                    >
+                      <legend
+                        class="PrivateNotchedOutline-legendLabelled"
+                      >
+                        <span>
+                          Enter URL
+                        </span>
+                      </legend>
+                    </fieldset>
+                  </div>
                 </div>
+                <p
+                  class="MuiFormHelperText-root"
+                >
+                  (Optional) The URL of the index file is automatically inferred from the URL of the main file if it is not supplied.
+                </p>
               </div>
               <div
                 class="makeStyles-actionsContainer"

package/src/AddTrackWidget/index.test.jsx

@@ -4,32 +4,51 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import Plugin from '@jbrowse/core/Plugin'
 import ViewType from '@jbrowse/core/pluggableElementTypes/ViewType'
 import stateModelFactory from './model'
+import Alignments from '@jbrowse/plugin-alignments'
+import SVG from '@jbrowse/plugin-svg'
+import Variants from '@jbrowse/plugin-variants'
+import Hic from '@jbrowse/plugin-hic'
 
 function standardInitializer() {
-  const pluginManager = new PluginManager([new FakeViewPlugin()])
+  const pluginManager = new PluginManager([
+    new FakeViewPlugin(),
+    new Alignments(),
+    new SVG(),
+    new Variants(),
+    new Hic(),
+  ])
   pluginManager.createPluggableElements()
   pluginManager.configure()
 
-  const SessionModel = types.model({
-    view: FakeViewModel,
-    widget: stateModelFactory(pluginManager),
-  })
+  const SessionModel = types
+    .model({
+      view: FakeViewModel,
+      widget: stateModelFactory(pluginManager),
+    })
+    .volatile(() => ({
+      rpcManager: {},
+      configuration: {},
+    }))
 
   // assemblyNames is defined on the view, which is done in LGV for example
   // this is really just used for convenience to automatically fill in the
   // assembly field in the form
-  return SessionModel.create({
-    view: {
-      id: 'testing',
-      type: 'FakeView',
-      assemblyNames: ['volvox'],
-    },
-    widget: {
-      type: 'AddTrackWidget',
-      view: 'testing',
+  return SessionModel.create(
+    {
+      view: {
+        id: 'testing',
+        type: 'FakeView',
+        assemblyNames: ['volvox'],
+      },
+      widget: {
+        type: 'AddTrackWidget',
+        view: 'testing',
+      },
     },
-  })
+    { pluginManager },
+  )
 }
+
 const realLocation = window.location
 
 // https://stackoverflow.com/a/60110508/2129219
@@ -71,7 +90,10 @@ describe('tests on an LGV type system with view.assemblyNames, using URL', () =>
 
   it('adds relative URL (BAM)', () => {
     const { widget } = session
-    widget.setTrackData({ uri: 'volvox-sorted.bam' })
+    widget.setTrackData({
+      uri: 'volvox-sorted.bam',
+      locationType: 'UriLocation',
+    })
     expect(widget.trackName).toBe('volvox-sorted.bam')
     expect(widget.isFtp).toBe(false)
     expect(widget.isRelativeUrl).toBe(true)
@@ -81,7 +103,10 @@ describe('tests on an LGV type system with view.assemblyNames, using URL', () =>
 
   it('adds full URL (BAM)', () => {
     const { widget } = session
-    widget.setTrackData({ uri: 'http://google.com/volvox-sorted.bam' })
+    widget.setTrackData({
+      uri: 'http://google.com/volvox-sorted.bam',
+      locationType: 'UriLocation',
+    })
     expect(widget.trackName).toBe('volvox-sorted.bam')
     expect(widget.isRelativeUrl).toBe(false)
     expect(widget.assembly).toBe('volvox')
@@ -89,7 +114,10 @@ describe('tests on an LGV type system with view.assemblyNames, using URL', () =>
 
   it('test wrongProtocol returning false', () => {
     const { widget } = session
-    widget.setTrackData({ uri: 'http://google.com/volvox-sorted.bam' })
+    widget.setTrackData({
+      uri: 'http://google.com/volvox-sorted.bam',
+      locationType: 'UriLocation',
+    })
     setWindowLoc('http://google.com')
 
     expect(widget.wrongProtocol).toBe(false)
@@ -97,7 +125,10 @@ describe('tests on an LGV type system with view.assemblyNames, using URL', () =>
 
   it('test wrongProtocol returning true', () => {
     const { widget } = session
-    widget.setTrackData({ uri: 'http://google.com/volvox-sorted.bam' })
+    widget.setTrackData({
+      uri: 'http://google.com/volvox-sorted.bam',
+      locationType: 'UriLocation',
+    })
     setWindowLoc('https://google.com')
     expect(widget.wrongProtocol).toBe(true)
   })
@@ -130,7 +161,10 @@ describe('tests on an view without view.assemblyNames', () => {
 
   it('adds url', () => {
     const { widget } = session
-    widget.setTrackData({ uri: 'volvox-sorted.bam' })
+    widget.setTrackData({
+      uri: 'volvox-sorted.bam',
+      locationType: 'UriLocation',
+    })
     expect(widget.trackName).toBe('volvox-sorted.bam')
     expect(widget.isRelativeUrl).toBe(true)
     expect(widget.assembly).toBe(undefined)
@@ -149,31 +183,46 @@ describe('tests different file types', () => {
 
   it('adds bam', () => {
     const { widget } = session
-    widget.setTrackData({ uri: 'volvox-sorted.bam' })
+    widget.setTrackData({
+      uri: 'volvox-sorted.bam',
+      locationType: 'UriLocation',
+    })
     expect(widget.trackType).toBe('AlignmentsTrack')
   })
 
   it('adds cram', () => {
     const { widget } = session
-    widget.setTrackData({ uri: 'volvox-sorted.cram' })
+    widget.setTrackData({
+      uri: 'volvox-sorted.cram',
+      locationType: 'UriLocation',
+    })
     expect(widget.trackType).toBe('AlignmentsTrack')
   })
 
   it('adds .vcf.gz', () => {
     const { widget } = session
-    widget.setTrackData({ uri: 'volvox-sorted.vcf.gz' })
+    widget.setTrackData({
+      uri: 'volvox-sorted.vcf.gz',
+      locationType: 'UriLocation',
+    })
     expect(widget.trackType).toBe('VariantTrack')
   })
 
   it('adds .gff3', () => {
     const { widget } = session
-    widget.setTrackData({ uri: 'volvox-sorted.gff3' })
+    widget.setTrackData({
+      uri: 'volvox-sorted.gff3',
+      locationType: 'UriLocation',
+    })
     expect(widget.trackType).toBe('FeatureTrack')
   })
 
   it('adds .hic', () => {
     const { widget } = session
-    widget.setTrackData({ uri: 'volvox-sorted.hic' })
+    widget.setTrackData({
+      uri: 'volvox-sorted.hic',
+      locationType: 'UriLocation',
+    })
     expect(widget.trackType).toBe('HicTrack')
   })
 })
@@ -185,7 +234,10 @@ describe('tests localpath', () => {
   })
   it('adds bam', () => {
     const { widget } = session
-    widget.setTrackData({ localPath: 'volvox-sorted.bam' })
+    widget.setTrackData({
+      localPath: 'volvox-sorted.bam',
+      locationType: 'LocalPathLocation',
+    })
     expect(widget.trackType).toBe('AlignmentsTrack')
     expect(widget.trackName).toBe('volvox-sorted.bam')
     // the localPath is not a "relativeUrl"

package/src/AddTrackWidget/model.ts

@@ -6,6 +6,7 @@ import {
   guessAdapter,
   guessTrackType,
   UNSUPPORTED,
+  getFileName,
 } from '@jbrowse/core/util/tracks'
 
 function isAbsoluteUrl(url = '') {
@@ -17,18 +18,6 @@ function isAbsoluteUrl(url = '') {
   }
 }
 
-function getFileName(track: FileLocation) {
-  const uri = 'uri' in track ? track.uri : undefined
-  const localPath = 'localPath' in track ? track.localPath : undefined
-  const blob = 'blobId' in track ? track : undefined
-  return (
-    blob?.name ||
-    uri?.slice(uri.lastIndexOf('/') + 1) ||
-    localPath?.slice(localPath.lastIndexOf('/') + 1) ||
-    ''
-  )
-}
-
 export default function f(pluginManager: PluginManager) {
   return types
     .model('AddTrackModel', {
@@ -88,7 +77,7 @@ export default function f(pluginManager: PluginManager) {
         const { trackData, indexTrackData, adapterHint } = self
 
         return trackData
-          ? guessAdapter(trackData, indexTrackData, getFileName, adapterHint)
+          ? guessAdapter(trackData, indexTrackData, adapterHint, self)
           : undefined
       },
 
@@ -148,7 +137,9 @@ export default function f(pluginManager: PluginManager) {
       get trackType() {
         return (
           self.altTrackType ||
-          (this.trackAdapter ? guessTrackType(this.trackAdapter.type) : '')
+          (this.trackAdapter
+            ? guessTrackType(this.trackAdapter.type, self)
+            : '')
         )
       },
     }))

package/src/AssemblyManager/AssemblyAddForm.tsx

@@ -149,6 +149,8 @@ const AdapterInput = observer(
   },
 )
 
+const blank = { uri: '' } as FileLocation
+
 const AssemblyAddForm = observer(
   ({
     rootModel,
@@ -169,18 +171,17 @@ const AssemblyAddForm = observer(
     const [assemblyName, setAssemblyName] = useState('')
     const [assemblyDisplayName, setAssemblyDisplayName] = useState('')
     const [adapterSelection, setAdapterSelection] = useState(adapterTypes[0])
-    const [fastaLocation, setFastaLocation] = useState({ uri: '' })
-    const [faiLocation, setFaiLocation] = useState({ uri: '' })
-    const [gziLocation, setGziLocation] = useState({ uri: '' })
-    const [twoBitLocation, setTwoBitLocation] = useState({ uri: '' })
-    const [chromSizesLocation, setChromSizesLocation] = useState({ uri: '' })
+    const [fastaLocation, setFastaLocation] = useState(blank)
+    const [faiLocation, setFaiLocation] = useState(blank)
+    const [gziLocation, setGziLocation] = useState(blank)
+    const [twoBitLocation, setTwoBitLocation] = useState(blank)
+    const [chromSizesLocation, setChromSizesLocation] = useState(blank)
 
     function createAssembly() {
       if (assemblyName === '') {
         rootModel.session.notify("Can't create an assembly without a name")
       } else {
         setFormOpen(false)
-        // setIsAssemblyBeingEdited(true)
         let newAssembly
         if (adapterSelection === 'IndexedFastaAdapter') {
           newAssembly = {

package/src/AssemblyManager/AssemblyManager.test.tsx

@@ -14,6 +14,7 @@ const mockRootModel = {
             type: 'testSeqAdapter',
             twoBitLocation: {
               uri: 'test.2bit',
+              locationType: 'UriLocation',
             },
           },
         },